Phage therapy, the use of bacteriophages (phages) to treat bacterial infections, is regaining momentum as a promising weapon against the rising threat of multidrug-resistant (MDR) bacteria. This comprehensive review explores the historical context, the modern resurgence of phage therapy, and phage-facilitated advancements in medical and technological fields. It details the mechanisms of action and applications of phages in treating MDR bacterial infections, particularly those associated with biofilms and intracellular pathogens. The review further highlights innovative uses of phages in vaccine development, cancer therapy, and as gene delivery vectors. Despite its targeted and efficient approach, phage therapy faces challenges related to phage stability, immune response, and regulatory approval. By examining these areas in detail, this review underscores the immense potential and remaining hurdles in integrating phage-based therapies into modern medical practices.

Metallo-β-lactamases (MBLs) are members of the structurally conserved but functionally diverse MBL-fold superfamily of metallohydrolases. MBLs are a major concern for global health care as they efficiently inactivate β-lactam antibiotics, including the “last-resort” carbapenems, and no clinically suitable inhibitors are currently available. Increasingly, promiscuous β-lactamase activity is also observed in other members of the superfamily, including from viruses, which represents an underexplored reservoir for future pathways to antibiotic resistance. Here, two such MBL-fold enzymes from Bacillus phages, the cyclic mononucleotide-degrading proteins ApycGoe3 and ApycGrass, are shown to efficiently degrade β-lactam substrates in vitro. In particular, ApycGrass displays a distinct preference for carbapenem substrates with a catalytic efficiency that is within one order of magnitude of that of the clinically relevant MBL NDM-1. Mutagenesis experiments also demonstrate that the loss of a metal-bridging aspartate residue reduces nuclease activity up to 35-fold, but improves carbapenemase activity. In addition, we propose that the oligomeric state significantly influences β-lactamase activity by modifying access to the active site pocket. Together, these observations hint at a possible new avenue of resistance via the spread of phage-borne MBL-fold enzymes with β-lactamase activity.

South Africa is a water stressed country experiencing mass urbanisation especially towards coastal cities. The country is already enduring the impacts of global warming and climate change with risk of water scarcity in many areas. The risk was evident with Cape Town near encounter with ‘Day Zero’ i.e., the day when water supplies would have been switched off and residents required to queue for daily water rations. The drought exposed the inadequa-cies of the existing water supply system. Paradoxically, in the same drought period, vast amounts of unutilized stormwater that could have augmented water supply run unabated into the ocean through rivers around the city. The study determined that the problem was not necessarily water shortage but lack of adequate water storage. This study investigated the suitability of coastal reservoirs for stormwater harvesting on the over 3000 km South African coastline. The objective was to identify suitable locations for coastal reservoirs. The study un-dertook a systematic process of selecting several candidate locations and eliminating unsuita-ble sites based on international best practice i.e., coastal topography, climate, hydrology, fluvi-al environment, catchment size and river water quality. Nine candidate sites were identified and ranked based on suitability and associated benefits. The identified locations in order of ranking include Knysna River, Berg River, Buffalo River, Kowie River, Thukela River, Orange River, Port of Richards Bay, Port of Durban, and Lourens River. The Knysna site, with a mean annual precipitation of 600 - 800 mm/annum and mean annual runoff of 100 - 500 Mm3/annum, was determined to be the most optimal location.

The sandwich format immunoassay is generally more sensitive and specific than more common assay formats, including direct, indirect, or competitive. A sandwich assay, however, requires two receptors to bind non-competitively to the target analyte. Typically, pairs of antibodies (Abs) or antibody fragments (Fabs) capable of forming a sandwiching with the target are identified through a slow, guess-and-check method with panels of candidate binding partners. Additionally, sandwich assays reliant on commercial antibodies can suffer from changes to reagent quality outside the researchers’ control. This report presents a reimagined and simplified phage display selection protocol that directly identifies sandwich binding peptides and Fabs. The approach yielded two sandwich pairs, one peptide-peptide and one Fab-peptide sandwich for the cancer and Parkinson’s disease biomarker DJ-1. Requiring just a few weeks to identify, the sandwich pairs delivered apparent affinity comparable to other commercial peptide and antibody sandwiches. The results reported here could expand the availability of sandwich binding partners for a wide range of clinical biomarker assays.

Bacteriophages (phages) are potential alternatives to chemical antimicrobials against pathogens of public health significance. Understanding the diversity and host specificity of phages is important for developing effective phage biocontrol approaches. Here, we assessed the host range, morphology, and genetic diversity of eight Salmonella enterica phages isolated from a wastewater treatment plant. The host range analysis revealed that six out of eight phages lysed more than 81% of the 43 Salmonella enterica isolates tested. The genomic sequences of all phages were determined. Whole genome sequencing data (WGS) data revealed that phage genome sizes ranged from 41 to 114 kb with GC contents be-tween 39.9 and 50.0 %. Two of the phages SB13 and SB28 represent new species Epsep-timavirus SB13 and genera Macdonaldcampvirus, respectively as designated by the In-ternational Committee for the Taxonomy of Viruses (ICTV) as per genome based taxonomic classification. One phage (SB18) belonged to the Myoviridae morphotype while the re-maining phages belonged to the Siphoviridae morphotype. The gene content analyses showed that none of the phages possessed virulence, toxin, antibiotic resistance, type I-VI toxin-antitoxin modules or lysogeny genes. Three (SB3, SB15 and SB18) out of the eight phages possessed tailspike proteins. Whole genome-based phylogeny of the eight phages with their 113 homologs revealed three clusters A, B, C and seven subclusters (A1, A2, A3, B1, B2, C1 and C2). While cluster C1 phages were predominantly isolated from animal sources, cluster B contained phages from both wastewater and animal sources. The broad host range of these phages highlights their potential use to control the presence of S. enterica in foods.

The conventional well placement was done manually by using a numerical reservoir simulator, and it required a lengthy trial-and-error process. It required great experience and expertise to manipulate the variables and uncertainties that lie on the reservoir to determine the best placement of the well. In addition, the traditional gradient-based methods such as Line-search and Trust-region were not viable in terms of maximum results obtained. Gradient-based methods were too dependent on the surface gradient of the solution and may only converge to local optima instead of global optima. Complex reservoirs have rough surfaces with high uncertainties, which hinders the traditional gradient-based method from converging to global optima. Thus, genetic algorithms were utilized to automate the manual trial-and-error process and to overcome the limitations of the traditional gradient-based method. The objectives of this study were to analyse the effect of different initial well placement distributions, the number of random solution sizes, and the crossover rate on cumulative oil production. A synthetic reservoir model built using CMG Builder was used as the testing platform for the optimization problems. Well-placement parameterization and optimization set-up were carried out using the CMG CMOST optimization tool. The integration of CMG IMEX and CMOST optimized cumulative oil production based on the objectives of the study. The results obtained showed that the higher number of random solutions used resulted in higher cumulative oil production, with more generations needed to reach the optimum solution. It can be concluded that the larger number of random solutions used increased the probability of reaching the optimum solution, but will take more generations.

: As antibiotic resistance undermines efforts to treat bacterial infections, phage therapy is being increasingly considered as an alternative in clinical settings and agriculture. However, a major concern in using phages is that pathogens will develop resistance to the phage. Due to the constant evolutionary pressure by phages, bacteria have evolved numerous mechanisms to block infection. If we determine the most common among them, we could use this knowledge to guide phage therapeutics. Here we compile data from 88 peer-reviewed studies where phage resistance was experimentally observed and linked to a bacterial gene, then assessed these data for patterns. In total, 141 host genes were identified to block infection against one or more of 80 phages (representing five families of the Caudovirales) across 16 microbial host genera. These data suggest that bacterial phage resistance is diverse, but even well-studied systems are understudied, and there are gaping holes in our knowledge of phage resistance across lesser-studied regions of microbial and viral sequence space. Fortunately, scalable approaches are newly available that, if broadly adopted, can provide data to power ecosystem-aware models that will guide harvesting natural variation towards designing effective, broadly applicable phage therapy cocktails as an alternative to antibiotics.

In this review we aim to address the current status of phage therapy in the management of multidrug-resistant infections, from compassionate use cases to ongoing clinical trials, as well as the challenges this approach presents in the particular context of CF patients.

The geological and hydrological conditions of tunnels near reservoirs are complex, and the impact of water level changes on the stability and leakage assessment of the lining structure is not considered in the current leakage evaluation. In order to construct an evaluation model for leakage level of tunnels near reservoirs, the influence of water level changes on tunnel stability and changes in environmental conditions on the leakage of tunnels were researched. Based on the AHP and extensibility theory, a hierarchical system for leakage assessment, incorporating values from nine indexes representing three aspects: geological conditions, hydrological conditions, and tunnel engineering. Numerical simulation was used to analyze the influence of water level changes. It was found that the water level change index greatly influences the displacement and stress distribution inside the tunnel structure. The leakage evaluation model was applied to the Tiebeishan Tunnel, resulting in a rating of 3, indicating medium-level leakage. Attention should be paid to water leakage in tunnels with changes in reservoir water levels. The leakage evaluation model for tunnels near reservoirs can effectively assess leakage levels under various conditions, providing a reference for safety assessments of tunnel leakage near reservoirs.

The mechanisms by which bacteriophage T4 converts the metabolism of its E. coli host to one dedicated to progeny phage production was the subject of decades of intense research in many labs from the 1950’s through the 1980’s. At this point, a wide range of phages are starting to be used therapeutically and in many other applications and also the range of available phage sequence data is skyrocketing. It is thus important to re-explore the extensive available data about the intricacies of the T4 infection process as summarized here, expand it to looking much more broadly at other genera of phages, and explore phage infections using newly-available modern techniques and a range of appropriate environmental conditions.

Factors affecting the host-virus interaction must be understood for the effective application of bacteriophages to combat bacterial pathogens. Two novel E. coli phages, the T1-like siphophage LL5 and the rV5-like myophage LL12, were subjected to forward genetic screens against the Keio collection, a library of single non-essential gene deletions in E.coli str. BW25113. These genome-wide screens and subsequent experiments identified eight genes required for efficient propagation of phage LL5 and six genes required for propagation of LL12. The majority of the genes identified were involved in production of the phage receptors. E. coli mutants deficient in heptose II and the phosphoryl substituent of heptose I of the inner core lipopolysaccharide (LPS) were unable to propagate phage LL5, as were mutants deficient in the outer membrane protein TolC. Mutants lacking glucose I of the LPS outer core failed to propagate LL12. Two cytoplasmic chaperones, PpiB and SecB, were found to be required for efficient propagation of phage LL5 but not LL12. This approach may be useful for identifying phage receptors and required host factors in other phages, which would provide valuable information for their potential use as therapeutics and for phage engineering.

Keywords: leptophages; Cas system; bacteriophages; Leptospira interrogans

The ongoing global pandemic caused by coronavirus disease 2019 (COVID-19) has once again demonstrated the significance of the Coronaviridae family in causing human disease outbreaks. As SARS-CoV-2 was first detected in December 2019, information on its tropism, host range, and clinical presentation in animals is limited. Given the limited information, data from other coronaviruses may be useful to inform scientific inquiry, risk assessment and decision-making. We review the endemic and emerging alpha- and betacoronavirus infections of wildlife, livestock, and companion animals, and provide information on the receptor usage, known hosts, and clinical signs associated with each host for 15 coronaviruses discovered in people and animals. This information can be used to guide implementation of a One Health approach that involves human health, animal health, environmental, and other relevant partners in developing strategies for preparedness, response, and control to current and future coronavirus disease threats.

This study aims to investigate the interfacial tension, emulsion stability, and the impact on oil displacement effectiveness of mixed systems containing nonionic surfactants and amphoteric surfactants at different ratios. To achieve this, three different emulsion stability formulations were prepared by mixing betaine and nonionic surfactants in ratios of 1:1, 3:2, and 3:1 respectively. By adjusting the proportions of betaine and nonionic surfactants, variations in interfacial tension and emulsion formation among the three mixed systems were studied to analyze the mechanism of interaction between betaine and nonionic surfactants and evaluate their effects on crude oil displacement and enhanced oil recovery in reservoirs. Subsequently, microscopic and macroscopic oil displacement experiments were conducted on the three mixed systems, along with experiments on emulsion flow resistance. The aim was to verify the oil displacement effectiveness of different mixed systems and further understand their potential applications in reservoirs. By comprehensively analyzing the experimental results, optimal ratios and conditions for the mixed systems were determined. The experimental results indicate that the emulsification system formed by mixing betaine and nonionic surfactants at a ratio of 3:1 achieves molecular synergies through electrostatic interactions and mixed adsorption with betaine, resulting in a compact arrangement of interface membranes and demonstrating a synergistic effect in reducing interfacial tension to an ultra-low value of 10 -4 mN/m. Additionally, as the proportion of betaine surfactant increases, the viscosity of the aqueous phase liquid film increases, the rate of thinning of the liquid film slows down, the rate of water release slows down, and the stability of the emulsion increases. Microscopic oil displacement experiments verified that the three mixed systems increase oil washing efficiency through low interfacial tension and emulsification stripping action, thereby increasing the oil displacement mechanism's coefficient. Emulsion flow resistance experiments demonstrated that as the proportion of betaine surfactant increases, the system exhibits better plugging ability. However, macroscopic oil displacement experiments revealed differences in compatibility between different emulsion stability solutions and rocks with different permeabilities. The mixed system of betaine and nonionic surfactants at a ratio of 3:1 exhibits the best emulsification plugging ability in rocks with a permeability of 109mD, while the 1:1 mixed system performs best in rocks with a permeability of 12mD. This holds significant theoretical and practical significance for reservoir development and enhanced production.

Enterococcus faecalis is a growing cause of nosocomial and antibiotic-resistant infections. Treating drug-resistant E. faecalis requires novel approaches. The use of bacteriophages (phages) against multidrug-resistant (MDR) bacteria has recently garnered global attention. Biofilms play a vital role in E. faecalis pathogenesis as they enhance antibiotic resistance. Phages eliminate biofilms by producing lytic enzymes, including depolymerases. In this study, Enterococcus phage vB_Efs8_KEN04 (ФKEN04), isolated from a sewage treatment plant in Nairobi, Kenya, was tested against clinical strains of MDR Enterococcus faecalis. This phage had a broad host range against 100% (26/26) of MDR E. faecalis clinical isolates and cross-species activity against Enterococcus faecium. It was able to withstand acidic and alkaline conditions, from pH 3 to 11, as well as temperatures between -80ᵒC and 37ᵒC. It could inhibit and disrupt the biofilms of MDR E. faecalis. Its linear double-stranded DNA genome of 142,402 bp contains 238 coding sequences with a G+C content and coding gene density of 36.01% and 91.46%, respectively. Genomic analyses showed that ФKEN04 belongs to the genus Kochikohdavirus in the family Herelleviridae. It lacked antimicrobial resistance, virulence, and lysogeny genes, and its stability, broad host range, and cross-species lysis indicate strong potential for the treatment of Enterococcus infections.

Eutrophication, a global concern, impacts water quality, ecosystems, and human health. It’s crucial to monitor algal blooms in freshwater reservoirs, as they indicate the trophic condition of a waterbody through Chlorophyll-a (Chla) concentration. Traditional monitoring methods, however, are expen-sive and time-consuming. Addressing this hindrance, we developed models using remotely sensed data from the Sentinel-2 satellite for large-scale coverage, including its bands and spectral indexes, to estimate the Chla concentration on 149 freshwater reservoirs in Ceará, Brazil. Several machine learning models were trained and tested, including k-nearest neighbours, random forests, extreme gradient boosting, the least absolute shrinkage, group method of data handling (GMDH), and sup-port vector machine models. A stepwise approach determined the best subset of input parameters. Using a 70/30 split for the training and testing datasets, the best-performing model was the GMDH, achieving an R2 of 0.91, MAPE of 102.34%, and RMSE of 20.38 g/L, which are values consistent with the ones found in the literature. Nevertheless, the predicted Chla concentration values were most sensitive to the red, green, and near infra-red bands.

The formation of hydrogen sulfide (H₂S) in petroleum reservoirs by anaerobic microbial activity is called biogenic souring of reservoirs and is a risk in the oil and gas industry as the compound is extremely toxic, flammable and corrosive. In this paper, we present a workflow and the tools to assess biogenic souring from a pragmatic engineering perspective. The retention of H₂S in the reservoir due to the reactions with iron-bearing rock minerals (e.g. siderite) is shown in a theoretical approach here and supported with literature data. Cases are given for two fields under secondary (waterflooding) and tertiary flooding with microbial enhanced oil recovery (MEOR). The use of the Monte Carlo method as a numerical modelling tool to incorporate uncertainties in the measured physical/chemical/ biochemical data is demonstrated as well. A list of studies conducted with different chemicals alone or in combination with various biocides to mitigate biogenic souring provides an overview of potential inhibitors as well as possible applications. Furthermore, the results of static and dynamic inhibition tests using molybdate are presented in more detail due to its promising mitigation ability. Finally, a three-step workflow for the risk assessment of biogenic souring and its possible mitigation is presented and discussed.

Staphylococcus aureus and Pseudomonas aeruginosa are opportunistic pathogens commonly associated with burn wound infections. These bacteria can form biofilm and contribute a high-level drug resistance to available antibiotics. This study focused on the bacteriolytic activity of phages vB_SAnS_SADP1 and vB_PAnP_PADP4 on 24 h old single or dual-species biofilms of Staphylococcus aureus and Pseudomonas aeruginosa in alone and in combination. Scanning and confocal laser scanning microscopic studies confirmed the structural organization of biofilms in single or dual-species combinations in in-vitro conditions. Single species biofilms are more robust and densely packed at 24 h of incubation. In contrast, dual-species biofilms (0.67± 0.02) are weakly associated due to their inter-species competition and are easily affected by phage cocktails (0.16 ± 0.02). In Invitro conditions, dual-species biofilms were more easily affected by phage cocktail than single phage. Scanning electron microscopic studies revealed the complete diminishment of biofilm formation by four h treatment with single phage or phage cocktails on single species or dual-species biofilms. Confocal laser scanning microscopic images with stains Syto®9 and propidium iodide revealed that phage treatment showed significant uptake of propidium iodide, indicating massive cell death mediated by respective phage or phage cocktail.

Prostate cancer (PC) is the second most diagnosed cancer among men. It was observed that early diagnosis of disease is highly beneficial for survival of cancer patients. Therefore, extension and increasing quality of life of PC patients can be achieved by broadening the Cancer Screening programs that are aimed at the identification of cancer manifestation in patients at earlier stages before they demonstrate well-understood signs of the disease. Therefore, there is an urgent need in standard, sensitive, robust, and commonly available screening and diagnosis tools for identification of early signs of cancer pathologies. In this respect, “Holy Grail” of cancer researchers and bioengineers for decades have been molecular sensing probes that would allow diagnosis, prognosis, and monitoring of cancer diseases by their interaction with cell-secreted and cellassociated PC biomarkers, e.g. PSA and PSMA correspondinly. At present, most PSA tests are performed at centralized laboratories using high throughput Total PSA immune analyzers which are suitable for dedicated laboratories and are not readily available for the broad health screening. Therefore, the current trend in detection of PC is developments of the portable biosensors for mobile laboratories and individual use. Phage display since its conception by George Smith in 1985 has emerged as a premier tool in molecular biology with widespread applications. This review describes how the paradigm of molecular evolution and phage display revolutionized the methods of early diagnosis and monitoring of PC.

Leptospira, which are known to be important disease-causing agents transmitted between animals and humans, results in significant illness and, in some cases, significant death in human populations. This study aims to examine the genomic structure of Leptospira interrogans serovar Copenhageni strain FDAARGOS_203 to identify the specific genetic factors that contribute to antimicrobial resistance (AMR) and defense against phages. The genome, consisting of two contigs totaling 4,630,574 base pairs, underwent thorough examination for protein-coding sequences, transfer RNA genes, and ribosomal RNA genes. A total of twenty-two antibiotic resistance genes that specifically target essential cellular processes such as cell wall synthesis, DNA replication, and protein synthesis have been identified. Significant among these were gidB, GdpD, and PgsA, each involved in separate aspects of antibiotic resistance. In addition, the investigation explored the defense mechanisms of bacteriophages, revealing the presence of defense islands that contain a range of anti-phage systems, including RM_Type_IV, PrrC, Borvo, CAS_Class1-Subtype-IC, and CAS_Class1-Subtype-IB. This comprehensive genomic analysis enhances our understanding of the molecular mechanisms that determine Leptospira's ability to adapt to various environments. The identified genetic factors linked to AMR and defense against phages not only enhance our scientific comprehension but also provide a basis for focused interventions to reduce the impact of leptospirosis.

Anthropogenic activities such as the damming of rivers have resulted in the formation of depositional systems for sediments that are naturally transported along river channels all over the world. The steady accumulation of sediments has profound effects on how reservoirs function. As the reservoir ages, the impact of sedimentation becomes more pronounced. In an alluvial channel, the dynamics of sediment movement, scour, and deposition are exceedingly complicated. The quantitative and qualitative management of river engineering heavily relies on sediment motion. One of the key concerns affecting reservoir storage capacity is reservoir sedimentation. Understanding the form and behavior of the river or reservoir is necessary for a scientific approach to sedimentation. An overview of reservoir sedimentation processes, and models of reservoir and shallow water bodies is provided in this article. More research in the developing fields is advised for continuing studies on reservoir sedimentation due to climate change effects

In antimicrobial-peptide/protein engineering, understanding the peptide/protein’s adaptability to harsh environmental conditions such as urea, proteases, fluctuating temperatures, high salts provide enormous insight into the pharmacokinetics and pharmacodynamics of the engineered peptide/protein and its ability to survive the harsh internal environment of the human body such as the gut or the harsh external environment to which they are applied. A previous work in our laboratory demonstrated that our cloned Eɛ34 TSP showed potent antimicrobial activity against Salmonella newington, and more so, could prevent biofilm formation on decellularized tissue. In this work, the effects of urea-acid on the Eɛ34 stability is studied, and the results demonstrates that at lower pHs of 3 and 4 with urea the protein was denatured into monomeric species. However, the protein withstood urea denaturation above pH of 5 and thus remained as trimeric protein. The mechanism of denaturation of Eɛ34 TSP seems to show that urea denatures proteins by depleting hydrophobic core of the protein by directly binding to the amide units via hydrogen bonds. The results of our in-silico investigation determined that urea binds with Eɛ34 TSP with relative free energies range of -3.4 to -2.9 kcal/mol at the putative globular head binding domain of the protein. The urea molecules interacts with with the protein’s predicted hydrophobic core, thus, disrupting and exposing the shielded hydrophobic moieties of Eɛ34 TSP to the solvent. We further showed that after the unfolding of Eɛ34 TSP via urea-acid, renaturation of the protein to its native conformation was possible within few hours. This unique characteristic of refolding of Eɛ34 TSP which is similar to that of the P22 phage tailspike protein is of special interest to protein scientists and can also be exploited in antimicrobial-protein engineering.

The prevalence of multidrug resistant bacterial diseases is a major global health risk. Multidrug resistant bacterial diseases are prevalent, and the need for novel methods of treatment is essential to the preservation of public health. Annually foodborne pathogens cause 1.35 million infections and 26,500 hospitalizations in the United States alone. Foodborne pathogens such as Salmonella spp. are a major threat to public health. Bacteriophages offer a unique method for the treatment of these multidrug resistant bacteria. We studied the infection dynamics of a potential mono-phage therapy of Salmonella typhimurium under various pathophysiological conditions. Furthermore, we determined the resistance dynamics of Salmonella typhimurium against P22 phage treatment. We also determined synergy with antibiotics such as ampicillin and kanamycin. This research helps to further define and show the versatility of bacteriophages as potential novel treatment methods.

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.

Tuberculosis (TB), caused by Mycobacterium tuberculosis, is an infectious disease that seriously affects human life and health. Despite centuries of efforts to control it, in recent years the emergence of multidrug-resistant bacterial pathogens of M. tuberculosis due to various factors has exacerbated the disease, posing a serious threat to global health. Therefore, a new method to control M. tuberculosis is urgently needed. Phages, viruses that specifically infect bacteria, have emerged as potential biocontrol agents for bacterial pathogens due to their host specificity. In this study, a Mycobacterium phage, Henu3, was isolated from soil around a hospital. The particle morphology, biological characteristics, genomics and phylogeny of Henu3 were characterized. Additionally, to explore the balance between phage resistance and stress response, phage Henu3-resistant strains 0G10 and 2E1 were screened by sequence passage and bidirectional validation methods, which significantly improved the sensitivity of phage to antibiotics (cefotaxime and kanamycin). By whole genome resequencing of strains 0G10 and 2E1, 12 genes involved in cell wall synthesis, transporter-encoded genes, two-component regulatory proteins and transcriptional regulatory factor-encoded genes were found to have mutations. These results suggest that phage Henu3 has the potential to control M. tuberculosis pathogens, and phage Henu3 has the potential to be a new potential solution for the treatment of M. tuberculosis infection.

Acinetobacter baumannii is a multidrug-resistant and invasive pathogen associated with the etiopathology of both an increasing number of nosocomial infections and of relevance to poultry production systems. Multidrug-resistant Acinetobacter baumannii has been reported in connection to severe challenges to clinical treatment, mostly due to an increase rate of resistance to carbapenems. Amid the possible strategies aiming to reduce the insurgence of antimicrobial resistance, phage therapy has gained particular importance for the treatment of bacterial infections. This review summarises the different phage-therapy approaches currently in use for multiple-drug resistant Acinetobacter baumannii, including single phage therapy, phage cocktails, phage -antibiotic combination therapy, phage coding Acinetobacter baumannii and the novel phage enzyme treatment. Although phage therapy represents a potential treatment solution for multidrug-resistant Acinetobacter baumannii, further research is needed to unravel some unanswered questions especially in regard to its in vivo applications, before possible routine clinical use.

Salmonella can cause acute and chronic infections in humans. Salmonella species are known to cause food poisoning and other diseases in developing countries. Their role in the pathogenesis of these diseases has received increased international attention. Despite numerous advances in sanitation, they still can infect humans and cause outbreaks in developed countries. For example, Salmonella causes about 1.2 million illnesses in the US each year with over 450 deaths. Additionally, Salmonella outbreaks cause significant losses to chicken producers globally. The Salmonella species is also prone to acquiring resistance to various classes of antibiotics. Hence, the need for a paradigm shift from antibiotics to bacteriophages to manage, control and treat bacterial infections. The ɛ34 phage belongs to Podoviruses and categorized into the P22-like phages. The P22-like phages include ɛ34, ES18, P22, ST104, and ST64T. In this work, we investigated the antibacterial property of ɛ34 phage tailspike protein against Salmonella newington (S. newington). We demonstrate here that, the phage’s tailspike protein enzymatic property as a LPS hydrolase synergizes with Vero Cell culture supernatant in killing S. newington. Using decellularized cartilage scaffold as an ex vivo tissue model, the ɛ34 TSP protected the scaffold from S. newington biofilm formation. Computational analysis of the ɛ34 TSP interaction with membrane proteins of S. newington demonstrated a higher probability (0.7318) of binding to ompA of S. newington, and when docked to ompA extracellular component, it produced a high free energy of -11.3kcal/mol. We also demonstrate the resistance/sensitivity of the tailspike to the digestive enzyme trypsin. The data obtained in this work indicates that the trypsin resistant tailspike protein of Ɛ34 phage can be formulated as a novel antibacterial agent against S. newington.

Bacteriophages, viruses that are widespread throughout the world, are highly specific for bacteria, usually of a single species and often of a particular strain. After being discovered and isolated 100 years ago, their use, called phage therapy, was instituted in medicine two years later and quickly used around the world to treat various bacterial infections. In the West, phage therapy was overshadowed in the second half of the 20th century by antibiotic therapy, which was then thought to be the definitive solution. But because of the increase in bacterial resistance to antibiotics, the idea of using bacteriophages in medicine has been reawakened. The innumerable observations reported over the years in the literature constitute an invaluable experience. We and some of our colleagues have, in the last decade treated some patients compassionately. With the available documentation and our own experience we discuss the potential indications and limitations of phage therapy. The observation of the increasing number of therapeutic failures in the announced perspective of a post-antibiotic era, we believe, that the introduction of bacteriophages into the therapeutic arsenal seems conceivable today to two preconditions: that their production as biologic drug meets current regulatory standards and that the benefit-risk assessment was conducted in a modern setting. Phage therapy could be applied as a substitution or supplement to antibiotic therapy under multiple circumstances in different modes, precise indications and limits.

Phage therapeutics offer a potentially powerful approach to combat multidrug-resistant bacterial infections. However, to be effective, phage therapy must overcome existing and developing phage resistance. While phage cocktails can reduce this risk by targeting multiple receptors in a single therapeutic, bacteria have mechanisms of resistance beyond receptor modification. A rapidly growing body of knowledge describes a broad and varied arsenal of antiphage systems encoded by bacteria to counter phage infection. We sought to understand the types and frequencies of antiphage systems present in a highly diverse panel of Pseudomonas aeruginosa clinical isolates utilized to characterize novel antibacterials. Using web-server tool PADLOC (Prokaryotic Antiviral Defense Locator), putative antiphage systems were identified in these P. aeruginosa clinical isolates based on sequence homology to a validated and curated catalog of known defense systems. Coupling this host bacterium sequence analysis with host range data for 70 phages, we observed a correlation between existing phage resistance and the presence of higher numbers of antiphage systems in bacterial genomes. We were also able to identify antiphage systems that were more prevalent in highly phage-resistant P. aeruginosa strains, suggesting their importance in conferring the resistance.

Immunohistochemistry is a widely used technique for research and diagnostic purposes that relies on the recognition by antibodies of antigens expressed in tissues. However, tissue processing and particularly formalin fixation affect the conformation of these antigens through the formation of methylene bridges. Although antigen retrieval techniques can partially restore antigen immunoreactivity, it is difficult to identify antibodies that can recognize their target especially in formalin-fixed paraffin-embedded tissues. Most of the antibodies currently used in immunohistochemistry have been obtained by animal immunization; however, in vitro display techniques represent alternative strategies that have not been fully explored yet. This review provides an overview of phage display-based antibody selections using naïve antibody libraries on various supports (fixed cells, dissociated tissues, tissue fragments, and tissue sections) that have led to the identification of antibodies suitable for immunohistochemistry.

Fractured media are seldom considered viable for storing excess thermal energy seasonally, compared to the more commonly used porous aquifers, due to their heterogeneity, lower storage capacity, and potential for unpredictable flow paths. This study employs COMSOL Multiphysics to create a numerical model of a fractured granite reservoir located below the Bedretto underground laboratory. The energy efficiency of both single-well and doublet systems was evaluated over 25 cycles, each comprising four 91-day phases: injection, storage, production, and resting. Results indicated that the single-well system was more efficient, with energy efficiency increasing with the flow rate. For an injection temperature of 60 °C, the system achieved energy efficiencies of up to 59.3% and 67.7%, after 10 and 25 cycles, respectively, aligning with porous Aquifer Thermal Energy Storage (ATES) system efficiencies at this temperature. Exploration of electricity production using water injected at 120 °C revealed it to be uneconomical and ineffective. However, the most promising use of the retrieved water was found to be direct ground heating for a greenhouse. This technology offers a potential alternative for thermal energy storage in regions lacking suitable porous aquifers, although identifying appropriate locations with the necessary geological characteristics may present significant challenges.

Increasing rates of infection by antibiotic resistant bacteria have led to a resurgence of interest in bacteriophage (phage) therapy. Several phage therapy studies in animals and humans have been completed over the last two decades. We conducted a systematic review of safety and toxicity data associated with phage therapy in both animals and humans reported in English-language publications from 2008 – 2021. Overall, 69 publications met our eligibility criteria including 20 animal studies, 35 clinical case reports or case series, and 14 clinical trials. After summarizing safety and toxicity data from these publications, we discuss potential approaches to optimizing safety and toxicity monitoring with the therapeutic use of phage moving forward. In our systematic review of the literature, we found few, but no serious, adverse events associated with phage therapy. Comprehensive and standardized reporting of potential toxicities associated with phage therapy has generally been lacking in the published literature. Structured safety and tolerability endpoints are necessary when phages are administered as anti-infective therapeutics.

The rise of antibiotic-resistant strains demands new alternatives in antibacterial treatments. Bacteriophages, with their precise host specificity and ability to target and eliminate bacteria safely, present a valuable option. Meanwhile, hydrogels, known for their excellent biodegradability and biocompatibility, serve as ideal carriers for bacteriophages. The combination of bacteriophages and hydrogels ensures heightened phage activity, concentration, controlled release, and strong antibacterial properties, making it a promising avenue for antibacterial treatment. This article provides a comprehensive review of different cross-linking methods for phage hydrogels and focuses on their application in treating infections caused by various drug-resistant bacteria.

The chemically synthesized polymer polyacrylamide (HPAM) in conventional reservoirs has achieved excellent oil displacement, but its oil displacement is poor in extreme reservoir environments. To develop biopolymer oil flooding agent under extreme reservoir conditions, the viscosity increasing and rheological properties of three biopolymers, diutan gum, xanthan gum, and scleroglucan, were studied under extreme reservoir conditions (high salt, high temperature, strong acid, and alkali), and the effects of temperature, mineralization, pH, and other factors on their viscosities and long-term stability properties were analyzed and compared. The results showed that under the temperature of 90℃ and below, the three kinds of biopolymers had the best viscosity-increasing ability. The viscosity of the three kinds of biopolymers was 80.94, 11.57, and 59.83mPa·s, respectively, when the concentration was 1500mg/L and the salinity was 220g/L. At the shear rate of 250s-1,100℃~140℃, scleroglucan has the best viscosification. At 140℃, the solution viscosity is 19.74mPa·s, and the retention rate can reach 118.27%. The results of the long-term stability study showed that the solution viscosity of scleroglucan with mineralization level of 220 mg/L was 89.54% viscosity retention in 40 days, and the diutan gum could be stabilized for 10 days, and the viscosity was maintained at 90 mPa·s. All three biopolymers are highly acid and alkali-resistant, with viscosity variations of less than 15% in the pH3~10 range. Rheological tests have shown that both of them have better viscoelastic properties than xanthan gum due to the peculiar double-helix structure of xanthan gum and the rigid triple-helix structure of scleroglucan. Therefore, the two biopolymers, diutan gum, and scleroglucan have the potential for extreme reservoir oil displacement applications, and it is recommended to use diutan gum for oil displacement in reservoirs up to 90℃ and scleroglucan for oil displacement in reservoirs between 100℃ and 140℃.

Using the fluorescent method in the modification of Krasnoyarsk State University, we study development (as chlorophyll content, ∑CHL) and photosynthetic activity of phytoplankton in seven large flat reservoir of the Volga River cascade (Russia) in August 2915–2017. In period of maximal warming of water, average ∑CHL varied in limits of 19.4–33.7 μg L–1 in the Upper Volga, 8.5–27.8 μg L–1 in the Middle Volga, and 5.2–11.3 μg L–1 in the Lower Volga. Photosynthetic activity coefficient (PhAC) varied mostly in limits of 0.12–0.59 with average of 0.22–0.38 and only in 2017 decreased to minimal <0.10 and average <0.20. The average PhAC values shows the normal physiological state of the phytoplankton of the Upper Volga during all periods of observation, occasional decrease of PhAC in the Middle Volga, and low photosynthetic activity in the Lower Volga. A decrease in the average ∑Chl and PhAC in 2017 was under cyclonic windy weather with a large amount of precipitation, low solar radiation, and large volume of flow. Trend towards a decrease in ∑CHL, like decrease in PhAC from the Upper Volga to the Lower Volga is explained by increasing in the flow rate and volume of runoff downstream the Volga River.

CO₂ enhanced oil recovery (EOR) has been proven its capability to explore the unconventional tight oil reservoirs and potential for geological carbon storage. Meanwhile, the extremely low permeability pores exaggerate the difficulty CO₂ EOR and geological storage processing in the actual field. This paper initiates the ultrasonic-assisted approach to facilitate the oil-gas miscibility development and finally contribute to unlock more tight oils. First, the physical properties of crude oil with and without ultrasonic treatments were experimentally analysed through gas chromatography (GC), Fourier-transform infrared spectroscopy (FTIR) and viscometer. Second, the oil-gas minimum miscibility pressures (MMPs) were measured from the slim-tube test and the miscibility developments with and without ultrasonic treatments were interpreted from the mixing-cell method. Third, the nuclear-magnetic resonance (NMR) assisted coreflood tests were conducted to physically model the recovery process in porous media and directly obtain the recovery factor. Basically, the ultrasonic treatment (40KHz and 200W for 8 hours) was found to substantially change the oil properties, with viscosity (at 60°C) reduced from 4.1 to 2.8mPa·s, contents of resin and asphaltene decreased from 27.94% and 6.03% to 14.2% and 3.79%, respectively. The FTIR spectrum shows the unsaturated C-H bond, C-O bond and C≡C bond in macromolecules were broken from ultrasonic, which caused the macromolecules (e.g., resin and asphaltenes) to be decomposed into smaller carbon-number molecules. Accordingly, the MMP was determined to be reduced from 15.8 to 14.9MPa from the slim-tube test and the oil recovery factor increased by over 10%. This study reveals the mechanisms of ultrasonic-assisted CO₂ miscible EOR in producing tight oils.

Streptococcus mutans is a key bacterium in dental caries- one of the most prevalent chronic infectious diseases. Conventional treatment both fails to specifically target the pathogenic bacteria and at-tempts to eradicate commensal bacteria as well. Thus, caries remains one of most common and challenging diseases. The use of bacterial viruses as anti-bacterial agents, is gaining interest worldwide. Hardly any phages were described against S. mutans. The objective of this study was to isolate anti-S. mutans phages and to characterize their antimi-crobial properties. Human saliva samples were filtered and screened for potential phages. Standard double-layered agar method was used for isolation. Whole genome sequence analysis and morphology visualization by TEM, were used for anti-S. mutans phage identification. Antibacterial properties were evaluated using clinical strains and ATCC strains of S. mutans in various states. Antibacterial effect was also tested on human cariogenic dentin. One phage against S. mutans was isolated and termed SMHBZ8. This phage showed effective lytic activity in vitro against both planktonic and biofilm S. mutans cultures. Moreover, the phage showed antibacterial effect when used on cariogenic dentin. The isolation and characterization of SMHBZ8 may be the first step in developing a potential phage therapy for dental caries.

The emergence of multidrug-resistant bacterial strains, especially in the clinical setting, has renewed interest in alternative treatment methods. The utilization of prokaryotic viruses in phage therapy has demonstrated potential as a novel treatment method against multidrug-resistant bacterial infections. As the post-antibiotic era quickly approaches, the development and standardization of phage therapy is critically relevant to public health. This review serves to highlight the development of phage therapy against methicillin-resistant Staphylococcus aureus (MRSA), an antibiotic-resistant bacterial strain responsible for severe clinical infections.

Directed evolution methods are becoming increasingly popular, as they are extremely powerful toward developing new biomolecules with altered/novel activities, e.g., proteins with new catalytic functions or substrate specificities, and nucleic acids that recognize an intended target. Especially useful are systems that have incorporated continuous evolution, where the protein to be evolved undergoes continuous mutagenesis to evolve a desired trait with little to no input from the researcher once the system is started. However, continuous evolution methods can be challenging to implement in the lab and daunting for researchers to invest time and resources. Our intent is to provide basic information and helpful suggestions that we have gained from our experience with bacterial phage-assisted continuous evolution (PACE). Specifically, we review factors to consider before adopting PACE for a given evolution scheme, different types of selection circuits that can be utilized with particular focus on the PACE-B1H selection system, what optimization of a PACE selection circuit may look like using directed evolution of ME47 as a case study, and additional techniques that may be incorporated into a PACE experiment. With this information, researchers will be better equipped to determine if PACE is a valid strategy to use to evolve their proteins and how to set up a valid selection circuit.

Phage, which is often used therapeutically, has begun to receive interest as an alternative to antibiotic growth promoters (AGPs) to enhance chicken growth. Another option that has been extensively studied as a growth promoter in chicken is probiotics. However, there are no studies using phages and probiotics as prospective feed additives for broiler chickens. Therefore, this study demonstrated the effects of phage cocktail, probiotics and their combinations on growth performance and gut microbiota of broiler chickens. A total of 288 one-day-old male Cobb 500 broilers were randomly allotted to 1 of 6 treatments in a completely randomised design. The treatments were: (i) C (basal diet (BD) only), (ii) 1ɸ (BD + 0.1% phage cocktail), (iii) 2ɸ (BD + 0.2% phage cocktail), (iv) P (BD + 0.1% probiotic), (v) 1ɸP (BD + 0.1% phage cocktail + 0.1% probiotic), (vi) 2ɸP (BD + 0.2% phage cocktail + 0.1% probiotic). The 1ɸP treatment had significantly (P < 0.05) better BW (35 d), BWG (22 – 35 d, 1 – 35d), and FCR (1-21 d. 22-35 d, 1-35 d) compared to C. Unique gut microbiota diversity was also found between the ɸP (1ɸP and 2ɸP) and non-ɸP groups (C, 1ɸ, 2ɸ and P) in ilea, particularly in the 35 d chickens. Microorganisms associated with short-chain fatty acid (SCFA) producers were significantly (P <0.05) present in the ɸP group than in the non- ɸP group. The carbohydrate and amino acid metabolism predicted genes were significantly upregulated in ɸP groups compared to non- ɸP groups. These genes were involved in the digestion and absorption of nutrients as well as the production of energy. Our findings showed that 1ɸP treatment could be a potential alternative to AGPs for poultry where growth performance was enhanced, and gut microbiota was positively modulated.

China is rich in coal resources under water bodies. However, for a long time, the safety prediction of high-intensity mining under water bodies is one of the problems encountered by the coal industry. It is of great significance to realize safe mining under water bodies, improve the recovery rate of coal resources and protect reservoir resources. Therefore, this article takes the No. 5 coal seam and No. 11 mining area of Wangwa Coal Mine as the research object, and integrates physical simulation, numerical simulation, theoretical analysis and other methods to study the development height of water-conducting fracture zones in fully mechanized top coal caving mining. Solid-liquid coupling physical simulation test reveals the failure characteristics of overlying strata in goaf and the seepage law of reservoir water under the influence of mining. By comparing the monitoring data of borehole leakage, the measured data obtained by borehole peeping with the height data of water-conducting fracture zone obtained by the traditional empirical formula of three-under standard, the error between the two is as high as -29.39 %. In this case, the variance correction coefficient is used to correct the empirical formula, and on this basis, in order to effectively protect the surface water dam and water body, the mining height of coal seam in the working face with limited height mining is inversely derived. The research results provide a basis for the safety prediction of high-intensity mining under the reservoir dam in the ecologically fragile areas of western China and provide a scientific guarantee for the formulation of safety measures under such conditions.

With the popularization of natural gas and the requirements for environmental protection, the development and utilization of natural gas is particularly important. The status of natural gas in China's oil and gas exploration and development is constantly improving, and the country is paying more and more attention to the exploitation and utilization of natural gas. The Upper Paleozoic tight sandstone in the Ordos Basin is characterized by low porosity, low permeability and large area of concealed gas reservoirs. By injecting CO2 into the formation, the recovery of natural gas can be improved, and at the same time, the stable storage of CO2 can be achieved to achieve a win-win situation of CO2 emission reduction and utilization. Injecting greenhouse gas CO2 into gas reservoirs for storage and improving recovery has also become a hot research issue. In order to improve the recovery efficiency of tight sandstone gas reservoir, this paper takes the complex tight sandstone of Upper Paleozoic in Ordos Basin as the research object, through indoor physical simulation experiments, carried out the influence of displacement rate, fracture dip angle, core permeability, core dryness and wetness on CO2 gas displacement efficiency and storage efficiency, and analyzed the influence of different factors on CO2 gas displacement efficiency and storage efficiency to improve the recovery and storage efficiency. The research results show that under different conditions, when the CO2 injection pore volume is less than 1PV, the relationship between the CH4 recovery rate and the CO2 injection pore volume is linear, and the tilt angle is 45 °. When the CO2 injection pore volume exceeds 1PV, the CH4 recovery rate increases slightly with the increase of displacement speed, the recovery rate of CO2 displacement CH4 is between 87% - 97%, and the CO2 breakthrough time is 0.7PV-0.9PV. In low-permeability and low-speed displacement cores, the diffusion of CO2 molecules is more significant. The lower the displacement speed is, the earlier the breakthrough time of CO2 is, and the final recovery of CH4 slightly decreases. Gravity has a great impact on CO2 storage and enhanced recovery. The breakthrough of high injection and low recovery of CO2 is earlier, and the recovery of CH4 is about 3.3% lower than that of low injection and high recovery. The bound water makes the displacement phase CO2 partially dissolved in the formation water, and the CO2 breakthrough lags about 0.1PV. Ultimately, CH4 recovery factor and CO2 storage rate are higher than those of dry core displacement. The research results provide theoretical data support for CO2 injection to improve recovery and storage efficiency in complex tight sandstone gas reservoirs.

Bacteria are engaged in a constant battle against preying viruses, called bacteriophages (or phag-es). These remarkable nano-machines pack and store their genomes in a capsid and inject it into the cytoplasm of their bacterial prey following specific adhesion to the host cell surface. Tailed phages possessing dsDNA genomes are the most abundant phages in the bacterial virosphere, particularly those with long, non-contractile tails. All tailed phages possess a nano-device at their tail tip that specifically recognizes and adheres to a suitable host cell surface receptor, being pro-teinaceous and/or saccharidic. Adhesion devices of tailed phages infecting Gram-positive bacte-ria are highly diverse and, for the majority, remain poorly understood. Their long, flexible and multi-domain encompassing tail limits experimental approaches to determine their complete structure. We have previously shown that the recently developed protein structure prediction program AlphaFold2 can overcome this limitation by predicting the structures of phage adhesion devices with confidence. Here, we extend this approach and employ AlphaFold2 to determine the structure of a complete phage, the lactococcal P335 phage TP901-1. Herein we report the structures of its capsid and neck, its extended tail, and the complete adhesion device, the baseplate, which was previously partially determined by X-ray crystallography.

In this article, the quality of water in the reservoirs of Lake Arpi, Lake Yerevan, Akhuryan, Azat, Aparan and Kechut was estimated with usage of the Armenian Water Quality Index. It was established that in the waters of reservoirs the the maximum permissible concentration of copper, vanadium, aluminum, chromium, manganese, iron, NH4+ and NO2- regularly increases. The following computational algorithm was used for determination of the Armenian Water Quality Index values: to determine the number of cases of MPC excess of i-substance or indicator of water –n; to estimate the total amount of cases of the maximum permissible concentration (N) – N = ∑n; to computes log2N, nlog2n and ∑nlog2n; to determine geoecological syntropy (I) and entropy (H): I = ∑ nlog2n/N and H = log2N – I. Then, Geo-Ecological Evolving Organized index index was determined: G = H/I. Further, the total amount multiplicity of MAC exceedances was estimated: (M) - M=∑m and log2M was computed. Finally, Armenian Water Quality Index was obtained: AWQI = G + 0.1log2M. It was established that the Armenian Water Qquality Index showed a linear dependence on the Water Contamination Index, the Specific Combinatory Water Quality Index, the Geo-Ecological Evolving Organized index and an inverse dependence on the Canadian Water Quality Index.

Reservoirs are characterized by accumulation of sediments where micropollutants may concentrate, with potential toxic effects on downstream river ecosystems. However, sediment management such as flushing is needed to maintain storage capacity. Climate change is expected to increase sediment loads, but potential effects on their quality are scarcely known. In this context, sediment contamination by trace elements (As, Cd, Cr, Cu, Hg, Ni, Pb, Zn) and organics (PAHs, PCBs, C>12) was analyzed in 20 reservoirs located in Italian Central Alps. A strong As and a moderate Cd, Hg and Pb enrichment was emphasized by Igeo, with potential ecotoxicological risk according to PEC quotients. Siltation, granulometry, total organic carbon (TOC) and altitude resulted as the main drivers governing pollutant concentrations in sediments. According to climate change models, expected increase of rainfall erosivity will enhance soil erosion and consequently the sediment flow to reservoirs, potentially increasing coarse grain fractions and thus potentially diluting pollutants. Conversely, increased weathering may enhance metal fluxes to reservoirs. Increased vegetation cover will potentially result in higher TOC concentrations, which may contrast contaminant bioavailability and thus toxicity. Our results may provide elements for a proper management of contaminated sediments in a climate change scenario aiming at preserving water quality and ecosystem functioning.

Antimicrobial resistance (AMR) has become a worldwide health problem. Consequently, there is a global interest in the study of the antimicrobial activity of natural compounds as an alternative to antibiotics. One of the possibilities studied during the last years is the use of bacteriophages and their derived proteins. More specifically, phage lytic proteins or endolysins are specific enzymes that cause cell lysis and can be easily produced and purified after overexpression in bacteria. However, one of the major disadvantages of these proteins is their sensitivity to some environmental conditions that can reduce their efficiency. The use of vesicles for endolysin encapsulation could help overcome this disadvantage, offering an additional protection to the protein and allowing its controlled release and long-term stability.

Tick-borne diseases are a growing concern worldwide, affecting both human and animal populations. Ticks are known to harbor a wide range of pathogens and are considered one of the most important vectors of disease. Lyme disease, caused by Borrelia burgdorferi sensu lato, is the most common tick-borne disease in the US and Europe. However, accurate diagnosis of Lyme disease can be challenging due to the complex immune evasion strategies employed by Borrelia species and the limitations of existing diagnostic tests. To address this issue, researchers are exploring novel approaches, including the use of bacteriophages as diagnostic tools. Bacteriophages are highly specific and offer advantages over traditional methods for detecting bacteria, including Borrelia. In particular, the use of multicopy bacteriophages as molecular markers for Borrelia detection is a promising approach that may provide greater sensitivity than targeting single-copy bacterial genes. Nonetheless, the task of identifying trace amounts of bacteriophages in blood samples necessitates attention, and scientists are devising innovative techniques to surmount this hurdle. In summary, employing bacteriophages as a diagnostic tool for tick-borne diseases, such as Lyme disease, by specifically targeting free circulating bacteriophages in blood samples, offers significant potential for enhancing patient outcomes and public health.

The problem of antimicrobial resistance has created a new need for alternative/ complementary treatments. To this end, bacteriophages offer an exciting prospect, as they can infect and kill specific bacteria without harming the host. This survey aimed to evaluate the state of applied phage research in Africa, among the members of the Africa phage Forum (APF). This was a cross-sectional survey whereby a google form was created for the members of the Africa Phage forum to fill so as to access the stage of phage research in Africa. Data was collected between June and July 2021 using a structured questionnaire form. A total of 65 out of a total of 101 forum members completed the questionnaire. The survey indicated that a majority 68% of phage researchers in Africa were at the training stages of their career. Some available participants were limited (8%). Most of the members identified funding, lack of skill set, near absence of adequate laboratory infrastructure as major hurdles for phage research. Despite these challenges, 73.3% of APF members work with the ESKAPE group with the majority of its members carrying out research in Phage in Biocontrol (80%), whereas others perform research related to human phage therapy (60%). However, it appeared this research has not yet reached the stage of commercialization. Overall, Phage research is in its infancy in Africa. Key challenges included poor laboratory infrastructure, lack of capacity building in the phage field, and lack of local awareness on the significance of phages for policymakers and governments. APF could, therefore, play a role in creating phage awareness in Africa; mobilizing resources; enhancing networks and collaborations amongst APF members and beyond, especially with more experienced phage mentors in the Western countries, to greatly reduce the gap in knowledge and enhance phage research in Africa.

Bacteria develop various defense mechanisms against stresses, including the bacteriophage infection. The giant phiKZ phage infection induced the appearance of a pseudo-nucleus inside the bacterial cytoplasm. Here, we used FISH, electron tomography and analytical electron microscopy to study the morphology of this unique nucleus-like shell and to demonstrate the distribution of phiKZ and bacterial DNA in infected P. aeruginosa cells. The maturation of the pseudo-nucleus was traced in short intervals for 40 min after infection. This study was accompanied by the identification of phiKZ and bacterial DNA by real-time RCR. We demonstrated that phage DNA that isolated from the cytoplasm during all infection stages were compacted within the pseudo-nucleus in a specific structure. Bacterial DNA was diminished in the course of infection, but did not completely degrade until at least 40 min after phage application. The content of the total phage DNA, on the other hand, increased. EDX analysis confirmed these results and revealed that, during the infection, Sulfur content in the bacterial cytoplasm increased, which suggests the increase of DNA-binding Met-reach proteins synthesis, which could protect bacterial DNA from stress.

Background: Dual function tail tubular proteins (TTP) belonging to the lytic bacteriophages are the interesting group of biologically active enzymes. Surprisingly, apart from their structural function, they are also polysaccharide hydrolyzes destroying bacterial extracellular components. One of the representatives of this group is TTPB from Klebsiella pneumoniae phage – KP32. TTPB hydrolyzes exopolysaccharide (EPS) of Klebsiella pneumoniae and Enterococcus faecalis strain. This depolymerizing feature was associated with the activity to prevent bacterial biofilm formation. TTPB can inhibit biofilm formation by K. pneumoniae, Enterobacter cloacae, Staphylococcus aureus, Enterococcus faecalis and Pseudomonas aeruginosa strains. Moreover, synergistic activity with antibiotic action has been observed, most likely due to depolymerases’ facilitation of contact of antibiotic with bacterial cells. Methods: TTPB was overexpressed in E coli system, purified and tested towards the bacterial strains using agar overlay method. The hydrolytic activity of TTPB was performed using EPSs of K. pneumoniae PCM2713 and E. cloacae ATCC 13047 as the substrates. Next, we determined the reducing sugar (RS) levels in the TTPB/EPS mixtures, regarding the RS amount obtained after acidic hydrolysis. The antibiofilm activity of TTPB has been set down on bacterial biofilm using a biochemical method. Finally, we have demonstrated the synergistic activity of TTPB with kanamycin. Results: For the first time, the hydrolytic activity of TTPB towards bacterial EPSs has been shown. TTPB releases about a half of the whole RS amount of EPSs belonging to K. pneumoniae PCM 2713 and E. cloacae ATCC 13047 strains. 1.12 µM of the phage protein reduces biofilm of both strains by over 60%. Destroying the bacterial biofilm the phage protein improves the antibiotic action increasing kanamycin effectiveness up to four times.

Climate change in the coming decades could intensify extreme events such as severe droughts. Combined with the possible increase of water demands, these changes exert a large pressure on the water systems. In order to confirm this assumption, a set of scenarios was proposed in this study to consider the combined impact of climate changes and the increase in water demand on the main multiple-use reservoirs of São Francisco River, Brazil. For this purpose, five CMIP6 climate models were used considering two greenhouse gas emissions scenarios: the SSP2-4.5 and SSP5-8.5. The naturalized and withdraw streamflows were estimated to the adopted reser-voirs considering all existing, new and projected demands. The conjunction of scenarios indicat-ed an increase in Potential Evapotranspiration, a possible significant reduction in water availa-bility, a growth in water demand mainly for irrigation and a substantial reduction in the perfor-mance of the evaluated reservoirs.

Probiotics are increasingly used by consumers and practitioners to reduce gastrointestinal (GI) distress and improve gut function. Here, we sought to determine whether addition of supplemental bacteriophages (PreforPro) could enhance the effects of a common probiotic, Bifidobacterium animalis subsp. lactis (B. lactis) on GI health. We conducted a 4-week, randomized, parallel-arm, double-blind, placebo-controlled trial where primary outcomes included self-assessments of GI health, a daily stool log, and 16s rRNA analysis of gut microbial populations. We observed within group improvements in GI inflammation (p=0.01) and a trending improvement in colon pain (p=0.08) in individuals consuming B. lactis with PreforPro, but not in the group consuming only the probiotic. There was also a larger increase in Lactobacillus and short chain fatty acid-producing microbial taxa detected in stool of participants taking PreforPro with B. lactis compared to the probiotic alone. Overall, these results suggest the addition of PreforPro as a combination therapy may alter gut ecology to extend the GI benefits of consuming B. lactis or other probiotics.

Lytic bacteriophages have the efficacy to act and eradicate pathogenic bacteria as an attractive tool in the near future. Bacteriophages specifically kill multidrug-resistant bacteria even which have the capacity to form biofilms. The present review mainly focused on the efficacy of bacteriophages and cocktails as therapeutic agents against predominate MDR-bacteria and their biofilms which are isolated from septic wound infections. The body of evidence includes data from studies investigating bacteriophages from sewage samples as novel antibacterial and antibiofilm agents against pathogenic bacteria. The goal of this review is to present an overview on predominant bacteria from septic wound infection, the biofilm-forming capacity of bacteria, lytic effect of bacteriophages and phage cocktails with an emphasis on the application of bacteriophages against septic wound causing bacteria.

Data-driven models (DDMs) are extensively used in environmental modeling but face challenges due to limited training data and potential results not adhering to physical laws. To address this challenge, this study developed a process-guided deep learning (PGDL) model, integrating a long short-term memory (LSTM) neural network and a process-based model (PBM), CE-QUAL-W2 (W2), to predict water temperature in a stratified reservoir. The PGDL included an energy constraint term from W2's thermal energy equilibrium into the cost function of the LSTM, besides the mean square error term. In PGDL, parameters were optimized by penalizing deviations from the energy law, ensuring adherence to physical constraints. Compared to LSTM, PGDL demonstrated enhanced satisfaction with the energy balance and superior performance in water temperature prediction. Even with less field data for training, PGDL outperformed both LSTM and calibrated W2 after pre-training with data generated using the uncalibrated W2. Therefore, integration of DDM with a PBM ensured physical consistency in water temperature prediction for complex stratified reservoirs with limited data. Moreover, pre-training the PGDL with PBM proved highly effective in mitigating bias and variance due to insufficient field measurement data.

Microorganisms inhabiting subsurface petroleum reservoirs are key players in biochemical transformations. The interactions of microbial communities in these environments are highly complex and still poorly understood. This work aimed to assess publicly available metagenomes from oil reservoirs and implement a robust pipeline of genome-resolved metagenomics to deci-pher metabolic and taxonomic profiles of petroleum reservoirs worldwide. Analysis of 301,2 Gb of metagenomic information derived from heavily flooded petroleum reservoirs in China and Alaska to non-flooded petroleum reservoirs in Brazil enabled us to reconstruct 148 MAGs of high and medium quality. At the phylum level, 74% of MAGs belonged to bacteria and 26% to ar-chaea. The profiles of these MAGs were related to the physicochemical parameters and recovery management applied. The analysis of the potential functional core in the reservoirs showed that the microbiota was specialized for each site, with 31.7% of the total KEGG orthologies annotated as functions (1,690 genes) common to all oil fields, while 18% of the functions were site-specific, i.e., present only in one of the oil fields. The oil reservoirs with lower level of intervention were the most similar to the potential functional core, while the oil fields with longer history of water in-jection had greater variation in functional profile. These results show how key microorganisms and their functions respond to the distinct physicochemical parameters and interventions of the oil field operations such as water injection and expand the knowledge of biogeochemical trans-formations in these ecosystems.

For the purpose of clean energy hydropower development, the construction of reservoirs has been continuously promoted in the Jinsha River basin for many years, and how the reservoirs affect the water and sediment process is a very necessary topic to study. This study is based on the gauged water and sediment data (span from the 1960’s to 2020) at Shigu, Panzhihua, and Xiangjiaba stations downstream located in the trunk channel of the river, and uses Mann-Kendall trend test method and double cumulative curve method to comprehensively judge the variation trends of runoff and suspended sediment load and reveal their credible mutation years. The linear regression method is used to reveal the variation characteristics of the relationship between water and sediment before and after the abrupt change years. The results show that the variations in runoff at Shigu and Panzhihua stations have significant and relatively obvious increasing trends, respectively, and that at Panzhihua station has a mutation year of 1985. The runoff at Xiangjiaba Station slightly increased but not significantly. The variation of suspended sediment load showed a temporal and spatial differentiation. The variation of sediment discharge at Shigu Station showed an increasing trend with a mutation year of 1997. For Panzhihua Station, it showed an increasing trend before 1998, but has significantly decreased since 1998. The fluctuation of sediment transport at Xiangjiaba Station was significant before 1998, but the trend is unclear. In the period of 1998−2020, it showed a significant decreasing trend, especially since 2013, when the mean annual suspended sediment load only accounted for 0.61% of its multi-year average. The variations of mean annual sediment concentration and sediment inflow coefficient at the hydrological stations is consistent with the variation trend of sediment transport. Before 2013, the correlation between water and sediment was strong, but thereafter it was extremely weak. The two sudden years of 1998 and 2013 are consistent with the year when large reservoirs were built in the river basin. The construction of large reservoirs and their large amount of sediment retention are the key reasons for the sudden changes in the water-sediment relationship and the sharp decrease in sediment transport in the downstream reach of the reservoir dam. The climate and underlying surface changes in the study area are not significant, and their impact on the water and sediment processes in the watershed is limited.

We present a generic and open-source framework for the numerical modeling of the expected transport and storage mechanisms in unconventional gas reservoirs. These unconventional reservoirs typically contain natural fractures at multiple scales. Considering the importance of these fractures in shale gas production, we perform a rigorous study on the accuracy of different fracture models. The framework is validated against an industrial simulator and is used to perform a history-matching study on the Barnett shale. This work presents an open-source code that leverages cutting-edge numerical modeling capabilities like automatic differentiation, stochastic fracture modeling, multi-continuum modeling and other explicit and discrete fracture models. We modified the conventional mass balance equation to account for the physical mechanisms that are unique to organic-rich source rocks. Some of these include the use of an adsorption isotherm, a dynamic permeability-correction function, and an embedded discrete fracture model (EDFM) with fracture-well connectivity. We explore the accuracy of the EDFM for modeling hydraulically-fractured shale-gas wells, which could be connected to natural fractures of finite or infinite conductivity, and could deform during production. Simulation results indicates that although the EDFM provides a computationally efficient model for describing flow in natural and hydraulic fractures, it could be inaccurate under these three conditions: 1. when the fracture conductivity is very low. 2. when the fractures are not orthogonal to the underlying Cartesian grid blocks, and 3. when sharp pressure drops occur in large grid blocks with insufficient mesh refinement. Each of these results are very significant considering that most of the fluids in these ultra-low matrix permeability reservoirs get produced through the interconnected natural fractures, which are expected to have very low fracture conductivities. We also expect sharp pressure drops near the fractures in these shale gas reservoirs, and it is very unrealistic to expect the hydraulic fractures or complex fracture networks to be orthogonal to any structured grid. In conclusion, this paper presents an open-source numerical framework to facilitate the modeling of the expected physical mechanisms in shale-gas reservoirs. The code was validated against published results and a commercial simulator. We also performed a history-matching study on a naturally-fractured Barnett shale-gas well considering adsorption, gas slippage & diffusion and fracture closure as well as proppant embedment, using the framework presented. This work provides the first open-source code that can be used to facilitate the modeling and optimization of fractured shale-gas reservoirs. To provide the numerical flexibility to accurately model stochastic natural fractures that are connected to hydraulically-fractured wells, it is built atop other related open-source codes. We also present the first rigorous study on the accuracy of using EDFM to model both hydraulic fractures and natural fractures that may or may not be interconnected.

The design flood estimation should consider the regulation of upstream cascade reservoirs which has significantly altered downstream hydrologic regime. The current flood regional composition (FRC) methods do not consider the unfavorable reservoir operation conditions for flood prevention. In this paper, a novel framework, the most unfavorable flood regional composition (MUFRC) method, was proposed based on the flood risk analysis to estimate design flood in cascade reservoir operation period. The results of case study in Yalong River basin indicated that: (1) The proposed MUFRC method would allocate more flood volume into downstream uncontrolled sub-basin, and the precise definition of flood loss could make great difference on MUFRC method for rational estimation of design flood. (2) The 1000-year design flood peak, 3-day and 7-day flood volume of the outlet section estimated by MUFRC method are 15400 m3/s, 3.91, and 8.42 billion m3 respectively, which are all greater than values estimated by other FRC methods; (3) The reduction of design floods in reservoir operation period result the adjustment of flood control water level in downstream reservoirs, which could additionally generate 460 million kW·h (+1.82%) hydropower during flood season. Comparison study and sensitivity analysis further proves that the MUFRC method could rationally allocate flood volume and meanwhile balance the flood prevention risk and comprehensive utilization benefits, which is worth for further study and practical application.

Leak of carbon dioxide (CO2) from conventional underground carbon storage reservoirs is an increasing concern. It is highly desirable to inject CO2 into low-temperature reservoirs so that CO2 can be locked inside the reservoir in solid state as CO2-hydrates. Marine gas hydrate reservoirs and surrounding water aquifers are attractive candidates for this purpose. However, the nature of low-permeability of these marine sediments hinders injection of CO2 in commercial scale due to the low-injectivity of wells with conventional completions. This study investigates injection of CO2 into the low-permeability marine reservoirs using a new type of well namely radial-lateral wells (RLW). An analytical model was developed for predicting CO2 injectivity of the RLW to assess well injectivity improvement. A case study and sensitivity analysis were performed with field data from the South China Sea. Result of analysis reveals that the injectivity of the RLW is nearly proportional to reservoir permeability, lateral wellbore length, and number of laterals. CO2 injection rate is predicted to be 19 tons/day to 250 tons/day, which is 3 to 15 times higher than the injectivity of frac-packed wells. It is feasible to inject CO2 into the low-permeability-low-temperature marine reservoirs at commercial flow rates. This work provides an analytical tool to predict CO2-injectivity of RLW in low-temperature marine reservoirs for leak-free CO2 storage.

HIV-1 protease (PR) is a viral enzyme that cleaves viral polyprotein precursors to convert them into functional forms, a process essential to generate infectious viral particles. Due to its broad substrate specificity, HIV-1 PR can also cleave certain host cell proteins. Several studies have identified host cell substrates of HIV-1 PR and described the potential impact of their cleavage on HIV-1-infected cells. Of particular interest is the interaction between PR and the caspase recruitment domain-containing protein 8 (CARD8) inflammasome. While PR typically has low levels of intracellular activity prior to viral budding, induction of premature PR activation to trigger CARD8-mediated cell killing may help eliminate latent reservoirs in people living with HIV. In this review, we discuss the viral and host substrates of HIV-1 protease and highlight potential applications and advantages of targeting CARD8 sensing of HIV-1 PR.

Especially for drought periods, the higher the accuracy of reservoir inflow forecasting, the more reliable the water supply from a dam. The article focuses on probabilistic forecasting of seasonal inflow to reservoirs and determines estimates from the probabilistic seasonal inflow according to drought forecast results. The probabilistic seasonal inflow was forecasted by a copula-based Bayesian network employing a Gaussian copula function. Drought forecasting was performed by calculation of the standardized streamflow index value. The calendar year is divided into four seasons; the total inflow volume of water to a reservoir for a season is referred to as the seasonal inflow. Seasonal inflow forecasting curves conforming to drought stages produce estimates of probabilistic seasonal inflow according to the drought forecast results. The forecasted estimates of seasonal inflow were calculated by using the inflow records of Soyanggang and Andong dams in the Republic of Korea. Under the threshold probability of drought occurrence ranging from 50 to 55 %, the forecasted seasonal inflows reasonably matched critical drought records. Combining the drought forecasting with the seasonal inflow forecasting may produce reasonable estimates of drought inflow from the probabilistic forecasting of seasonal inflow to a reservoir.

Multi-step ahead streamflow forecasting is of practical interest for the operation of hydropower reservoirs. We provide generalized results on the error evolution in multi-step ahead forecasting by conducting several large-scale experiments based on simulations. We also present a multiple-case study using monthly time series of streamflow. Our findings suggest that some forecasting methods are more useful than others. However, the errors computed at each time step of a forecast horizon within a specific case study strongly depend on the case examined and can be either small or large, regardless of the forecasting method used and the time step of interest.

From the hospital wastewater, a novel bacteriophage was isolated and characterized. According to characterization properties, this bacteriophage belongs to the Siphoviridae family, the maximum bacteriophage titer was recorded at 37°C and a pH of 7.2, had a 44,789 bp linear double-strand DNA genome, and within the genome sequence, there are 61 genes, all of which are encoded into proteins. Although this bacteriophage does not have any virulence factors or antimicrobial resistance genes and had specific lytic activity against some antimicrobial resistance S. aureus clinical isolates.

Fire blight, caused by Erwinia amylovora, is a devastating bacterial disease that threatens world-wide production of apples and pears. In Canada and the US, streptomycin and kasugamycin are commonly used for the control of this pathogen. There is an urgent need for development of biocontrol agents (BCAs) that can be easily incorporated into integrated pest management pro-grams with high efficacy against streptomycin sensitive and resistant strains of E. amylovora. In addition, excessive use of antibiotics in agriculture has increased awareness of the possibility of antibiotic resistance gene transfer to human, animal and environmental microbes. To address this issue, a phage-carrier system (PCS) that combines Pantoea agglomerans as an antagonistic bacterial carrier of Erwinia phages as a double-pronged treatment for fire blight have been de-veloped. The low viability of P. agglomerans cells following spray drying challenged the industrial scale production of this PCS. In the present research, a spray drying protocol was developed for P. agglomerans by modifying the growth medium and the bacterial cell formulation using D(+)-trehalose and maltodextrin. The developed protocol is amenable to industrial scale pro-duction of the BCA/PCS. The P. agglomerans viability was greater than 90% after spray drying, had a prolonged shelf life of 4 months at 4 C, and the reconstituted cells showed an approximate 3 log reduction in E. amylovora counts with a green pear disc challenge assay.

The global health emergency caused by multi-drug resistant bacteria has led to the search for and development of new antimicrobial agents. Phage therapy is an abandoned antimicrobial therapy that has been resumed in recent years. In this study, we mutated a lysogenic phage from Acinetobacter baumannii into a lytic phage (Ab105-2phiΔCI) showing antimicrobial activity against A.baumannii clinical strains (such as Ab177_GEIH-2000 which showed MICs to meropenem and imipenem of 32 µg/ml and 16 µg/ml, respectively as well as belonging to GEIH-REIPI Spanish Multicenter A. baumannii Study II 2000/2010, Umbrella Genbank Bioproject PRJNA422585). We then enhanced the time kill curves (in vitro) and in Galleria mellonella survival assays (in vivo) antimicrobial activity of the new lytic phage by combining it with carbapenem antibiotics (meropenem and imipenem). We observed in vitro, an antimicrobial synergistic effect (from 4 log to 7 log CFU/ml) with meropenem plus lytic phage in all combinations analysed (0.1, 1 and 10 MOI of Ab105-2phiΔCI mutant as well as 1/4 and 1/8 MIC of meropenem). Moreover, we had a decrease in bacterial growth of 8 log CFU/ml for the combination of imipenem at 1/4 MIC plus lytic phage (Ab105-2phiΔCI mutant) and of 4 log CFU/ml for the combination of imipenem at 1/8 MIC plus lytic phage (Ab105-2phiΔCI mutant) in both MOI 1 and 10. These results were confirmed in in vivo (G. mellonella) obtaining a higher effectiveness in the combination of imipenem and Ab105-2phiΔCI mutant (P<0.05 by Log Rank-Matel Cox test). This approach could help to reduce the emergence of phage resistant bacteria and restore sensitivity to the antibiotics when used to combat multiresistant strains of Acinetobacter baumannii.

In contrast to lytic phages, filamentous phages are assembled in the inner membrane and secreted across the bacterial envelope without killing the host. For assembly and extrusion of the phage across the host cell wall, filamentous phages code for membrane-embedded morphogenesis proteins. In the outer membrane of E. coli, the protein gp4 forms a pore-like complex, while gp1 and gp11 form a complex in the inner membrane of the host. By comparing sequences with other filamentous phages, we identified putative Walker A and B motifs in gp1 with a conserved lysine in the Walker A motif (K14), and a glutamic and aspartic acid in the Walker B motif (D88, E89). In this work we demonstrate that both, Walker A and Walker B, are essential for phage production. The crucial role of these key residues suggest that gp1 is likely to be a molecular motor driving phage assembly. We further identified essential residues for the function of the assembly complex. Mutations in three out of six cysteine residues abolish phage production. Similarly, two out of six conserved glycine residues are crucial for gp1 function. We hypothesise that the residues represent molecular hinges allowing domain movement for nucleotide binding and phage assembly.

Microemulsions with excellent properties have shown significant potential for enhancing oil recovery from tight formations through spontaneous imbibition. This work present a high-temperature-tolerant lower-phase microemulsion (HTLP-ME) using a microemulsion dilution method. The properties and morphological characteristics of HTLP-ME were evaluated and proposed a enhanced spontaneous imbibition oil recovery mechanism using imbibition tests and CT scanning technology. The results show that the optimum concentration of HTLP-ME is 0.2wt% has a superior thermal stability, small particle size, lower IFT, good wettability alteration ability, and minimum adsorption loss. Imbibition and CT experiments showed that the longer the imbibition distance, the better is the effect on spontaneous imbibition oil recovery. Furthermore, the solubilization coefficient and self-driving force were defined and calculated to quantitatively analyze the imbibition mechanisms. The imbibition mechanisms demonstrate that the reduction of oil/solid adhesion is due to the synergistic effect of IFT reduction and wettability alteration, and the ability to increase the imbibition distance through a larger self-driving force.

Well placement optimization in a given geological setting for a fractured geothermal reservoir is a prerequisite for enhanced geothermal operations. High computational cost associated in the framework of fully coupled thermo-hydraulic-mechanical (THM) processes in a fractured reservoir simulation, makes the well positioning as a missing point in developing a field scale investigation. Here, in this study, we shed light on this topic through examining different injection-production well (doublet) position in a given real fracture network. Water and CO2 are used as working fluids for geothermal operations and importance of well positions are examined using coupled THM numerical simulations for both the fluids. Results of this study are examined through the thermal breakthrough time, mass flux and the energy extraction potential to assess the impact of well position in a two-dimensional reservoir framework. Almost ten times of the difference between the final amount of heat extraction is observed for different well position but with the same well spacing and geological characteristics. Furthermore, stress field is be a strong function of well position that is important with respect to the possibility of unwanted stress development. As part of the MEET project, this study recommends to perform similar well placement optimization study for each fracture set in a fully coupled THM manner before a field well drilling.

Abstract: Coal bed methane (CBM) reservoirs are complex systems whose properties differ from those of conventional reservoirs. Coal seams are dual-porosity systems that comprise the porosities of the matrix and cleat system. Gas in the coal seams can be stored as free gas in the cleat system and as adsorbed gas in the porous medium. The flow mechanisms of the natural gas through the formation include desorption, diffusion, and Darcy’s flow regimes. The permeability of CBM reservoirs is more sensitive to pressure variations than conventional gas reservoirs. To study the flow behavior of CBM reservoirs it is mandatory to use a model that considers their unique characteristics. The objective of this study was to propose a physical and mathematical model of production performance for horizontal wells in CBM reservoirs whose permeability is dependent on pressure. A solution for the model was obtained by applying Pedrosa´s transformation, perturbation theory, Laplace transformation, the point source method, and Sthefest´s algorithm. The solution to this problem was validated with previous work thoroughly. The type curves of the model were built and the pressure transient behavior of the model was analyzed and discussed. The effects of several parameters on pressure behavior were also discussed.

Diversity-generating retroelements (DGRs) are prokaryotic systems providing rapid modification and adaptation of target proteins. In phages, the main targets of DGRs are receptor-binding proteins that are usually parts of tail structures and the variability of such host-recognizing structures enables phage adaptation to changes on the bacterial host surface. Sometimes, more than one target gene containing a hypermutated variable repeat (VR) can be found in phage DGRs. The role of mutagenesis of two functionally different genes is unclear. In this study, several phage genomes that contain DGRs with two target genes were found in the gut virome of healthy volunteer. Bioinformatics analysis of these genes indicated that they encode proteins with different topology; however, both proteins contain the C-type lectin (C-lec) domain with a hypermutated beta-hairpin on its surface. One of the target proteins belongs to a new family of proteins with a specific topology: N-terminal C-lec domain followed by one or more immunoglobulin domains. Proteins from the new family were named tentaclins after TENTACLe+proteIN. The genes encoding such proteins were found in the genomes of prophages and phages from the gut metagenomes. We hypothesized that tentaclins are involved in binding either to bacterial receptors or intestinal/immune cells.

The phytoplankton community in 66 reservoirs ubicated at the hydrographic basin of the Ebro River (Spain) was analyzed. Samples were collected in the summer season during the period 2010-2015, with the main purpose of evaluate the Trophic State and Ecological Potential according to the Water Framework Directive of the European Union. In this work we presented a representative overview of several consecutive years of the state of the reservoirs and their associated trophic status; methodology was to obtain statistically significant relationships between the phytoplankton community and main physicochemical water quality variables (water transparency, pH, chlorophyll a, total and soluble phosphorus, anoxic zone depth, nitrite, nitrate and ammonium concentrations). We provide data for retrospective comparative of the state of the reservoirs with previous and current studies in order to improve the management of these reservoirs, and to serve as data reference for future works in a context of global change (climate and pollution).

We aimed at analyzing Chlorophyll-a and CDOM dynamics from field measurements and at assessing the potential of multispectral satellite data for retrieving water-quality parameters in three small surface reservoirs in the Brazilian semiarid region. More specifically, this work comprises i) analysis of Chl-a and trophic dynamics; ii) characterization of CDOM; iii) estimation of Chl-a and CDOM from OLI/Landsat-8 and RapidEye imagery. The monitoring lasted 20 months within a multi-year drought, which contributed to water-quality deterioration. Chl-a and trophic state analysis showed a highly eutrophic status for the perennial reservoir during the entire study period, while the non-perennial reservoirs ranged from oligotrophic to eutrophic, with changes associated with the first events of the rainy season. CDOM characterization suggests that the perennial reservoir is mostly influenced by autochthonous sources, while allochthonous sources dominate the non-perennial ones. Spectral-group classification assigned the perennial as CDOM-moderate and highly eutrophic reservoir, whereas the non-perennial ones were assigned as CDOM-rich and oligotrophic-dystrophic reservoirs. The remote sensing initiative was partially successful: the Chl-a was best modelled using RapidEye for the perennial; whereas CDOM performed best with Landsat-8 for non-perennial reservoirs. This investigation showed high potential for retrieving water quality parameters in dry areas with small reservoirs.

The microscopic pore structure of tight sandstone reservoir significantly influences the characteris-tics of CO2 flooding after water flooding. The research was conducted using various techniques such as casting thin sections, high pressure mercury injection, scanning electron microscopy, Nu-clear magnetic resonance (NMR) testing, and a self-designed high-temperatures and high-pressures microscopic visualization displacement system. Three type cores with different pore structures were selected for the flooding experiments and the microscopic visualization displace-ment experiments, including CO2 immiscible flooding, near-miscible flooding, and miscible flood-ing after the conventional water flooding. The characteristics of CO2 flooding and the residual oil distribution after water flooding were quantitatively analyzed and evaluated. The results show that: (1) During the water flooding process, the oil produced from type I and type III samples mainly comes from large and some medium pores. Oil utilization of all pores is significant for type II samples. The physical properties and pore types have a greater impact on water flooding. Type I and II samples are more suitable for near-miscible flooding after water flooding. Type III samples are more suitable for miscible flooding after water flooding. (2) In the CO2 flooding, oil recovery increases gradually with increasing pressure for all three types of samples. Type II core samples have the highest recovery. Before miscibility, the oil recovered from type I and type II samples was primarily from large pores, however, the oil recovery mainly comes from medium pores when reaching miscibility. As for the type III samples, the oil produced in the immiscible state mainly comes from large and medium pores, and the enhanced oil recovery mainly comes from medium and small pores after reaching the near-miscible phase. (3) It can be seen from the microscopic re-sidual oil distribution that oil recovery will increase as the petrophysical properties of the rock model improve. The oil recovery of near-miscible flooding after water flooding regarding the type II model is up to 68.11%. The oil recovery of miscible flooding after water flooding about type III model is the highest at 74.57%. With increasing pressure, the proportion of flake residual oil grad-ually decreases, while the proportion of droplet-like and film-like residual oil gradually increases. Type II samples have a relatively large percentage of reticulated residual oil in the near-miscible stage.

In this work, we analyzed non-Darcy two-component single-phase isothermal flow in naturally fractured tight gas reservoirs for enhanced gas recovery (EGR) and carbon dioxide storage as a possible application. We used the Peng-Robinson equation of state to evaluate the thermodynamic properties of the components, and we performed the discretization of the governing partial differential equations using the Finite Volume Method. This process leads to two subsystems of algebraic equations, which, after linearization and use of an operator splitting method, are solved by the Conjugate Gradient (CG) and Biconjugate Gradient Stabilized (BiCGSTAB) methods for determining the pressure and fraction molar, respectively. We include inertial effects using the Barree and Conway model, gas slippage via a more recent model than Klinkenberg’s and we use a simplified model for the effects of effective stress. We also utilize a mesh refinement technique to represent the discrete fractures. Finally, we implemented simulations to show the influence of inertial, slippage and stress effects on production in fractured tight gas reservoirs.

A single geological carbon dioxide (CO2) storage within salinity aquifer as a paramount stratagem in the context of forthcoming CO2 sequestration initiatives. Within the expansive tapestry of terrestrial salinity aquifers in China, replete with nuances in mineral composition and structural diversity, a paradigm distinct from the marine sedimentary basins of North America, a labyrinthine stratigraphic environment of elevated complexity unfolds. Consequently, conspicuous lacunae and insufficiencies manifest within the existing knowledge reservoir pertaining to CO2-water-rock (mineral) reaction mechanisms. Notably, a conspicuous dearth of insights prevails concerning the dissolution kinetics inherent to individual minerals embroiled in these reactions. The present investigation undertakes a scrupulous exploration into the dissolution and erosive processes manifest within four emblematic terrestrial minerals in conjunction with CO2. Furthermore, the study meticulously scrutinizes the evolution of ionic composition and pH within the formation water throughout the trajectory of the geochemical reactions. To accomplish this, a simulation apparatus is configured to emulate conditions germane to temperature, pressure, and mineralization characteristics characteristic of a prototypical salinity aquifer reminiscent of the Daqing oilfield in China. The findings that emerge from this scrutiny reveal that the erosive action of CO2 fluid begets varying degrees of dissolution within the four minerals under investigation. Moreover, our meticulous inquiry lays bare that, in the terminal phases of the reaction process, feldspar precipitates secondary minerals, characterized primarily by dawsonite, in response to the aquatic milieu typifying the profound salinity stratum of terrestrial sedimentation. This milieu is notably enriched with Na+ ions and NaHCO3. This phenomenon suggests that feldspar, under these specific conditions, assumes the mantle of a mineral amenable to carbon sequestration, thus enriching the reservoir for CO2 mineralization within the salinity stratum of terrestrial sedimentation.

Here are analysed data taken in two hydrocarbon fields ("A" and "B"), located in the western part of Sava Depression (North Croatia). They are in the secondary phase of production. The selected reservoirs "L" (in the “A” Field) and "K" (“B”) are of the Lower Pontian (Upper Miocene) age and belong to Kloštar-Ivanić Formation. Due to strong tectonics, there are numerous tectonic block, relatively rarely sampled with well and laboratory tests. Here are selected two variables for interpolation - reservoirs permeabilities and the injected volumes of field water. The following interpolation methods are described, compared and applied: Nearest Neighbourhood, Natural Neighbour (the first time in the Sava Depression) and Inverse Distance Weighting. The last one has been proven as the most appropriate for datasets with size lower than 20 points.

The gas-water relative permeability curve plays a crucial role in reservoir simulation and development for condensate gas reservoirs. In this study, we conducted a series of high temperature and high pressure analysis experiments on real gas cores from Wells A and B in Block L of the Yinggehai Basin to investigate the effects of temperature, pressure, and different types of gas media on gas-water seepage. The experimental results demonstrate that: Temperature has a significant impact on both gas and water relative permeability, particularly on the former. As temperature increases, gas relative permeability shows a substantial increase while water relative permeability remains relatively unchanged. Under the same effective stress, increasing pressure causes downward shifts in both the gas and water relative permeability curves; however, there is a more pronounced decrease in gas relative permeability. Gas type has minimal influence on phase permeability except at higher water saturation where differences become apparent. When water saturation ranges from 80% to 50%, there is no significant variation observed in the measured relative permeability of different displacement gases; however, as water saturation exceeds 80%, distinctions gradually emerge. At bound water saturation conditions, nitrogen exhibits lower relative permeability compared to simulated gases with approximately 92% similarity between them. This investigation into the characteristics of gas-water relative permeability in high temperature and high pressure condensate reservoirs within Yinggehai Basin provides valuable insights for efficient development strategies for similar reservoirs.

Coal permeability data are critical in the prevention and control of coal and gas outbursts in mines and are an important reservoir parameter for the development of coalbed methane. The mechanism by which permeability is affected by gas pressure is complex. We used a self-developed true triaxial seepage experimental device that collects lignite and anthracite coal samples, sets fixed axial pressure and confining pressure, and changes gas pressure by changing the orientation of the coal seam to study the influence of the gas pressure on the permeability of the coal seam under the conditions of different coal types and different bedding orientations. Coal permeability decreased rapidly and then decreased slowly and tended to be stable with the increase in gas pressure. This conforms to the power exponential fitting relationship, and the fitting degree reaches more than 99%. The permeabilities of lignite and anthracite were basically the same under various pressure conditions, indicating that the influence of coal type on coal permeability was not significant. The comparison of the two anthracite coal samples showed that the sample's permeability with a bedding plane vertical to the seepage direction was significantly lower than that of the bedding plane parallel to the seepage direction, indicating that gas seeped more easily along the bedding. The sensitivity coefficient of permeability with the change in gas pressure was calculated. The analysis showed that coal permeability was sensitive to changes in gas pressure during the low-pressure stage. When the gas pressure was greater than 0.8 MPa, the sensitivity coefficient was significantly reduced, which may be related to the slow increase in the amount of gas absorbed by the coal seam in the high-pressure stage. A theoretical calculation model of coal seam permeability considering adsorption/desorption and seepage effects was proposed and then verified with experimental results showing that the theoretical model better reflected the permeability characteristics of coal and predicted its permeability. Using the finite element simulation software COMSOL, the extraction efficiency of the coal seam gas under different gas pressure conditions was simulated. The results showed that with an increase in gas pressure, coal permeability and extraction efficiency decreased. In the low-pressure stage, the reduction in the extraction efficiency was more obvious than that in the high-pressure stage.

Buruli ulcer (BU), caused by Mycobacterium ulcerans, is a neglected tropical disease associated with freshwater habitats. A variety of limnic organisms harbor this pathogen, including aquatic bugs (Hemiptera: Heteroptera), which have been hypothesized to be epidemiologically important reservoirs. Aquatic Hemiptera exhibit high levels of diversity in the tropics, but species identification remains challenging. In this study, we collected aquatic bugs from emerging foci of BU in the Southwest Region of Cameroon, which were identified using morphological and molecular methods. The bugs were screened for mycobacterial DNA and a selection of 20 mycobacteria-positive specimens from the families Gerridae and Veliidae were subjected to next-generation sequencing. Only one individual revealed putative M. ulcerans DNA, but all specimens contained sequences from the widespread alpha-proteobacterial symbiont, Wolbachia. Phylogenetic analysis placed the Wolbachia sequences into supergroups A, B and F. Circularized mitogenomes were obtained for seven gerrids and two veliids, the first from these families for the African continent. This study suggests that aquatic Hemiptera may have a minor role (if any) in the spread of BU in Southwest Cameroon. Our metagenomic analysis provides new insights into the incursion of Wolbachia into aquatic environments and generates valuable resources to aid molecular taxonomic studies of aquatic Hemiptera.

Smear-ripened cheeses host complex microbial communities that play a crucial role in the ripening process. Although bacteriophages have been frequently isolated from dairy products, their diversity and ecological role in such type of cheese remain underexplored. In order to fill this gap, the main objective of this study was to isolate and characterize bacteriophages from the rind of a smear-ripened cheese. Thus, viral particles extracted from cheese rind were tested against a collection of bacterial isolates through a spot assay. In total, five virulent bacteriophages infecting Brevibacterium aurantiacum, Glutamicibacter arilaitensis, Leuconostoc falkenbergense and Psychrobacter aquimaris species were obtained. All exhibit a narrow host range, being only able to infect a few cheese-rind isolates within the same species. The complete genome of each phage was sequenced using both Nanopore and Illumina technologies, assembled and annotated. Sequence comparison with known phages revealed that four of them may represent at least new genera. The distribution of the five virulent phages into the dairy-plant environment was also investigated by PCR and three potential reservoirs were identified. This work provides new knowledge on the cheese rind viral community and an overview of the distribution of phages within a cheese factory.

The paper investigates the possible use of a low strength domestic sand (D) (up to today useless – not considered as proppant source) of small particle sizes, instead to that of high strength imported commercial sand (C), as a prospective micro-proppant for low permeability reservoirs in Poland. There is need to develop national unconventional gas resources like tight gas, shale gas and coalbed methane. An important energy source of value and readily available in Poland is coal. The basins of this resource are large and bears low permeability coalbed methane reservoirs which needs to be developed to contribute to the energy security, economy and environmental needs of the country. These reservoirs need technological assistance such as hydraulic fracturing which makes use of proppants for development. Most of the commonly used proppants over the years for fracturing have been large grain size commercial proppants of high strength material content bought abroad. Investigated finer proppants are known to have the ability to penetrate narrow fracture networks to ensure effective high reservoir volume and conductivity for production. Results from presented laboratory research shows the D - proppant, which is cheaper and readily available, has the 3K class with low settling rates as a potential micro-proppant for effective transportation, enhancement of conductivity and production rate in the narrow fractures of low permeability reservoirs. Future using of domestic proppant will decrease stimulation cost and will have positive impact on the environment due to omitting long distance transportation from abroad.

The Oil reservoirs with low permeability account for a large proportion in the world, they surpass half of the total number of the oil reservoirs in China, it is important to exploit this kind of reservoir effectively. The exploitive results of these reservoir using normal water flooding methods are very poor because of the thine pores, bad connections and so on. However, these problems can be well solved by applying gas injection techniques. In this paper, the effects on the recovery effects exerted by the injection parameters such as the oxygen content in the injected air, the injection speed etc. were studied by several experiments using independently designed equipments aiming at one low permeable sandstone reservoir in China. Several conclusions were made from the experiment results: the best recovery effects can be achieved by injecting the oxygen reduced air with 8% of oxygen at the speed of 0.3ml/min (7.41×10-4PV/min) using the methods of injecting the air slugs and the foaming agent slugs alternately; the best oxidation time of the oil was 168 hours and the final oil recovery could be enhanced by 26.5% in this method. It was also showed by the experiments that the larger the permeability ratio is, the larger the recovery factor will be increased. At last, several equations about relationships between the EOR and the air injection parameters were revealed according to the results of the experiments which may offer some references to the LTO process mechanisms study in the similar oil reservoir.

Mesozoic-Palaeozoic marine carbonate rocks are important hydrocarbon reservoirs in the Central Uplift area of the South Yellow Sea Basin (SYSB). Due to the lack of boreholes and the great heterogeneity of carbonate reservoirs, the distribution of porous carbonate reservoirs and their related key controlling factors remain unclear. Based on seismic inversion and isotope analysis, this study explores the factors affecting the distribution of porous Carboniferous-Early Permian carbonate reservoirs in the SYSB. In this study, the log-seismic characteristics of porous carbonate reservoirs, sensitive lithology parameters, and physical property parameters are extracted and analyzed. The pre-stack simultaneous inversion technique is applied to predict the lithology properties and physical properties of the porous carbonate reservoirs. Moreover, the sedimentary of carbonate is analyzed using isotopes of carbon, oxygen, and strontium. The results indicate that porous carbonate reservoirs with porosities of 3%~5% mainly occur at the paleo-highland (Huanglong Formation and Chuanshan Formation) and the slope of paleo-highland (Hezhou Formation). The porous carbonate reservoirs of the Qixia Formation are only locally developed. In addition, the study area was dominated by a warm and humid tropical climate from the Carboniferous to Early Permian, with four sea-level eustatic fluctuation indicated by the negative and positive δ13C excursions. When the sea level fell, the study area was exposed and denuded, and the supply of terrigenous detrital was dominated, which significantly influenced the carbonate deposit and diagenesis. This study highlights that sedimentation was a key factor in controlling the quality of Carboniferous-Early Permian carbonate reservoirs. The methods proposed in this study can be used in other carbonate-dominated strata worldwide.

The Burkholderia cepacia complex (Bcc) are a group of increasingly multi-drug resistant opportunistic bacteria that can cause severe pulmonary infections. This resistance is driven through a combination of intrinsic factors and the carriage of a broad range of conjugative plasmids harbouring virulence determinants. Therefore, novel treatments are required to not only treat Bcc infection but also to prevent further spread of these virulence determinants. In the search for phages infective for two clinical Bcc isolates, CSP1 phage, a PRD1-like phage was isolated. CSP1 phage was found to require pilus machinery commonly encoded on conjugative plasmids to facilitate infection of multiple Gram-negative bacteria genera including Escherichia and Pseudomonas. Whole genome sequencing and characterisation of one of the clinical Burkholderia isolates revealed it to be Burkholderia contaminans. B. contaminans 5080 was found to contain a genome of over 8 Mbp encoding multiple intrinsic resistance factors, such as efflux pump systems, but more interestingly, carried three novel plasmids encoding multiple putative virulence factors for increased host fitness, including antimicrobial resistance. Even though PRD1-like phages are broad host range, their use in novel antimicrobial treatments shouldn’t be dismissed, as the dissemination potential of conjugative plasmids is extensive. Continued survey of clinical bacterial strains is

The development of antibody therapies against SARS-CoV-2 remains a challenging task during the ongoing COVID-19 pandemic. All approved therapeutic antibodies are directed against the receptor binding domain (RBD) of Spike and lost neutralization efficacy against continuously emerging SARS-CoV-2 variants, which especially mutate in the RBD region. Previously, phage display has been used to identify epitopes of antibody responses against several diseases. Such epitopes have been applied to design vaccines or neutralizing antibodies. Here, we constructed an ORFeome phage display library for the SARS-CoV-2 genome. Open reading frames (ORFs) representing the SARS-CoV-2 genome were displayed on the surface of phage particles in order to identify enriched immunogenic epitopes from COVID-19 patients. Library quality was assessed by both, NGS and epitope mapping of a monoclonal antibody with known binding site. The most prominent epitope captured represented parts of Spike´s fusion peptide (FP). It is associated with the cell entry mechanism of SARS-CoV-2 into the host cell and the serine protease TMPRSS2 cleaves Spike within this sequence. Blocking of this mechanism could be a potential target for non-RBD binding therapeutic anti-SARS-CoV-2 antibodies. As mutations within the FP amino acid sequence were rather rare among SARS-CoV-2 variants so far, this may be an advantage in the fight against future virus variants.

Cholera is an acute enteric infectious disease caused by the Gram-negative bacterium Vibrio Cholerae. Despite a huge body of research, the precise nature of its transmission dynamics has yet to be fully elucidated. Mathematical models can be useful to better understand how an infectious agent can spread and be properly controlled. We develop a compartmental model describing a Human population, a bacterial population as well as a phage population. We show that there might be eight equilibrium points; one of which is a disease free equilibrium point. We carry out numerical simulations and sensitivity analyses and we show that the presence of phage can reduce the number of infectious individuals. Moreover, we discuss the main implications in terms of public health management and control strategies.

In order to understand the impact of lithologic heterogeneity of continental mixed fine-grained sedimentary rocks on reservoir brittleness in western Qaidam basin, the mechanical properties of the rocks and their correlation with mineral composition and petrographic characteristics were studied by measns of mineralogy, petrography and triaxial stress test. The results show that the reservoir rocks can be divided into 5 different types according to the mechanical properties of the reservoir (characteristics of stress-strain curves), among them Type I and III belong to similar elastoplastic failure model, type II shows a special pulse failure mode for plastic material, type IV shows a failure mode of mixed characteristics, and type V exhibits a typical plastic failure model. The correlation between minerals and mechanical properties indicates that quartz and feldspar, which are often considered brittle minerals, do not contribute much to the brittleness of continental fine-grained sedimentary rocks. The main minerals affecting reservoir brittleness are dolomite and clay minerals, and their contributions to reservoir brittleness are positive and negative, respectively. The petrographic analysis results prove that the abnormal correlation between rock mechanical properties and quartz and feldspar is caused by the different rock fabrics. When dolomite forms a rock skeleton, it typically exhibits greater strength, brittleness and physical properties than other minerals. Based on the results, a brittleness evaluation standard for continental fine-grained sedimentary rock reservoir is proposed, and the validity of the standard is verified by the spatial correlation between the lithology probability model and the micro-seismic monitoring data, indicating that the spatial heterogeneity of dolomite-rich rock is the main controlling factor for the development of ‘sweet spot’ in the Cenozoic continental fine-grained sedimentary rock reservoir in the Western Qaidam Basin.

Interpolation is procedure that depends on spatial and/or statistical properties of analysed variable(s). It is special challenging task for data that included low number of samples, like dataset with less than 20 data. This problem is especially emphasized in the subsurface geological mapping, i.e. in the cases where data are taken solely from wells. Successful solutions of such mapping problems ask for knowledge about interpolation methods designed primarily for small datasets and dataset itself. Here are compared two methods, namely Inverse Distance Weighting and Modified Shepard’s Method, applied for three variables (porosity, permeability, thickness) measured in the Neogene sandstone hydrocarbon reservoirs (Northern Croatia). The results showed that pure cross-validation is not enough condition for appropriate map selection, but also geometrical features need to be considered, for datasets with less than 20 points.

Pollution of sub-surface water reservoirs mainly rivers and streams through contaminated water point sources (CWPS) was studied. The objective was to formulate a discrete time delay mathematical model which describes the dynamics of reservoir pollution using mixing-problem processes that involve single species contaminants such as nitrates, phosphorous and detergents. The concentration of pollutants was expressed as a function of the inflow and outflow rates using the principle for the conservation of mass. Systems of ODEs generated from principles of mixing problems were refined into a system of DDEs so that the concentration of pollutant leaving the reservoir at time would be determined at some earlier instant, for the delay. The formulated model is a mathematical discrete time delay model which would be used to describe the dynamics of sub-surface water reservoir pollution. The results from the validation of the model were analyzed to determine how time delays in the mixing processes affect the rate of particle movement in water reservoirs.

This study presents a numerical analysis of rock deformation and damage behaviors induced by dynamic loadings, specifically focusing on the fracturing of tight oil reservoirs. An elastoplastic model based on finite element methods was utilized to simulate the effects of varying loading and perforation parameters. Three distinct scenarios were modeled: a single perforation, boundary loading on three sides, and multiple perforations, each providing unique insights into the mechanical responses of the rock material. The analysis revealed that dynamic effects are highly localized around perforations and loaded boundaries across all scenarios. Acceleration magnitudes are captured with rapid attenuation observed as the distance from the perforation increased. This indicated that the highest stress concentrations and deformation occurred close to the points of loading or perforation. Strain rate analysis in the x direction showed significant fluctuations near the perforations, reflecting intense stress redistributions and compressive deformation, especially prominent in the scenario with multiple perforations. Plastic strain, representing irreversible damage, was found to concentrate near perforation tips and loaded boundaries. However, the pattern of plastic strain accumulation varied: in the small domain scenario with boundary loading, plastic strain did not immediately accumulate next to the loading boundary, whereas in scenarios with single and multiple perforations, damage developed from the loading boundaries. These findings highlight the need for precise control in perforation and dynamic loading processes to manage stress and deformation effectively. It is concluded that optimizing perforation patterns and loading strategies can enhance reservoir stimulation efficiency while minimizing unintended damage to the surrounding formation.

Staphylococcal bacteriophages of Kayvirus genus are candidates for therapeutic applications. One of their proteins, Tgl, is slightly similar to staphylococcal virulence factors, secreted autolysins of lytic transglycosylase motifs, IsaA and SceD. We show that Tgl is also a lytic enzyme secreted by bacterial transport system and localizes to cell peripheries, like IsaA and SceD. It caused lysis of E. coli cells expressing the cloned tgl gene, but could be overproduced when depleted of signal peptide. S. aureus cells producing Tgl lysed in the presence of nisin, which mimics the action of phage holin. In vitro, Tgl protein was able to destruct S. aureus cell walls. The production of Tgl decreased S. aureus tolerance to vancomycin, unlike the production of SceD, which is associated with the decreased sensitivity to vancomycin. In the genomes of kayviruses, the tgl gene is located a few genes away from gene lysK, encoding the major endolysin. While lysK is a late phage gene, tgl can be transcribed by a host RNA polymerase, as are phage early genes. Taken together our data indicate that tgl is a part of kayviruses lytic module and encodes an additional endolysin which can act in concert with LysK in cell lysis.

Geothermal energy aims at harnessing the heat of the Earth to produce energy, from the near-surface to great depths. Emphasis is put on geothermal reservoirs in crystalline rocks, hence vol-canic islands and crystalline basements of sedimentary basins based on three examples world-wide. Hot brines circulate in those rocks and are responsible for their hydrothermal alteration because of fluid-rock interactions. This includes dissolution of preexisting minerals and crystal-lization of newly formed ones which provide many information of crucial importance for a better exploration of those reservoirs. For example, the crystallization of clay minerals results from the dissolution of preexisting minerals (feldspar and ferro-magnesian minerals in plutonic, volcanic or metamorphic rocks) or from the direct precipitation from geothermal brines, in specific condi-tions. Clay minerals are found in both the geothermal reservoirs and in the clay-cap found above them. Other newly formed minerals such as quartz, carbonates or sulfates have also recorded the conditions of temperature and salinity encountered by fossil reservoirs which can be evaluated thanks to the study of fluid inclusions trapped during their crystallization. This paper presents results from several geothermal deep sites and surface analogues to pinpoint the role played by newly-formed minerals in the characterization of geothermal reservoirs and their cap-rock.

Brine-dependent recovery process has seen much global research efforts in the past two decades because of their benefits over other oil recovery methods. The process involves the tweaking of the ionic composition and strength of the injected water to improve oil production. In recent years, several studies ranging from laboratory coreflood experiments by many researchers to field trials by several companies admit to the potential of recovering additional oil in sandstone and carbonate reservoirs. Sandstone and carbonate rocks are composed of completely different minerals, with varying degree of complexity and heterogeneity, but wettability alteration has been widely considered as the consequence rather than the cause of brine-dependent recovery. However, there is no consensus on the cause as several mechanisms have been proposed to relate the wettability changes to the improved recovery. This review paper aims to provide a state-of-the-art development in published research and various efforts of the industry. This review outlines an overview of laboratory and field observations, descriptions of underlying mechanisms and their validity, the complexity of the oil-brine-rock interactions, modelling works, and comparison between sandstone and carbonate rocks. The provided information is intended to provide the reader with up-to-date information, point to relevant studies for those who are new and those implementing either laboratory- or field-scale projects to speed up the process of further investigations in this research area. Overall, the outcome of this review would potentially be of immense benefit to the oil industry.

The power generation from hydroelectric plants has increased worldwide, contributing to the participation of the renewable sources to the energy matrix. In the semiarid Brazilian Northeast (NEB), thousands of small dams have been built over time as a solution for water supply. Although incompatible with hydropower generation due to the conflict with human water supply in the region, small reservoirs accumulate water and hydraulic energy at high altitudes. In this work, simulations were performed to assess how the arrangement of various sized reservoirs impact the power demand for water distribution in the Banabuiú River Basin – BRB (19,800 km²), Brazil. The power required to pump water from all 1,405 reservoirs to the districts is 6.5 GWh/year, whereas in the scenario with the 12 larger strategic reservoirs only, the power demand reaches 45.3 GWh/year. Although representing roughly 60% of the water availability of the BRB and being able to supply all the districts, the Arrojado Lisboa reservoir alone would demand 195 GWh/year to supply water to the entire basin, i.e. 30 times the power required in the real reservoir arrangement. By storing water at high altitudes and distributing it spatially, the small reservoirs increase the energy efficiency on the water distribution system.

Antimicrobial resistance is a major public health concern. Rodents and shrews live in closer proximity to humans and animals and serve as reservoirs for the transmission of several diseases, including AMR pathogens. There is no data available from India on surveillance of AMR bacteria in rodents and shrews. In this study, bacterial pathogens viz, Staphylococcus sp, Escherichia coli and Salmonella sp were isolated from rodents and shrews and genetic elements conferring antimicrobial resistance in the pathogens were screened by PCR. Bacterial pathogens in the oropharyngeal and anal swabs collected from the rodents and shrews trapped (n=100) were cultured on selective media such as Mannitol salt, Mac Conkey and Xylose lysine deoxycholate media to isolate Staphylococcus sp., E. coli and Salmonella sp. respectively. A total of 76 (80%) S. aureus and 19 (20%) Staphylococcus non aureus were isolated. E. coli was isolated in 89 samples and among the Salmonella sp (n=59), 16 (27%) were S. enteritidis and 29 (49.1%) were S. typhimurium. In S. aureus isolates, mec A and mec C (MRSA) were detected in 40 (52.6%) and 6 (7.9%) isolates respectively. Also, 7 (36.84%) and 1 (5.3%) Staphylococcus non aureus isolates were tested to harbour mec A and mec C genes. A total of 77 (86.5%) E. coli isolates had genes encoding ESBL [TEM in 21 (23.59%), SHV in 45 (50.6%) and CTXM in 11 (12.4%)]. Among the 45 pathogenic Salmonella sp, 44 (97.78%) harboured AMR genes [tet in 13 (28.9%), sul3 & sul4 in 20 (44.4%) and qnrA in 11 (24.4%)]. Thirty-eight animals harboured more than one zoonotic pathogen and 21 with multi-drug resistant genes. Our findings signify that these rodents and shrews may serve as sentinels to screen environment spillover of AMR pathogens and also act as reservoir to transmit MRSA, ESBL, Salmonella sp. human/animals. Also these animals aid in the transfer of antimicrobial resistance genetic elements to non-pathogenic organisms.

The model of T4 phage, Lambda phage and Escherichia coli is often used in research on virus-host interactions. This paper reports for the first time the thermodynamic driving force of biosynthesis, catabolism and metabolism for the three organisms, on the M9 medium. Moreover, the influence of activities of nutrients and metabolic products is analyzed. All three organisms were found to have very similar Gibbs energies of metabolism. Moreover, since they share the same catabolism, their Gibbs energies of catabolism are identical. However, Gibbs energies of biosynthesis differ. The calculated thermodynamic properties have been used to explain the coexistence of both bacteria and phages in a dynamic equilibrium in natural ecosystems.

During the development of horizontal wells in bottom water reservoirs, the strong heterogeneity of reservoir permeability leads to premature bottom water breakthrough at locations with high permeability in the horizontal wellbore, and the water content rises rapidly, which seriously affects production. In order to cope with this problem, a new technology has emerged in recent years that utilizes gravel filling to block the flow in the annulus between the horizontal well and the borehole, and utilizes the Inflow Control Device (ICD) completion tool to carry out segmental water control in horizontal wells. Unlike conventional horizontal well ICD completions that use packers for segmentation, gravel pack combined with ICD completions breaks the original seg-mentation routine and increases the complexity of production dynamic simulation. In this paper, the flow in different spatial dimensions such as reservoir, gravel packed layer, ICD completion section and horizontal wellbore is modeled separately, and the annular pressure at different locations is used as the solution variable for the coupled solution, which realizes the prediction of oil production, water production and water content of gravel pack combined with ICD completions of horizontal wells. The model was used to calculate the effects of different crude oil viscosities, different reservoir permeabilities, different permeabilities of gravel packed layers, and different development stages on the water control effects of gravel pack combined ICD completions and conventional ICD completions at field conditions. This study provides a basis for using gravel pack combined ICD completions in horizontal wells in bottom water reservoirs.

Leptospirosis is a zoonosis with global public health impact, particularly in poor socio-economic settings of tropical regions. Transmitted through urine-contaminated water or soil from rodents, dogs, and livestock, leptospirosis causes over a million clinical cases annually. Risk factors include outdoor activities, livestock production, and substandard housing that foster high densities of animal reservoirs. This One Health study in southern Chile examined Leptospira serological evi-dence of exposure people from urban slums, semi-rural, and farm settings, using the Extreme Gradient Boosting algorithm to identify key influencing factors. In urban slums, age, shrub terrain, distance to Leptospira-positive households, and neighborhood housing density were contributing factors. Human exposure in semi-rural communities was linked to environmental factors (tree, shrub, and lower vegetation terrain) and animal variables (Leptospira-positive dogs and rodents, and proximity to Leptospira-positive households). On farms, dog counts, animal Leptospira preva-lence, and proximity to Leptospira-contaminated water samples were significant drivers. The study underscores that disease dynamics vary across landscapes, with distinct drivers in each community setting. This case study demonstrates how the integration of machine learning with comprehensive cross-sectional epidemiological and geospatial data provides valuable insights into leptospirosis eco-epidemiology. These insights are crucial for informing targeted public health strategies and for generating hypotheses for future research.

Infill drilling is one of the most effective methods to improve the performance of poly-mer flooding. The difficulties related to infill drilling are determining the optimal numbers and placements of infill wells. In this study, an improved archimedes optimization algorithm with Halton sequence (HS-AOA) was proposed to overcome the aforementioned difficulties. First, to optimize the infill well placement for polymer flooding, an objective function that considered the economic influence of infill drilling was developed. Then, the novel optimization algorithm (HS-AOA) for infill well placement was developed by combining the AOA with the Halton se-quence. The codes were developed in MATLAB and connected to a commercial reservoir simula-tor CMG STARS to carry out the infill well placement optimization. Finally, the HS-AOA was compared to the basic AOA to confirm its reliability and then used to optimize the infill well placements for polymer flooding in a typical offshore oil reservoir. The results showed that the introduction of the Halton sequence into AOA effectively increased the diversity of the initial ob-jects in the AOA and avoided the HS-AOA trapping into the local optimal solutions. The HS–AOA outperformed the AOA. It was an effective approach to optimize the infill well placement for polymer flooding processes. In addition, infill drilling could effectively and economically im-prove the polymer flooding performance in offshore oil reservoirs. The NPV of the polymer flooding case with infill wells determined by HS-AOA reached 3.5 × 108 $, which was an increase of 7% over that of the polymer flooding case. This study presents an effective method for opti-mizing infill well placement for polymer flooding processes. It also can serve as a valuable refer-ence for other optimization problems in the petroleum industry, such as joint optimization of well control and placement.

In deep geological analysis of data, these are input data that are few and include a small set of data. In a small set of case data, it is necessary to obtain reliable data of individual geological variables from this type of data. The paper analyzes the possibility of applying the bootstrap method on variables that are important in the exploration and production of hydrocarbons. The variables analyzed were the following: porosity and total costs of disposal formation water. The case study was made on the data of reservoir "K", field "B" located in the western part of the Sava Depression. The analysis of the results showed the possibility of applying the bootstrap method in the analysis of deep geological data with the application of three different sizes of resampling dataset.