Proteomics research has become one of the most important topics in the fields of life science and natural science. At present, research on protein–protein interaction networks (PPINs) mainly focuses on detecting protein complexes or function modules. However, existing approaches are either ineffective or incomplete. In this paper, we investigate function module detection mechanisms in PPIN, including open databases, existing detection algorithms and recent solutions. After that, we describe the proposed solution based on simplified swarm optimization (SSO) algorithm and gene ontology knowledge. The proposed solution implements SSO algorithm for clustering proteins with similar function, and imports biological gene ontology knowledge for further identifying function complexes and improving detection accuracy. Furthermore, we use four different categories of species dataset for experiment: Fruitfly, Mouse, Scere, and Human. The testing and analysis result show that the proposed solution is feasible, efficient and could achieve a higher accuracy of prediction than existing approaches.

SOC stock (SOCS) changes caused by land use changes are still unclear, and understanding this response is essential for many environmental policies and land management practices. In this study, we investigated the temporal-spatial and vertical distribution characteristics of SOCS on the Western Sichuan Plateau (WSP) using the sparrow search algorithm-random forest regression (SSA-RFR) models with excellent model applicability and accuracy. The temporal-spatial varia-tions in the SOCS were modeled using 1080 soil samples and a set of nine environmental covariates. We analyzed the effect of land use changes on the SOCS on the WSP. The total SOCS increased by 18.03 Tg C from 1990 to 2020. The results of this study confirmed that the SOCS in the study area has increased significantly since 2010, with an increase of 27.88 Tg C compared to the total SOCS in 2010. We found that the spatial distribution of the SOCS increased from southeast to northwest, and the vertical distribution of the SOCS in the study area decreased with increasing soil depth. Forest and grassland are the main sources of SOCS, the total SOCS in the forest and grassland accounted for 37.53 and 59.39% of the total SOC pool in 2020, respectively. Expansion of the wetlands, forest, and grassland areas could increase SOCS in the study area.

Bicyclic peptides have attracted the interest of pharmaceutical companies because of their remarkable properties putting them on a new path in medicine. Their conformational rigidity that improves proteolytic stability, leads to rapid penetration into tissues via any possible route of administration and elimination, occurring by renal metabolism, is of great importance for people with a history of liver diseases. In addition, each ring can function independently, making them extremely versatile molecules for further optimization. In this paper we compared the potentiometric and spectroscopic properties studied by UV-Vis, MCD, and EPR, of four synthetic analogues of the bi-cyclic peptide c(PKKHP-c(CFWKTC)-PKKH). In particular we correlated the structural and spectral properties of complexes with coordinating abilities toward Cu(II) ions of MCL (Ac-PKKHPc(CFWKTC)PKKH-NH2) that contains the unbinding cycle and N- and C-terminal linear parts, with two histidine residues, one per part; two monocyclic ligands containing one histidine residue, both in the N-terminal position i.e., MCL2 (Ac-PKKHPc(CFWKTC)PKKS-NH2) and in the C-terminal position i.e., MCL3 (Ac-PKKSPc(CFWKTC)PKKH-NH2), respectively, and the linear structure LNL (Ac-PKKHPSFWKTSPKKH-NH2).

The European Union's recent decision to renew the authorization for the use of glyphosate until 15 December 2033 stimulates the scientific discussion all around the world regarding its toxicity or otherwise for humans. Glyphosate is a chemical used by millions of tons in the last 50 years worldwide to drying weeds in cultivated fields, greenhouses, roadsides. Concern has been raised in many quarters about the possible presence in the food chain and the consequent adverse effects on health: both aspects that argue in favor of toxicity and those that instead may indicate limited toxicity of glyphosate are here discussed. The great debate that has been generated requires further investigations and field measurements to understand its fate once dispersed in the environment and its concentration in the food chain. Hence the need for validated analytical methods that are available to analysts in the field. In the present review, methods for the analytical determination of glyphosate and its main metabolite, AMPA, are discussed, with a specific focus on chromatographic techniques applied to cereal products. The experimental procedures are explained in any detail, including cleanup, derivatization, and instrumental conditions to give the laboratories involved enough information to proceed with the implementation of this line of analysis. The prevalent chromatographic methods used are LC-MS/MS, GC-MS/SIM, and GC-MS/MS but sufficient indications are also given to those laboratories that wish to use the simpler HPLC-FLD, HPLC-UV, GC-NPD or GC-FPD techniques for screening purposes. Concentrations from literature measured in wheat, corn, barley, rye, oats, soybean, and cereal-based foods are reported together with the regulatory status in various parts of the world and the accumulation mechanism. As for the accumulation in cereals, available data show that glyphosate tends to accumulate more in wholemeal flours than in refined ones, that its concentration in the product strictly depends on the treatment period (the closer it is to the time of harvesting, the higher the concentration) and that in cold climates the herbicide tends to persist in the soil for a long time.

Respiratory Syncytial Virus (RSV) causes severe inflammation and airway pathology in children and the elderly by infecting the epithelial cells of the upper and lower respiratory tract. RSV replication is sensed by intracellular pattern recognition receptors upstream of the IRF and NF-B transcription factors. These proteins coordinate an innate inflammatory response via Bromodomain containing protein 4 (BRD4), a protein that functions as a scaffold for unknown transcriptional regulators. To better understand the pleiotropic regulatory function of BRD4, we examine the BRD4 interactome and identify how RSV infection dynamically alters it. To accomplish these goals, we leverage native immunoprecipitation and Parallel Accumulation – Serial Fragmentation (PASEF) mass spectrometry to examine BRD4 complexes isolated from human alveolar epithelial cells in the absence or presence of RSV infection. In addition, we explore the role of BRD4’s acetyl-lysine binding bromodomains in mediating these interactions by using a highly selective competitive bromodomain inhibitor. We identify 101 proteins that are significantly enriched in the BRD4 complex and are responsive to both RSV-infection and BRD4 inhibition. These proteins are highly enriched in transcription factors and transcriptional coactivators. Among them, we identify members of the AP1 transcription factor complex, a complex important in innate signaling and cell stress responses. We independently confirm the BRD4/AP1 interaction in primary human small airway epithelial cells. We conclude that BRD4 recruits multiple transcription factors during RSV infection in a manner dependent on acetyl-lysine binding domain interactions. This data suggests that BRD4 recruits transcription factors to target its RNA processing complex to regulate gene expression in innate immunity and inflammation.

This study provides a detailed investigation into the pathways through which microplastics from urban sources are transported to marine ecosystems, their distribution across different environments, and their impacts on marine life. Utilizing a combination of water and sediment sampling across urban, riverine, and marine environments, the research quantitatively assesses the concentration and types of microplastics present, and evaluates the ecological consequences of their accumulation in marine ecosystems. The findings reveal a significant concentration of microplastics in all examined environments, with the highest levels detected in urban areas, closely linked to industrial activities and inadequate waste management practices. The study documents a variety of microplastic polymers, with polyethylene (PE), polypropylene (PP), and polyethylene terephthalate (PET) being the most prevalent. A substantial impact on marine organisms was observed, including evidence of microplastic ingestion across a wide range of species and indications of stress and physical damage to coral reefs. Seasonal variations indicate that microplastic concentrations peak during periods of high rainfall, suggesting urban runoff as a critical pathway for microplastic transport. The study concludes with recommendations for improving waste management practices, enhancing public awareness and engagement in plastic recycling efforts, and implementing policies aimed at reducing the production and use of single-use plastics. This research underscores the urgent need for coordinated actions to mitigate the pervasive issue of microplastic pollution, highlighting the role of urban management and policy interventions in safeguarding marine ecosystems.

Lipid droplet (LD) accumulation in hepatocytes is one of the major symptoms associated with fatty liver disease. Mitochondria play a key role in catabolizing fatty acids for energy production through β-oxidation. The interplay between mitochondria and LD assumes a crucial role in lipid metabolism, while it is obscure how mitochondrial morphology affects systemic lipid metabolism in the liver. We previously reported that cilnidipine, an already existing anti-hypertensive drug, has potency to prevent pathological mitochondrial fission by inhibiting protein-protein interaction between dynamin-related protein 1 (Drp1) and filamin, an actin-binding protein. Here, we found that cilnidipine and its new dihydropyridine (DHP) derivative, 1,4-DHP, which lacks Ca2+ channel blocking action of cilnidipine, prevent the palmitic ac-id-induced Drp1-filamin interaction, LD accumulation and cytotoxicity of human hepatic HepG2 cells. Cilnidipine and 1,4-DHP also suppressed the LD accumulation accompanied by reducing mitochondrial contact with LD in obese model and high fat diet-fed mouse livers. These results propose that targeting Drp1-filimin interaction becomes a new strategy for the prevention or treatment of fatty liver disease.

Rice prolamins are categorized into three groups by molecular size (10, 13, or 16 kDa), while the 13 kDa prolamins are assigned to four subgroups (Pro13a-I, Pro13a-II, Pro13b-I, and Pro13b-II) based on cysteine residue content. Here, we generated four knockout strains of rice using CRISPR-Cas9, each of which demonstrated selectively reduced expression of specific subgroups of the 13 kDa prolamins. These four mutant rice lines also demonstrated compensatory expression of glutelins and non-targeted prolamins, which resulted in low grain weight, altered starch content and atypically-shaped starch granules and protein bodies. Transcriptome analysis identified 746 transcripts that were differentially expressed in the mutant rice lines during development. These transcripts played roles primarily in RNA processing, protein synthesis, stress response, and transport. After selective suppression/knockout of genes in the Pro13a-I subgroup, compensatory upregulation of genes in the Pro13a-II and Pro13b-I/II subgroups was observed. Compensatory expression of 9 ER stress and 17 transcription factor genes was also observed in mutant rice in which expression of 13 kDa prolamin genes was suppressed. Our results provide valuable insight into the regulatory mechanisms underlying rice seed development and the specific roles played by 13 kDa rice prolamins and their target genes.

Hybrid reinforcement in a composite material (CM), in many situations, allows better govern material mechanical properties. Polymer matrix CM plate is reinforced with small particles and macro-fibers. Particles are oil shale ash (OSA) powder, macro-fibers – basalt fiber threads im-pregnated by matrix material. With the goal to find out elastic properties of the matrix- polymer with OSA, samples with its different concentrations were experimentally fabricated and their elastic properties were experimentally measured. Obtained data were used in numerical model-ling. Was observed polymer matrix composite slab, reinforced with OSA and three-dimensional (3D) basalt fiber fabric. Fabric are forming threads impregnated by matrix (polymer resin mixed with OSA particles). Damage accumulation in the stretched slab was modelled. Impregnated thread, in the modelling, is observed as a macro-fiber (MF) with averaged elastic properties. With the load increase MF in the material began to break. At first, appeared isolated single breaks. A probabilistic sequential MF rupture accumulation model was accepted and numerical-ly realized. The geometry of the reinforcing knitted fabric was modeled using the Leaf and Glaskin approach. In the knitted fabric highly, stressed MF cross-sections are observed as po-tential location where thread breakage can occur. If one thread breaks, the cross-sections of the adjacent threads experience the overload caused by this rupture. More overloaded crossection in the adjacent overloaded thread breaks and we obtain two adjacent broken MF designated as a defect with the size j=2. The probabilities of obtaining defect consisting of at least 2, 3, … j adjacent broken MF in the plate were calculated. The calculations continued until the rupture process becomes unstable (j→∞). The overstresses on adjacent threads in the CM were calculat-ed using the FEM three-dimensional numerical approach. Analytical and stochastic methods were used for the load-carrying capacity determination and different size defects accumulation in the hybrid composite material (HCM) plate. Also, was calculated the probability of the plate rupture.

The long-term use of fertilizers and pesticides in conventional cultivation has resulted in a decrease in soil productivity and vegetable yields in greenhouses. However, only a limited number of studies have explored the impacts of organic cultivation on greenhouse soil. Specifically, there is a scarcity of research examining the alterations in soil aggregate mediated organic carbon and microbial communities, which are known to enhance soil productivity. This study investigated the properties of soil aggregates, including the levels of organic carbon fractions, microbial community, and enzyme activity with the three aggregate classes microaggregates (<0.25 mm), small macroaggregates (2-0.25 mm) and large macroaggregates (>2 mm). These investigations were conducted under three different cultivation methods in a greenhouse: conventional cultivation (CC), integrated cultivation (IC), and organic cultivation (OC) in greenhouse. The results showed that (1) OC and IC promoted the formation of small macro-aggregates and enhanced aggregate stability compared to CC, (2) SOC in the three size fractions of OC increased by 98.99%-92.06% compared to CC; EOC increased by 98.47%-117.59%; POC increased by 138.59%-208.70%; MBC increased by 104.71%-230.61%; DOC increased by 21.93%-40.90%, respectively; (3) Organic cultivation significantly increased enzyme activity in all three particle size aggregates and increased the relative abundance of bacteria in micro-aggregates as well as the relative abundance of fungi in small macro-aggregates. Structural equation model (SEM) analysis revealed that organic farming practices fostered the development of smaller macro-aggregates, elevated microbial and enzyme activities within soil aggregates, and facilitated the conversion of soil nutrients and carbon sequestration. consequently, this led to an increase in soil organic carbon content and improved vegetable yield in greenhouse environments. In conclusion, the soil carbon content and vegetable yield are enhanced through long-term organic cultivation in greenhouses, primarily by increasing the proportion of small macro-aggregates.

The p53 tumor suppressor protein shows antiviral activity. The replication of viruses is also antagonized by interferons (IFNs) – cytokines, which control immunity genes by the STAT transcription factors. The best studied interferons belong to type I (e.g. IFNα) and type II (IFNγ) groups. IFNα and IFNγ both induce activating phosphorylation of STAT1 on Tyr701. Previously, we noticed that p53 activates SOCS1, which is a negative regulator of STAT1 phosphorylation. Thus, we hypothesized that p53 by activating SOCS1 expression reduces phosphorylation of STAT1 and attenuates activation of genes stimulated either by IFNα or IFNγ. To test this hypothesis, we exposed p53-proficient and p53-deficient cells to strong p53 activators, and either to IFNα or IFNγ. Subsequently, we estimated the phosphorylation status of STAT1 and the expression of genes regulated by either of these cytokines. Strong activation of p53 reduced the phosphorylation of STAT1 on Tyr701, however surprisingly it did not lead to reduced expression of most tested interferon-stimulated genes. On contrary, p53 and IFNγ synergized in the activation of CASP1, IFIT1 and IFIT3 genes. We conclude that the interactions between p53 and interferon-activated pathways are more complicated than initially expected, but the apparent cooperation between p53 and IFNγ deserves further studies.

A theoretical model to translate the evolution over time, in early stages, of growth and accumulation of biofilm bacterial mass is introduced. The model implies the solution of a system of differential-difference master equations. The application of an algorithm like Miller´s tree term recurrence, already known for Bessel functions of first kind, allows an exact calculation of the solutions of such equations, for a wide range of parameters values and time. For biofilm model a five term recurrence is deduced and applied in a backwards computation. A suitable normalisation condition completes the reach of the solution.

The apicomplexan parasite, Sarcocystis neurona causes the degenerative neurological equine protozoal myeloencephalitis (EPM) disease of horses. Due to its host range expansion, S. neurona is an emerging threat that requires close monitoring. In apicomplexans, protein kinases (PKs) have been implicated in a myriad of critical functions such as host cell invasion, cell cycle progression and host immune responses evasion. Here, we used various bioinformatics methods to define the kinome of S. neurona and phylogenetic relatedness of its PKs to other apicomplexans. Further, three-dimensional (3D) homology models for selected S. neurona putative PKs were constructed and evaluated for inhibitor docking. We identified 92 putative PKs clustering within the AGC, CAMK, CK1, CMGC, STE, TKL, aPK and OPK groups. Although containing the universally conserved PKA (AGC group), S. neurona kinome was devoid of PKB and PKC, but contained the six apicomplexan conserved CDPKs (CAMK group). The OPK group was represented by ROPKs 19A, 27, 30, 33, 35 and 37, but was devoid of the virulence-associated ROPKs 5, 6, 18 and 38. Two out of the three S. neurona CK1 enzymes had high sequence similarities to T. gondii TgCK1-α and TgCK1-β and the Plasmodium PfCK1. Docking of four inhibitors onto homology models of putative ROP27 and PKA indicated that inhibition of S. neurona PKs is feasible, but needs to be experimentally tested. The essentiality of apicomplexan PKs makes the elucidation of S. neurona kinome a key milestone for development of novel therapeutics for EPM.

Zika virus (ZIKV) infection and pathogenesis are linked to the disruption of neurogenesis, congenital Zika syndrome and microcephaly by affecting neural progenitor cells. Nonstructural protein 5 (NS5) is the largest product encoded by ZIKV-RNA and is important for replication and immune evasion. Here, we studied the potential effects of NS5 on microtubules (MTs) and autophagy flux, together with the interplay of NS5 with histone deacetylase 6 (HDAC6). Fluorescence microscopy, biochemical cell-fractionation combined with the use of HDAC6 mutants, chemical inhibitors and RNA interference indicated that NS5 accumulates in nuclear structures and strongly promotes the acetylation of MTs that aberrantly reorganize in nested-like structures. Similarly, NS5 accumulates the p62 protein, an autophagic-flux marker. Therefore, NS5 alters events that are under the control of the autophagic tubulin-deacetylase HDAC6. HDAC6 appears to degrade NS5 by autophagy in a deacetylase- and BUZ domain-dependent manner and to control the cytoplasmic expression of NS5. Moreover, NS5 inhibits RNA-mediated RIG-I interferon (IFN) production, resulting in greater activity when autophagy is inhibited (i.e., effect correlated with NS5 stability). Therefore, it is conceivable that NS5 contributes to cell toxicity and pathogenesis, evading the IFN-immune response by overcoming HDAC6 functions. HDAC6 has emerged as an anti-ZIKV factor by targeting NS5.

The criteria of “Distinctness, Uniformity and Stability” as well as a high "overall quality index” are used to register the Italian modern varieties to the national register. Differently, local conservation varieties can be certified under different EU Directives having, as overall objective, the preservation of biodiversity and the containment of genetic erosion. In recent years, products derived from an-cient grains are perceived to be healthier and more sustainable by consumer, especially in Italy, with consequent higher market prices. Ancient tetraploid wheat varieties registered in the national reg-ister of conservation varieties are 28, 24 of which are Sicilian. They are supposed to have a wide genetic variability compared to modern ones, making them vulnerable of fraud because they are difficult to trace. It is therefore important to have tools able to discriminate the autochthonous Si-cilian varieties. This can be done by gluten proteins composition, which also gives information on the technological properties of derived products. Fifty-one accessions belonging to 22 ancient va-rieties of Sicilian tetraploid (mostly durum) wheat were analyzed. Although a wide intra-accession and intra-varietal variability was assessed, the gliadin pattern of bulks of seeds belonging to each variety was discriminatory. Moreover, differences in technological attitudes were found between landraces. This paves the way to use gluten protein patterns for traceability allowing local farmers and producers to valorize their products and assure consumers about the transparency of the entire supply chain.

Proteins need to be located in appropriate spatiotemporal contexts to carry out their diverse biological functions. Mislocalized proteins may lead to a broad range of diseases, such as cancer and Alzheimer’s disease. Knowing where a target protein resides within a cell will give insights into tailored drug design for a disease. As the gold validation standard, the conventional wet lab uses fluorescent microscopy imaging, immunoelectron microscopy, and fluorescent biomarker tags for protein subcellular location identification. However, the booming era of proteomics and high-throughput sequencing generates tons of newly discovered proteins, making protein subcel-lular localization by wet-lab experiments a mission impossible. To tackle this concern, in the past decades, artificial intelligence (AI) and machine learning (ML), especially deep learning methods, have made significant progress in this research area. In this article, we review the latest advances in AI-based method development in three typical types of approaches, including sequence-based, knowledge-based, and image-based methods. We also elaborately discuss existing challenges and future directions in AI-based method development in this research field.

Insulin signaling plays a crucial role in cellular uptake of glucose and different metabolic pathways. Impairment in cellular insulin sensitivity due to various molecular pathways leads to Insulin resistance (IR) as well as fatty liver. In this review, mechanisms by which zinc involved in decreasing IR are described, focusing on oxidative stress, inflammation, immune system, gut flora and hepatic lipophagy. This study reviews the cause of IR and highlights the role of zinc in mechanisms diminishing IR and fatty liver.

The photosystem I (PSI) of the green alga Chlamydomonas reinhardtii associates with 10 light-harvesting proteins (LHCI) to form the PSI-LHCI complex. Binding of LHCII to PSI may also occur and is controlled by a process called state transitions. Hereby, two LHCII trimers bind to the PSAL, PSAH and PSAO side of PSI to produce the PSI-LHCI-LHCII complex. In this work, we took advantage of chemical crosslinking of proteins in conjunction with mass spectrometry to identify protein-protein interactions between the light-harvesting proteins of PSI and PSII. We detected binding of LHCBM proteins to the LHCA1-PSAG side of PSI and identified protein-protein interactions of LHCSR3 with LHCA5 and LHCA3. Our data indicate that the binding of LHCII to PSI is more versatile as anticipated and reveal that LHCSR3 likely regulates excitation energy transfer to the PSI core via LHCA5/LHCA3.

The pace of implementation of renewable electricity storage in Europe is disappointingly slow. Several factors influence it, but there is a need to speed up the rate and increase the volumes in order to promote a 100% transition to renewable energy resources, expand the practice of using renewable energy, and contribute to the improvement of the user's quality of life. Also, an important factor is significantly reducing the global impact on the environment and climate change. Electricity from renewable energy sources such as solar and wind has a seasonal nature that cannot provide the necessary electricity consumption and cover peak loads. Also, the so-called "energy resource crisis" is a very topical problem at the moment, which reinforces the global need to increase the share of renewable energy resources in the overall balance of primary energy resources. It is precisely the wider integration of renewable electricity storage in practice that can help stimulate this. The availability of renewable electricity is constantly increasing and the level of technological innovation is rapidly developing, therefore it is valuable to analyze, look for connections and at the same time the main differences in the ways of accumulation in order to promote its availability from a private house to the national and European scale as a whole. Therefore, this article analyses and compares the different options for renewable electricity storage, from small batteries to large storage systems, arriving at the best solution according to needs, using analysis methods such as multicriteria decision analysis (MCDA) and TOPSIS. After comparing nine criteria, such as the amount of investment required, existing power density, efficiency, duration of operation and others, in both groups, it was concluded that lithium-ion batteries are currently the best solution among batteries, while in the group of large accumulation systems – pumped hydro storage.

Chlamydia trachomatis (Ct) infections are the most common sexually-transmitted infection (STI). Despite effective antibiotics for Ct, undetected infections or delayed treatment can lead to infertility, ectopic pregnancies, and chronic pelvic pain. Besides humans, chlamydia poses similar health challenges in animals such as C. suis (Cs) in pigs. Based on the similarities between humans and pigs as well as their chlamydia species, we use pigs as a large biomedical animal model for chlamydia research. In this study, we use the pig model to develop a vaccine candidate against Ct. The vaccine candidate consists of TriAdj-adjuvanted chlamydial protease-like activity factor (CPAF) protein. We tested two weekly administration options – twice intranasal (IN) followed by twice intramuscular (IM), or twice IM followed by twice IN. We assessed the humoral immune response not only in serum by CPAF-specific IgG including antibody avidity determination but also in cervical and rectal swabs by CPAF-specific IgG and IgA ELISAs. The systemic T-cell response was analyzed upon in vitro CPAF-restimulation via IFN-γ and IL-17 ELISpots as well as intracellular cytokine staining flow cytometry. Our data demonstrate that while the IN/IM vaccination mainly led to non-significant systemic immune responses, the vaccine candidate is highly immunogenic if administered IM/IN. This vaccination strategy induced high serum anti-CPAF IgG levels with strong avidity as well as high IgA and IgG levels in vaginal and rectal swabs and in uterine horn flushes. In addition, this vaccination strategy prompted a pronounced cellular immune response: Besides inducing IL-17 production, the vaccine candidate induced a strong IFN-γ response by CD4 T cells. In the IM/IN vaccinated pigs, these cells also significantly downregulated their CCR7 expression – a sign for differentiation into peripheral tissue homing effector/ memory cells. Conclusively, this study demonstrates strong immunogenicity of the IM/IN administered TriAdj-adjuvanted Ct CPAF vaccine candidate. Future studies will test vaccine efficacy of this promising Ct vaccine candidate. In addition, this project demonstrates suitability of the Cs pre-exposed outbred pig model for Ct vaccine development. Thereby, we aim to open the bottleneck of large animal models to facilitate the progression of Ct vaccine candidates into clinical trials.

Few studies have examined the dietary protein intake and sources in combination with the longitudinal changes in brain structure markers. Our study aimed to examine the association between dietary protein intake and different sources of dietary protein with the longitudinal rate of change in brain structural markers. A total of 2723 and 2679 participants from the UK Biobank were included in the analysis. The relative and absolute amounts of dietary protein intake were calculated through a 24-hour dietary recall questionnaire. The longitudinal change rates of brain structural biomarkers were computed using two waves of brain imaging data. We utilized multiple linear regression to examine the association between dietary protein and different sources and the longitudinal changes in brain structural biomarkers. Restrictive cubic splines were used to explore nonlinear relationships, and stratified and sensitivity analyses were conducted. Increasing the proportion of animal protein in dietary protein intake is associated with a slower reduction in the total hippocampus volume (THV, β: -0.02524, P<0.05), left hippocampus volume (LHV, β: -0.02435, P<0.01) and right hippocampus volume (RHV, β: -0.02544, P<0.05).Higher intake of animal protein relative to plant protein is linked to a lower atrophy rate in THV (β: -0.01249, P<0.05) and LHV (β: -0.01173, P<0.05) and RHV (β: -0.01193, P<0.05). Individuals with higher intake of seafood exhibit lower longitudinal rate of change in HV compared to those with no consume (THV, β: -0.004514; P<0.05; RHV, β: -0.005527, P<0.05). In subgroup and sensitivity analyses, there was not a significantly alteration. A moderate increase in the intake and proportion of animal protein in the diet, especially from seafood, is associated with a lower longitudinal change rate in hippocampus volume.

Protein tyrosine phosphatase receptor type E (PTPRE) is a member of the “classical” protein tyrosine phosphatase subfamily and regulates a variety of cellular processes in a tissue-specific manner by antagonizing the function of protein tyrosine kinases. PTPRE plays a tumorigenic role in different human cancer cells, but its role in retinoblastoma (RB), the most common malignant eye cancer in children, remains to be elucidated. Etoposide resistant RB cell lines and RB patients display significant higher PTPRE expression levels compared to chemosensitive counterparts and the healthy human retina, respectively. PTPRE promotor methylation analyses revealed that PTPRE expression in RB is not regulated via this mechanism. Lentiviral PTPRE knockdown (KD) induced a significant decrease in growth kinetics, cell viability, and anchorage independent growth of etoposide resistant Y79 and WERI RB cells. Caspase-dependent apoptosis rates were significantly increased and a re-sensitization for etoposide could be observed after PTPRE depletion. In vivo chicken chorioallantoic membrane (CAM) assays revealed decreased tumor formation capacity as well as reduced tumor size and weight following PTPRE KD. Expression levels of miR631 were significantly downregulated in etoposide resistant RB cells and patients. Transient miR631 overexpression resulted in significantly decreased PTPRE levels and concomitantly decreased proliferation and increased apoptosis levels in etoposide resistant RB cells, impacts mirroring PTPRE KD effects and indicating PTPRE regulation via this miR. Additionally, PTPRE KD led to altered phosphorylation of protein kinase SGK3 and - dependent on the cell line - also AKT and ERK1/2, suggesting potential PTPRE downstream signaling pathways. In summary, these results indicate an oncogenic role of PTPRE in chemoresistant retinoblastoma.

Extant research pays little attention to migrant workers’ skill accumulation/upgrading from the perspective of the labor supply. This paper takes China as an example to explore the factors influencing skill accumulation of rural-urban migrant workers (RUMWs), with a purpose to discover how to sustain or reshape regional competitive advantage through improving RUMWs’ skill accumulation. Structured questionnaire surveys were adopted for data collection in Suzhou City, Jiangsu Province and Taizhou City, Zhejiang Province located in the Yangtze River Delta in the east of China. 900 questionnaires were issued and 491 effective questionnaires were recovered totally. This paper takes a perspective of global production networks, and gets a broad viewpoint containing intra-firm coordination, inter-firm partnership and extra-firm bargaining with non-firm actors, beyond what the extant literature on laborers’ human capital focuses on. The finding indicates that firms’ skill-oriented preference, which concerns about employees’ skills and innovation ability and stimulates them to learn initiatively, have a significant influence on RUMWs’ skill accumulation. In terms of collective efficiency based on co-competitive relationship between local firms, the more intensive interactions are, the more opportunities of skill accumulation RUMWs get. The accessibility of local institutions and favorable policies benefit RUMWs’ skill accumulation. Besides, the place itself, as a synthesized space of labor-management relations inside a firm and inter-organization relations, exerts an influence on and cause the regional differences in RUMWs’ skill accumulation.

Lumpy skin disease (LSD), caused by a virus within the Poxviridae family and Capripoxvirus genus, induces nodular skin lesions in cattle, spreading through direct contact and insect vectors, significantly affecting global cattle farming. Despite available vaccines, their effectiveness is limited by poor bioavailability and adverse effects. Our study aimed to identify potential inhibitors targeting LSD-associated DNA polymerase protein, selecting LSDV039 for further investigation through comprehensive analysis and computational methods. Virtual screening revealed rhein and taxifolin as potent binders among 380 phytocompounds, with respective affinities of -8.965 and -7.195 kcal/mol. Canagliflozin and tepotinib exhibited strong affinities (-9.858 and -8.856 kcal/mol) among 718 FDA-approved antiviral drugs. Molecular dynamics simulations of canagliflozin, tepotinib, rhein, and taxifolin highlighted taxifolin's superior stability and binding energy. Rhein displayed compactness in RMSD and RMSF but fluctuations in Rg and SASA, while canagliflozin demonstrated stability compared to tepotinib. The study highlights the promising potential of repurposed drugs and phytocompounds as LSD therapeutics. However, extensive validation through in-vitro, in-vivo, and clinical trials is crucial for their practical application.

The p53 tumor suppressor protein is an activator of transcription. Diverse stress factors lead to various sets of posttranslational modifications of p53 what results in different sets of upregulat-ed genes. We noticed that actinomycin D and nutlin-3a (A+N) synergize in inducing activating phosphorylations of p53 and upregulation of selected p53-target genes. Here we found that one of these genes is DUSP13, which codes for poorly-studied, dual-specificity phosphatase having at least two isoforms, one expressed in testis and the other in skeletal muscles. In cancer cells ex-posed to A+N, DUSP13 is expressed from an alternative promoter in intron, what results in ex-pression of isoform named TMDP-L1. The luciferase reporter tests demonstrated that this pro-moter is activated by both endogenous and ectopically expressed p53. We showed for the first time that mRNA expressed from this promoter actually produces the protein, which can be de-tected by Western blotting in all examined cancer cell lines with wild-type p53 exposed to A+N. In some cell lines it is also induced by clinically relevant camptothecin or by nutlin-3a acting alone. This isoform, fused with green fluorescent protein localizes in perinuclear region of cells. Thus, TMDP-L1 isoform may be an important element of p53-regulated stress response system.

Optical sensor data can be used to determine changes in anthocyanins, chlorophyll and soluble solids content (SSC) in apple production. In this study, visible and near-infrared spectra (729 to 975 nm) were transformed to SSC values by advanced multivariate calibration models i.e. partial least square regression (PLSR) in order to test the substitution of destructive chemical analyses through non-destructive optical measurements. Spectral field scans were carried out from 2016 to 2018 on marked ’Braeburn’ apples in Southwest Germany. The study combines an in-depth statistical analyses of longitudinal SSC values with horticultural knowledge to set guidelines for further applied use of SSC predictions in the orchard to gain insights into apple carbohydrate physiology. The PLSR models were investigated with respect to sample size, seasonal variation, laboratory errors and the explanatory power of PLSR models when applied to independent samples. As a result of Monte Carlo simulations, PLSR modelled SSC only depended to a minor extent on the absolute number and accuracy of the wet chemistry laboratory calibration measurements. The comparison between non-destructive SSC determinations in the orchard with standard destructive lab testing at harvest on an independent sample showed mean differences of 0.5 % SSC over all study years. SSC modelling with longitudinal linear mixed-effect (LME) models linked high crop loads to lower SSC values at harvest and higher SSC values for fruit from the top part of a tree.

The COVID-19 pandemic over the past years has shown a great need for rapid, low-cost and on-site detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this paper, an aptamer-based colloidal gold nanoparticle lateral flow test strip was well developed to realize the visual detection of wild type SARS-CoV-2 spike protein (SP) and multiple variants. Under the optimal reaction conditions, a low detection limit of SARS-CoV-2 S protein of 0.68 nM was acquired, and the actual detection recovery was 83.3% to 108.8% for real world samples. This suggests a potential tool for the prompt detection of SARS-CoV-2 with good sensitivity and accuracy, and a new method for the development of alternative antibody test strips for the detection of other viral targets.

COVID-19 has rapidly spread worldwide since December 2019. During the pandemic, SARS-CoV-2 repeatedly mutated from Alpha to Omicron. The severity and mortality are related to age, sex, and underlying diseases (respiratory, cerebrovascular, cardiovascular, metabolic, cancer, and immune diseases). We retrospectively studied 44 hospitalized stroke patients infected with the SARS-CoV-2 Omicron variant. The mortality rate of hospitalized stroke patients with COVID-19 was 6 (13.6%). The cause of death was coagulopathy in 3 cases of ischemic stroke. High modified Rankin Scale score（mRS）of stroke patient was correlated with severity of COVID-19. The timing of vaccination is inversely correlated with COVID-19 severity. In conclusion, stroke patients with COVID-19 have high mortality rates attributed to coagulopathy. Stroke patients with high mRS scores are more likely to develop severe COVID-19. In high mRS scores, therapy for severe COVID-19 should be administered.

Maintaining sufficient levels of plant nutrients in the soil and controlling certain heavy metals, which can be toxic to the environment, are critical to ensure sustainable agricultural production. The study aimed to assess the linkage of crop-specific agricultural practices established by farmers in the Kvemo Kartli region (Georgia) with metal accumulation in soils of agricultural lands being subject to influence from polluted irrigation water in the past. In particular, we tried to identify the primary sources of micronutrients, including iron (Fe), copper (Cu), manganese (Mn), nickel (Ni), and zinc (Zn), and toxic elements such as cadmium (Cd) and lead (Pb), and share of the contaminated irrigation water and other factors related to agricultural practices under different land uses, such as intensive and extensive arable farming, vineyards, orchards, and permanent pastures having the least disturbed soil. Based on principal component analysis, five primary sources were identified and categorized according to farmers' interviews and previous studies conducted in the region. The results showed that increased concertation of plant-available Cu, Zn, Cd and Pb were mainly associated with irrigation water and intensive use of fungicides; Fe, Mn, and Ni were closely linked to several factors, such as the mineralogical composition of soils, mineral and organic fertilizers inputs, and atmospheric deposition from diffuse sources, where exhausts from transport are probably the primary source. During our study, we attempted to differentiate irrigation water inputs from fungicides using simulation based on irrigation pattern and irrigation water quality on the one hand and fungicide application rate and their metal content on the other. The simulation revealed that the intensive application of fungicides, especially in vineyards, is more significant in enriching soils with Cu and Zn than irrigation water. Identification of factorial dependences was supported by statistical analysis and application of a number of contamination assessment methods: Contamination Factor (CF), Pollution Load Index (PLI), single-factor Pollution Index (PI), Nemerow’s comprehensive pollution index (PIN), Enrichment Factor (EF), and Geo-Accumulation Index (Igeo). Applied environmental indices indicate that the soils under the former and existing vineyards are the most enriched with Cu and Zn, highlighting the significance of agricultural practices on heavy metals accumulation in soils of agricultural lands.

Proteins have the ability to adsorb on the surface of materials, such as soft contact lenses (SCLs), and can affect the hydrophobicity, roughness and surface properties of the contact lenses (CLs), which, in turn, can influence the friction between the lenses and the ocular surface. Excessive friction between contact lenses and the ocular surface can lead to discomfort for the wearer and may cause irritation or inflammation of the cornea, better known as corneal ulcers (keratitis). Bovine serum albumin (BSA) is often used as a standard protein in biocompatibility testing of materials, including contact lenses. One standard commercial contact lenses was tested under lubricated conditions to access the coefficient of friction (CoF), being the contact lubricated with a tear like fluid (TLF) solution containing six different concentrations of BSA. In all cases, a good linearity of the results of the friction force was verified, so the first friction law can be applied to determine the value of the coefficient of friction. It was found that friction increases with increasing protein concentration.

Genetic enhancement of grain production and quality is a priority in wheat breeding projects. In this study, we assessed two key agronomic traits - grain protein content (GPC) and thousand kernel weight (TKW) - across 179 Bulgarian contemporary and historic varieties, and landraces in three growing seasons. Significant phenotypic variation existed for both traits among genotypes and seasons, and no discernible difference was evident between the old and modern accessions. To understand the genetic basis of the traits, we conducted a genome-wide association study with MLM using phenotypic data from the crop seasons, best linear unbiased estimators, genotypic data from the 25K Infinium iSelect array, and a Bonferroni-adjusted p-value. As a result, 776 significant quantitative trait nucleotides (QTNs) organized into quantitative trait loci were discovered, including 25 loci associated with GPC, and 35 loci linked to TKW. Additionally, 14 environmentally stable QTNs were identified for TKW. Certain loci on chromosomes 2A, 3A, and 6B favorably in-fluenced GPC, while the locus on chromosome 6D impacted TKW positively. These loci may reflect novel associations to the two traits. Annotations for proteins involved in the remobilization of carbon and nitrogen from vegetative tissues to developing grain during senescence, as well as in the following buildup of resources required for seed germination, have been found for selected pu-tative candidate genes. These include genes coding for 11S globulin seed storage protein, glutamine synthetase, metalloendopeptidase, components of the ubiquitin/proteasome system, sucrose transporter, alpha-amylase, NAC and bZIP transcription factors. Our findings highlight promising genomic regions for targeted breeding programs aimed at improving grain yield and protein content.

Nitrogen (N) strongly affects plant growth and metabolism. For shikonin biosynthesis, although the ammonium toxicity phenomenon has been reported, the effects of nitrogen on the shikonin synthesis remains obscure. In this study, we carried out four different concentrations of NH4+ treatments on Arnebia euchroma hairy roots (AEHR) to clarify the influence of NH4+ on the growth and shikonin accumulation in A. euchroma and the possible mechanism. The results showed that compared with the 0% NH4+ treatment (only nitrate as nitrogen source), 10% NH4+ treatment increased the fresh weight and the dry weight of AEHR, and promoted the synthesis of shikonins; 20% NH4+ treatment started to show the inhibition effects on growth and shikonin accumulation of AEHR and 30% NH4+ treatment exhibited the strongest inhibition effects. With increased percentage of NH4+, AEHRs became shorter and thicker with more branches. To further elucidate the mechanism, we analyzed the time-course of nitrogen assimilation, gene expression level of key enzymes involved in the shikonin biosynthesis pathway, and contents of various endogenous hormones under NH4+ toxicity condition. Results indicated that auxin and cytokinin might regulate the growth and architecture of AEHR under NH4+ toxicity, and jasmonate level was reduced along with the inhibition of shikonin biosynthesis. This first comprehensive investigation into the effects of ammonium/nitrate ratio on shikonin biosynthesis not only provided valuable data for optimizing the in vitro culture and shikonin production in A. euchroma, but also suggested potential fertilizer strategies for its cultivation.

Flavonoids are major secondary metabolites in plants, which play important roles in maintaining the cellular redox balance in cells. Chalcone synthase (CHS) is the key enzyme in the flavonoids biosynthesis pathway, and has been proved to monitor the changes to drought stress tolerance. In this work, we overexpressed a CHS gene in tobacco (Nicotiana tabacum). The transgenic tobacco plants were more tolerant than the control plants to drought stress. The transcription levels of the key genes involved in the flavonoids pathway and the contents of seven flavonoids were also significantly raised in the transgenic tobacco plants. In addition, overexpression of the CHS gene lead to a lower concentration of the oxidative stress product malondialdehyde. Overall, the NtCHS gene studied in this work was considered as a candidate gene for genetic engineering to enhance drought tolerance of plants and improve response to oxidative stress.

The paper investigated the components of savings accumulation in Nigeria over the period 1980 to 2017. Secondary data were collated from World Development Index (WDI). In evaluating the objectives, the study employed the Auto Regressive Distributive Lag (ARDL) and Vector Error Correction Model (VECM) estimation methods. The key findings of the study show that the components of savings identified in literature understudied in the paper specifically, GDP per capita, foreign direct investment, financial deepening, interest rate, inflation rate exchange rate significantly influence savings accumulation in Nigeria either in short run, long run or both. Financial deepening was found statistically significant but influences savings negatively. Inflation rate was statistically insignificant although negative. The result from the VECM causality test revealed that short run and long run causal relationship exist between savings and the afore mentioned components in Nigeria. Hence, the study recommends careful manipulation of the identified savings components in a manner that they will not yield a counterproductive result in the economy rather contribute to the growth of savings and ultimately, the growth of Nigeria economy as a whole. It further recommends that the Nigerian government through its financial institutions encourage savings from both small and big savers which to large extent will assuage the perceived undeserved influence of financial deepening on savings accumulation.

The expanding global population has increased the demand for sustainable protein sources, and microbial protein (MP) has emerged as a promising alternative. However, conventional carbon (glucose) and nitrogen (ammonia, urea) sources needed for MP production pose environmental and economic issues. This study aims to produce protein using lignocellulosic biomass (LCB) as a carbon source and the nitrogen fixation ability of Klebsiella oxytoca M5A1 as a nitrogen source. The study investigates the pretreatment of LCB (switchgrass), enzymatic hydrolysis, protein quantification, and high-performance liquid chromatography system (HPLC) analysis to track glucose utilization and organic acid production. K. oxytoca M5A1 harnessed free nitrogen from the atmosphere through nitrogen fixation and used abundant, cheap glucose from LCB to produce MP and organic acids as by-products. Protein production occurred in two phases: first within the initial 8 hours and secondly, within the last 16 hours. The highest protein concentration was at 40 hours, with approximately 68.3% protein content. HPLC analysis revealed a dynamic profile of glucose utilization and organic acids (Lactic acid, Propionic acid, Acetic acid, and Succinic acid). K. oxytoca M5A1 exhibited an early high rate of glucose consumption, and conversion to organic acids that were later used for second-phase protein production. The acids profile revealed intra-conversion from one acid to another via metabolic pathways (glycolysis and tricarboxylic acid cycle). Overall, leveraging LCB and the nitrogen-fixing ability of K. oxytoca M5A1 for MP production offers an eco-friendly and cost-effective alternative to traditional protein sources, contributing to a sustainable circular economy.

The paper presents the results of experimental studies and mathematical modeling of the effect of stress accumulation in thermosetting epoxy polymer "hot" curing on anhydride hardener. Stress accumulation occurs under cyclic thermomechanical action in a locked rod, similar effects are observed, for example, in thermoplastic elements subjected to the combined effect of mechanical loads and variable temperatures. Experimental results have shown that under cyclic thermomechanical loading during exploitation it is possible to accumulate residual stresses in the thermosetting polymer. A multi-element structural mathematical model with memory for thermomechanical load, which allows to consider the accumulation of residual thermal stresses, has been proposed. The results of modeling and experiment are compared. Based on the results, corrections are made in the approach to the application of this model to thermosetting polymers such as the epoxy resin under study. Considering the corrections, a good agreement (the difference is from 1 to 6%) with the results of experimental determination of stresses under complex cyclic thermomechanical load was obtained.

Plastic pollution of the ocean is currently one of the most serious environmental threat. Analysis of observations in the Arctic ocean shows that microplastic particles have been found in Arctic snow cover, sea ice, water and sediments. Possible pathways and deposition locations of microplastics in the Arctic Ocean can be assessed based on 3D numerical modeling of thermohaline structure and water circulation, sea ice conditions and drift. The problem is that in addition to transport by currents, a number of other processes affect the state of microplastics. These include mechanical fragmentation, freezing into sea ice and release back into the water, biofouling, adsorption of contaminants and other factors. In this study, based on scenario calculations for a 5-year period, we analyzed the possible spread of microplastics brought by Siberian rivers to the Kara Sea shelf. The Lagrangian particle model used daily 3D numerical simulation data to simulate microplastic transport by ocean currents and by sea ice drift. The results of a series of scenario calculations show how the distribution of particles and their subsequent deposition depend on their type (density), size, processes of freezing into the ice and biofouling.

Based on the plate tectonic theory, using seismic, geology, and public literature data, the proto-type basins and lithofacies paleogeography during the main geological periods of the passive continental margin of East Africa are restored, and the architecture characteristics of the basins and the differences in sedimentary fillings are analyzed. Combined with the dissection of discovered oil and gas reservoirs, four types of hydrocarbon accumulation models are established, the favorable hydrocarbon accumulation combinations (plays), and the next exploration directions in this region are explored. The passive continental margin basins in East Africa experienced three proto-type stages: intracontinental aborted rift during the Late Carboniferous-Triassic Karoo period, intracontinental-intercontinental rift during the Jurassic period, and passive continental margin basin since the Cretaceous period. Affected by the difference in sedimentary filling thickness between the rift period and depression period, four types of passive continental margin basins are formed: rifted type, depressed type, faulted depression type, and reformed delta type. The maximum sedimentary thickness of the rifted basins during the rift period is greater than 3500 m, and that during the depression period is less than 4000 m, forming a "single-source structure type" hydrocarbon accumulation model. The exploration of rifted basins should focus on giant structural traps at the top of the rifted sequences. The maximum sedimentary thickness of the depressed basins during the depression period exceeds 4000 m, forming a "single-source fan group type" hydrocarbon accumulation model. The dominant exploration directions of depressed basins are sedimentary sand bodies and structural-lithologic traps during the depression and drift periods. The maximum sedimentary thickness of the faulted depression basins during the rift period is greater than 3500 m, and that during the depression period is greater than 4000 m, forming a "double-source and double-combination type" hydrocarbon accumulation model. The exploration of rifted basins should focus on giant slip-collapse-debris flow sedimentary sand bodies on the upper and middle slopes. In addition to the large sedimentary thickness of the early rift and the central depression, the delta thickness of the reformed delta basins during the late depression period since the Miocene is more than 4000 m, and four structural belts (growth fault, mud diapir, thrust fold, and foredeep gentle slope) were formed from onshore to offshore, forming a "three-source and multi-combination type" hydrocarbon accumulation model. All four structural belts can form giant oil and gas fields.

Heavy metals have adverse effects on microalgae growth and metabolism. Photosynthesis and lipid profile are quite sensitive to heavy metal toxicity. The impact of chromium (Cr) on growth and photosynthetic activity of Dictyosphaerium pulchellum and Micractinium pusillum exposed to different concentrations (0 – 500 μg L-1) was investigated for 11 days. The influence of Cr on cell density and cell number followed similar trends, indicating a possible correlation among these growth responses. A significant (p < 0.05) increase in lipid content was observed with the increasing concentration of Cr however, growth was suppressed at higher concentrations exceeding 100 μg L-1. Addition of Cr in the cell culture medium showed a negative effect on quantum yield (Fv/Fm) and a photosynthetic inhibition of > 65% was noted in both species at 500 μg L-1. However, the lipid gravimetric analysis presented inner cell lipid content up to 36% and 30% of dry weight biomass for D. pulchellum and M. pusillum, respectively. The effects of chromium on growth and lipid accumulation in both microalgae species was concentration and exposure time dependent. This shows that an appropriate concentration of chromium in culture medium could be beneficial for higher lipid accumulation in freshwater eukaryotic microalgae species.

Plastic production is escalating tremendously throughout the globe and the reason behind this is its durability and multipurpose utility. But there is a severe scarcity of its management. Tonnes of plastics are dumped into water bodies across the world. These plastics breakdown because of different reasons and results in the plastic debris of size <5mm termed as microplastics (MPs) which are hazardous to aquatic life. They are a potential source of toxins as they offer a large surface area to various chemicals present in the water body when these MPs are ingested by fishes it causes serious health issues leading to mortality of the fishes. Therefore, we comprehensively reviewed the sources of MPs in freshwater systems and its various types and how they get accumulated inside the body of fishes. We found that fishes ingest these particles by mistaken for food or accumulated these particles by consuming from lower trophic organisms. Some of the commonly studied MPs are PE, PS, and PVC, examined from the body of fishes. MPs can cause various ecotoxicological effects on fishes like behavioral change, cytotoxicity, neurotoxicity effects, and liver stress etc. Our review study finds that there is a paucity of information on the accumulation of MPs by freshwater fishes and there are very few studies on its effects also there is a debate whether this accumulation is subjected to the bio-magnification process which ultimately affects human life.

Low-temperature accumulation is one of the essential stages in the growth process of woody ornamental plants. In this study, two different low-temperature treatments, 6℃ and 10℃, were used to analyze the effects of different low-temperature treatments on dormancy release and flowering of the 'Gulihong' plant using artificial low temperatures. Based on the experimental results, four typical early-blooming Prunus mume cultivars widely planted in Yangling area of Henan Province, China, including 'Zaoyudie', 'Zaohualve', 'Nanjing gongfen', and 'Gulihong', were selected as the experimental materials. The effects of low-temperature accumulation on the flowering characteristics of different cultivars were analyzed using a 6℃ artificial low-temperature treatment. The suitable cultivation temperature for early-blooming P. mume cultivars was screened to provide a theoretical basis for further exploration of P. mume bonsai cultivation techniques. The results showed that the flowering rate, flower diameter, flowering quantity, flowering uniformity, and bud development in the 6℃ treatment were significantly better than those in the 10℃ treatment. The flowering rate and quality of different cultivars gradually increased with the accumulation of low-temperature. Therefore, chill accumulation plays a significant role in promoting flowering quality.

The dimensional effect of the accumulation of an electric charge with a density of up to 270 μF/g by the system of compacted zirconium dioxide nanoparticles during exposure in an electric field (5000 V/m) under normal physical conditions is determined. Based on a qualitative complex analysis of the forms of appearance of the effect, it is shown that the place of localization of different charge carriers is the surface of nanoparticles. The supposed mechanism of this effect is considered using the theory of dispersed systems, the band theory, and the theory of contact phenomena in semiconductors. It was concluded that this mechanism is due to the phenomenon of localization of electron-type charge nanoparticles in the near-surface zone of the material in contact with the adsorption ion atmosphere. This effect is relevant for modern nanoelectronics, microsystem technology, and printed electronics.

Hepatitis B virus (HBV) is the dominant risk factor for hepatocellular carcinoma (HCC). HBV X protein (HBx) plays crucial roles in HCC carcinogenesis. HBx interferes with several signaling pathways including Notch1 pathway in HCC. In our study, we found that Notch1 was highly expressed in HCC especially in large HCC. Notch1 and HBx co-localized in HCC and their levels were positively correlated with each other. Notch1 expression was more elevated in HepG2.2.15 than that in HepG2. HBx activated Notch1 pathway in HepG2.2.15. Repression of HBx and Notch1 pathway attenuated the growth of HepG2.2.15. Notch1, ERK and AKT pathways were inhibited after a γ-secretase inhibitor treatment. Dual-specificity phosphatase 1 (DUSP1) and phosphatase and tensin homolog (PTEN) were up-regulated after the γ-secretase inhibitor treatment and Hes1 inhibition. Luciferase reporter assays showed that Hes1 repressed the promoters of DUSP1 and PTEN and this was reverted by γ-secretase inhibitor treatment. Western blotting demonstrated that DUSP1 dephosphorylated pERK and PTEN dephosphorylated pAKT. Collectively, we reported a link among HBx, Notch1 pathway, DUSP1/PTEN, and ERK/AKT pathways, which influenced HCC cell survival and could be a therapeutic target for HCC.

This study delves into the extraction and compositional analysis of soybean meal protein isolates (SMPI) compared to soy protein isolates (SPI), focusing on their functional and structural properties, digestibility, amino acid composition, and the impact of various proteases on antinutritional factors. By leveraging alkaline (0.25 % of NH4OH) extraction and isoelectric precipitation, SMPI was efficiently obtained. Compositional characteristics revealed that SMPI has high moisture, protein, and ash, but lower fat, and carbohydrate content compared to SPI. Alcalase, Neutrase and Pepsin hydrolysis indicated lower digestibility of SMPI than SPI. Fourier-transform infrared spectroscopy and sodium dodecyl sulfate-polyacrylamide gel electrophoresis provided similar molecular structure and protein molecular weight distribution. This comprehensive analysis underscores the valorization of soybean meal, promoting its use beyond conventional animal feed towards nutritional supplements and bio-based products, thereby contributing to environmental sustainability and the enhancement of global food systems.

The study of the impact of polyQ expansion driven proteotoxicity on cell metabolism has evi-denced NAD molecule as a central player in regulating metabolic response and cell repair in neurodegeneration. The decline in NAD intracellular levels represents a hallmark of ageing aris-ing from a dysregulation between NAD-consuming and biosynthetic enzymatic reactions in which NMNAT plays a key role. By an integrated bioanalytical and proteomic experimental design, the derangement of NAD metabolism deriving from the accumulation of polyQ-Htt protein has been analysed in Saccha-romices cerevisiae harbouring a 103Q-Htt and compared with wild-type Htt, in absence and in presence of a phenolic extract from EVOO, as a source of antioxidant bioactive compounds. Quantification of NAD and its precursors and proteomic analysis of the differential protein ex-pression has been performed by LC-DAD-MS. Chronological lifespan and NAD homeostasis was strongly impaired by proteotoxic polyQ-Htt, eliciting a depletion of NAD levels and accumulation of NaMN. In parallel a downregulation of Sirt2 expression levels has been observed. Phenolic extract administration had no meaningful ef-fects on NAD replenishment to prevent proteotoxicity. NaMN can represent a biomarker of accel-erated aging, and/or a signaling molecule for cell repair.

The combination of snowfall, snow water equivalent (SWE), and precipitation rate measurements from 39 Snow Telemetry (SNOTEL) sites in Alaska are used to assess the performance of various precipitation products from satellites, reanalysis, and rain gauges. Observation of precipitation from two water years (2018-2019) of the high resolution radar/rain gauge data (Stage IV) product was also utilized to add insights into scaling differences between various products. The outcomes were also used to assess two popular methods for rain gauge undercatch correction. It was found that SWE and precipitation measurements at SNOTELs, as well as precipitation estimates based on Stage IV data, are generally consistent and can provide a range in which other products can be assessed. Time-series of snowfall and SWE accumulation suggests that most of the products can capture snowfall events; however, differences exist in their accumulation. Reanalysis products tend to overestimate snow accumulation in the study area, while current combined passive microwave remote sensing products (i.e., IMERG-HQ) underestimate snowfall accumulation. We found that corrections factors applied to rain gauges are effective in improving their undercatch, especially for snowfall. However, no improvement in correlation is seen when correction factors are applied, and rainfall is still estimated better than snowfall. Even though IMERG-HQ has less skill in capturing snowfall than rainfall, analysis using Taylor plots showed that the combined microwave product does have skill in capturing the geographical distribution of snowfall and precipitation accumulation, so bias adjustment might lead to reasonable precipitation estimates. This study demonstrates that other snow properties (e.g., SWE accumulation at the SNOTEL sites) can complement precipitation data to estimate snowfall. In the future, gridded SWE and snow depth data from GlobSnow and Sentinel-1 can be used to assess snowfall and its distribution over broader regions.

In order to better understand the source-sink flow and relationships of Zinc (Zn) and other nutrients in wheat (Triticum aestivum L.) plants for biofortification and improving grain nutritional quality, effects of reducing photoassimilate source (through the flag leaf removal and spike shading) or sink (through 50% spikelets removal) in the field on accumulation of Zn and other nutrients in wheat grains of two cultivars (Jimai 22 and Jimai 44) were investigated under two soil Zn application levels. The single panicle weight (SPW), kernel number per spike (KNPS), thousand kernel weight (TKW), total grain weight (TGW), concentrations and yields of various nutrient elements (Zn, Fe, Mn, Cu, N, P, K, Ca and Mg), phytate phosphorus (phytate-P), phytic acid (PA) and phytohormones (ABA: abscisic acid, and the ethylene precursor ACC: 1-aminocylopropane-1-carboxylic acid), and C/N ratios were determined. Soil Zn application significantly increased concentrations of grain Zn, N and K. Cultivars showing higher grain yields had lower grain protein and micronutrient nutritional quality. SPW, KNPS, TKW (with an exception of TKW in half spikelets removal), TGW, and nutrient yields in wheat grains were most severely reduced by half spiklets removal, secondly by spike shading, and slightly by flag leaf removal. Grain concentrations of Zn, N and Mg consistently showed negative correlations with SPW, KNPS and TGW, but positively with TKW. There were general positive correlations among grain concentrations of Zn, Fe, Mn, Cu, N and Mg, and bioavailability of Zn and Fe (estimated by molar ratios of PA/Zn, PA × Ca/Zn, PA/Fe, or PA × Ca/Fe). Although concentrations of Zn and Fe were increased and Ca was decreased in treatments of half spikelets removal and spike shading, the simultaneously increased PA limited the increase in bioavailability of Zn and Fe. In general, different nutrient elements interact with each other and are affected to different degrees by source-sink manipulations. Elevated endogenous ABA levels and ABA/ACC ratios were associated with increased TKW and grain-filling of Zn, Mn, Ca and Mg, and inhibited K in wheat grains. However, effects of ACC were diametrically opposite. These results provide basis for wheat grain biofortification to alleviate human malnutrition.

This study aimed to investigate the appearance and frequencies of the booroola polymorphism of the bone morphogenetic protein receptor 1b (BMPR1B) gene (FecB) and the embrapa polymorphism of the growth differentiation factor 9 (GDF9) gene (FecGE) in sheep in Thailand. A total of 454 cross-bred sheep blood samples were collected from four provinces in Thailand during August 2022 to July 2023. The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was used to identify the FecB and FecGE genotype. The history of ewe birth types was collected from the owners to analyze the association between Fecundity (Fec) genotypes and the history of birth types. The genotypic frequencies of FecB for homozygous genotype (B/B), heterozygous genotype (+/B) and wild-type (+/+) were 0.22%, 1.54%, and 98.24%, respectively. Meanwhile, the genotypic frequencies of FecGE for homozygous genotype (E/E), heterozygous genotype (+/E), and wildtype (+/+) were 0.00%, 2.42%, and 97.58%, respectively. Furthermore, three ewes exhibited both FecB and FecGE genotypes. Fisher’s exact test revealed that the possessor of FecB genotype was associated with multiple births (p&lt;0.01). Both FecB and FecGE mutations were identified in crossbred sheep in Thailand. Sheep containing FecB allele is a better candidate to be selected to improve the prolificacy of crossbred sheep in Thailand.

In order to study the effects of irradiation on the physicochemical properties and digestion behavior of chickpea protein, chickpea protein concentrate (CPC) was treated with electron beam irradiation (EBI) at doses of 5, 10, 15 and 20 kGy, respectively. After irradiation, protein solubility first increased at 10 kGy and 15 kGy, and then decreased at higher dose of 20 kGy. This was supported by SDS-PAGE where the intensity of major protein bands first increased and then decreased. Increased does of EBI generally led to greater oxidative modification of proteins in CPC, indicated by reduced sulfhydryls and increased carbonyls. In addition, protein structure was modified by EBI shown by Fourier transform infrared spectroscopy analysis where α-helix generally decreased and β-sheet increased. Although the protein digestibility was not significantly affected by EBI, the peptidomic analysis of the digests revealed significant difference among CPC irradiated with varying doses. A total of 337 peptides were identified from CPC irradiated with 0 kGy, 10 kGy and 20 kGy, respectively, with 18 overlapping peptides and 60, 29 and 40 peptides specific to the groups of 0, 10 and 20 kGy respectively. Theoretical calculation showed that the distribution of peptide length, hydrophobicity, net charge, and C-terminal residues were affected by irradiation. The 2, 2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical scavenging activity showed a marginal decrease with increasing dose of irradiation. In conclusion, EBI led to oxidative modification and structural changes of the chickpea protein, which subsequently affected the physicochemical properties of peptides obtained from in-vitro digestion of CPC despite of similar digestibility.

This paper aims to investigate the coal thickness change area of the combined rock strata energy accumulation law. The method of connecting a uniaxial compression experiment with a theoret-ical analysis is used in this work. We employ a combination of coal and rock to carry out our studies. We investigate how different lithologies and ratios of coal-rock height affect the me-chanical properties of the mixture and the law governing energy accumulation. We have deter-mined the following facts: (1) The combination's peak strength and elastic modulus exceed that of coal and are inferior to that of rock but are nearer to that of coal. (2) When the coal-rock height ratios are dissimilar, the peak strength and modulus of elasticity of the combination show a negative correlation with the coal-thickness share, and the pre-peak energy accumulation and impact energy index of the combination shows a positive correlation with the coal-thickness share. (3) For the combination with the same coal-rock height ratio, the peak strength, elastic modulus, pre-peak energy accumulation, and impact energy index all increase with greater rock strength and elastic modulus. The presence of a hard rock layer affects the accumulation of pre-peak energy. ( 4 ) The stress in the surrounding rock gradually decreases as the coal thick-ness increases. In the area where coal thickness declines, the stress in surrounding rock is higher than that in the region where it thickens. The energy stored in the surrounding rock is directly proportional to the coal in the zone. Conversely, areas with thinner coal deposits exhibit a lower energy storage capacity in the surrounding rock than those with thicker coal deposits. The stress distribution of surrounding rock in coal thickness change is abnormal; substantial energy accu-mulation can swiftly initiate dynamic disasters, such as rock bursts. This study has important reference significance for preventing and controlling rock burst in coal thickness change areas.

This paper constructs a model of climate-related damage for small island developing states (SIDS). We focus on the loss of private productive capital stocks through extreme climate events. In contrast to most economic analyses of climate impacts, which assume temperature-dependent damage functions, we draw on the engineering literature to allow for a greater or lesser degree of anticipation of climate change when designing capital stocks and balancing current adaptation expenditure against future loss & damage. We apply the model to tropical storm damage in the small island developing state of Barbados and show how anticipatory behavior changes the damage to infrastructure for the same degree of climate change. Thus, in the model, damage depends on behavior as well as climate variables.

Cadmium accumulation in rice grain poses a serious threat to people’s health. Understanding the genetic basis on grain cadmium accumulation facilitates efforts to reduce it. Here, we show that OsCd1 is involved in Cd uptake and contributes to grain accumulation in rice. Natural variation in OsCd1 with a missense mutation Val449Asp is responsible for the divergence of rice grain cadmium accumulation between japonica and indica. Notably, near-isogenic line tests confirmed that the indica variety carrying the OsCd1^V449 allele could reduce the grain cadmium accumulation. The favorable allele OsCd1^V449 may be an important genetic resource to reduce grain cadmium accumulation for indica.

Neurodegeneration with brain iron accumulation (NBIA) is a group of rare neurogenetic dis-orders frequently associated with iron accumulation in the basal nuclei of the brain. Among NBIA subtypes, β -propeller protein-associated neurodegeneration (BPAN) is associated with mutations in the autophagy gene WDR45. The aim of this study was to demonstrate autophagic defects and secondary pathological con-sequences in cellular models derived from two patient harboring WDR45 mutations. Both protein and mRNA expression levels of WDR45 were decreased in patient-derived fibro-blasts. In addition, the increase of LC3B upon treatments with autophagy inducers or inhibitors was lower in mutant cells compared to control cells, suggesting decreased autophagosome formation and impaired autophagic flux. Transmission electron microscopy (TEM) analysis showed mitochondrial vacuolization associated with accumulation of lipofuscin-like aggregates containing undegraded material. Autophagy dysregulation was also associated with iron ac-cumulation and lipid peroxidation. In addition, mutant fibroblasts showed altered mitochon-drial bioenergetics. Antioxidants such as pantothenate, vitamin E and α-lipoic prevented lipid peroxidation and iron accumulation. However, antioxidants were not able to correct the ex-pression levels of WDR45 neither the autophagy defect nor cell bioenergetics. Our study demonstrated that WDR45 mutations in BPAN cellular models impaired autophagy, iron metabolism and cell bioenergetics. Antioxidant partially improved cell physiopathology, however autophagy and cell bioenergetics remained affected.

Cell-penetrating peptides (CPPs), a group of small peptides capable of promoting the transport of molecular cargo across the plasma membrane, have become important tools in promoting the cellular uptake of exogenously delivered macromolecules. GV1001, a peptide derived from a reverse-transcriptase subunit of telomerase (hTERT) and developed as a vaccine against various cancers, reportedly has unexpected CPP properties. Unlike typical CPPs, such as the HIV-1 TAT peptide, GV1001 enabled the cytosolic delivery of macromolecules such as proteins, DNA and siRNA via extracellular heat shock protein 90 (eHSP90) and 70 (eHSP70) complexes. The eHSP-GV1001 interaction may have biological effects in addition to its cytosolic delivery function. GV1001 was originally designed as a MHC class II-binding cancer epitope, but its CPP properties may contribute to its strong anti-cancer immune response relative to other telomerase peptide-based vaccines. Cell signaling via eHSP-GV1001 binding may lead to unexpected biological effects, such as direct anticancer or antiviral effects. In this review, we focus on the CPP effects of GV1001 bound to eHSP90 and ehsp70.

Gliomas are one of the most aggressive and treatment-resistant types of human cancer. One of the most promising field in gliomas cancer therapy is identification and evaluation of anticancer properties of compounds found in plants i.a. naringenin (N) and 8-prenylnaringenin (8PN). The prenyl group seem to be crucial to the anticancer activity of flavones, which may lead to enhanced cell membrane targeting and thus increased intracellular activity. Unfortunately, 8PN content in hop cones is from 10 to 100 times lower compared to other flavonoids i.e. xanthohumol. In this study we used a simple method for the synthesis of 8PN from isoxanthohumol, via O-demethylation with high, 97% of the isolated yield. Cellular accumulation and cytotoxicity of naringenin and 8-prenylnaringenin in normal (BJ) and cancer cells (U-118 MG) were also examined. Obtained data indicated that 8-prenylnaringenin exhibited higher toxicity against used cell lines than naringenin and both flavones inhibited stronger glioblastoma U-118 MG cells than normal fibroblasts. The anticancer properties of 8PN correlated with its significantly greater (37%), accumulation in glioblastoma cells than in normal fibroblasts. Additionally, naringenin indicated higher selectivity for glioblastoma as it was over 6 times more toxic for cancer than normal cells. Our results provide evidence that examined prenylated and non-prenylated flavanones have different biological activity against normal and cancer cell lines and this phenomenon may be useful in clinical practice to construct new, anticancer drugs for glioblastoma.

The biomethane accumulation of several combinations of whey and sugarcane molasses, inoculated with sludge from a treatment facility of one of the dairy enterprises of Imbabura, was assessed in the current experiment at a concentration of 0.5 g/l COD. The whey: molasses (W: M) ratios for each treatment were 0:100, 25:75, 50:50, 75:25, and 100:0, with a constant temperature of 37°C and an initial pH adjustment of 7.5. Half a litre of total mixes was used for each treatment in duplicate. Six kinetic models were evaluated to account biomethane accumulation in anaerobic co-digestion processes in batch of whey and sugarcane molasses. Five of these have been tested by other researchers, and one was developed by modifying a first-order model to consider changes in the biomethane accumulation profile. This proposed model, along with the modified two-phase Gompertz model, resulted in the ones that were best able to adjust the experimental data, obtaining in all cases an R² ≥ 0.949, indicating the accuracy of both models. In addition, the proposed here model has five parameters, one less than the modified two-phase Gompertz model, making it more straightforward and robust.

Metal hyperaccumulating plants should have extremely efficient defence mechanisms, enabling growth and development in a polluted environment. Brassica species are known to display hyperaccumulation capability. Brassica juncea (Indiana mustard) v. Malopolska plants were exposed to trace elements, i.e., cadmium (Cd), copper (Cu), lead (Pb), and zinc (Zn), at a concentration of 50 M and were then harvested after 96 hours for analysis. We observed a high index of tolerance (IT), higher than 90%, for all B. juncea plants treated with the four metals, and we showed that Cd, Cu, Pb and Zn accumulation was higher in the above-ground parts than in the roots. We estimated the metal effects on the generation of reactive oxygen species (ROS) and the levels of protein oxidation as well as on the activity and gene expression of antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT) and ascorbate peroxidase (APX). The obtained results indicate that organo-specific ROS generation was higher in plants exposed to essential metal elements (i.e., Cu and Zn), compared with non-essential ones (i.e., Cd and Pb), in conjunction with SOD, CAT and APX activity and expression at the level of encoding mRNAs and existing proteins. In addition to the potential usefulness of B. juncea in the phytoremediation process, the data provide important information concerning plant response to the presence of trace metals.

Deciphering protein–protein interactions (PPIs) in vivo is crucial to understand protein function. Bimolecular fluorescence complementation (BiFC) is one of extensively used PCAs over the last decade in many different native contexts, including human live cells. It is based on the reconstitution of a monomeric fluorescent protein (FP) such as cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP) from two complementary nonfluorescent sub-fragments (N- and C-terminal sub-fragments) upon spatial proximity. Interaction between a bait protein and a prey protein fused to such complementary sub-fragments is sufficient to lead to the reconstitution of the FP, resulting in an emission signal upon excitation (Figure 1). In this comprehensive review, we commence by tracing the development of fluorescent proteins (FPs) tailored for BiFC, followed by the highlighting of BiFC advantages over other PPI detection methods. Concurrently, the essential factors and nuanced considerations when employing BiFC are thoroughly explored. To vividly showcase the versatility of BiFC, the implementations at different throughputs are also presented, encompassing both single PPI experiments and large-scale studies, along with noteworthy variants of BiFC.

In this study we used a recently developed ex vivo-in vitro model to assess the effect of feeding older adults a casein protein hydrolysate (CPH) compared with non-bioactive non-essential amino acid (NEAA) supplement on Muscle Protein Synthesis (MPS) and Breakdown (MPB). Serum from six healthy older males following overnight fast and 60 min postprandial ingestion of CPH or NEAA (0.33 g.kg^-1 body mass) was used to condition C2C12 myotube media. CPH-fed serum significantly increased MPS compared to fasted serum. In addition, CPH-fed serum induced myotube growth and markedly suppressed atrogin-1, but not MuRF1, expression. Comparatively, no change in MPS, myotube growth and gene expression was observed following NEAA-fed serum treatment. CPH-fed serum from older adults stimulated de novo MPS, suppressed markers of protein breakdown and resulted in myotube growth, indicating a potential role for CPH as a dietary protein source to prevent age-related sarcopenia.

This manuscript addresses the phenomenon of masked priming in bilingual individuals. We employed a lexical decision task with masked translation priming, which serves as a valuable tool for elucidating the orthographic and lexical processes involved in the initial stages of reading. Our study builds upon previous research conducted on monolingual masked priming, which consistently demonstrates shifts in the response time (RT) distributions when comparing related and unrelated primes. Within the framework of a diffusion model, we implemented two theoretical positions. First, we posited that translation priming operates at the orthographic level, resulting in enhanced efficiency during the encoding process. Second, we explored the possibility that translation priming operates at the semantic level, influencing the accumulation of evidence during the lexical decision task. Our findings indicate that translation priming elicits outcomes similar to those observed in monolingual priming paradigms. Specifically, we observed that translation priming facilitation is manifested as shifts in the RT distributions. We interpret these findings as suggesting that the benefits derived from the encoding process are not specific to the accessed lexicon following brief stimulus presentation.

With permafrost degenerating caused by climate change, water accumulation increases in permafrost regions during last decades. Water accumulation will deteriorate existing status of engineering in cold regions. Water accumulation can make a thermal effect on permafrost under construction, even result in failure of the subgrade. Moreover, the thermal effect is related to water temperature. However, temperature variation of water accumulation is complex, and its influence factors include air temperature, environment, scope of water accumulation and so on. In order to make analysis of the damage mechanism of water accumulation on permafrost, it is necessary to explore the internal temperature change of water accumulation. This paper proposes a review about temperature calculation method of water accumulation in cold environment. The thermal calculation method between air and water boundary of water accumulation is summarized. Water temperature change of water accumulation with various type is analyzed. The thermal calculation considering phase transformation in water accumulation is discussed, and heat transfer from the bottom of water accumulation to the underlying soil is further studied. Finally, the key factors which are advantageous to make research about the thermal effect of water accumulation in permafrost is proposed to optimize calculation method.

Phytoene is a colourless natural carotenoid that absorbs UV light and provides antioxidant and anti-inflammatory activities as well as protection against photodamage. It is therefore valued for its skin health and aesthetic benefits by the cosmetic industry, as well as by the health food sector. The halotolerant green microalga Dunaliella salina is one of the richest sources of natural carotenoids. We have previously investigated over-production of phytoene in D. salina after cultivation with the well-characterised mitosis inhibitor, chlorpropham. In this study, 15 herbicides with different modes of action were tested for their potential to promote phytoene accumulation. All herbicides showed different levels of capabilities to support phytoene over-production in D. salina. Most significantly, the two mitosis inhibitors tested in this study, propyzamide and chlorpropham, showed similar capacities to support over-production of phytoene by D. salina cultures, as phytoene desaturase inhibitors. The cellular content of phytoene increased by over 10-fold within 48 h after treatment with the mitosis inhibitors compared to untreated cultures. Results indicate a general effect of mitosis inhibitors on phytoene accumulation in D. salina. Furthermore, red light was found to significantly enhance the phytoene yield when used in combination with effective inhibitor treatments. Red light can be applied to maximize the production of phytoene from D. salina.

Wooden breast is a muscle disorder affecting modern commercial broiler chickens that causes a palpably firm pectoralis major muscle and severe reduction in meat quality. Most studies have focused on advanced stages of wooden breast apparent at market age, resulting in limited insights into the etiology and early pathogenesis of the myopathy. Therefore, the objective of this study was to identify early molecular signals in the wooden breast transcriptional cascade by performing gene expression analysis on the pectoralis major muscle of two-week-old birds that may later exhibit the wooden breast phenotype by market age at 7 weeks. Biopsy samples of the left pectoralis major muscle were collected from a subset of 101 birds randomly selected from a total of 302 birds at 14 days of age, after which all birds were raised to 7 weeks of age for scoring of wooden breast. RNA sequencing was performed on 5 unaffected and 8 affected female chicken samples, selected based on wooden breast scores (0 to 4) assigned at necropsy where affected birds had scores of 2 or 3 (mildly or moderately affected) while unaffected birds had scores of 0 (no apparent gross lesions). Differential expression analysis identified 60 genes found to be significant at an FDR-adjusted p value of 0.05. Of these, 26 were previously demonstrated to exhibit altered expression or genetic polymorphisms related to glucose tolerance or diabetes mellitus in mammals. Additionally, 9 genes have functions directly related to lipid metabolism and 11 genes are associated with adiposity traits such as intramuscular fat and body mass index. This study suggests that wooden breast disease is first and foremost a metabolic disorder characterized primarily by ectopic lipid accumulation in the pectoralis major.

We investigate wealth accumulation in forestry, assuming that revenues are re-invested. Three different optimization criteria are compared, two of which are based on cash flows, the third financially grounded. Direct optimization of wealth appreciation rate always yields best results. Procedures gained by maximizing internal rate of return are only slightly inferior. With external discounting interest rate, the maximization of net present value yields arbitrary results, with at worst devastating financial consequences.

The evolution of human societal dynamics over the course of decades and centuries has led to an ever-increasingly complex digital modern life, one of the hallmark of which is the need for multi-tasking, inclusive of that with media. Is there an empirical mapping between this macroscopic (digital) evolution of the human societal dynamics (in terms of multi-tasking) and the microscopic evolution of the functional molecular units within cells (i.e., proteins) and their manifold cross-talks? Multi-tasking requires a certain degree of intrinsic or adapted flexibility which is as true at the bio-molecular level. Evolutionary diversification of structure-function relationship in proteins emphasizes the functional importance of intrinsically disordered entities (IDPs/IDRs) which are highly dynamic biological soft matters. Multi-functionality is favorably supported by their fluid-like shapes and other new malleable members of the protein family. The new wealth of knowledge coming from recent research on protein intrinsic disorder, fold-switching, moonlighting, hub proteins etc. has given us new insights into protein structure – functional relationship. This has led to a paradigm shift in protein science, clearly diverging from the traditional 'one structure – one function' model applicable to enzyme classes to a more complex understanding of protein functionality. This paradigm shift has caused scientists to delve deeper into the subject, exploring various evolutionary toys and tools to fit the cumulative multi-functional demands in higher organisms. This commentary covers the different evolutionary arsenals to achieve the growing multi-functionality and argues in favor of protein intrinsic disorder as probably the sharpest weapon of all.

Variable and sometimes contrasting effects of using artificial rhizobium inocula to increase grain legume performance have been reported. The objectives of this systematic review and meta-analysis were therefore to (i) estimate the overall effect of rhizobium inocula on grain yield and protein content and (ii) identify potential confounding factors that explain the observed variation. A web of Science database literature search was carried out in 2016. Data from all field experiments, greenhouse and pot experiments that compared grain yields and protein contents in Rhizobium/Bradyrhizobium-inoculated with non-inoculated control crops were extracted and analyzed using previously described unweighted and weighted meta-analysis protocols. GRADE assessments of the strength of evidence of results from the weighted meta-analyses were carried which included an assessment of the risk of publication bias. Results: For unweighted meta-analyses we identified eligible data in 236 and 36 studies for grain yield and protein content respectively. For weighted meta-analyses we identified eligible data in 92 and 8 studies for grain yield and protein content respectively. Rhizobium inoculation was found to (i) significantly increase grain yield in both the unweighted (mean percent difference: 41%, 95%CI 36,46, p&lt;0.0001) and weighted meta-analysis (Standardized mean difference: 1.56, 95%CI 1.26,1.87, p&lt;0.0001) and (ii) significantly increase protein content in the unweighted meta-analysis (mean percent difference: 11%, 95%CI 5,18, p&lt;0.0001), but not the weighed meta-analyses which only detected a trend (0.1&gt;p&gt;0.05) towards higher protein content in inoculated grain legume crops. Multi-level model-based weighted meta-analyses suggest that the (i) type of experiment, (ii) type of fertilizer used in experiments, (iii) grain legume type/species and (iv) the country in which experiments were carried out, were confounding factors. The main limitation of the evidence is that a large number of publications did not report measures of variation and could therefore not be included in the more scientifically sound weighted meta-analyses. However based on the large evidence-base available for grain yield it can be concluded that overall Bradyrhizobium/Rhizobium seed inoculation results can increase grain yield by ~40% compared with non-inoculated grain legume crops.

Bacteria can colonize and develop biofilm on a large variety of biotic and abiotic materials, it is accountable for nosocomial infections and chronic illness and consequently, it is a serious economic and public health problem. Staphylococcus epidermidis, thanks to its ability to form biofilm and colonize biomaterials, represents the most frequent causative agent involved in bio-film-associated infections of medical devices. Due to the biofilm presence, S. epidermidis infections are extremely difficult to treat and the research of new molecules able to interfere with its biofilm formation has a remarkable interest. In the present work, the attention was focused on Pseudomonas sp. TAE6080, an Antarctic marine bacterium able to produce and secrete an effective antibiofilm compound. The molecule responsible for this activity was purified by an activity-guided approach and it resulted to be a periplasmic protein, named Cold-Azurin. The Cold-Azurin was recombinantly produced in E. coli and purified. The recombinant protein was able to impair S. epidermidis attachment to the polystyrene surface and effectively prevent biofilm formation.

This research focussed on utilisation of salmon protein and lipid to manipulate pasta glycaemic index and protein digestibility. Salmon fish (Oncorhynchus tschawytscha) powder (SFP) supplemented pasta flour at the from 5% to 20% (w/w). Inclusion of SFP lead to a significant reduction in starch digestibility and hence the potential glycaemic values of pasta (experimental pasta being up to 143% lower than control values). SFP addition to pasta increased the release of phenolic compounds from pasta during both a gastric digestion (179%) and pancreatic digestion ( 133%) in comparison to the control sample. At the same time, the antioxidant activity of the digested pasta was increased by up to 263% (gastric) and 190% (pancreatic) in comparison to durum wheat pasta alone. Interestingly, although protein levels increased with incorporation of SFP, the digestibility values of the protein decreased from 86.41% for the control pasta to 81.95% for 20% SFP pasta. This may indicate that there are interactions between phenolic and protein in the pasta samples which affect overall protein digestibility levels.

Molecular visualisation is fundamental in the current scientific literature, textbooks and dissemination materials, forming an essential support for presenting results, reasoning on and formulating hypotheses related to molecular structure. Visual exploration has become easily accessible on a broad variety of platforms thanks to advanced software tools that render a great service to the scientific community. These tools are often developed across disciplines bridging computer science, biology and chemistry. Here we first describe a few Swiss Army knives geared towards protein visualisation for everyday use with an existing large user base, then focus on more specialised tools for peculiar needs that are not yet as broadly known. Our selection is by no means exhaustive, but reflects a diverse snapshot of scenarios that we consider informative for the reader. We end with an account of future trends and perspectives.

Herpesviruses usurp cellular stress responses to avoid immune detection while simultaneously promoting viral replication and spread. The unfolded protein response (UPR) is an evolutionarily conserved stress response that is activated when the protein load in the ER saturates its chaperone folding capacity causing an accrual of misfolded proteins. Through translational and transcriptional reprogramming, the UPR aims to restore protein homeostasis; however, if this fails the cell undergoes apoptosis. It is commonly thought that many enveloped viruses, including herpesviruses, may activate the UPR due to saturation of the ER with nascent glycoproteins and thus these viruses may have evolved mechanisms to evade the potentially negative effects of UPR signaling. Over the past fifteen years there has been considerable effort to provide evidence that different viruses may reprogram the UPR to promote viral replication. Here we provide an overview of the molecular events of UPR activation, signaling and transcriptional outputs, and highlight key findings that demonstrate that the UPR is an important cellular stress response that herpesviruses have hijacked to facilitate persistent infection.

Glutathione peroxidases (GPxs) form a broad family of antioxidant proteins essential for maintaining redox homeostasis in eukaryotic cells. In this study, we used an integrative approach that combines bioinformatics, molecular biology, and biochemistry to investigate the role of GPxs in reactive oxygen species detoxification in the unicellular eukaryotic model organism Tetrahymena thermophila. Both phylogenetic and mechanistic empirical model analyses provided indications about the evolutionary relationships among the GPXs of Tetrahymena and the orthologous enzymes of phylogenetically related species. In-silico gene characterization and text mining were used to predict the functional relationships between GPxs and other physiologically-relevant processes. The GPx genes contain conserved transcriptional regulatory elements in the promoter region, which suggest that transcription is under tight control of specialized signaling pathways. The bioinformatic findings were next experimentally validated by studying the time course of copper (Cu)-dependent regulation of gene transcription and enzymatic activity. Results emphasize the role of GPxs in the detoxification pathways that, by complex regulation of Cu-dependent GPx gene expression, enables Tetrahymena to survive in high Cu concentrations and the associated redox environment.

Fusarium graminearum is a dangerous pathogen of the cereals producing mycotoxins (trichothecene and zearalenone) harmful for human and animal health. There were evaluated sixteen winter wheat varieties for their response in conditions of natural infection with F. graminearum in the epidemic year 2019, being well known that accumulation of mycotoxins (DON, ZON and T-2) is induced by different biotic and abiotic factors. Field plot was organized in Latin rectangle randomized with three replicates. For all evaluated wheat varieties were collected field data (incidence, severity and infection degree of the fungus F. graminearum) and laboratory data (mycotoxins concentration in grains) that have been processed using the software JASP (Version 0.14) for descriptive statistics, and exploratory factor analysis (EFA). Microsoft Excel 2019 was used to calculate Pearson’s correlation coefficients. The results showed negative corelation between plants’ density and F. graminearum attack frequency. Positive correlations were found between DON and T-2 and between DON and fungus attack intensity. This work highlights that during a F. graminearum epidemic year some of the most influential factors in the contamination with harmful mycotoxins (DON, ZON and T-2) are: plants density, frequency of the attack on ear, diseased ears and attack intensity on ears.

Aflatoxins (AFs) contamination of cereals is considered one of the greatest food safety concerns worldwide. Occurrence of AFs in maize, wheat, rice and sorghum is highly prevalent with each commodity accounting for more than 10% of world’s AF exposure. Their occurrence as food contaminants is also associated with huge economic losses. AFs are highly stable compounds that cannot be eliminated by regular processing of grains. Hence, prevention of AFs in food and feed is now considered more important than the subsequent interventions to mitigate the deleterious health effects of AFs in human and animals. However, the development of an effective preventive strategy hinges on a clear understanding of the underlying factors influencing AFs production. Therefore, the present review aims to highlight the most significant factors influencing AFs contamination of cereals at pre-and post-harvest stages. This is crucial for effective monitoring of critical control points and optimisation of preventive strategies in food and feed supply chains. Several intrinsic and extrinsic factors have been reported of which nutritional composition, environmental factors (temperature, water activity and relative humidity) and climate change have been identified as primary factors, while pH of the substrate, carbon dioxide (CO2) levels in the gaseous environment, and agronomic and socioeconomic status are the main secondary factors promoting AFs biosynthesis in cereals. Additionally, an overview of global occurrence of AFs in cereals, with their health impacts and various preventive measures have also been highlighted.

Loess was deposited in the Negev during the Pleistocene, but such sediments seem to be missing for the Holocene. This could be due to erosion unless structures such as ruins offered protection. We studied soils developed on archaeological hilltop ruins in the Negev and the Petra region and compared them with local soils, paleosols, geological outcrops, and current dust. The ruin soils in both regions were found to consist of similarly complex mixtures of local and remote sediment sources. They differ from sediments deposited during current dust storms. This seems due to fixation processes: average accretion rates are estimated to ~0.14 mm/a, suggesting that only ~3% of the current dust that can be trapped with dry marble dust collectors is stored in the soils. Vegetation, biocrusts, and/or clast pavements associated with vesicular layers seem to act as sediment-fixing agents. As well, climate might play a role: rain, and in particular one snowstorm in the Petra region brought a high amount of sediment that was more similar to the ruin soils. Wet deposition and snow might catalyze dust deposition and enhance fixation by fostering vegetation and crust formation. Frequent snow during the Pleistocene might be one explanation of enhanced loess deposition.

The main objective of this study is to compare and investigate the proximate, sensory parameters of the biscuits fortified with (1) whey protein concentrate (WPC), (2) isolated soy protein (ISP) at various proportions as a source of protein enrichment. The fortified biscuits were analysed for sensory and proximate analysis. The study evaluated and compared the effect of fortifying whey protein concentrate and isolated soy protein at various proportions T0 control (0%), T1 (5%), T2 (10%), T3 (15%), T4 (20%). The protein content in both WPC and ISP samples tends to increase, but much higher in WPC formulated biscuits. At 20% WPC the protein content peaked to 29.11%, other nutritional components such as fat, ash, fibre and moisture content of WPC samples increased significantly, whereas no such significant changes were observed and only linear increase of protein content were in ISP fortified samples. The sensory analysis of ISP fortified samples were acceptable up to 10% proportion, exceeding 10% showed unacceptable results, on comparison WPC biscuits were acceptable at all proportions, more desirable at 20% WPC. Conclusively, fortifying biscuits with either WPC or ISP might be a source of protein without any significant effect on the quality of biscuits.

Proteins are the workhorses of the cell that perform biological functions by interacting with other proteins. Many statistical methods for protein-protein interaction (PPI) have been studied without considering time-dependent changes in networks and the functionalities. I introduced a novel method that models PPI networks as being dynamic in nature and evolving time-varying multivariate distribution with Conditional Random Fields (CRF). This research is directed towards implementing this new combinatorial algorithm on massively parallel architectures such as Graphics Processing Units (GPUs) for efficient computations for large scale bioinformatics datasets. I compared Conditional Random Fields (CRF) and the proposed novel method using CRF combined with the Block Coordinate Descent algorithm for human protein-protein interaction data set. Both are implemented on GPU-Accelerated Computing Architecture and the proposed novel method showed the advantages in predicting protein-protein interaction sites. I also show that the proposed approach is more efficient in 6.13% than standalone CRF++ in predicting protein-protein interaction sites.

We report the results of our study of approved drugs as potential treatments for COVID 19, based on the application of various bioinformatics predictive methods. The drugs studied include chloroquine, ivermectin, remdesivir, sofosbuvir, boceprevir, and α-difluoromethylornithine (DMFO). Our results indicate that these small molecules selectively bind to stable, kinetically active residues and residues adjoining them on the surface of proteins and inside protein pockets, and that some prefer hydrophobic over other active sites. Our approach is not restricted to viruses and can facilitate rational drug design, as well as improve our understanding of molecular interactions, in general.

Balanced nitrogen (N) and phosphorus (P) rates coupling with rational fertilization methodology could promote crop N accumulation, N use efficiency and yield production, particularly in semi-arid and arid regions. To test these characteristics, a two-year (2018 and 2019) pot experiment was therefore performed by growing summer maize in a rain-proof glass greenhouse, under 9 combined N (112, 150 and 187 kg ha-1, urea) and P (45, 60, 75 kg ha-1, calcium superphosphate) rates and three contrasting fertilizer placements. The fertilizers were placed by broadcast on soil surface (Broadcast), side band on 4 cm strip soil surface within 7 cm from sowing line (Side band) and deep band on 4 cm strip below 7 cm soil depth within 7 cm from sowing line (Deep band). Results from three maize growth stages (eight-leaf, 45 days after sowing, DAS; tasseling, 60 DAS; and harvest, 115 DAS) showed that leaf, stem, root N accumulation and total soil N were significantly increased under Deep band than under both Side band and Broadcast at N150P60, N187P60, N150P75 and N187P75, but not at N112P45, N150P45, N187P45, N112P60 and N112P75. Significantly greater leaf, stem, and root N accumulations were also displayed at N150 and N187 than at N112 for the same P60 or P75 under Deep band at 60 DAS and 115 DAS, while were for leaf and stem N accumulations at P75 and P60 than at P45 for the same N150 under Deep band at 45 DAS, 60 DAS and 115 DAS. Significantly greater agronomy N use efficiency, partial factor productivity and N use efficiency exhibited under Deep band than under Side band and Broadcast at N150P75 and N187P75, but at N150P60 and N187P60 for NUE only. In addition, leaf, stem, seed, root N concentrations positively correlated with their own N accumulations or soil N concentration at tasseling and harvest stages. Our results demonstrate that a synchronized N150P60, N187P60, N150P75 or N187P75 fertilization rate with Deep band placement can improve soil N availability and root N uptake, and hereby greater aboveground N accumulation, N use efficiency and yield production of maize particularly practical for small-holder farmers globally.

Hypoplastic left heart syndrome (HLHS) is a severe congenital heart disease (CHD) affecting 1 in 5,000 newborns. We constructed the interactome of 74 HLHS-associated genes identified from a large-scale mouse mutagenesis screen, augmenting it with 408 novel protein-protein interactions (PPIs) using our High-precision Protein-Protein Interaction Prediction (HiPPIP) model. The interactome is available on a webserver with advanced search capabilities (http://severus.dbmi.pitt.edu/wiki-HLHS). 364 genes including 73 novel interactors were differentially regulated in tissues/iPSC-derived cardiomyocytes of HLHS patients. Novel PPIs facilitated the identification of TOR signaling and endoplasmic reticulum stress modules. 60.5% of the interactome consisted of housekeeping genes that may harbor large-effect mutations and drive HLHS etiology but show limited transmission. Network proximity of diabetes, Alzheimer’s disease, and liver carcinoma-associated genes to HLHS genes suggested a mechanistic basis for their comorbidity with HLHS. Interactome genes showed tissue-specificity for sites of extracardiac anomalies (placenta, liver and brain). The HLHS interactome shared significant overlaps with the interactomes of ciliopathy and microcephaly-associated genes, with the shared genes respectively enriched for genes involved in intellectual disability and/or developmental delay, and neuronal death pathways. This supported the increased burden of ciliopathy variants and prevalence of neurological abnormalities observed among HLHS patients with developmental delay and microcephaly respectively.

Adeno-associated viruses (AAVs, genus dependoparvovirus) are promising gene therapy vectors. In strains AAV1-12, the capsid gene VP1 encodes a recently discovered protein, MAAP, in an overlapping frame. MAAP binds the cell membrane by an unknown mechanism. We discovered that MAAP is also encoded in bovine AAV and in porcine AAVs (which have shown promise for gene transfer into muscle tissues), in which it is probably translated from a non-canonical start codon. MAAP is predicted to be mostly disordered except for a predicted C-terminal, membrane-binding amphipathic α-helix. MAAP has a highly unusual composition. In particular, it lacks internal methionines, and is devoid of tyrosines in most strains. Unexpectedly, we discovered that the N-terminus of VP1 also lacks several amino acids. In all AAVs that encode MAAP, the first 200 aas of VP1 are devoid of internal methionines, probably owing to a selection against ATG codons that could prevent translation of MAAP and of capsid isoforms (VP2, VP3). The N-terminus of VP1 also lacks cysteines, likely to avoid the formation of disulfide bridges when it becomes exposed outside of the capsid during post-endocytic trafficking. Finally, the region common to VP1 and VP2 lacks tyrosine in the vast majority of AAVs that encode MAAP. Avoiding these "forbidden" aas in MAAP and VP1 when creating recombinant AAV capsids might increase the efficiency of capsid design. Conversely, the presence of "forbidden" aas in some rare strains probably indicates that they have unusual properties that could help us understand the viral cycle.

The amino acid sequences ARG of gag proteins of HTLV1, HTLV2, STLV1 and STLV2 match with its primer binding site GGGGGCTCG in the 3'-to-5' direction, and the amino acid sequences SPR of gag proteins of HIV1, HIV2, SIV and FIV match with its primer binding site GGCGCCCGA in the 3'-to-5' direction, and gag, gag-pol and gag-pro-pol proteins are promising for reawaken dormant retrovirus infection. The latency-reversing drugs were involved in the process of transcription of cancer, the genome which they actually reawaken is just happened to be contained genome of the retrovirus, they are essentially false reawaken. Use proteins of retroviruses to reawaken themselves are more reliable, just like androgen receptor activates IGF1R genome.

The efficient generation of high-quality random numbers is essential in the operation of cryptographic modules. The quality of a random number generator is evaluated by the min-entropy of its entropy source. Typical method used to achieve high min-entropy of the output sequence is an entropy accumulation based on a hash function. This is grounded in the famous Leftover Hash Lemma which guarantees a lower bound on the min-entropy of the output sequence. However, the hash function based entropy accumulation has slow speed in general. For a practical perspective we need a new efficient entropy accumulation with the theoretical background for the min-entropy of the output sequence. In this work, we obtain the theoretical bound for the min-entropy of the output random sequence through the very efficient entropy accumulation using only bitwise XOR operations, where the input sequences from the entropy source are independent. Moreover we examine our theoretical results by applying to the quantum random number generator that uses dark noise arising from image sensor pixels as its entropy source.

Liver receptor homolog-1 (LRH-1) has emerged as a regulator of hepatic glucose, bile acid, and mitochondrial metabolism. However, the functional mechanism underlying the effect of LRH-1 on lipid mobilization has not been addressed. This study investigated the regulatory function of LRH-1 in lipid metabolism during fasting. The wild-type (WT) and LRH-1 liver-specific knockout (LKO) mice were either fed or fasted for 24 h, and the liver and serum were isolated. During fasting, the LRH-1 LKO mice showed greater accumulation of triglycerides in the liver compared to that in WT mice. Interestingly, LRH-1 LKO liver decreased the perilipin 5 (PLIN5) expression and genes involved in β-oxidation. Additionally, the LRH-1 agonist dialauroylphosphatidylcholine also enhanced PLIN5 expression in human cultured HepG2 cells. To identify new target genes of LRH-1, these findings directed to analyze the PLIN5 promoter sequence, which revealed −1620/−1614 to be a putative binding site for LRH-1. This was confirmed by promoter activity and chromatin immuno-precipitation assays. Moreover, fasted WT primary hepatocytes showed increased co-localization of PLIN5 in lipid droplets (LDs) compared to that in fasted LRH-1 LKO primary hepatocytes. Overall, these findings suggest that PLIN5 might be a novel target of LRH-1 to mobilize LDs and manage the cellular needs.

Based on the geologic conditions of natural gas hydrate (NGH) accumulations in the Shenhu area, northern slope of the South China Sea, this paper used a method of combining reservoir stimulation technique (RST) with depressurization to investigate the conversion efficiency of marine NGH reservoirs in different intrinsic permeability and initial NGH saturation conditions, and analyze the influence of variably-stimulation effect on marine NGH conversion efficiency in different accumulation conditions, provided a reference scheme for improving the NGH conversion efficiency in the Shenhu area. In this work, we performed calculations for the variations in CH4 production rate and cumulative volume of CH4 in different initial NGH saturation, intrinsic permeability and stimulation effect conditions, variance analysis and range analysis methods were used to analyze the significance of these key factors and their interaction, and investigated the sensitivity of stimulation effect on NGH conversion efficiency, respectively. The simulation results showed that stimulation effect have a significant influence on NGH conversion efficiency, and the influence of interaction between these three factors were not obvious. Possibly most important, we clarified an optimum stimulation effect for higher NGH conversion efficiency under different accumulation conditions, especially in low-permeability and high-saturation, which corresponding stimulation effect were different.

Protein-protein interactions (PPIs) are associated with various diseases; hence, they are important targets in drug discovery. However, the physicochemical empirical properties of PPI-targeted drugs are distinct from those of conventional small molecule oral pharmaceuticals, which adhere to the ”rule of five (RO5).” Therefore, developing PPI-targeted drugs using conventional methods, such as molecular generation models, is difficult. In this study, we propose a molecule generation model based on deep reinforcement learning, specialized for generating PPI inhibitors. By introducing a scoring function that can represent the properties of PPI inhibitors, we successfully generated potential PPI inhibitor compounds. The generated virtual compounds possess the desired properties for PPI inhibitors, and show similarity to commercially available PPI libraries. These generated virtual compounds are freely available as a virtual library.

Silybum Marianum, is a plant belonging to the family Asteraceae. For many centuries it has been used a natural remedy for many diseases like Liver and Biliary tract diseases. It is effective as an anti-oxidant and is used in a variety of diseases. This study was conducted to check the effects of Silybum Marianum on PARP protein (4UND protein).The Molecular Docking techniques was chosen to check the effects of different chemical constituents of Silybum marianum on DNA damaging protein. For this purpose, different PARP inhibitor drugs were taken as standard. The Molecular Docking of the chemical constituents of Silybum marianum was performed using 4UND protein with the help of PyRx software along with BIOVIA Drug Discovery studio software. The result of molecular docking showed that some of the chemical constituent have higher binding affinity than standard PARP inhibitor drugs.

To investigate the differences in cadium (Cd) uptake and translocation among edible rapes and select suitable rape varieties for safe production, a field experiment was carried out with 25 varieties of edible rapes on a farmland polluted with Cd in the central souothern part of Hunan Province. The growing characteristics and Cd contents in rape tissues were measured, and the amount of Cd removed was calculated. The results showed that the growth of 25 rape varieties was not inhibited without withering or inconsistent changes in leaf and so on. The Cd contents in stem-leaf and root of rapes were in the range 0.05-0.26mg·kg-1 and 0.04-0.26mg·kg-1, respectively. Basing on BCF, the stem-leaf showed a greater capacity for Cd transport than root. And the total Cd removed by rape were 0.002-0.016 mg·plant-1. Except for plant height, BCF of soil available Cd from soil to stem-leaf, TCF of Cd from root to stem-leaf and Cd taken away by rape, there was no significant difference among edible rape varieties. Although Cd contents in stem-leaf of 25 rape varieties does not exceed the national safety standards, planting “Lvjin 1”, “Guanyou Qingjing” and “Guanyou brassica” not only reduced soil pollution but also allowed the production of safe leafy rape.

Rapid lignification occurring in the endocarp of dove tree results in the formation of a rigid and compact structure, which seriously hinders seed germination. A gene named DiCCoAOMT1, which encodes a hyperactive O-methyltransferase, was identified and thought to play a critical role in the process of endocarp lignification. In this study, the DiCCoAOMT1 gene was introduced into A. thaliana and poplar, respectively, to further verify its function. The lignin content was increased by 45% and 20% in the stems of transgenic A. thaliana and poplar lines, respectively. There was a positive correlation between the expression levels of DiCCoAOMT1 and lignin amount in transgenic lines. Furthermore, the shifts of lignin composition was indicated by the elevated S/G ratio in transgenic poplar lines. Lignin accumulation was promoted specifically in the phloem cells, and the cells in secondary xylem was thickened in transgenic plants. In addition, lengthened pods and elevated plant height, and elongated petioles and internodes were observed in transgenic A. thaliana and poplar lines, respectively. Taken together, our data indicated that an endocarp-specific DiCCoAOMT1 gene could effectively increase lignin accumulation and alter lignin composition in both herbs and woody plants, which provides new insights to understand the regulatory mechanism of lignin biosynthesis and the biological significance of lignification in specific tissues.

Dunaliella salina is a rich source of 9-cis β-carotene, which has been identified as important in the treatment of retinal dystrophies and other diseases. We previously showed that chlorophyll absorption of red light photons in D. salina is coupled to oxygen reduction and phytoene desaturation and increases the pool size of β-carotene [1]. Here we show for the first time that growth under red light also controls conversion of extant all-trans β-carotene to 9-cis β-carotene by β-carotene isomerases. Cells illuminated with red light from a light emitting diode (LED) during cultivation contained a higher 9-cis β-carotene content compared to cells illuminated with white or blue LED light. The 9-cis/all-trans β-carotene ratio in red light treated cultures reached >2.5:1 within 48 hours and was independent of light intensity. Illumination using red light filters that eliminated blue wavelength light also increased the 9-cis/all-trans β-carotene ratio. With norflurazon, a phytoene desaturase inhibitor which blocked downstream biosynthesis of β-carotene, extant all-trans β-carotene was converted to 9-cis β-carotene during growth with red light and the 9-cis/all-trans β-carotene ratio was ~2:1. With blue light under the same conditions, 9-cis β-carotene was likely destroyed at a greater rate than all-trans β-carotene (9-cis/all-trans ratio 0.5:1). Red light perception by the red light photoreceptor, phytochrome, may increase the pool size of anti-oxidant, specifically 9-cis β-carotene, both by upregulating phytoene synthase to increase the rate of biosynthesis of β-carotene and to reduce the rate of formation of reactive oxygen species (ROS), and by upregulating β-carotene isomerases to convert extant all-trans β-carotene to 9-cis β-carotene.

Forest vegetation plays a key role in the cycling of mercury (Hg) and organic matter (OM) in terrestrial ecosystems. Litterfall has been indicated as the major transport vector of atmospheric Hg to forest soils, which is eventually transported and stored in the sediments of forest lakes. Hence, it is important to understand how changes in forest vegetation affect Hg in soil and its biogeochemical cycling in lake systems. We investigated the pollen records and the geochemical compositions of sediments from two lakes (Schurmsee and Glaswaldsee) in the Black Forest (Germany) to evaluate whether long-term shifts in forest vegetation induced by climate or land use influenced Hg accumulation in the lakes. We were particularly interested to determine whether coniferous forests were associated with a larger export of Hg to aquatic systems than deciduous forests. Principal components analysis followed by principal component regression enabled us to describe the evolution of the weight of the latent processes determining the accumulation of Hg over time. Our results emphasize that the in-lake uptake of Hg during warm climate periods, soil erosion after deforestation and emissions from mining and other human activities triggered changes in Hg accumulation during the Holocene stronger than the changes caused by forest vegetation alone.

Copper(II), nickel(II) and zinc(II) complexes of various peptide fragments of tau protein were studied by potentiometric and spectroscopic techniques. All peptides contained one histidyl residue and represented the sequences of tau(91-97) (Ac-AQPHTEI-NH2), tau(385-390) (Ac-KTDHGA-NH2) and tau(404-409) (Ac-SPRHLS-NH2). Imidazole-N donors of histidine were the primary metal binding sites for all peptides and all metal ions but in case of copper(II) and nickel(II) the deprotonated amide groups were also involved in metal binding by increasing pH. The most stable complexes were formed with copper(II) ion but the presence of prolyl residues resulted in significant changes in the thermodynamic stability and speciation of the systems. It was also demonstrated that nickel(II) and especially zinc(II) complexes have relative low thermodynamic stability with these peptides. Copper(II) catalyzed oxidation of the peptides was also studied. In the presence of H2O2 the fragmentation of peptides can be detected in all cases. In the simultaneous presence of of H2O2 and ascorbic acid the extent of the fragmentation of the peptide is less preferred, and the formation of 2-oxo-histidine also occurs.

Plants endogenous hormones play an important role in resistance to soil lead (Pb) contamination. In order to explore the response of plant hormones to Pb stress, pot experiment was conducted to analysis the hormones contents, related gene expressions and Pb accumulation of Arabis alpina under Pb treatment and transporter (CAX(cation exchangers), HMA(heavy metal ATPase) and ABC(ATP-binding cassette transporter)) activities under foliage spraying auxin (IAA). The results showed that contents of total Pb and soluble components Pb (vacuoles) in roots and leaves of Arabis alpina increased with increase of Pb treatment concentrations. Compering to 100 mg·kg-1 Pb2+ treatment, Pb contents in soluble components of roots and leaves under 300 mg·kg-1 Pb2+ treatment increased by 896.3% and 238.8%, respectively. The contents of endogenous hormones in leaves and roots increased under Pb treatment concentrations. Comparing to control (0 mg·kg-1 Pb2+ treatment), contents of auxin in roots and leaves under 100 mg∙kg-1 Pb treatment increased by 176.19% and 585.29%, respectively. Auxin contents in xylem saps under 100 and 300 mg∙kg-1 Pb treatments increased by 283.14% and 100.30%, respectively. Gene expression related to auxin transport was up-adjusted. The expressions of three gene related to auxin-repressed 12.5 kDa protein and auxin-responsive GH3 family were down-adjusted. Under foliage spraying IAA, Pb contents in leaves increased by 29.81% and Pb content in symplast sap was higher than that with non spraying IAA treatment. The activities of CAX and HMA in roots of A. alpina increased by 9.62% and 8.79% with foliage spraying IAA treatment, while activity of ABC decreased by 21.94%. In general, contents of auxin and related genes expressions of A. alpina increased under Pb treatment, which enhanced activities of CAX and HMA resulting in Pb translocation through symplast pathway.

Black horehound (Ballota nigra L.) is one of the important medicinal plants, which is a rich source of health-promoting essential oils. Salinity stress affects plant development and alters the quality and quantity of plants extracts and their composition. This study was aimed to investigate the effect of salinity on morphological, physiological characteristics, and secondary metabolites of B. nigra under greenhouse, and in vitro culture conditions. The plants were treated with different concentrations of NaCl (25, 50, 75, 100 mM) and fresh and dry weight of leaf and stem were measured as well as morphological characteristics of the plant. Plant growth was reduced with the increased salinity concentrations. The results showed that all growth-related traits and SPAD were decreased both in vivo and in vitro. Additionally, increased salt concentration affected the cell membrane integrity. Total phenolics content of plants growing in the greenhouse, increased by 21% at 50 mM NaCl, but at higher stress levels (100 mM NaCl), the amounts were decreased significantly. Total flavonoids contents followed similar patterns, with a slight difference. In addition, the maximum and minimum total phenolics contents of plants growing under in vitro condition were observed at 50 mM NaCl and control treatments, respectively. Increasing the salt concentration significantly affected the total flavonoids content, and as a result, the highest amount was observed in 50 and 75 mM NaCl treatments. Antioxidant activity was also measured. Among the NaCl treatments, the highest DPPH scavenging activities (IC50) under greenhouse and in vitro conditions were detected at 50 mM and 25 mM concentrations, respectively. In general, based on the results, with increasing the salinity level to 75 mM, the activities of CAT and APX were significantly upregulated in both greenhouse and in vitro culture conditions. A correlation between total phenolics and flavonoids contents as well as antioxidant activity were obtained. With shifting salinity stress, the type and the amount of the identified essential oil compounds changed. Compounds such as styrene, tridecanol, germacrene-D, beta-Ionone, beta-bisabolene, and caryophyllene oxide increased compared to the controlled treatment.

Peptides of hydrolysates of food proteins are an easily digestible source of amino acids necessary for the body to adapt to physical stress. Commercially significant hydrolysates include whey protein, casein, and other animal proteins. Hydrolysates of plant proteins are gaining popularity, but they are less common, then animal ones. Soy protein isolate is promising for obtaining the hydrolysates due to its affordable price and balanced amino acid profile. However, there are no direct studies showing an improvement in the result of physical activity when eating soy protein isolate hydrolysate (SPIH). In this work, for the first time, the study was conducted on the safety and efficacy of SPIH during physical load on model animals (rats). It was shown that the hydrolysate did not lead to pathological changes in the viscera, food intake, and weight of animals did not differ from the control group (animals consumed whey protein). Under physical load rats enteral fed SPIH showed a tendency to adapt more quickly to physical stress than the control group and the group of animals that was fed by free amino acids. The metabolites of animal blood serum were studied by NMR spectroscopy. It was shown that by the 95th minute after feeding in the group of rats receiving SPIH, the difference of proteinogenic amino acids concentrations in blood between individuals was significantly less than in the groups receiving whey protein or a mixture of amino acids. In other words, individual biochemical and physiological characteristics of individuals did not affect the assimilation of amino acids of hydrolysate.

The outbreak of COVID-19, the disease caused by SARS-CoV-2, continues to affect millions of people around the world. The absence of a globally distributed effective treatment makes the exploration of new mechanisms of action a key step to address this situation. Stabilization of non-native Protein-Protein Interactions (PPIs) of the nucleocapsid protein of MERS-CoV has been reported as a valid strategy to inhibit viral replication. In this study, the applicability of this unexplored mechanism of action against SARS-CoV-2 is analyzed. During our research, we were able to find three inducible interfaces of SARS-CoV-2 N protein NTD, compare them to the previously reported MERS-CoV stabilized dimers, and identify those residues that are responsible for their formation. A drug discovery protocol implemented consisting of docking, molecular dynamics and MM-GBSA enabled us to find several compounds that might be able to exploit this mechanism of action. In addition, a common catechin skeleton was found among many of these molecules, which might be useful for further drug design. We consider that our findings could motivate future research in the fields of drug discovery and design towards the exploitation of this previously unexplored mechanism of action against COVID-19.

Understanding the mechanism, how entirely new (EntNew) gene/protein or the first ancestral gene/protein of a family was created, should be one of the most important issues in the biological sciences. However, the mechanism is totally unknown still now. On the other hand, it is well known that mature protein is generally rigid and one catalytic center exists on the protein. Creation of such a mature EntNew gene/protein should be, of course, carried out through random process, because it cannot be designed in advance. However, the EntNew gene/protein never be created by random polymerization of the respective monomeric units, because of the extraordinary large sequence diversities of ~10¹⁸⁰ and ~10¹³⁰, respectively. Protein 0^th-order structure or a specific amino acid composition, in which immature but water-soluble protein can be produced even through random process, holds the key for solving the difficult problem. As it was fragmentally described in the previous papers how and where EntNew gene/protein was created, I describe in detail in this review three processes generating EntNew gene/protein with some flexibility under three genetic codes, the universal genetic code, SNS primitive code and GNC primeval code, and discuss why the mature gene/protein could be created through the processes.

Prenatal maternal feeding plays an important role in fetal development and has potential to cause long-lasting epigenetic modifications. MicroRNAs (miRNAs) are non-coding, single-stranded RNAs that serve as one epigenetic mechanism. Though miRNAs have crucial roles in fetal programming, growth, and development, there are limited data regarding maternal diet and sheep miRNA expression. Therefore, weanalyzed high and low maternal dietary protein for miRNA expression in sheep fetal longissimus dorsi. Pregnant ewes were fed an isoenergetic high-protein (HP, 160–270 g/day), low-protein (LP, 73–112 g/day), or standard protein diet (SP, 119–198 g/day) during pregnancy. miRNA expression profiles were evaluated using the Affymetrix GeneChip miRNA 4.0 Array. Twelve up-regulated, differentially expressed miRNAs (DE miRNAs) were identified targeting 65 genes. The oar-3957-5p miRNA was highly up-regulated in LP and SP compared to HP. Previous transcriptome analysis identified integrin and non-receptor protein tyrosine phosphatase genes targeted by miRNAs detected in the current experiment. A total of 28 GO terms and 10 pathway-based gene sets were significantly (padj &lt; 0.05) enriched in target genes. Most genes targeted by identified miRNAs are involved in immune and muscle disease pathways. Our study shows dietary protein intake during pregnancy affects fetal skeletal muscle epigenetics via miRNA expression.

The lengthy maturation period is the key cause of the reduced hot pepper market value. An experiment was performed to assess the effects of R/B/W light qualities on reducing the maturation period. The maturation period was shortened by 16 days under 4R:1B:5W compared to the control. The appearance of the first flower is a limiting factor affecting the maturation period. It exhibited a dark purple color and an abnormal petal under 4R:1B:5W compared to the control, which was associated with increased contents of flavonoids, total organic acids, and phenolics and decreased total amino acid and carbohydrate contents. Plant hormone, flavonoid, ABC transporters, key metabolites (such as amino acid, carbohydrate, organic acid) was associated with first flower development. Ethylene response factors (ERFs) mediated by light, especially ERF021, were identified as potential hub regulators during the development of the first flower due to their involvement in all the associated metabolic pathways.

We studied peat stratigraphy at the Mukhrino peatland, which is a typical ombrotrophic bog for the middle taiga zone of Western Siberia, to gain insights about its history, hydrology and carbon fluxes. Seven cores were collected from locations chosen to represent the typical present-day vegetation types, for dating of separated dissolved (DOC) and particulate (POC) organic carbon fractions using the Accelerator Mass Spectrometer (AMS) radiocarbon ($^{14}$C) method. The oldest peat was found at the bottoms of an underlying lake (10,053 cal. year BP) and an ancient riverbed (10,989 cal. year BP). For the whole history of the peatland the average peat accumulation rate was estimated to be 0.067±0.018 cm yr-1 (0.013-0.332 cm yr-1) and the carbon accumulation rate was 38.56±12.21 g m-2yr-1 (28.46–57.91 g m-2 yr-1). There were clear age differences between the separated samples of DOC and POC. DOC was older than POC in the uppermost 150 cm of the peat deposit, and younger in the deeper layers. The difference in age increased with depth, reaching 2,000–3,000 years at the bottom of the peat deposit (depth 430--530 cm). Following consideration of a range of factors that could potentially cause the dating discrepancy, we hypothesised that DOC continuously moves down into the mineral sediment beneath the peat, as an additional carbon flux that results in mixing of younger and older carbon. On this basis we estimated the apparent rate of DOC downward movement and the associated rate of carbon loss. The first estimate of the average rate of DOC downward movement in Western Siberia is 0.047±0.019 cm yr-1.

Pore fluid pressure is very important to the generation, migration and accumulation of petroleum. The previous studies indicate that the Chezhen sag region is typically characterized by pore fluid overpressure (the difference between pore fluid pressure and hydrostatic pressure). To date, the formation mechanism of pore overpressure and the accumulation regularity of “upper source-lower reservoir” type in this region remains unknown. In order to investigate these problems, a 2-D finite element model is established with regards to the fluid-solid coupling in Chegu 25 block of Chezhen depression, fully considering the existing seismic, logging data and regional tectonic stress environment. Meanwhile, we calculate the abnormal overpressure generated at the source rock during hydrocarbon generation and the process of hydrocarbon migration and accumulation along the faults, analyzing the dynamic conditions of hydrocarbon downward accumulation. The results show that overpressure can accelerate migration of hydrocarbon and improve the efficiency of hydrocarbon accumulation. However, when the overpressure is too large, tensile fractures and shear fractures may occur, resulting in hydrocarbon dissipation, and changing the results of oil and gas accumulation. The overpressure at the source rock is mainly caused by hydrocarbon generation, while the overpressure at the reservoir is primarily created by unbalanced compaction. As the dominant channel of hydrocarbon migration, overpressure will change the direction and path of hydrocarbon migration in the fault. Therefore, the “upper source-lower reservoir” hydrocarbon accumulation model is strongly explained by the high permeability of faults and the presence overpressure. In summary, the simulated overpressure results are in good agreement with the mud weight equivalent overpressure and the drill stem tests (DSTs).