Legume plants enter symbiosis with soil nitrogen-fixing bacteria (rhizobia), thereby gaining access to the assimilable atmospheric nitrogen. This symbiosis is important for agriculture, thus, biofertilizers with effective strains of rhizobia are created for crop legumes to increase their yield and minimize the amounts of mineral fertilizers used. In this work, we sequenced and characterized the genome of Rhizobium leguminosarum bv. viciae strain RCAM1022, a component of the ‘Rhizotorfin’ biofertilizer produced in Russia and used for pea (Pisum sativum L.).

Pumpo is a Simmental breed and an essential livestock resource in the nucleus genetic cattle of Peru. This study provides a draft genome sequence of a top bull using a de novo assembly approach on the Illumina Novaseq X platform, yielding 208 GB of raw sequencing data with 150 bp paired-end reads. The final genome assembly resulted in a size of 2.06 Gb with an N50 contig length of 108 Mb and a completeness of 95.7% according to BUSCO analysis. A total of 973,925 simple sequence repeats (SSRs) were identified, with a predominance of mononucleotide repeats. The genome showed low heterozygosity (0.568%) and moderate repeatability (11.5%), aligning with other Bos taurus genomes. Reference-guided scaffolding improved the assembly quality significantly, producing an N50 scaffold value of 108 Mb. The SSR analysis of the Pumpo genome identified 973,925 SSRs with a frequency of 2,808 SSRs per kilobase, predominantly mononucleotide repeats, and 85,453 found in compound formations. Obtaining knowledge of the genome of a breeding Simmental bull is essential to optimize breeding programs and improve productivity.

"Medusaviridae" is a proposed family of large DNA viruses so far represented by a sole virus isolated from a hot spring. In the present study, we report the isolation and genome sequencing of a new member of this family, medusavirus stheno, discovered from a freshwater sample with Acanthamoeba castellanii coculture.

Paenibacillus sp. tmac-D7 was isolated from coastline growing Trifolium macraei (double-head clover) root nodules from Bodega Bay, California. The draft genome is 5,567,337 bp with a G+C% of 52.4%, an N50 of 114,261 bp, and 5,282 predicted protein-coding genes. Paenibacillus, while found in many other environments, is frequently isolated from root nodules, with many acting as plant pathogen antagonists. Paenibacillus sp. tmac-D7 is the first genome of a non-rhizobial endophyte isolate from wild Trifolium macraei (double-head clover).

Here, we report the draft genome sequence of the type strain of Ideonella azotifigens DSMZ21438^T (formally 1a22^T = JCM15503^T). Ideonella azotifigens DSMZ21438T a novel betaproteobacterial non-symbiotic nitrogen-fixing grass rhizosphere dwelling microbe. The 891,561 paired-end shotgun reads were quality filtered and decontaminated with the ATLAS pipeline, then assembled with Unicycler. The genome size is 6,257,981 bp, an N50 size of 7,849 bp, with a G+C content of 66.71%, and with 5,882 predicted protein-coding genes. I. azotifigens DSMZ21438^T represents the first member of the genus isolated from rhizosphere soil, providing a framework for further study into non-alphaproteobacterial nitrogen fixation and synthetic biology applications.

We describe the draft genome of a Bovine enterovirus (EV) recovered from sewage in Nigeria. The virus replicates on both RD and L20B cell lines, but is negative for all EV screens in use by the GPEI. It contains 7,368nt, with 50.2% G+C content and an ORF with 6,525nt (2,174aa).

The nucleosome is a major modulator of DNA accessibility to other cellular factors. Nucleosome positioning has a critical importance in regulating cell processes such as transcription, replication, recombination or DNA repair. The DNA sequence is a major factor influencing the position of nucleosomes on genomes. Different sequence motifs can promote or inhibit the nucleosome formation, thus influencing the accessibility to the DNA. Sequence-encoded nucleosome positioning having functional consequences on cell processes can then be selected or counter-selected during evolution. We review the interplay between sequence evolution and nucleosome positioning evolution. We first focus on the different ways to encode nucleosome positions in the DNA sequence, and to which extent these mechanisms are responsible of genome-wide nucleosome positioning in vivo. Then, we discuss the findings about selection of sequences for their nucleosomal properties. Finally, we illustrate how the nucleosome can directly influence sequence evolution through its interactions with DNA damage and repair mechanisms. This review aims to provide an overview of the mutual influence of sequence evolution and nucleosome positioning evolution, possibly leading to complex evolutionary dynamics.

Escherichia coli phage Eco_BIFF was isolated from several laboratory stocks of E. coli K-12 MG1655 derivatives. The source of the contamination is unknown. Eco_BIFF is a lytic phage that shows effective growth inhibition of E. coli K-12. Here, we announce the complete genome sequence of Eco_BIFF, and major findings from its genome annotation.

Butirosins are naturally occurring aminoglycoside (AG) antibiotics featuring a 4,5-disubstituted 2-deoxystreptamine (2-DOS) with a (2S)-4-amino-2-hydroxybutyrate (AHBA) side chain. This side chain has been shown to confer resistance against AG modifying enzymes, leading to ongoing studies on the butirosin biosynthetic pathway and the corresponding enzymes. Butirosin is produced by Niallia (formerly Bacillus) circulans and Bacillus vitellinus, with most research focused on the former strain. To date, no whole genome analysis has been performed on B. vitellinus. In this study, we sequenced the complete genome of B. vitellinus NBRC 13296 and performed a comparative analysis of different butirosin biosyntheric gene clusters (BGCs), including those from N. circulans. The complete genome of B. vitellinus NBRC 13296 comprises a 6,331,192 base circlular chromosome with a GC content of 52.68%. The annotation revealed the presence of 5,605 CDSs, 70 tRNA genes, 30 rRNA genes, and 3 ncRNA genes in NBRC 13296. The highest dDDH and ANI values between NBRC 13296 and the most closely related type strain, Paenibacillus chitinolyticus KCCM 41400, were 97.8% and 98.66%, respectively. Based on these genome-based comparative analyses, we propose reclassifying B. vitellinus NBRC 13296 as P. chitinolyticus. Genome mining revealed 18 gene clusters encoding the biosynthesis of diverse secondary metabolites in the genome of B. vitellinus NBRC 13296, indicating the enormous biosynthetic potential of this strain. The predicted structural diversity of secondary metabolites includes aminoglycoside, PKS, NRPS, PKS-NRPS hybrids, metallophores, phosphonates, terpenes, β-lactones, and RiPP peptides. We then comparatively characterized butorosin BGCs previously studied in several N. circulans strains. Additionally, comparative genome analysis revealed complete butirosin BGCs identified from P. chitinolyticus KCCM 41400, P. chitinolyticus NRRL B-23119, P. chitinolyticus NRRL B-23120, P. chitinolyticus B-14908, P. chitinolyticus YSY-3.1, P. chitinolyticus JMW06, Paenibacillus sp. GbtcB18, Paenibacillus sp. HGH0039, Paenibacillus sp. MZ04-78.2. Finally, we identified the core region consisting of BtrS, BtrN, BtrM, BtrL, BtrA, BtrB, BtrC, BtrD, BtrD, BtrE, BtrF, BtrG, BtrH, BtrI, BtrI, BtrJ, BtrK, BtrO, BtrP, and BtrV, followed by an upstream region organizing BtrQ, BtrW, BtrX, BtrY, and BtrZ in the same transcriptional direction and sequential genetic arrangement, and a downstream region organizing various proteins based on BtrT, BtrR2, BtrU, and BtrR1. Our study provided insights into the reclassification of B. vitellinus NBRC 13296 to P. chitinolyticus and suggested the need for continued studies on butirosin biosynthesis from an enzymatic perspective.

We presented here the first draft genome sequence of the trypanosomatid Herpetomonas muscarum ingenoplastis. This parasite was isolated repeatedly in the black blowfly, Phormia regina. This is the first draft genome of a flagellate from the phylogenetically distinct clade of Trypanosomatidae.

Clupeiformes, such as sardines and herrings, represent an important share of worldwide fisheries. Among those, the European sardine (Sardina pilchardus, Walbaum 1792) exhibits significant commercial relevance. While the last decade showed a steady and sharp decline in capture levels, recent advances in culture husbandry represent promising research avenues. Yet, the complete absence of genomic resources from sardine imposes a severe bottleneck to understand its physiological and ecological requirements. We generated 69 Gbp of paired-end reads using Illumina HiSeq X Ten and assembled a draft genome assembly with an N50 scaffold length of 25579 bp and BUSCO completeness of 82.1% (Actinopterygii). The estimated size of the genome ranges between 655 and 850 Mb. Additionally, we generated a relatively high-level liver transcriptome. To deliver a proof of principle of the value of this dataset, we established the presence and function of enzymes (elovl2, elovl5 and fads2) that have pivotal roles in the biosynthesis of long chain polyunsaturated fatty acids, essential nutrients particularly abundant in oily fish such as sardines. Our study provides the first omics dataset from a valuable economic marine teleost species, the European sardine, an essential resource for their effective conservation, management and sustainable exploitation.

The world is facing a major health crisis, the global pandemic of COVID-19 caused by the SARS-CoV-2 coronavirus, for which no approved antiviral agents or vaccines are currently available. Here we describe a collection of codon-optimized coding sequences for SARS-CoV-2 cloned into Gateway-compatible entry vectors, which enable rapid transfer into a variety of expression and tagging vectors. The collection is freely available via Addgene. We hope that widespread availability of this SARS-CoV-2 resource will enable many subsequent molecular studies to better understand the viral life cycle and how to block it.

The Peruvian creole cattle (PCC) is a neglected breed, and is an essential livestock resource in the Andean region of Peru. To develop a modern breeding program and conservation strategies for the PCC, a better understanding of the genetics of this breed is needed. We sequenced the whole genome of the PCC using a paired-end 150 strategy on the Illumina HiSeq 2500 platform, obtaining 320 GB of sequencing data. The obtained genome size of the PCC was 2.77 Gb with a contig N50 of 108Mb and 92.59% complete BUSCOs. Also, we identified 40.22% of repetitive DNA of the genome assembly, of which retroelements occupy 32.39% of the total genome. A total of 19,803 protein-coding genes were annotated in the PCC genome. We downloaded proteomes and genomes of the Bovinae subfamily, and conducted a comparative analysis with our draft genome. Phylogenomic analysis showed that PCC is related to Bos indicus. Also, we identified 7,746 family genes shared among the Bovinae subfamily. This first PCC genome is expected to contribute to a better understanding of its genetics to adapt to the tough conditions of the Andean ecosystem, and evolution.

Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder, with a highly variable expression of phenotypes (restricted interest or activity and repetitive behavior in communication and social interactions), genes (mutation), markers (alteration of transcription) and pathways. Loss of function of the CC2D1A gene appears to primarily affect the brain, leading to a range of behavioral problems in humans. In our study published in 2020; we found that the expressions of miR-19a-3p, miR-361-5p, miR-150-5p, miR-3613-3p, miR-126-3p and miR-499a-5p were downregulated in the serum samples of autistic patients and their families. Here, acquired non-Mendelian hereditary character in a genetically defined mouse model of autism (Cc2d1a +/-) correlates with the transcriptional alteration of five miRNAs. We seek to test the hypothesis that miRNA levels are varying by changes in RNA/DNA structure during development, thereby creating transcription alteration. Behavioral tests were conducted on the offspring of Cc2d1a +/- mutant and control mice, such as novel object, social interaction, marble burying and tail suspension behavior. Two RNA fractions were isolated from mouse hippocampal tissues and sperm cells by standard TRIzol extraction: total RNA and fraction of RNA bound to DNA in the form of a DNA/RNA hybrid (R-loop). The expression levels of miR-19a-3p, miR-361-5p, miR-150-5p, miR-126-3p and miR-499a-5p were investigated by quantitative real-time RT-PCR. We report differences in the distribution of five miRNAs in the hippocampus between male and female mice in RNA fractions, particularly in colonies of Cc2d1a +/- mice. Furthermore, the number of miRNAs engaged in the DNA/RNA hybrid fraction is generally higher in the mutant pedigree than in the control group. On the other hand, in sperm both fractions are at lower levels than in controls. R-loops contribute to the physiology and pathology of organisms including human disease. Here we report a variation in five miRNA levels between gender and tissue. Our results suggest that the transcription levels of these five miRNAs are directly regulated by their RNA.

Electricity load forecasting is a crucial undertaking within all the deregulated markets globally. In contemporary times, the transition from conventional electricity grids to Smart Grids constitutes an area where extensive research is conducted on a global scale. Among the research challenges, the investigation of Deep Transfer Learning (DTL) in the field of electricity load forecasting represents a fundamental effort that imparts generality to Artificial Intelligence applications, due to new capabilities, such as knowledge transfer and computational power reduction. In this paper a comprehensive study is conducted for day-ahead electricity load forecasting. For this purpose, three Sequence-to-Sequence (Seq2seq) Deep Learning (DL) models are used, namely the Multilayer Perceptron (MLP), the Convolutional Neural Network (CNN) and the Ensemble Learning Model (ELM), which is consisted of the weighted combination of the outputs of MLP and CNN models. Also, the study focuses on the development of different forecasting strategies based on DTL and emphasizing the way the datasets are trained and fine-tuning for higher forecasting accuracy. In order to implement the forecasting strategies using Deep Learning models, load datasets from three Greek islands, Rhodes, Lesvos, and Chios, are used. The main purpose is to apply DTL for day-ahead predictions (1-24 hours) for each month of the year for Chios dataset after training and fine-tuning the models using the datasets of the three islands in various combinations. After several trials, four DTL strategies are illustrated. In the first strategy (DTL Case 1), each of the three DL models is trained using only Lesvos dataset, while fine-tuning is performed on the dataset of Chios island, in order to create day-ahead predictions for Chios load. In the second strategy (DTL Case 2), data from both Lesvos and Rhodes concurrently are used for the DL model training period, and fine-tuning is performed on the data from Chios. The third DTL strategy (DTL Case 3) contains the training of the DL models using Lesvos dataset, and the testing period performed directly on the Chios dataset without fine-tuning. The fourth strategy is a Multi-task Deep Learning (MTDL) approach, which has been extensively studied in recent years. In MTDL, the three DL models are trained simultaneously on all three datasets and the final predictions are made on the unknown part of the dataset of Chios. In this paper, we explore the performance of DTL and compare the results with those produced with MTDL. The results demonstrated that DTL can be applied with high efficiency for day-ahead load forecasting. Specifically, the two cases with fine-tuning (DTL Case 1 and 2) outperformed MTDL in terms of load prediction accuracy. Regarding the DL models, all three exhibit very high prediction accuracy, especially in the two cases with fine-tuning. The ELM excels compared to the single models. More specifically, for conducting day-ahead predictions, it has been concluded that the MLP model presents best monthly forecasts with a MAPE of 6.24% and 6.01% for the first two cases, the CNN model presents best monthly forecasts with a MAPE of 5.57% and 5.60% respectively and the ELM model achieves best monthly forecasts with a MAPE of 5.29% and 5.31%, respectively, indicating the very high accuracy it can achieve.

The chloroplast genome is conservative and stable, which can be employed to resolve genotypes. Currently, published nuclear sequences and molecular markers failed to differentiate the species from taxa robustly, including Machilus leptophylla, Hanceola exserta, Rubus bambusarum, and Rubus henryi. In this study, the four chloroplast genomes were characterized, and then their simple sequence repeats (SSRs) and phylogenetic positions were analyzed. The results demonstrated the four chloroplast genomes consisted of 152.624 kb, 153.296kb, 156.309 kb, and 158.953 kb in length, involving 124, 130, 129, and 131 genes, respectively. Moreover, the chloroplast genomes contained typical four regions. Six classes of SSR were identified from the four chloroplast genomes, in which mononucleotide was the class with the most members. The types of the repeats were various within individual classes of SSR. Phylogenetic trees indicated that M. leptophylla was clustered with M. yunnanensis, and H. exserta was confirmed under family Ocimeae. Additionally, R. bambusarum and R. henryi were clustered together, whereas they did not belong to the same species due to the differing SSR features. This research would provide evidence for resolving the species and contributed new genetic information for further study.

Abstract: The study used whole-genome sequencing (WGS) and bioinformatics analysis for the genomic characterization of 60 isolates of Listeria monocytogenes isolated from cattle farms, cattle abattoirs, and retail outlets in Gauteng province, South Africa. The isolates' sequence types (STs), clonal complexes (CCs), and lineages were determined using in silico multilocus sequence typing (MLST). We used BLAST-based analyses to identify virulence and antimicrobial genes, plasmids, proviruses, and the CRISPR-Cas system. The study investigated any association of the detected genes to the origin in the beef production chain of the L. monocytogenes isolates. Overall, in 60 isolates of Listeria monocytogenes, there were 7 STs, 6 CCs, 44 putative virulence factors, 2 resistance genes, 1 plasmid with AMR genes and 3 with conjugative genes, 1 CRISPR gene, and all 60 isolates were positive for proviruses. Among the 7 STs detected, ST204 (46.7%) and ST2 (21.7%) were the most prominent, with ST frequency varying significantly (p<0.001). The predominant CC detected were CC2 (21.7%) and CC204 (46.7%) in lineages I and II, respectively. Of the 44 virulence factors detected, 26 (across Listeria Pathogenicity Islands, LIPIs) were present in all the isolates. The difference in the detection frequency varied significantly (P<0.001). The two AMR genes (fosX and vga(G)) detected were present in all 60 (100%) isolates of L. monocytogenes. The only plasmid, NF033156, was present in 3 (5%) isolates. A CRISPR-Cas system was detected in 6 (10%), and all the isolates carried proviruses. Significant differences were detected in the frequencies of STs and virulence factors regarding the source and sample type of the L. monocytogenes isolates. The presence of both fosX and vga(G) genes in all the isolates from the three industries (cattle farms, abattoirs, and retail outlets) can potentially cause therapeutic implications. Our study, which characterized L. monocytogenes recovered from the three levels in the beef production chain in the country, provides the first evidence of the distribution of the pathogen with potential food safety and therapeutic implications.

In this work we looked for a stable and accurate procedure to perform feature selection in datasets with a much higher number of predictors than individuals, as in Genome-Wide Association Studies. Due to the instability in feature selection when many potential predictors are measured, a variable selection procedure is proposed that combines several replications of shrinkage regression models. A weighted formulation is used to define the final predictors. The procedure is applied to investigate Single Nucleotide Polymorphisms (SNPs) predictors associated to Alzheimer’s disease in the Alzheimer’s disease Neuroimaging Initiative (ADNI) dataset. Two data scenarios are investigated: one considering only the set of SNPs and another with the covariates age, sex, educational level and APOE4 genotype. The SNP rs2075650 and the APOE4 genotype are given as risk factors for AD, which is in line with the literature, and other four new SNPs are pointed, opening new hypotheses for in vivo analyses. These experiments demonstrate the potential of the new method for stable feature selection.

Cercospora beticola Sacc. is an ascomycete pathogen that causes Cercospora leaf spot in sugar beets (Beta vulgaris L.) and other related crops. The disease symptoms are characterized by circular lesions with an ash-gray centre and dark brown to purple margins on the leaves. It can lead to significant yield losses if not effectively managed. This study aims to characterize and assess the impact of bacterial biological control agents against C. beticola. Following a dual-culture screening, 18 bacteria exhibiting over 50% inhibition were selected, with six of them demonstrating more than 80% control. Identification of the bacteria was carried out through sequencing of the16S rDNA, revealing potentially 12 species belonging to six genera including Bacillus which was represented by four species. Additionally, the bacteria underwent in-depth characterization of biochemical and molecular properties, as well as plant-growth promotion. PCR detection of genes responsible for producing antifungal metabolites revealed that 83%, 78%, 89%, and 56% of the selected bacteria possessed the bacillomycin, iturin, fengycin, and surfactin encoding genes, respectively. Infrared spectroscopy analysis confirmed the presence of lipopeptide structure in the bacteria supernatant filtrate. Subsequently, the bacteria were assessed for their effect on sugar beet plants in controlled conditions. The bacteria exhibited notable capabilities, promoting growth in both roots and shoots, resulting in significant increases in root length, weight, and shoot length. The field experiment with four bacterial candidates demonstrated good performance against C. beticola compared to difenoconazole fungicide. These bacteria played a significant role in disease control, achieving a maximum efficacy of 77.42%, slightly below the 88.51% efficacy attained by difenoconazole. Additional field trials are necessary to verify the protective and growth-promoting effects of these candidates, whether applied individually, combined in consortia, or integrated with chemical inputs in sugar beet crop production.

The purpose of this study was to identify candidate novel species performing beneficial ecological functions from soil. The hypothesis was that novel culturable species with antibiotic production potential could be readily found from soil in the Nature Canyon at Los Angeles Pierce College. 137 bacterial isolates from soil were grown on nutrient agar, ISP-6 medium, or LB agar and partial 16S was ascertained using the Sanger platform for regions V1-V4. One of the potentially novel isolates, Pseudomonas sp. 21-C3-ER, was isolated on nutrient agar from fallow soil in an agricultural nature preserve in Los Angeles. The soil conditions were 3.7% moisture, clay texture by touch, 13.37% organic matter, pH=6.63, TDS=638, 150 ppm nitrogen, 114 ppm phosphate, and 42 ppm potash. Whole genome sequencing was performed on the DNBseq platform and species identification was performed with TRUEBacID; the closest relative was Pseudomonas brassicacearum subsp. neoaurantiaca which was 92.05% similar by genomic evidence. 197 virulence factors were identified including flagellar biosynthesis, motor proteins, Beta-lactamase, Fosfomycin, copper, and sulfur drug resistance. Gram stain of strain 21-C3-ER revealed gram negative rods. Rods were visualized with scanning electron microscopy, revealing individuals approximately 1 µm in length. Secondary metabolite analysis using antiSMASH showed a variety of post-translationally modified proteins and a promysalin analog. The qualitative test for pyoverdine siderophore production using UV light was positive. Metabolic analysis using RAST indicated genes were present for pyoverdine production, antimicrobial resistance, and ammonification. The nitrate reduction test was positive. Denitrifying bacteria may prevent leaching of nitrates from soil, since ammonia has a higher affinity to soil and organic matter than nitrate. We propose Pseudomonas fernandeno as a novel species. The type stain is 21-C3-ER.

The Chinese honeybee (Apis cerana cerana) sacbrood virus (CSBV) causes death of larvae and colony collapse, and could damage the beekeeping industry in China. We sequenced complete genomes of CSBV strains derived from the Maerkang area, Wenjiang area, and Wanyuan area of Sichuan province of China. The genome length of CSBV strains from Sichuan was 8863bp, and it contained one complete Open Reading Frame of a gene with 8544 bp that encoded a protein with 2848 amino acids. The (G+C) % and (A+T) % composition ranged from 40.6 to 40.7 and 59.3 to 59.4, respectively. A phylogenetic tree was constructed using the three CSBV strains and previously reported SBV and CSBV sequences from other regions. We found that viral strains clustered based on their region of origin and host species. The genetic sequences of the CSBV strain from Maerkang were 98.7% and 99.6% similar to CSBV strains from Wanyuan and Wenjiang, respectively. In addition, CSBV from Maerkang had 88.4%-95.2% sequence similarity to previously published genomes of CSBV or SBV from other areas. The VP1 gene sequenced in our study had a 43 bp deletion compared to VP1 sequences of CSBV from other regions in Asia. We detected 10 antigenic determinants on the VP1 protein of CSBV form Aba. Our study provides new insight into the diversity of CSBV strains in China and may help with identifying methods to prevent infection of honeybee colonies.

Idiopathic granulomatous mastitis (IGM) is a rare condition characterised by chronic inflammation and granuloma formation in the breast. The aetiology of IGM is unclear. By focusing on the protein-coding regions of the genome, where most disease-related mutations often occur, whole-exome sequencing (WES) is a powerful approach for investigating rare and complex conditions, like IGM. We report WES results on paired blood and tissue samples from eight IGM patients. Samples were processed using standard genomic protocols. Somatic variants were called with two analytical pipelines: nf-core/sarek with Strelka2 and GATK4 with Mutect2. Our WES study of eight patients did not find evidence supporting a clear genetic component. The discrepancies between variant calling algorithms, along with the considerable genetic heterogeneity observed amongst the eight IGM cases, indicate that common genetic drivers are not readily identifiable. With only three genes, CHIT1, CEP170, and CTR9, recurrently altered in multiple cases, the genetic basis of IGM remains uncertain. The absence of validation for somatic variants by Sanger sequencing raises further questions about the role of genetic mutations in the disease. These observations suggest that IGM may be influenced by non-genetic factors, such as environmental triggers or immune system dysregulation, rather than being primarily a genetic disorder.

Nyssa yunnanensis is a deciduous tree species in the family Nyssaceae within the order Cornales. As only eight individual trees and two populations have been recorded in China’s Yunnan province, this species has been listed among China’s national Class I protection species since 1999 and also among 120 PSESP (Plant Species with Extremely Small Populations) in the Implementation Plan of Rescuing and Conserving China’s Plant Species with Extremely Small Populations(PSESP) (2011-2-15). Here, we present the draft genome assembly of N. yunnanensis. Using 10X Genomics linked-reads sequencing data, we carried out the de novo assembly and annotation analysis. The N. yunnanensis genome assembly is 1475 Mb in length, containing 288,519 scaffolds with a scaffold N50 length of 985.59 kb. Within the assembled genome, 799.51 Mb was identified as repetitive elements, accounting for 54.24% of the sequenced genome, and a total of 39,803 protein-coding genes were predicted. With the genomic characteristics of N. yunnanensis available, our study might facilitate future conservation biology studies to help protect this extremely threatened tree species.

The origin of SARS-CoV-2 is debated, even after 18 months into the COVID-19 pandemic and a special investigation conducted by the World Health Organization. The RaTG13 sequence has been a highlight of discussions surrounding the origin of SARS-CoV-2. Here we express our opinion about the need for better reporting standards for information about sequencing data, especially for pathogens, citing our findings with the reported RaTG13 genome.

RaTG13 (a bat derived SARS-like CoV) is the closest relative sequence of SARS-CoV-2 reported till date. The sample from which RaTG13 was sequenced was a bat fecal swab collected in 2013 from Tongguan, Mojiang, Yunnan province, China. The Illumina based sequence of RaTG13, MN996532.1, was deposited on 27^th Jan 2020 and the raw data (Illumina), https://www.ncbi.nlm.nih.gov/sra/SRX7724752[accn]. There are discrepancies in dates about when the metagenome sequencing of RaTG13 sample was done (2018 or 2020), both stated by the same corresponding author. Comparison of the RNA Seq data of RaTG13 fecal swab to the corresponding data from the bat fecal swabs deposited by the same working group using the same methods indicated that the RaTG13 raw data seemed to be different in various aspects. The fecal swab sample showed abnormally less read of bacterial reads in the swab was exceptionally low, i.e. 0.7%, compared to the 20-90% abundance in other fecal swabs from bats processed by similar methods. Also, another raw data in the form of amplicon sequences was deposited in May 2020; however, the dates mentioned on the files of the sequenced amplicons were older (2017, 2018). The genome assembly of RaTG13 could not be done de-novo and the average coverage of the genome ~8%. Also, literature indicates that RaTG13 RBD cannot bind to Rhinolophus ACE-2 receptors. Collectively, the anomalies in the raw data of RaTG13 and other issues pose an important question about the overall authenticity of the RaTG13 genome sequence.

Recently we have seen a relaxation of the historic restrictions on the use and subsequent research on the Cannabis plants, generally classified as Cannabis sativa and Cannabis indica. What research has been performed to date has centered on chemical analysis of plant flower products, namely cannabinoids and various terpenes that directly contribute to phenotypic characteristics of the female flowers. In addition, we have seen many groups recently completing genetic profiles of various plants of commercial value. To date, no comprehensive attempt has been made to profile the proteomes of these plants. We report herein our progress on constructing a comprehensive draft map of the Cannabis proteome. To date we have identified over 17,000 potential protein sequences. Unfortunately, no annotated genome of Cannabis plants currently exists. We present a method by which “next generation” DNA sequencing output and shotgun proteomics data can be combined to produce annotated FASTA files, bypassing the need for annotated genetic information altogether in traditional proteomics workflows. The resulting material represents the first comprehensive annotated protein FASTA for any Cannabis plant. Using this annotated database as reference we can refine our protein identifications, resulting in the confident identification of 13,000 proteins with putative function. Furthermore, we demonstrate that post-translational modifications play an important role in the proteomes of Cannabis flower, particularly lysine acetylation and protein glycosylation. To facilitate the evolution of analytical investigations into these plant materials, we have created a portal to host resources we have developed from proteomic and metabolomic analysis of Cannabis plant material as well as our results integrating these resources. All data for this project is available to view or download at www.CannabisDraftMap.Org

Abstract The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in people in the city of Wuhan at the end of December 2019, and it has since spread to all continents. Global interest has been focused on discovering a treatment and developing a successful coronavirus vaccine as a result of the emergence of this new coronavirus. In this research, we sequenced the whole genome of the SARS-COV-2 virus that were isolated from 40 patients in Duhok, Iraq. 95 different mutations were identified in our isolation when such the whole genome sequence of the SARS-COV-2 isolated from the city of Wuhan, China (Accession number: NC 045512.2) was matched to the virus's sequence using Sequencing technology (Illumina , USA ) and Assembly method (iVar 1.3.1). Sequence analysis revealed that 38 mutations were found at spike glycoprotein (S), 30 of which were found in the ORF1b , 11 mutations were found in ORF1b ,7,3,2,1 mutations were found in ( N,M,ORF6 ,ORF9 /E ) genes which had been linked to structural changes at various places. The conclusion that the cases in Iraq were of different origins of infections and had a close relationship with the isolates from different country and state were further confirmed by phylogenetic analysis and transmission. The whole genome sequence of the SARS-CoV-2 , which were identified from the Iraqi Kurdistan region, and reported as a first study in Kurdistan region.

The complete genomic sequence of a Cassava common mosaic virus Linggao isolate (CsCMV-LG) was determined from cassava (Manihot esculenta Crantz) with mild leafy mosaic symptom to no symptom in China. Excluding the poly(A) tail, the CsCMV-LG genome (GenBank accession No. MT038420) is 6374 nucleotides (nts) in length, with five major open reading frames encoding a 1450-amino acids (aa) RNA-dependent RNA polymerase (RdRp), three triple gene block (TGB) proteins (231-aa, 110-aa and 95-aa), and a 229-aa coat protein (CP). Phylogenetic analysis indicated that the complete genome of the CsCMV-LG is closely related to that of CsCMV-Brazilian which has been assigned to the genus Potexvirus, but the sequence identity shared only 88.0%. Notable, the mild CsCMV-LG isolate can also infect Nicotiana benthamiana in laboratory through rub inoculation causing mild vein yellowing at 15-day post inoculation. This is the first full-length genome sequence of a distinct isolate of Cassava common mosaic virus (CsCMV) infecting cassava in Hainan, China.

Astroviruses (AstVs) are occurs globally and are common causes of gastroenteritis in human and animals. The genetic diversity and epidemiology of AstVs in Africa is not well known, hence, we aimed to genetically characterize astroviruses in asymptomatic smallholder piglets in East Africa. Twenty-four samples randomly selected from 446 piglets (<6 months old), initially collected for rotavirus study, was sequenced for metagenomic analysis. Thirteen (13/24) samples had contigs with high identity to genus Mamastrovirus. Analysis of 7 strains with complete (or near complete) genome revealed variable nucleotide and amino acid sequence identities with known PoAstV strains. The U083 and K321 strains had nucleotide sequence similarities ranging from 66.4 to 75.4 % to the known PoAstV2 strains, nucleotide sequence similarity of U460 strain with known PoAstV3 ranged 57.0 to 65.1 % to the, while K062, K366, K451, and K456 strains showed nucleotide sequence similarities of 63.5 to 80 % to the known PoAstV4 strains. The low sequence identities (<90 %) indicate that novel genotypes of PoAstVs are circulating in the study area. Multiple recombination events were detected in our PoAstV4 strains, indicating that the genetic diversity observed in these strains may be due to recombination. Importantly, we identified potential candidate epitopes with conserved peptides in our PoAstV strains that could aid in the design of immune diagnosis tools and subunit vaccines. Our data provide new intuitions into the genetic structure of porcine astroviruses in East African.

Classifying network flow subsequences in an Industrial IoT gateway is an effective method for identifying Industrial IoT faults. This paper proposes a subsequence classification algorithm SSGBUL-IKNN based on unsupervised learning encoding to address the problem of low classification accuracy. Firstly, we built a network module based on unsupervised learning to encode the flow sequence of the Industrial IoT gateway. In the encoding module, a subsequence calibration algorithm controls the increasing error during the coding process. Then, the specific fault type is obtained through an improved KNN classification algorithm based on the indication distance source from the integrated coding sequences converted by multi-dimensional network flow sequences. The test result on three Industrial IoT datasets of a sewage treatment plant shows that the accuracy of SSGBUL-IKNN in this paper exceeds 92%, significantly higher than the algorithm DTW and TSF. It reaches the classification requirements of Industrial IoT fault diagnosis.

Oligopeptide transporters (OPTs) are a group of membrane localized proteins that have a broad range of substrate transport capabilities and contribute to numerous biological processes. However, limited information has been reported on OPTs in higher plants. In this study, a comprehensive analysis of the OPT gene family in Medicago truncatula was performed. A total of 26 OPT genes (MtOPT01-MtOPT26) have been identified in the Medicago truncatula genome. Phylogenetic analyses indicated that MtOPTs consisted of two distinct subgroups, 12 MtOPTs belonged to the peptide transport subgroup (PT-OPT) based on their predicted amino acid sequences containing the two highly conserved motifs (NPG and KIPPR) and 14 MtOPTs belonged to yellow stripe subgroup (YS-OPT). The MtOPTs distributed on each of 8 chromosomes in Medicago truncatula. Sequence analysis verified that MtOPTs significant similar to those in other plants. The copy number of MtOPTs was low and the multiply of MtOPTs was simple relatively. Gene structure analysis showed that most of the MtOPTs have various numbers of introns. The multiple of MtOPTs might play different biological roles which were supported by the fact that MtOPTs have a distinct tissue-specific expression pattern. The data obtained in this study will help to better understand the complexity of the MtOPTs gene family and provide new evidence for the function and evolution of the OPT gene family in higher plants.

The utilization of electroporation for delivering the CRISPR/Cas9 system components has enabled efficient gene editing in mammalian zygotes, facilitating the development of genome-edited animals. In our study，This research focused on targeting the ACTG1 and MSTN genes in sheep, revealing a threshold phenomenon in electroporation with a voltage tolerance in sheep in vitro fertilization (IVF) zygotes. Various poring voltages near 40V and pulse durations were examined for electroporating sheep zygotes. The study concluded that stronger electric fields required shorter pulse durations to achieve the optimal conditions for high gene mutation rates and reasonable blastocyst development. The investigation also assessed the quality of Cas9/sgRNA ribonucleoprotein complexes (Cas9 RNPs) and their influence on genome editing efficiency in sheep early embryos. It was highlighted that pre-complexation of Cas9 proteins with single-guide RNA (sgRNA) before electroporation was essential for achieving a high mutation rate. The use of suitable electroporation parameters for sheep IVF zygotes led to significantly high mutation rates and heterozygote ratios. By delivering Cas9 RNPs and single-stranded oligodeoxynucleotides (ssODNs) to zygotes through electroporation, targeting the MSTN (Myostatin) gene, a knock-in efficiency of 26% was achieved. The successful generation of MSTN-modified lambs was demonstrated by delivering Cas9 RNPs into IVF zygotes via electroporation.

Thorough and precise gene structure annotations are essential for maximizing the benefits of genomic data and unveiling valuable genetic insights. The cucumber genome was first released in 2009 and updated in 2019. To increase the accuracy of predicted gene models, 64 published RNA-seq data and 9 new strand-specific RNA-seq data from multiple tissues were used for manual comparison with the gene models. The updated annotation file (version 2.0) contains increased 24,145 predicted genes from previous version (24317 genes) with a higher BUSCO value of 96.9%. 6231 and 1490 transcripts were adjusted and newly added, respectively, accounting for 31.99% of the overall gene tally. These newly added and adjust genes were renamed (CsaV3.1_XGXXXXX), while genes remaining unaltered preserve their original des ignations. A random selection of 21 modified/added genes were validated using RT-PCR analyses. Additionally, tissue-specific patterns of gene expression were examined using newly obtained transcriptome data with the revised gene prediction model. This improved annotation of cucumber genome will provide essential and accurate resources for studies in cucumber.

Background: Alfalfa, the most economically important forage legume worldwide, features modest genetic progress due to long selection cycles and large extent of non-additive genetic variance associated with its autotetraploid genome. Methods: To improve the efficiency of genomic selection in alfalfa, we explored the effects of genome parametrization (as autotetraploid and diploid dosage, plus allele ratios) and SNP marker subsetting (all available SNPs; only genic regions; only non-genic regions) on genomic regressions, together with various levels of filtering on reading depth and missing rates. We used Genotyping by Sequencing-generated data and focused on traits of different genetic complexity, i.e., dry biomass yield in moisture-favorable (FE) and drought stress (SE) environments, leaf size, and onset of flowering, assessed on 143 genotyped plants from a genetically-broad European reference population and their phenotyped half-sib progenies. Results: On average, allele ratio improved the predictive ability compared with other genome parametrizations (+7.9% vs. tetraploid dosage, +12.6% vs. diploid dosage), SNP subsetting offered an advantage compared with any tested subsettings (+3.7% vs. genic regions, +7.6% vs. non-genic regions). However, when focusing on specific traits, different combinations of genome parametrization and subsetting reached better performances. We also released Legpipe2, a SNP calling pipeline tailored for reduced representation (GBS, RAD) medium-sized genotyping experiments.

Callus induction (CI) is the critical trait for the transformation of desirable genes in plants. A genome-wide association study (GWAS) analysis was conducted on the rice germplasm of 110 diverse indica rice accessions. Three tissue culture media, including B5, MS, and N6, were used for CI in those rice panels. Seven quantitative trait loci (QTLs) on chromosomes 2, 6, 7, and 11 were found to confer a CI percentage in these three media. For the B5 medium, one QTL (qCI-B5-Chr6) was identified on the rice chromosome 6. For the MS medium, two QTLs were identified on the rice chromosomes 2 and 6 (qCI-MS-Chr2 and qCI-MS-Chr6, respectively). For the N6 medium, four QTLs were identified on the rice chromosomes 6, 7, and 11 (qCI-N6-Chr6.1, qCI-N6-Chr6.2, qCI-N6-Chr7, and qCI-N6-Chr11, respectively). Fifty-five genes were identified within the haplotype blocks corresponding to these QTLs. Thirty-one genes showed haplotypes associated with different CI in those media. The qCI-B5-Chr6 was located in the same region as the qCI-N6-Chr6.2. The caleosin-related family protein was identified in this region. Analysis of the gene-based haplotype reveals the association of this gene with different CI in both B5 and N6 media, suggesting that the gene may play a critical role in the CI mechanism. Moreover, several genes, including the beta-tubulin, the zinc finger proteins, the RNP-1 domain-containing protein, and the Lysophosphatidic acid acyltransferase, were associated with different CI in the N6 media. Results from this study provide insight into the potential QTLs and candidate genes for callus induction in rice that will fulfill the understanding of the physiological and biochemical processes involved in callus formation, which is an essential tool in the molecular breeding of rice.

This study aimed to determine shifts in microbial populations regarding richness and diversity from the daily use of a popular over-the-counter nasal spray. In addition, the finding of nasal commensal bacterial species that overlap with the oral microbiome may prove to be potential probiotics for the “gateway microbiomes.” Nasal swab samples were obtained before and after using the most popular over-the-counter (OTC) nasal spray in 10 participants aged 18–48. All participants were healthy volunteers with no significant medical histories. The participants were randomly assigned a number by randomizing software and consisted of five men and five women. The sampling consisted of placing a nasal swab atraumatically into the nasal cavity. The samples were preserved and sent to Northwestern University Sequencing Center for whole-genome deep sequencing. After 21 days of OTC nasal spray use twice daily, the participants returned for further nasal microbiome sampling. The microbial analysis included all bacteria, archaea, viruses, molds, and yeasts via deep sequencing for species analysis. The Northwestern University Sequencing Center utilized artificial intelligence analysis to determine shifts in species and strains following nasal spray use that resulted in changes in diversity and richness.

The genus Vigna is penta-tropical having more than 200 species with many desirable economically important traits. The aim of study was to validate the in-silico polymorphism of whole genome sequence developed mungbean specific SSR markers and their transferability among the different Vigna species. The present study utilized a set of 200 SSR markers developed from whole genome sequence of mungbean and validated using a diversity panel of 25 accessions which belongs to 13 Vigna species. Out of 200 SSR markers, 130 markers (65%) were polymorphic across the various Vigna species and the number of alleles amplified varied between 7 to24. The SSR markers showed more than 90 percent transferability across the different Vigna species accessions. Based on allelic data, the 25 Vigna accessions grouped into three clusters based upon the unweighted pair group method with arithmetic mean (UPGMA) phylogenetic tree. The principal co-ordinates analysis (PCA) biplot graph and UPGMA based neighbor joining clustering diagram showed similar pattern of Vigna accessions distribution. The population structure assessment has grouped the cultivated and wild species accessions into two sub-population. The estimated marker parameters such as polymorphic information content (0.09 – 0.84), marker index (0.091 – 3.342) and effective multiplex ratio (1.0 – 4.0) suggested their adequacy in several genetic studies such as parental selection, hybrid testing, genetic mapping and marker aided breeding programmes for genetic enhancement of species belonging to the Vigna genus.

In order to improve the performance of the draft tube in hydraulic turbine, a multi–objective optimization method for the draft tube is developed by combining the design of experiment (DOE), the radial basis function (RBF) and the non–dominated sorting genetic algorithm (NSGA–II) in this paper. The geometrical design variables of the median section in the draft tube and the cross section in its exit diffuser are considered as design parameters in this optimization, which objective function is to maximize the pressure recovery factor (Cp) and minimize the energy loss coefficient (ζ). The limited numbers of design matrix required for the shape optimization of the draft tube is generated by optimal Latin hypercube (OLH) method of the DOE technique, of which performances are evaluated through computational fluid dynamic (CFD) numerical simulation. For reducing of the computational consumption, the approximate model is used based on the RBF. The Pareto optimal solutions are finally performed using the NSGA–II for obtaining the best geometrical parameters of the draft tube. The optimization result of the draft tube shows a marked performance improvement over the original, which verifies the theoretical validity and feasibility of the proposed method in this paper.

Background: Intrauterine transfusion (IUT) of the donor and partial exchange (pET) of the recipient is a temporizing treatment for pregnancies with Twin Anemia Polycythemia Sequence (TAPS). We sought to give a detailed description of the procedural approach and outcomes for sequential donor IUT and recipient pET in TAPS. Methods: Retrospective study of spontaneous TAPS referred to the Johns Hopkins Center for Fetal Therapy treated with donor IUT followed by recipient pET utilizing a double-syringe set up. Procedure characteristics and outcomes as well as accuracy of existing transfusion formulas were analyzed and compared with the literature. Results: 5 of 78 patients with spontaneous TAPS underwent a total of 19 combined IUT/pET procedures (median first procedure to delivery interval 5.6 weeks [interquartile range IQR 1.9-6.0]). One pET was stopped for fetal decelerations. Patients delivered at 33.0 weeks [IQR 31.9-33.3] with two survivors and no neonatal transfusion requirements. IUT volumes were 48 ml [IQR 39-63 ml] and pET volumes 32 ml [IQR 20-50] utilizing aliquots of 5 – 20 mls for the latter (p=0.021). For IUTs, assumption of a fetal blood volume below 150 ml/kg underestimated required transfusion volume. For pETs, all formulas required adjustment of dilution volume based on bedside testing (p&lt;0.05 for all). Conclusions: Donor transfusion followed by partial exchange in the recipient can prolong pregnancy in spontaneous TAPS and obviate the need for neonatal transfusion. A double-syringe setup facilitates efficient saline exchange. Because the accuracy of volume formulas is limited, bedside testing is recommended to achieve the target hemoglobin.

Today massive amounts of sequenced metagenomic and -transcriptomic data from different ecological niches and environmental locations are available. Scientific progress depends critically on methods that allow extracting useful information from the various types of sequence data. Here, we will first discuss types of information contained in the various flavours of biological sequence data, and how this information can be interpreted to increase our scientific knowledge and understanding. We argue that a mechanistic understanding is required to consistently interpret experimental observations, and that this understanding is greatly facilitated by the generation and analysis of dynamic mathematical models. We conclude that, in order to construct mathematical models and to test mechanistic hypotheses, time-series data is of critical importance. We review diverse techniques to analyse time-series data and discuss various approaches by which time-series of biological sequence data was successfully used to derive and test mechanistic hypotheses. Analysing the bottlenecks of current strategies in the extraction of knowledge and understanding from data, we conclude that combined experimental and theoretical efforts should be implemented as early as possible during the planning phase of individual experiments and scientific research projects.

Scientists can use the Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) protein 9 system, which is a powerful and flexible tool for changing the genome, to change only certain parts of the genome. This has helped researchers figure out how target genes work in biology and disease. CRISPR/Cas9 is made up of a sequence-specific CRISPR RNA (crRNA) set and a generic Cas9 nuclease. The crRNA set tells Cas9 where to cut DNA and cause double-strand breaks. In the next step of cellular DNA repair, insertions, deletions, and swaps are made at specific spots. For CRISPR/Cas9-mediated DNA cleavage to be specific, the target sequences must match the crRNA, and a protospacer nearby motif must be placed after the target sequences. In this article, we talk about how CRISPR/Cas9 works at the molecular level, what it can be used for, what it can't do, and what its future clinical treatment promise might be.

Spontaneous tumours in higher plants can develop depending on plant genotype without any pathogen invasion. Spontaneous tumour formation on the taproots is consistently observed in certain inbred lines of radish (Raphanus sativus var. radicula Pers.). In this work, we have sequenced the genomes of two closely related radish inbred lines that differ in their ability to spontaneously form tumours. We have identified numerous single nucleotide variants (amino acid substitutions, insertions or deletions) that are likely to be associated with the spontaneous tumour formation. Furthermore, we performed the identification of CLE and WOX genes the genomic sequences of the radish inbred lines and, as a result, identified two unique radish CLE genes which probably encode proteins with multiple CLE domains. The results obtained provide a basis for investigating the mechanisms of plant tumour formation and also for future genetic and genomic studies of radish.

Open source software such as OpenDSS has given a lot of help to distribution network researchers and educators. With high penetration of distributed renewable energy resources into distribution network, tradition distribution steady state analysis software such as OpenDSS is faced with difficulty in handling distributed generators. Three-phase distributed generators are often modeled in sequence frame while unbalanced distribution network are usually modeled in phase frame. So a load flow in sequence-phase coupled frame is proposed to handle models described in both frames. Voltage controlled DGs which are difficult to cope with in OpenDSS are handled in proposed program. The steady state analysis platform is programmed with open source Modelica language and the main aim of this paper is to introduce an open source platform for active distribution network steady analysis include load flow and short circuit analysis which can be easily adopted and improved by other educators and researchers.

The flowering period of rice significantly impacts variety adaptability and yield formation. Properly shortening the reproductive period of rice varieties can expand their ecological range without significant yield reduction. Targeted genome editing, like CRISPR/Cas9, is an ideal tool to fine-tune rice growth stages and boost yield synergistically. In this study, we developed a CRISPR/Cas9-mediated multiplex genome editing vector containing five genes related to three traits: Hd2, Ghd7, and DTH8 (flowering stage genes), along with the recessive rice blast resistance gene Pi21 and the aromatic gene BADH2. This vector was introduced into the high-quality Geng rice variety in Zhejiang province, Jiahe212 (JH212), resulting in 34 T0 plants with various effective mutations. Among the 17 mutant T1 lines, several displayed diverse flowering dates, but most exhibited undesirable agronomic traits. Notably, three homozygous mutant lines (JH-C15, JH-C18, and JH-C31) showed slightly earlier flowering dates without significant differences in yield-related traits compared to JH212. Through special Hyg and Cas marker selection of T2 plants, we identified 7, 6, and 2 fragrant glutinous plants devoid of transgenic components, respectively. These single plants will serve as sib lines of JH212 and potential resources for breeding applications, including maintenance lines for Xian-Geng interspecific three-line hybrid rice. In summary, our research offers practical insights and potential resources for targeted improvement of Geng rice varieties, and would also promote the Geng rice varieties expending from the southward to the northward.

Magnetic resonance (MR) image acquisitions are usually time-consuming, limiting utilization in neuroimaging. For multiple sclerosis (MS) patients, MR imaging plays a major role in drug therapy decision-making. The purpose of this study was to evaluate whether an ultrafast, T2-weighted (T2w), deep-learning-enhanced (DL), echo-planar-imaging-based (EPI) fluid-attenuated inversion recovery (FLAIR) sequence (FLAIRUF) that has been targeting neurological emergencies so far might even be an option to detect MS lesions of the brain compared to conventional FLAIR sequences. Therefore, 17 MS patients were enrolled prospectively in this exploratory study. Standard MR protocols and ultrafast acquisitions were conducted at 3 tesla (T), including three-dimensional (3D)-FLAIR, turbo/fast spin echo (TSE)-FLAIR, and FLAIRUF. Inflammatory lesions were grouped by size and location. Lesion conspicuity and image quality were rated on an ordinal five-point Likert scale, and lesion detection rates were calculated. Statistical analyses were performed to compare results. Altogether, 568 different lesions were found. Data indicated no significant differences in lesion detection (sensitivity and positive predictive value [PPV]) between FLAIRUF and axially reconstructed 3D-FLAIR (lesion size ≥ 3 mm × ≥ 2 mm) and no differences in sensitivity between FLAIRUF and TSE-FLAIR (lesion size ≥ 3 mm total). Lesion conspicuity in FLAIRUF was similar in all brain regions except for superior conspicuity in the occipital lobe and inferior conspicuity in central brain regions. Further findings include location-dependent limitations of signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) as well as artifacts such as spatial distortions in FLAIRUF. In conclusion, FLAIRUF could potentially be an expedient alternative to conventional methods for brain imaging in MS patients since the acquisition can be performed in a fraction of time while maintaining good image quality.

Genetic engineering has become an essential element in developing climate-resilient crops and environmental sustainable solutions to respond to the increasing need for global food security. Genome editing using CRISPR/Cas [Clustered regulatory interspaced short palindromic repeat (CRISPR)-associated protein (Cas)] technology is being applied to a variety of organisms, including plants. This technique has become popular because of its high specificity, effectiveness, and low production cost. Therefore, this technology has the potential to revolutionize agriculture and contribute to global food security. Over the past few years, increasing efforts have been seen in its application in developing higher-yielding, nutrition rich, disease resistant, stress-tolerant “crops” fruits and vegetables. Cas proteins such as Cas9, Cas12, Cas13, and Cas14, among others, have distinct architectures and have been used to create new genetic tools that improve features that are important for agriculture. The versatility of Cas has accelerated genomic analysis and facilitated the use of CRISPR/Cas to manipulate and alter nucleic acid sequences in cells of different organisms. This review provides the evolution of CRISPR technology exploring its mechanisms and contrasting it with traditional breeding and transgenic approaches to improve different stress tolerance. We have also discussed the CRISPR/Cas system and explored three Cas proteins that are currently known to exist: Cas12, Cas13, and Cas14 and their potential to generate foreign DNA free or non-transgenic crops that could be easily regulated for commercialization in most countries.

The aim of this paper is to use the elementary method and the properties of the second kind Stirling numbers to study the congruence properties of a new sequence, which is closely related to Fubini polynomials and Euler numbers, and give some interesting congruences for it. This solves a problem proposed by the first author at an unpublished paper.

Most non-infectious diseases are associated with dysfunction of proteins or protein complexes. Аssociation between sequence and structure is analyzed since a long time, and analysis of sequence organization in domains and motifs is actual research area. A mathematical method is proposed here to identify the hierarchical organization of protein sequences. The method is based on pentapeptide as a unit of protein sequences. This method was applied on a non-homologous dataset of protein sequences. The analysis revealed 11 hierarchical levels of protein sequence organization, showing the relationship of these multiple fragments of sequences. Using different examples, we illustrated how the fragments of the spatial structure of protein correspond to the elements of the hierarchical structure of the protein sequence. A hierarchical structure is observed in the protein sequence. This methodology is an interesting basis for mathematically based classification of elements of spatial organization of proteins. Elements of the hierarchical structure of different levels of the hierarchy can be used for biotechnological and medical problems.

The UK government and many international experts have pointed out that nuclear energy has an important role to play in the transition towards a decarbonized energy system since it is the only freely manageable very low-carbon energy technology with 24/7 availability to complement renewables. Besides current investments in light water reactor technologies, we need innovation for improved fuel usage and reduced waste creation, like offered by iMAGINE, for the required broad success of nuclear technologies. To allow quick progress into innovative technologies like iMAGINE and their regulation, a timely investment into urgently needed experimental infrastructure and expertise development will be required to assure the availability of capacities and capabilities. The initial steps to start the development of such a new reactor physics experimental facility to investigate molten salt fast reactor technology are discussed and a stepwise approach for the development of the experimental facility is described. The down selection to the choice for a diverse control and shutdown system is described through manipulating the reflector (control) and splitting the core (shutdown). The developed innovative core design of having the two core parts in two different rooms opens completely new opportunities and will allow to manifest the request for separated operational and experimental crews, as nowadays requested by regulators into the built environment. The proposed physical separation of safety relevant operational systems from the experimental room should on the one hand help to ease the access to the facility for visiting experimental specialists. On the other hand, the location of all safety relevant systems in a now separated access-controlled area for the operational team will limit the risk of misuse through third party access. The planned experimental programme described with the major steps: core criticality experiments, followed by experiments to determine the neutron flux, neutron spectrum, and power distribution as well as experiments to understand the effect of changes in reactivity and flux as a function of salt density, temperature and composition change.

The overall cost of a hydropower plant is mainly due to the expenses for civil works, mechanical equipment (turbine and control units) and electrical components. The goal of a new draft tube design is to obtain a geometry that reduces investment costs, especially the excavation ones, but the primary driver is to increase the overall machine efficiency allowing for reduced payback time. In the present study, an optimization study of the elbow-draft tube assembly of a Kaplan turbine was conducted. A CFD model for the complete turbine has been developed and validated; next, an optimization of the draft tube alone was performed using a Design of Experiments technique; finally, several optimum solutions for the draft tube were obtained using a Response Surface technique aiming at maximizing pressure recovery and minimizing flow losses. A selection of optimized geometries was subsequently post-checked using the validated model of the entire turbine and a detailed flow analysis on the obtained results could make it possible to provide insight into the improved designs. It was observed that efficiency could be improved by 1% (in relative terms), and the mechanical power increased by 1,8% (in relative terms) with respect to the baseline turbine.

The Aspergillus genus comprises fungi that are widely distributed in nature. The Terrei section is particularly important due to its functions in recycling organic matter. Aspergillus hortae is a species from this section that has been isolated from clinical samples, but its role as a pathogenic agent is unclear. In this study, three clinical A. hortae isolates from Colombia, initially identified as A. terreus, were characterised by micro and macro-morphological analysis at 26°C and 37°C. A bioinformatic pipeline was used for molecular typing, which included analysis of whole genome sequences for accurate species identification. Susceptibility assays were also conducted using the microdilution broth method (EUCAST). It was confirmed that this species is intrinsically resistant to Amphotericin B with a minimum inhibitory concentration (MIC) of 2-4 mg/L, and is also thermotolerant. We obtained the in vitro susceptibility profiles for three azole drugs (MIC, 0.25-1 mg/L). The three isolates showed phylogenetic divergence from the reference genome strain. A mutation (M769K) in the MelA ortholog of a hypopigmented isolate, which had the lowest MIC value for AmB (2 mg/L), was identified. This study presents the morphological characterization, molecular typing through whole-genome analysis and identification of susceptibility profiles to azoles and amphotericin B of three clinical isolates of A. hortae from Colombia.

Personalized recommendation is an important part of ecommerce platform. In the recommendation system, the neural network is used to enhance collaborative filtering to accurately capture user preferences, so as to obtain better recommendation performance. Traditional recommendation methods focused on the results of a single user behavior, ignoring the modeling of multiple interactive behaviors of users, such as click, add to cart and purchase. Although many studies had also focused on Multi-Behavior modeling, two important challenges remained. 1)Since multiple behavioral context information was ignored, it was still a challenge to identify the multimodal relationships of behaviors. 2) Surveillance signals were still sparse. In order to solve this problem, this paper proposes Two-path Multi-behavior Sequence Modeling(TP_MB). First, a two-path learning strategy is introduced to maximize the multiple interaction information of user items learned by the two paths, which effectively enhances the robustness of the model. Second, a multi-behavior dependent encoder is designed. Contextual information is obtained through behavior dependencies in the interaction of different user. In addition, three contrastive learning methods are designed, which not only obtain additional auxiliary supervision signals, but also alleviate the problem of sparse supervision signals. Extensive experiments on two real datasets demonstrate that our method outperforms state-of-the-art multi-behavior recommendation methods.

We study various properties of the polygonal numbers; such as their recurrence relations; fundamental identities; weighted binomial and ordinary sums; partial sums and generating functions of their powers; and a continued fraction representation for them. A feature of our results is that they are presented naturally in terms of the polygonal numbers themselves and not in terms of arbitrary integers; unlike what obtains in most literature.

The Ylistrum japonicum is a commercially valuable scallop known for its long-distance swimming abilities. Despite its economic importance, genetic and genomic research on this species is limited. This study presents the first complete mitochondrial genome of Y. japonicum. The mitochondrial genome is 19,475 bp long and encompasses 13 protein-coding genes, 3 ribosomal RNA genes, and 23 transfer RNA genes. By selecting 15 Pectinidae species and additional outgroup taxa, we have constructed phylogenetic trees to elucidate the evolutionary placement of Ylistrum within the family Pectinidae. Our analysis reveals that Ylistrum is a basal lineage to the Pectininae clade, distinct from its previously assigned tribe, Amusiini. This study offers critical insights into the genetic makeup and evolutionary history of Y. japonicum, enhancing our knowledge of this economically vital species.

Diacylglycerol kinase (DGK) is a lipid kinase that phosphorylates diacylglycerol (DAG) to generate phosphatidic acid (PA). Based on converting one important signaling molecule (DAG) to another (PA), DGK plays an important role in plant responses to abiotic stress including waterlogging stress. However, no studies have been reported on the characterization of the DGK gene family in the waterlogging-tolerant kiwifruit germplasm, Actinidia valvata Dunn. Here, we identified 18 AvDGK genes in the A. valvata genome. The phylogenetic analysis showed that AvDGKs can be classified into three clusters, and members within the same cluster have similar domain distribution, exon-intron structures and conserved motif compositions. Chromosome localization analysis revealed that all the AvDGK genes are located across 18 different chromosomes. There were 29 duplicated gene pairs in kiwifruit and all had undergone purifying selection during evolution. Promoter cis-element analysis revealed that the cis-elements within AvDGK genes are associated with multiple functions, including phytohormone signal transduction, stress response, and plant growth and development. The expression pattern analyses indicated that AvDGK play an important role in the fruit development and plant response to waterlogging stress. AvDGKs gene family in the tetraploid A. valvata genome might promote PA synthesis and subsequent signal transduction both under short-term and long-term waterlogging stress. These results provide information regarding the structural characteristics and potential function of DGK genes within kiwifruit and lay a fundamental basis for further research into breeding for enhancing the kiwifruit’s tolerance to waterlogging stress.

Capulus danieli, a distinct member of Capulidae, exhibits a unique ecological behaviour by attaching and drilling onto the pecten, distinguishing itself from other gastropods. Herein, we present the first characterisation of the mitochondrial genome of Capulus danieli. The results showed that the genome spans 15600 base pairs, with an A + T content of 71.12% and a G + C content of 28.88%. Within this genetic makeup, we identified 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes. Phylogenetic analysis revealed a close evolutionary relationship between Capulus danieli and members of the Ficoidea superfamily. The divergence time estimation suggested that Capulus danieli diverged approximately 52.29 million years ago. These findings significantly contribute to our understanding of the evolutionary history and genetic architecture of Capulus danieli, shedding light on its unique ecological adaptations to the marine environment.

Aim: Streptococcus pneumoniae and influenza H1N1 virus are common organisms associated with human infections. These infections could play a significant role in immune regulation. The study was performed to analyse the genome sequences of these organisms with human genome and study its functional significance. Methods: The study was performed to analyse the overlapping of genome sequences in Streptococcus pneumoniae and Influenza (H1N1) virus against human genome sequences by BLASTn sequence analysis. The alignments are studied against the corresponding genes for their functional significance with DAVID and NDEx software.Results: Several hits or overlapping nucleotide segments were identified. Between streptococcus and homo sapiens 287 overlaps were identified, and among influenza and homo sapiens 124 hits were identified. A wide range of functional significance of these genes were identified, and the results are presented in this study. The results show insights into functional pathways and biological activities associated with the respective vaccinations or infections by these microorganisms. Conclusion: The common organisms like Streptococcus pneumoniae and Influenza H1N1 virus actively interact with the immune system and result in a wide range of immune regulations.

Purpose: Investigation for the co-occurrence of two unrelated genetic disorders of muscular dystrophy and Prader-Willi syndrome (PWS) (OMIM # 176270) using joint whole genome sequencing (WGS). Methods: Trio WGS joint analysis was performed to investigate the genetic etiology in a proband with PWS, prolonged muscular hypotonia associated hyperCKemia, and early-onset obesity. The parents were unaffected. Results: Results showed maternal isodisomy uniparental disomy (UPD) in chromosome 15 expanding from 15q11.2 to 15q22.2, including PWS regions at 15q11.2-15q13. Maternal heterodisomy was detected from 15q22.2 to 15q26.3. A pathogenic variant, NM_000070.3(CAPN3):c.550del (p.Thr184fs), was identified at 15q15.1 in a heterozygous state in the mother that was homozygous in the proband due to maternal isodisomy. Conclusion: This is the first study of the concurrent molecular etiology of PWS and calpainopathy (OMIM # 253600) in the same patient. This report highlights the utility of joint analysis and need for the assessment of autosomal recessive disease in regions of isodisomy in patients with complex and unexplained phenotype.

This comprehensive overview of the historical milestones in cell culture underscores key breakthroughs that have shaped the field over time. It begins with Wilhelm Roux's seminal experiments in the 1880s, followed by the pioneering efforts of Ross Granville Harrison, who initiated groundbreaking experiments that fundamentally shaped the landscape of cell culture in the early 20th century. Carrel's influential contributions, notably the immortalization of chicken heart cells, mark a significant advancement in cell culture techniques. Holtfreter, Moscona, and Leighton introduced innovations such as 3D cell culture, laying the groundwork for further exploration. The advent of induced pluripotent stem cells by Takahashi and Yamanaka in 2006 was revolutionary, enabling the reprogramming of differentiated cells into a pluripotent state. Since then, recent innovations include spheroids, organoids, and organ-on-a-chip technologies, aiming to mimic the structure and function of tissues and organs in vitro, pushing the boundaries of biological modeling and disease understanding. In this review, we overview the history of cell culture shedding light on the main discoveries, pitfalls and hurdles that were overcome during the transition from 2D to 3D cell culture techniques. Finally, we discussed the future directions for cell culture research that may accelerate the development of more effective and personalized treatments.

Reptilians or reptoids are staple characters of Hollywood cinema, science fiction literature, ufology and conspiracy theories. Despite its popularity, the reptoid has been dismissed by the scientific community as a figment of the imagination; born out of a speculation, paranoia and wanton anthropocentricism. In this paper, however, the Life Sequence Conjecture is advanced as a supportive framework for the notion of reptilian extraterrestrials. This paper is not an argument in support of the existence of extraterrestrials. Rather, it proposes that if extraterrestrials do exist, then a reptilian morphology is not untenable.

This article presents description of social structures such as, for example, states, in the context of their consideration as systems. Moreover, it seeks to develop K. Marx’s model in terms of systematic approach, as well as to justify the application of the Fibonacci sequence to systems in general and, in particular, to social systems. The description covers a wide range of issues, ranging from the assertion of the basic principle of living systems as patterns in resources flows to description of functions of various aspects of states and their economics in terms of objective needs of such structures. In addition, this article justifies synergetic effect based on proposed model, and the way this effect is applied to state systems. Moreover, it includes the description of main changes of socio-economic formations throughout the history as a natural development of social systems, including possible modern stages. The fundamental tool of this description is description of essence of the mechanism of property rights and its formation options. The differences of two extreme directions of such development are also described on the basis of the objective factor of resource provision. Special attention is given to the concept of surplus value as a feature of social production systems.

The induced draft (ID) fan is important auxiliary equipment in the thermal power plant. It is of great significance to monitor the operation of the ID fan for safe and efficient production. In this paper, an adaptive warning model is proposed to detect early faults of ID fans. First, a non-parametric monitoring model is constructed to describe the normal operation states with the multivariate state estimation technique (MSET). Then, an early warning approach is presented to identify abnormal behaviors based on the results of the MSET model. As the performance of the MSET model is heavily influenced by the normal operation data in the historic memory matrix, an adaptive strategy is proposed by using the samples with a high data quality index (DQI) to manage the memory matrix and update the model. The proposed method is applied to a 300 MW coal-fired power plant for early fault detection, and it is compared with the model without an update. Results show that the proposed method can detect the fault earlier and more accurately.

Mitochondrial carriers facilitate the transfer of small molecules across the inner mitochondrial membrane (IMM) to support mitochondrial function and core cellular processes. In addition to the classical mitochondrial carrier family SLC25, the past decade led to the discovery of additional protein families that exhibit IMM localization and transporter-like properties. These include mitochondrial pyruvate carriers, sideroflexins and mitochondrial cation/H+ exchangers that have been linked to vital physiological functions and disease. Their structures and transport mechanisms are still largely unknown and understudied. Protein sequence analysis per se can often pinpoint hotspots that are of functional or structural importance. In this review, we summarize current knowledge about sequence features of mitochondrial transporters with a special focus on the newly included SLC54, SLC55 and SLC56 families of the SLC solute carrier superfamily. Taking a step further, we combined sequence conservation analysis with transmembrane segment and secondary structure prediction methods to extract residue positions and sequence motifs that likely play a role in substrate binding, binding site gating or structural stability. We hope that our review will help guide future experimental efforts by the scientific community to unravel the transport mechanism and structure of these novel mitochondrial carriers.

Garcinia indica (Thouars) Choisy (commonly known as Kokum) is an important medicinal plant in Ayurvedic medicine and belonging to the Clusiaceae family. Kokum is a highly traded medicinal plant species of India, dried rind of fruits and butter from seeds are traded in the markets. This study aimed to assemble the complete chloroplast (cp) genome of G. indica and compare it with the previously published cp genome within the Garcinia taxa to identify the potential species-specific barcode marker for Kokum authentication. The assembled cp genome, with a size of 1,56,891 bp, exhibits a typical quadripartite structure. The large single-copy (LSC) region spans 85,580 bp, and the small single-copy (SSC) region spans 17,181 bp, together comprising 64.5% of the genome. The pair of inverted repeats (IRA and IRB) are each 27,065 bp, covering the remaining 35.5% of the genome. A total of 126 unique genes were identified, including 86 protein-coding genes, 32 tRNA genes, and 8 rRNA genes. Phylogenetic analysis using complete cp genomes from 12 species in the Clusiaceae family indicated that 10 Garcinia species form a sister clade. Notably, the ycf1 gene in the LSC region was more divergent within the Garcinia species. This study presents the first report on the chloroplast genome of G. indica. This chloroplast genome resource provides a basis for identifying new DNA barcode marker as well as species-specific marker for herbal drug authentication of Kokum, and species delineation within the Garcinia genus.

To fully appreciate genetics, one must understand the link between genotype (DNA sequence) and phenotype (observable characteristics). Advances in high-throughput genomic sequencing technologies and applications, so-called “-omics”, have made genetic sequencing readily available across fields in biology from applications in non-traditional study organisms to precision medicine. Thus, understanding these tools is critical for any biologist, especially those early in their career. This comprehensive review discusses the chronological development of different sequencing methods, the bioinformatics steps to analyzing this data, and social and ethical issues raised by these techniques that must be discussed and evaluated.

Lecanicillium lecanii KMZW-1, is recognized for its potential as a bio-control agent against agricultural and forestry pests, particularly due to its compatibility with integrated pest management (IPM) strategies. This study aimed to investigate the complete genome of L. lecanii KMZW-1 and assess its pathogenicity against Bactrocera dorsalis. Whole genome sequencing revealed a genome size of 47,239,278 bp, comprising 27 contigs, with a GC content of 51.16%. The genome completeness was assessed as 97.93% using BUSCO analysis, AntiSMASH analysis identified 29 gene clusters associated with secondary metabolite biosynthesis providing insights into the genetic basis of its pathogenic mechanisms and biocontrol potential. The pathogenicity of L. lecanii KMZW-1 was assessed using concentrations ranging from 1×10^4 to 1×10^11 spores/mL. Higher-concentrations (1×10^10 to 1×10^11 spores/mL), resulted in significantly increased cumulative mortality rates of B. dorsalis adults compared to the control group. Notably, the pathogenicity was higher in male adults than in females. Probit regression analysis yielded LogLC50 values as 5.662 for female and 4.486 for male B. dorsalis adults. In summary, L. lecanii KMZW-1 exhibits strong insecticidal activity against B. dorsalis and shows potential as a biocontrol agent with IPM strategies. These findings provide robust genomic evidence supporting the use of L. lecanii KMZW-1in managing against B. dorsalis populations.

Histone deacetylases inhibitors (HDACi) have shown promising therapeutic outcomes in haematological malignancies such as leu-kaemia, multiple myeloma and lymphoma, with dis-appointing results in solid tumours when used as monotherapy. As a result, combination therapies either with radiation or other deoxyribonucleic acid (DNA) damaging agents have been suggested as ideal strategy to improve their efficacy in solid tumours. Numerous in vitro and in vivo studies have demonstrated that HDACi can sensitise malignant cells to both electromagnetic and particle types of radiation by inhibiting DNA damage repair. Although the radiosensitising ability of HDACi has been reported as early as 1990s, the mechanisms of radiosensitisation are yet to be fully understood. This review brings forth the various protocols used to sequence the administration of radiation and HDACi treatments in the different studies. The possible contribution of these various protocols on the ambiguity that surrounds the mechanisms of radiosensitisation is also highlighted.

In archaea, the interaction of HerA helicase and NurA nuclease is required for 3' end resection during DNA double-stranded break repair, and its disruption results in unfaithful DNA repair. Interactions transpire by the four conserved domains, including the N-terminal HAS domain (HerA-ATP synthase), which serves as a binding site for the exonuclease NurA. As a HerA hexamer between its two subunits, the conserved C-terminal brace extension functions as an adjacent brace. DBD serves as a location for DNA binding, which causes the DNA strands to be propelled into the HerA pocket to begin unwinding. The putative pore entrance is made up of four helix coils, which provide a suitable charged surface for guiding DNA into the pore. The crystal structure of the complex HerA-NurA allows for the identification of key residues for protein-protein interaction. This allows us to predict that most archaeal HerA orthologs will be able to interact with one another. Archaeal HerA is a homo-hexameric assembly featuring a DNA-binding domain that is conserved. It also features distinctive ATP and NurA binding domains. Following the structure and sequence conservation criteria, we find one HerA ortholog in Pyrobaculum calidifontis and multiple HerA paralogs, but the role of none is established yet.Interestingly, orthologous HerA is part of an Mre11-Rad50 gene neighborhood while paralogous HerA is not, which could be misleading. As a result, it sought to describe the criteria that may be used as a possible fingerprint for identifying orthologous genes, as well as the cloning procedures and tactics that would aid in the confirmation of the HerA helicase in P. calidifontis. Their confirmation is based on PCR cloning and characterization following HerA construct creation.

The nutrient absorption and utilization efficiency in the roots of seedlings are beneficial for increasing crop yield. Creating marker assisted selection for wheat root traits can assist wheat breeders in choosing robust roots to maximize nutrient uptake. Exploring and identifying the effect of different nitrogen applications on RSA is of great significance for breeding nitrogen efficient wheat varieties. In this study, A total of 243 wheat varieties native to the Yellow and Huai Valley regions of China were utilized for genome-wide association studies (GWAS). Furthermore, a recombinant inbred line (RIL) population of 123 lines derived from the cross between Avocet and Chilero was utilized for linkage examination and confirmation of the hereditary loci distinguished by GWAS. Five RSA traits include the relative number of root tips (RNRT); relative total root length (RTRL); relative total root surface area (RTRS); relative total root volume (RTRV) and relative average root diameter (RARD) where evaluated under two N conditions—normal N (NN) supply and low N (LN)—to characterize the NUE of each accession. GWAS and linkage analysis were performed by integrating data from the wheat 660k single nucleotide polymorphism (SNP) chip and diversity arrays technology (DArT) to identify genetic loci associated with RSA. The results showed that based on the ratio of RSA related traits under two N supply conditions, a total of 598 SNP markers, which are significantly associated with RSA related traits, were detected at 160 genetic loci by GWAS. A total of 10 QTL loci related to RSA were dis-covered and identified by linkage mapping. In which, three significant RSA related Quantitative Trait Locus (QTL) were identified, namely qRtrl-3D, qRnrt-3D, and qRtrl-7D. The study has the potential to enhance the effectiveness of selecting root traits in wheat breeding programs, offering valuable insights into the genetic underpinnings of nitro-gen use efficiency (NUE) in wheat. This could lead to the creation of NUE wheat varieties by implementing focused breeding strategies.

Let an odd integer be represented as $\sum \limits_{n > m} 2^n + 2^m - 1$ for $m \geq 1$. To transform $2^m - 1$ according to the Collatz rules, the $3x + 1$ step is applied, resulting in the even integer $2^{m + 1} + 2^m - 2$. This even integer, being exactly once divisible by 2, becomes the next odd integer $2^m + 2^{m - 1} - 1$. This represents the growth phase, as exactly one even step follows an odd step. However, while the overall value of the integer increases, terms with decreasing indices are generated after each odd-even cycle. After $m$ such cycles, a term $2^{m - m}$ (which equals 1) is generated, canceling the negative 1. Additional even steps are then performed until the integer becomes odd again, which occurs when the next smallest index becomes zero. The positive 1 thus obtained is written as $2^1 - 1$. If uninterrupted, the term $2^1 - 1$ has the trivial cycle $2^1 - 1 \rightarrow 2^2 \rightarrow 2^1 \rightarrow 2^1 - 1$. This represents the shrinkage phase, as two even steps follow an odd step. To interrupt the trivial cycle, a sequence such as $2^1 + 2^2 + \cdots$ must be available to combine with $2^1 - 1$ and produce $2^{\mathcal{M}} - 1$. This starts another growth phase that lasts for $\mathcal{M}$ odd-even cycles. Finally, there is an attempt to craft an integer that can escape the shrinkage phase in the Collatz dynamics.

In this paper, we investigate the recurrence properties of the generalized Tribonacci sequence and present how the generalized Tribonacci sequence at negative indices can be expressed by the sequence itself at positive indices.

Sequence alignment and comparison through pairwise, multiple, global and local techniques are the main principles that underpin comparative genomics. However, most of the algorithms used are alignment-based which imposed some limitations on their use and application. In an attempt to provide an alignment-free alternative approaches, a methodology of comparative optinalysis and statistical mirroring was used and adopted to provide a suitable alternative for multiple genomic sequence comparison. In this article, methods comparison with MUSCLE, MUFFT, Clustal Omega, and T-Coffee was designed to assess the suitability and statistical power of statistical mirroring as an alternative method for multiple genomic sequences comparison using different sets of logically generated biological sequence datasets with different problems and computational complications. The results of the comparisons validate that statistical mirroring is a suitable alignment-free alternative approach for multiple genomic sequence comparison. The applied method (statistical mirroring) distinguishes itself over MUSCLE, MUFFT, Clustal Omega, and T-Coffee in specificity to a position-specific changes, specificity to a base-specific changes, cladogram and phylogenetic linearity, alignment independency, computational simplicity, and limit of input capacity.

Taking a DNA-sequence, a word with letters/bases A, T, G and C, as the relation between the generators of an infinite group $\pi$, one can discriminate two important families: (i) the cardinality structure for conjugacy classes of subgroups of $\pi$ is that of a free group on $1$ to $4$ bases and the DNA word, viewed as a substitution sequence, is aperiodic. (ii) The cardinality structure for conjugacy classes of subgroups of $\pi$ is not that of a free group, the sequence is generally not aperiodic and topological properties of $\pi$ have to be determined differently. The two cases rely on DNA conformations such as A-DNA, B-DNA, Z-DNA, G-quadruplexes, etc. We found a few salient results: Z-DNA, when involved in transcription, replication and regulation in a healthy situation implies (i). The sequence of telomeric repeats comprising $3$ distinct bases, most of the time, satisfies (i). For $2$-base sequences in the free case (i) or non free case (ii), the topology of $\pi$ may be found in terms of the $SL(2,\mathbb{C})$ character variety of $\pi$ and the attached algebraic surfaces. The linking of two unknotted curves --the Hopf link-- may occur in the topology of $\pi$ in cases of biological importance, in telomeres, G-quadruplexes, hairpins and junctions, a feature we already found in the context of models of topological quantum computing. For $3$- and $4$ base sequences, other knotting configurations are noticed and a building block of the topology is the $4$-punctured sphere. Our methods have the potential to discriminate potential diseases associated to the sequences.

Assessment of the genetic distinctiveness of a cultivar through morphological descriptors is an important tool for both the registration and the protection. New mango genotypes have been improved using valuable diverse germplasm resources to ensure food security. DNA fingerprinting based simple sequence repeats (SSR)-markers have been the most broadly used, effective and accurate in evaluation of genetic characterization of a cultivar. Molecular breeding is an effective source of genetic gain after improvement of fruit trees using marker assisted genomic selection. Mango (Mangifera indica L.) is an allotetraploid (2n = 4X= 40) drupe fruit and has high nutritional value belongs to genus Mangifera and family Anacardiaceae. Mango cultivars are used with worldwide acceptance to pharmacological, ethnomedical, and phytochemical industries. This study investigated the molecular evaluation of a new mango cultivar ‘Azeem Chaunsa’ using a set of the most effective 50 hyper-variable polymorphic SSR markers. Highly specific DNA fingerprints were identified in the genome of this mango cultivar, ‘Azeem Chaunsa’ compared with three standard cultivars such as Sindhri, Samar Bahisht (S.B) Chaunsa and Sufaid Chaunsa. Our results showed that SSR markers could efficiently assess genetic diversity in mango. An agglomerative hierarchical clustering method was used to construct dendrogram based on the ‘Unweighted Pair- Group Method with Arithmetic Mean’ (UPGMA). The genetic similarity coefficients were recorded between the mangos cultivars ranged from 0.49 to 0.67. Cultivar identification (CID) evaluates association among standard cultivars and Azeem Chaunsa and further concludes significant variations. CID results concluded that cultivar ‘Azeem Chaunsa’ varied significantly from the check cultivar, Sindhri (46.2%), S.B Chaunsa (45%) and Sufaid Chaunsa (46.7%). The results obtained in this study will orient cultivar identification strategies for a successful future mango breeding programmes in the context of climate change.

The heat transfer and fluid mechanics analysis in agitated vessels is usually performed using the Dittus-Boelter correlation. In this study, we propose the analysis of an agitated vessel with a draft tube through the analysis of dimensionless numbers correlations. The heat transfer and fluid mechanics simulation was conducted using ANSYS Fluent software. The simulation used the Sliding Mesh approach and the SST k-ω turbulent model to capture the vessel's fluid flow and heat transfer phenomena. A grid independence study was conducted by varying the number of time steps to obtain an appropriate time step size for the simulation. The convective heat transfer coefficient, as indicated by the mean values of the Nusselt number, was calculated. The local values along the radial coordinate of the heat transfer surface were also determined. These results provide insights into the distribution of heat transfer rates within the vessel, which can help optimize process efficiency and equipment design. The simulation results were analyzed by varying the c and m coefficients in the Nusselt correlation presented as Nu= c Rem Pr1/3. Furthermore, correlations describing the mean Nusselt number at the bottom and wall of the vessel are presented and compared with existing literature, contributing to advancing knowledge in this field.

Whole genome alignment (WGA) is a critical process in comparative genomics, facilitating the detection of genetic variants and aiding our understanding of evolution. This paper offers a detailed overview and categorization of WGA techniques, encompassing suffix tree-based, anchors-based, and graph-based methods. It elaborates on the algorithmic properties of these tools, focusing on performance and methodological aspects. The paper underscores the latest progress in WGA, emphasizing the increasing capacity to manage the growing intricacy and volume of genomic data. However, the field still grapples with computational and biological hurdles affecting the precision and speed of WGA. We explored these challenges and potential future solutions. This paper aims to provide a comprehensive resource for researchers, deepening our understanding of WGA tools and their applications, constraints, and prospects.

Recently, there have been revolutions in the development of both gene therapy and genome surgical treatments for inherited diseases. Much of this progress has been centered around hereditary retinal dystrophies, because the eye is an immune-privileged and anatomically ideal target. Gene therapy treatments, already demonstrated to be safe and efficacious in numerous clinical trials, are benefitting from the development of new viral vectors, such as dual and triple AAVs. CRISPR/Ca9, which revolutionized the field of gene editing, is being adapted into more precise “high fidelity” and catalytically dead variants. New CRISPR endonucleases, such as CjCas9 and Cas12a, are generating excitement in the field as well. Stem cell therapy has emerged as a promising alternative, allowing human embryo derived stem cells and induced pluripotent stem cells to be edited precisely in vitro and then reintroduced into the body. This article highlights recent progress made in gene therapy and genome surgery for retinal disorders, and it provides an update on precision medicine FDA treatment trials.

To address the response of small RNAs (sRNAs) biogenesis to drought stress, we identified sRNAs biogenesis genes, including 11 encoding argonauts (AGO), 8 encoding dicer-like proteins (DCL), and 9 encoding RNA-dependent RNA polymerases (RDR) in the peach genome. Notably, the largest numbers of sRNAs biogenesis genes are located to chromosome 1. The PAZ, PIWI, and MID domains were identified in PpAGOs, while the ribonuclease IIIa and IIIb domains were characterized in PpDCLs. The RDRP domain was recognized in PpRDRs. Orthologous similarity and collinearity analyses between Arabidopsis and peach revealed 5, 1, and 2 collinear blocks in AGOs, DCLs, and RDRs, respectively. Moreover, 41, 40, and 42 cis-acting elements were located in the promoters of PpAGOs, PpDCLs, and PpRDRs, respectively, with the majority related to drought stress response. Analysis of RNA sequencing (RNA-seq) data revealed that sRNAs biogenesis genes were involved in drought stress response in different tissues. Furthermore, the expression of candidate genes was verified in two peach cultivars, Beijing 2-7 (BJ2-7) and Sinai (SN), which are drought tolerance and sensitive, respectively. Interestingly, the expression of PpAGO2b, PpDCL2b, PpDCL4, and PpRDR4 genes was induced in ‘BJ2-7’ but inhibited in ‘SN’ under drought stress. Overall, this study provides insight into the roles of sRNA biogenesis genes in response to drought stress in peach.

An addition sequence is an important operation in many applications of computer science, such as multi-modular exponentiation and outsourcing protocols. Finding an addition sequence for a set of positive integers with the shortest length is challenging due to the high computational time required to find the solution. In this paper, a new metaheuristic algorithm is designed based on the simulated annealing strategy to generate a short addition sequence. The efficiency of the proposed algorithm was proved experimentally by comparing it with the previous exact and heuristic algorithms in terms of running time and the length of the addition sequence.

While the language model using the stop sign as an independent token has been widely used to decide when the model should stop, it may lead to the growth of vocabulary dimensions and further problems. Similarly, present research on game algorithms usually estimate stopping point related problems based on the evaluation of the winning rate. However, information redundancy may also exist in such models, thus increasing the training difficulty. Above two types of tasks (and similar autoregressive tasks) show a common problem of stopping point prediction. In this paper, we describe a design of separated model, trying to separate the complexity of stopping point prediction from the main task model, so that the information used for estimating stopping point can be reduced. On this basis, in order to verify the rationality of using separated model, we propose a model-free test method. It judges the separability of transformed data based on point difference and sequence difference metrics. In this way, it can predict the credibility of the separated model inference.

Background SARS-CoV-2 has generated a life-treating pandemic and is the main challenge of this century. Some untranslated regions (UTRs) in SARS-CoV-2 genome, specifically leader sequence and transcription regulatory sequence (TRS) in 5’UTR, can be considered as Achilles' heel of virus. Leader sequence are found at the 5' ends of all encoded transcripts that highlights its importance. TRS can explain the host range and pathogenicity of coronavirus. However, our knowledge on the evolution and the role of UTRs in SARS-CoV-2 pathogenicity is very limited. This study is a pioneering attempt to unravel the evolution of key regions in 5' UTR of SARS-CoV-2 and discover the inhibitory microRNAs against 5' UTR of virus. Methods Evolution of TRS and leader sequence was compared between human pathogenic (SARS-CoV-2, SARS, and MERS) and non-pathogenic (bovine) coronaviruses. Profiling of microRNAs that can inactive the key UTR regions of coronaviruses, UTR-inhibitory microRNAs, was carried out. Findings We found a distinguished pattern of evolution in leader sequence and TRS of SARS-CoV-2, compared to the other coronaviruses. Mining all available microRNA families against leader sequences of coronaviruses resulted in discovery of 39 microRNAs with an acceptable thermodynamic binding energy against SARS-COV-2, SARS, MERS, Bat Coronavirus, or Bovine Coronavirus. Multivariate analysis demonstrated a distinguished pattern of binding of leader sequence of SARS-CoV-2 against microRNAs, with a lower binding stability. hsa-MIR-5004-3p was the only human microRNA that can target leader sequence of SARS and SARS-CoV-2. However, its binding stability remarkably decreased in SARS-COV-2 (-19.4 kcal/mol), compared to SARS-COV-2 (-25.9 kcal/mol). We found an insertion-type mutation in leader sequence of SARS-COV-2 that results in lower binding stability and escaping of viral leader sequence from hsa-MIR-5004-3p. Altogether, we suggest lack of innate human inhibitory microRNAs to bind to leader sequence and TRS of SARS-CoV-2 contributes to its high replication in infected human cells. On the other hand, mining of two hundred million deposited human genomic variants led us to discovery of 49 missense and splice-disrupt mutations in genomic structure of hsa-MIR-5004-3p. These mutations can negatively affect hsa-MIR-5004-3p function in preventing SARS-CoV-2 replication. Interpretation This study unravels the evolution of key regions in 5’UTR of SARS-CoV-2. Inducing microRNAs to bind to the leader sequence and TRS regions by drugs or food supplements can reduce virus replication. Enhancing the microRNA defence machinery against TRS and leader of virus has a potential to prevent SARS-CoV-2 infection at the first place. The mentioned strategy is rapidly achievable against COVID-19. Missense variation in genomic sequence of 5’UTR inhibitory microRNAs, such as hsa-MIR-5004-3p, can be considered as risk factor of COVID-19.

The global antibiotic resistance crisis, driven by antibiotic overuse and misuse, is multifaceted. This study aimed to assess the microbiological and genetic characteristics of raw retail pork meat, including the isolation, antibiotic susceptibility testing (AST), whole genome sequencing (WGS) of selected indicator bacteria, antibiotic residue testing, and metagenomic sequencing. Samples were purchased from 10 randomly selected retail stores in Gauteng, South Africa. Samples were aseptically separated, with a portion sent to an external laboratory for isolating indicator bacteria and antibiotic residue testing. Identification of the isolated bacteria was reconfirmed using matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). AST was performed using the Microscan Walkaway system. WGS and metagenomic sequencing were performed using the Illumina NextSeq 550 instrument. The isolated E. coli and enterococci exhibited little phenotypic resistance, with WGS revealing tetracycline resistance genes. Isolated bacteria and meat samples all harboured tetracycline resistance genes, and the antibiotic residue concentrations were within acceptable limits for human consumption. In the metagenomic context, most identified bacteria were of food/meat spoilage and environmental origin, with the resistome analysis primarily indicating beta-lactam, tetracycline and multidrug resistance genes. Further research is needed to understand the broader implications of these findings on environmental health and antibiotic resistance.

Bioinformatics is a rapidly developing field enabling scientific experiments through computer models and simulations. Considering the vast databases of biological data available, it is ex-tremely important to develop efficient methods and algorithms for their processing. Sequence comparison is the best method for studying the evolutionary interaction between genes. It is based on alignment – the process of arranging two or more sequences to achieve the maximum level of identity and degree of similarity. The paper presents a new version of the algorithm for pairwise DNA sequences alignment, based on a new method called CAT, where a dependency with a previous match and the closes neighbor are taken in consideration to increase uniqueness of the CAT profile and to reduce possible collisions, i.e. two or more sequence having same CAT profiles. This makes proposed algorithm suitable for finding exact match of a concrete DNA se-quence in a big set of DNA data faster. The generation of CAT profiles is made once before data has been uploaded to the database, allowing the profiles to be used as metadata for the sequenc-es. It consists of an algorithm to calculate a CAT profile against the selected reference sequences and an algorithm to compare two sequences based on the calculated CAT profiles. Improve-ments in generation of the CAT profiles, are detailed described in the paper. Block scheme, pseudo code tables and figures were updated according to the proposed new version and ex-perimental results. Experiments have been carried out with the new version of the method and different datasets to align DNA sequences based on the CAT method. New experimental results in terms of collisions, speed, and efficiency of the proposed solutions are presented. Experiments related to the performance comparison with Needleman-Wunsch were re-executed with the new version of the algorithm to confirm that we have the same performance. An analysis of the per-formance of the proposed CAT based algorithm against Knuth–Morris–Pratt algorithm, which has a complexity of O(n) and is one of the most widely used for searching biological data, was performed. The impact of prior matching dependencies on uniqueness for generated CAT pro-files is investigated. The analysis of the experimental results obtained by sequence alignment shows a small deviation of the proposed algorithm based on the CAT method, which can be ig-nored if this deviation is acceptable at the expense of performance. The time efficiency of the CAT algorithm remains constant, regardless of the length of the sequences. Therefore, the ad-vantage of the proposed method is its fast processing in the alignment of large sequences, for which the execution of the exact algorithms takes a long time. The example code realization of the CAT Method, under the protection of the GNU General Public License v3.0, can be accessed on GitHub at: https://github.com/HristoS/CATSequenceAnalysis.

In response to a threefold increase in osteoporotic vertebral fractures (OVF) at our institution over the past decade and the subsequent development of new fractures within a year in a third of cases, we evaluated the effectiveness of STIR MRI scans in conjunction with CT scans for initial OVF diagnosis. This study, conducted over five months, involved full spine sagittal STIR MRI scans alongside CT scans for patients over 50 with minor injury-related vertebral fractures. The independent assessments by radiologists and neurosurgeons of 64 patients revealed that while CT scans identified 161 fresh fractures, of which only 68 were previously reported, MRI detected 266 fractures, 1.65 times more than CT. CT scans showed single fractures in 27% of patients and multiple fractures in 73%, whereas MRI identified single fractures in 9% and multiple fractures in 91% of patients. Additionally, MRI demonstrated a 1.5-fold increase in adjacent fracture detection. The use of MRI influenced treatment plans in 67% of cases. Given these findings, we advocate for including a STIR MRI of the entire spine alongside CT scans in OVF cases, as it significantly enhances fracture detection and can alter treatment strategies.

Many cryptographic systems require random numbers, and weak random numbers lead to insecure systems. In the modern world, there are several techniques for generating random numbers, of which the most fundamental and important methods are deterministic extractors proposed by von Neumann, Elias, and Peres. Elias’s extractor achieves the optimal rate (i.e., information theoretic upper bound) h(p) if the block size tends to infinity, where h(·) is the binary entropy function and p is probability that each bit of input sequences occurs. Peres’s extractor achieves the optimal rate h(p) if the length of input and the number of iterations tend to infinity. The previous researches related to both extractors did not mention practical aspects including running time and memory-size with finite input sequences. In this paper, based on some heuristics, we derive a lower bound on the maximum redundancy of Peres’s extractor, and we show that Elias’s extractor is better than Peres’s one in terms of the maximum redundancy (or the rates) if we do not pay attention to time complexity or space complexity. In addition, we perform numerical and non-asymptotic analysis of both extractors with a finite input sequence with any biased probability under the same environments. For doing it, we implemented both extractors on a general PC and simple environments. Our empirical results show that Peres’s extractor is much better than Elias’s one for given finite input sequences under the almost same running time. As a consequence, Peres’s extractor would be more suitable to generate uniformly random sequences in practice in applications such as cryptographic systems.

Objective: The main purpose of the study is to investigate the combined effects of polydeoxyribonucleotide (PDRN) and extracorporeal shock wave therapy (ESWT) sequences on the regenerative processes in atrophied animal muscles. Methods: Thirty male New Zealand rabbits, aged 12 weeks, were divided into five groups: normal saline, PDRN, ESWT, PDRN injection before ESWT, and PDRN injection after ESWT. Following 2 weeks of cast immobilization, the respective treatments were administered to the atrophied calf muscles. Radial ESWT was performed twice weekly. The evaluation included measurements of calf circumference, tibial nerve compound muscle action potential (CMAP), and gastrocnemius (GCM) muscle thickness after 2 weeks of treatment. Histological and immunohistochemical staining, as well as Western blot analysis, were conducted 2 weeks post-treatment. Staining intensity and extent were assessed using semi-quantitative scores. Results: Groups 4 and 5 demonstrated significantly greater calf muscle circumference, GCM muscle thickness, tibial nerve CMAP, and GCM muscle fiber cross-sectional area (types I, II, and total) than in the remaining three groups (p < 0.05), while they did not did not differ significantly in these parameters. Groups 2 and 3 showed the higher values for all the observations compared to group 1 (p < 0.05). Group 4 had the greatest ratio of vascular endothelial growth factor (VEGF) to platelet endothelial cell adhesion molecule-1 (PECAM-1) in the gastrocnemius muscle fibers than in the other four groups (p < 0.05). Western blot analysis revealed significantly higher expression of angiogenesis cytokines in groups 4 and 5 than in the remaining (p < 0.05). Conclusion: The combination of ESWT and PDRN injection demonstrated superior regenerative efficacy for atrophied calf muscle tissue in rabbit models than these techniques alone or saline. Particularly, administering ESWT after PDRN injection yielded the most favorable outcomes in specific parameters.

The Mobius function is commonly used to define Euler's totient function and the Mangoldt function. Similarly, the summatory Mobius function (the Mertens function) can be used to define the summatory totient function and the summatory Mangoldt function (the second Chebyshev function).

Sutherlandia frutescens (S. frutescens) has been traditionally used as an herbal medicine to ameliorate symptoms associated with cancer, infectious diseases, as well as inflammation. The objective of this investigation was to explore the impact of S. frutescens on the expression of genes in a murine macrophage cell line (i.e., RAW 264.7). We found that treatment with an ethanolic-extract of S. frutescens (SFE) 1 h prior to the stimulation with LPS and IFNγ for 24 h significantly affected the expression of 715 genes in RAW 264.7 cells. When the post-stimulation period was shortened to 8 h, the number of genes that were significantly impacted by SFE diminished to 50. Pathway analysis revealed that inflammatory signaling pathways, such as NF-κB, MAPK, and TNF, as well as signaling pathways associated with immune-related responses, were inhibited by SFE treatment. These findings are consistent with previously reported anti-inflammatory activity of SFE and enable better understanding of the immune-modulating properties of this botanical. To our knowledge, this represents the first report on the impact of S. frutescens on global gene expression in an immune cell population.

An analysis of 1300+ existing ACE mutations revealed that 400+ are damaging and led us to hy-pothesize that carriers of heterozygous loss-of-function (LoF) ACE mutations (which result in low ACE levels) could be at risk for the development of late-onset Alzheimer’s disease (AD) [Danilov, 2024]. Here we quantified blood ACE levels in EDTA-plasma from 41patients with 10 different heterozygous ACE mutations, as well as 33 controls, and estimated the effect of these mutations on ACE phenotype using a set of mAbs to ACE and two ACE substrates. We found that relatively frequent (~1%) AD-associated ACE mutations in the N domain of ACE, Y215C and G325R are truly damaging and, likely, transport-deficient, with ACE levels in plasma only ~50% of controls. Another AD-associated ACE mutation, R1250Q, in the cytoplasmic tail, did not cause a decrease in ACE and, likely, did not affect surface ACE expression. We have also developed a method to identify patients with anti-catalytic mutations in the N domain. These mutations may result in reduced degradation of amyloid beta peptide Aβ42, an important component for amyloid deposition. Consequently, these could pose a risk factor for the development of AD. Therefore, a systematic analysis of blood ACE levels in patients with all ACE mutations has potential to identify individuals at an increased risk of late-onset AD. These individuals may benefit from future preventive or therapeutic interventions involving a combination of chemical and pharmacological chaperones, as well as proteasome inhibitors, aiming to enhance ACE protein traffic. This approach has been previously demonstrated in a cell model of the transport-deficient ACE mutation, Q1069R [Danilov, 2010].

A genome represents the complete collection of genetic material in an organism or cell. This genetic information is encoded in nucleic acids, which can be either single or double-stranded and arranged in linear or circular forms. DNA, the most common type of genetic material, consists of just four nucleotides: adenine, guanine, thymine, and cytosine. These nucleotides are organized in a double helix structure, a discovery made by Watson and Crick. The sequence of these nucleotides forms the basic blueprint of a gene or genome. The process of determining this sequence is known as genome sequencing. The field of genome sequencing has evolved dramatically over time, advancing from sequencing short DNA fragments to analyzing millions of base pairs. Initially, efforts were focused on determining the sequence of individual genes, but now whole genome sequencing is both rapid and widely accessible. Recent improvements in sequencing technology emphasize faster, more accurate results, lower costs, and better data analysis. Sanger sequencing, which became the gold standard for DNA sequencing for about thirty years, was instrumental in completing various genome sequences, including the human genome. It laid the groundwork for newer sequencing methods. Today, these newer methods, known collectively as “Next-Generation Sequencing” (NGS), include several generations of technology. Second-generation methods, such as Illumina, Pyrosequencing, ABI/SOLiD, and Ion Torrent Sequencing, and third-generation methods like PacBio and Helicos Sequencing, have advanced the field further. Fourth-generation technology, such as Nanopore sequencing, is also emerging. Most modern research now relies on NGS for analyzing biological sequences, and understanding these technologies offers insight into current methods and future developments.

With an ever increasing amount of research data available, it becomes constantly more important to possess data literacy skills to benefit from this valuable resource. An integrative course was developed to teach students the fundamentals of data literacy through an engaging genome sequencing project. Each cohort of students performed planning of the experiment, DNA extraction, nanopore sequencing, genome sequence assembly, prediction of genes in the assembled sequence, and assignment of functional annotation terms to predicted genes. Students learned how to communicate science through writing a protocol in the form of a scientific paper, providing comments during a peer-review process, and presenting their findings as part of an international symposium. Many students enjoyed the opportunity to own a project and to work towards a meaningful objective.

Major depressive disorder (MDD) is a prevalent mental health condition with substantial social and economic consequences. This study focuses on the interplay between genetic and environmen-tal factors in MDD, with particular emphasis on epigenetic mechanisms such as stochastic epige-netic mutations (SEMs), epigenetic age acceleration, and epigenetic drift. We conducted a meta-analysis of DNA methylation patterns across six datasets (n=1125 MDD cases, 398 controls in whole blood; n=95 MDD cases, 96 controls in brain tissues) from the Gene Expression Omnibus. The analysis did not reveal significant global methylation differences between MDD cases and controls. However, a brain-specific probe (cg25801113) near the SHF gene consistently exhibited hypomethylation, suggesting its potential relevance to MDD. SEMs were assessed, revealing a dis-tinct burden at the gene level in MDD cases, though no significant findings emerged for epigenetic age acceleration, indicating it may not play a central role in MDD. The study also identified rare epivariations in specific genes unique to MDD cases. In blood tissue, 51 genes were associated with these unique epivariations, while 1 gene was highlighted in the brain tissue. These results un-derscore the importance of exploring rare epivariations in understanding the molecular mecha-nisms underlying MDD and offer potential targets for further investigation.

Escherichia coli is an indicator microorganism in One Health antibiotic resistance surveillance programmes. The purpose of the study was to describe and compare E. coli isolates obtained from pigs and human contacts from a commercial farm in South Africa using conventional methods and whole genome sequencing (WGS). Porcine E. coli isolates were proportionally more resistant phenotypically and harboured a richer diversity of antibiotic resistance genes, as compared to human E. coli isolates. Different pathovars, namely ExPEC (12.43%, 21/169), ETEC (4.14%; 7/169), EPEC (2.96%, 5/169), EAEC (2.96%, 5/169) and STEC (1.18%, 2/169) were detected at low frequencies. Sequence type complex (STc) 10 were the most prevalent (85.51%, 59/169) among human and porcine isolates. Six STcs (STc10, STc86, STc168, STc206, STc278 and STc469) were shared at the human-livestock interface according to multilocus sequence typing (MLST). Core genome MLST and hierarchical clustering (HC) showed that human and porcine isolates were overall genetically diverse, but some clustering at HC2 to HC200 were observed. In conclusion, even though the isolates shared a spatio-temporal relationship, there were still differences in the virulence potential, antibiotic resistance profiles, and cgMLST and HC according to the source of isolation.

Scale drop disease virus (SDDV), a double-stranded DNA virus in the family Iridoviridae, has been reported widely in southeast Asian countries as a causative agent of scale drop syndrome (SDS) in Asian seabass. SDS have resulted in high mortality and significant economic losses to the aquaculture industry. This study demonstrated the use of metagenomic methods to investigate bacterial and viral communities present in infected fish tissues and recovering a complete genome of the causative agent named SDDV TH7_2019. Characterization of the TH7_2019 genome revealed a genome size of 131 kb with 134 putative ORFs encoding viral proteins potentially associated with host apoptosis manipulation. A comparative genome analysis showed a high degree of amino acid identity across SDDV strains, with variations in number of repeat sequences and mutations within core genes. Phylogenetic analyses indicate a close relationship among SDDV genomes. This research enhances our understanding of the genetic diversity and evolutionary relationship of SDDV, contributing valuable insights for further development of effective control strategies of SDDV.

Species identification and phylogenetic relationships clarification are fundamental goals in species delimitation. Yet these tasks pose challenges when based on morphologies, geographic distribution, and genomic data. Previously, two new species of fern genus Bolbitis, B. × multipinna and B. longiaurita, were described based on morphological traits, are phylogenetically intertwined with B. sinensis and fail to form monophyletic groups. To address the unclear phylogenetic relationships within the B. sinensis species complex, RAD sequencing was performed on 65 individuals from five populations. Our integrated analysis of phylogenetic tree, neighbor net, and genetic structure, indicate that the B. sinensis species complex should not be considered as separate species. Moreover, our findings reveal differences in the degree of genetic differentiation among five populations, ranged from low to moderate, which might be influenced by geographical distance and gene flow. The Fst values also confirmed that genetic differentiation intensifies with increasing geographic distance. Collectively, this study clarifies the complex phylogenetic relationships within the B. sinensis species complex, elucidates the genetic diversity and differentiation across the studied populations, and offers valuable genetic insights that contribute to the broader study of evolutionary relationships and population genetics within the Bolbitis species.

Snakes are a vital component of wildlife resources and are widely distributed across the globe. Bungarus multicinctus, a highly venomous snake, is found in central and southern China. B. multicinctus is a highly venomous snake and is distributed in central and southern China. Snakes are an ancient group of reptiles, and their genome resources can provide important clues for understanding the evolutionary history of reptiles. Meanwhile, genomic resources play a crucial role in comprehending the evolution of species. So far, the genomic resources of snakes are a rarity. In 2021, a snake sample was collected from Beiliu Longgukeng, Guangxi, which was identified as B. multicinctus through morphological identification. In this study, we present a highly contiguous genome of B. multicinctus with a size of 1.51 Gb. The genome contains a repeat content of 40.15%, with a total length exceeding 620 Mb. Additionally, we annotated a total of 24,869 functional genes. This research is of great significance for comprehending the evolution of B. multicinctus and provides a genomic basis for the genes involved in venom gland function.

Enterovirus A71 (EV-A71) infection is a major cause of hand, foot and mouth disease (HFMD) which may be occasionally associated with severe neurological complications. There are currently a lack of treatment options for EV-A71 infection. The Raf-MEK-ERK signaling pathway, in addition to its critical importance in the regulation of cell growth, differentiation and survival, has been shown to be essential for virus replication. In this study, we investigated the anti-EV-A71 activity of vemurafenib, a clinically approved B-Raf inhibitor used in the treatment of late stage melanoma. Vemurafenib exhibits potent anti-EV-A71 effect in cytopathic effect inhibition and viral load reduction assays, with half maximal effective concentration (EC50) at nanomolar concentration. Mechanistically, vemurafenib interrupts both EV-A71 genome replication and assembly. These findings expand the list of potential antiviral candidates of anti-EV-A71 therapeutics.

Cardiomyopathies are diseases of heart muscle, a significant percentage of which are genetic in origin. Cardiomyopathies can be classified as dilated, hypertrophic, restrictive, arrhythmogenic right ventricular or left ventricular non-compaction, although mixed morphologies are possible. A subset of neuromuscular disorders, notably Duchenne and Becker muscular dystrophies, are also characterized by cardiomyopathy aside from skeletal myopathy. The global burden of cardiomyopathies is certainly high, necessitating further research and novel therapies. Genome editing tools, which include zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR) systems have emerged as increasingly important technologies in studying this group of cardiovascular disorders. In this review, we discuss the applications of genome editing in the understanding and treatment of cardiomyopathy. We also describe recent advances in genome editing that may help improve these applications, and some future prospects for genome editing in cardiomyopathy treatment.

Two strongly curved areas of the Carpathians in Romania are earthquake-prone: Vrancea - in the South-Eastern Carpathians, and Danubian – in the western edge of the Southern Carpathians. By far the highest seismicity episode in 2023 was recorded in the Southern Carpathians, near Targu Jiu city, of more than 4000 earthquakes. A first ML 5.2 mainshock was recorded on 13 February, followed by a second one, ML 5.7, on 14 February. Our purpose is to provide a first analysis of this sequence in order to explain its extent and unusual development, in time. The possible role of fluids in the middle crust, is discussed in connection with the rather unusual character of the space-time distribution of aftershocks. A large and high-quality dataset is provided by the dense array of seismic stations which has been gradually improved by adding new stations in the epicentral area. The thorough revision of the phase picking and location reveals a few interesting and intriguing features of seismicity that still remain worthy to be further investigated. The database built within this paper provides excellent information not only for Targu Jiu area, but for any other investigation in intra-continental regions characterized by diffuse and sporadic seismic activity.

The bacterial composition of oral samples has traditionally been determined by PCR amplicon sequencing of 16S rRNA genes. Recent amplicon sequence variant (ASV)-based analyses of 16S rRNA genes differ from that based on operational taxonomic unit (OTU) clustering in the way it deals with sequences having potential errors. However, little information is available on its application in oral microbiome studies. Here, we conducted ASV-based analysis of oral microbiome samples using QIIME 2. We investigated the optimal parameters for sequence denoising, using DADA2, and found the trimming of the first 20 nucleotides from 5′-end of both paired reads avoided excessive sequence loss during chimera removal. Truncating reads at positions 240–245 allowed the removal of low-quality sequences while maintaining sufficient length to merge matching paired ends. Taxonomic assignment, using the naïve Bayes classifier trained with the V3-V4 region of reference 16S rRNA sequences in the extended human oral microbiome database (eHOMD), resulted in bacterial compositions similar to those of OTU-based analyses. Contrary to OTU-based clustering, ASV-based analysis showed taxonomic abundance at the genus or species level to not differ significantly in tongue microbiomes, regardless of brushing. QIIME 2 can, therefore, be a standard pipeline for ASV-based analysis of oral microbiomes.