Metagenomic profiling of antibiotic resistance genes in Red Sea brine pools.

Antibiotic resistance (AR) is an alarming global health concern, causing an annual death rate of more than 35,000 deaths in the US. AR is a natural phenomenon, reported in several pristine environments. In this study, we report AR in pristine Red Sea deep brine pools. Antimicrobial resistance genes (ARGs) were detected for several drug classes with tetracycline and macrolide resistance being the most abundant. As expected, ARGs abundance increased in accordance with the level of human impact with pristine Red Sea samples having the lowest mean ARG level followed by estuary samples, while activated sludge samples showed a significantly higher ARG level. ARG hierarchical clustering grouped drug classes for which resistance was detected in Atlantis II Deep brine pool independent of the rest of the samples. ARG abundance was significantly lower in the Discovery Deep brine pool. A correlation between integrons and ARGs abundance in brine pristine samples could be detected, while insertion sequences and plasmids showed a correlation with ARGs abundance in human-impacted samples not seen in brine pristine samples. This suggests different roles of distinct mobile genetic elements (MGEs) in ARG distribution in pristine versus human-impacted sites. Additionally, we showed the presence of mobile antibiotic resistance genes in the Atlantis II brine pool as evidenced by the co-existence of integrases and plasmid replication proteins on the same contigs harboring predicted multidrug-resistant efflux pumps. This study addresses the role of non-pathogenic environmental bacteria as a silent reservoir for ARGs, and the possible horizontal gene transfer mechanism mediating ARG acquisition.

IntFOLD: an integrated web resource for high performance protein structure and function prediction.

The IntFOLD server provides a unified resource for the automated prediction of: protein tertiary structures with built-in estimates of model accuracy (EMA), protein structural domain boundaries, natively unstructured or disordered regions in proteins, and protein-ligand interactions. The component methods have been independently evaluated via the successive blind CASP experiments and the continual CAMEO benchmarking project. The IntFOLD server has established its ranking as one of the best performing publicly available servers, based on independent official evaluation metrics. Here, we describe significant updates to the server back end, where we have focused on performance improvements in tertiary structure predictions, in terms of global 3D model quality and accuracy self-estimates (ASE), which we achieve using our newly improved ModFOLD7_rank algorithm. We also report on various upgrades to the front end including: a streamlined submission process, enhanced visualization of models, new confidence scores for ranking, and links for accessing all annotated model data. Furthermore, we now include an option for users to submit selected models for further refinement via convenient push buttons. The IntFOLD server is freely available at: http://www.reading.ac.uk/bioinf/IntFOLD/.

Estimation of model accuracy in CASP13.

Methods to reliably estimate the accuracy of 3D models of proteins are both a fundamental part of most protein folding pipelines and important for reliable identification of the best models when multiple pipelines are used. Here, we describe the progress made from CASP12 to CASP13 in the field of estimation of model accuracy (EMA) as seen from the progress of the most successful methods in CASP13. We show small but clear progress, that is, several methods perform better than the best methods from CASP12 when tested on CASP13 EMA targets. Some progress is driven by applying deep learning and residue-residue contacts to model accuracy prediction. We show that the best EMA methods select better models than the best servers in CASP13, but that there exists a great potential to improve this further. Also, according to the evaluation criteria based on local similarities, such as lDDT and CAD, it is now clear that single model accuracy methods perform relatively better than consensus-based methods.

A Multi-crosslinking Nanocapsule-Based Serial-Stimuli-Responsive Leakage-Free Drug-Delivery System In Vitro.

As some stimuli utilized in conventional drug delivery systems can also be found in normal cells, it is inevitable that encapsulated drugs escape from carriers into normal cells. Based on mutual interactions among proteins, polyphenol compounds, and metal ions, we developed a serial-stimuli-responsive drug delivery system. With multi-crosslinking structure, nanocapsules can maintain the integrity of the framework, even with a certain amount of stimuli present, and eventually reach tumor cells to initiate apoptosis, and protect normal cells from being damaged. Meanwhile, the fluorescence of DOX will be quenched when encapsulated in nanocapsules. This property means that the DOX that is released from nanocapsules can be monitored in real-time based on the recovery of fluorescence. These versatile nanocapsules exhibit great potentials to treat cancer.

ModFOLD6: an accurate web server for the global and local quality estimation of 3D protein models.

Methods that reliably estimate the likely similarity between the predicted and native structures of proteins have become essential for driving the acceptance and adoption of three-dimensional protein models by life scientists. ModFOLD6 is the latest version of our leading resource for Estimates of Model Accuracy (EMA), which uses a pioneering hybrid quasi-single model approach. The ModFOLD6 server integrates scores from three pure-single model methods and three quasi-single model methods using a neural network to estimate local quality scores. Additionally, the server provides three options for producing global score estimates, depending on the requirements of the user: (i) ModFOLD6_rank, which is optimized for ranking/selection, (ii) ModFOLD6_cor, which is optimized for correlations of predicted and observed scores and (iii) ModFOLD6 global for balanced performance. The ModFOLD6 methods rank among the top few for EMA, according to independent blind testing by the CASP12 assessors. The ModFOLD6 server is also continuously automatically evaluated as part of the CAMEO project, where significant performance gains have been observed compared to our previous server and other publicly available servers. The ModFOLD6 server is freely available at: http://www.reading.ac.uk/bioinf/ModFOLD/.

Accurate template-based modeling in CASP12 using the IntFOLD4-TS, ModFOLD6, and ReFOLD methods.

Our aim in CASP12 was to improve our Template-Based Modeling (TBM) methods through better model selection, accuracy self-estimate (ASE) scores and refinement. To meet this aim, we developed two new automated methods, which we used to score, rank, and improve upon the provided server models. Firstly, the ModFOLD6_rank method, for improved global Quality Assessment (QA), model ranking and the detection of local errors. Secondly, the ReFOLD method for fixing errors through iterative QA guided refinement. For our automated predictions we developed the IntFOLD4-TS protocol, which integrates the ModFOLD6_rank method for scoring the multiple-template models that were generated using a number of alternative sequence-structure alignments. Overall, our selection of top models and ASE scores using ModFOLD6_rank was an improvement on our previous approaches. In addition, it was worthwhile attempting to repair the detected errors in the top selected models using ReFOLD, which gave us an overall gain in performance. According to the assessors' formula, the IntFOLD4 server ranked 3rd/5th (average Z-score > 0.0/-2.0) on the server only targets, and our manual predictions (McGuffin group) ranked 1st/2nd (average Z-score > -2.0/0.0) compared to all other groups.

Methods for estimation of model accuracy in CASP12.

Methods to reliably estimate the quality of 3D models of proteins are essential drivers for the wide adoption and serious acceptance of protein structure predictions by life scientists. In this article, the most successful groups in CASP12 describe their latest methods for estimates of model accuracy (EMA). We show that pure single model accuracy estimation methods have shown clear progress since CASP11; the 3 top methods (MESHI, ProQ3, SVMQA) all perform better than the top method of CASP11 (ProQ2). Although the pure single model accuracy estimation methods outperform quasi-single (ModFOLD6 variations) and consensus methods (Pcons, ModFOLDclust2, Pcomb-domain, and Wallner) in model selection, they are still not as good as those methods in absolute model quality estimation and predictions of local quality. Finally, we show that when using contact-based model quality measures (CAD, lDDT) the single model quality methods perform relatively better.

Insertion sequences enrichment in extreme Red sea brine pool vent.

Mobile genetic elements are major agents of genome diversification and evolution. Limited studies addressed their characteristics, including abundance, and role in extreme habitats. One of the rare natural habitats exposed to multiple-extreme conditions, including high temperature, salinity and concentration of heavy metals, are the Red Sea brine pools. We assessed the abundance and distribution of different mobile genetic elements in four Red Sea brine pools including the world's largest known multiple-extreme deep-sea environment, the Red Sea Atlantis II Deep. We report a gradient in the abundance of mobile genetic elements, dramatically increasing in the harshest environment of the pool. Additionally, we identified a strong association between the abundance of insertion sequences and extreme conditions, being highest in the harshest and deepest layer of the Red Sea Atlantis II Deep. Our comparative analyses of mobile genetic elements in secluded, extreme and relatively non-extreme environments, suggest that insertion sequences predominantly contribute to polyextremophiles genome plasticity.

Protective potency of clove oil and its transcriptional down-regulation of Aeromonas sobria virulence genes in African catfish (Clarias gariepinus L.).

Disease episodes of fish caused by Aeromonas species are moved to the top list of limiting problems worldwide. The present study was planned to verify the in vitro antibacterial activities as well as the in vivo potential values of clove oil and ciprofloxacin against Aeromonas sobria in African catfish (Clarias gariepinus). The in vitro phenotypic virulence activities and the successful amplification of aerolysin and hemolysin genes in the precisely identified A. sobria strain were predictive for its virulence. In the in vivo assay, virulence of A. sobria strain was fully demonstrated based on constituent mRNA expression profile of tested virulence genes and typical septicemia associated with high mortalities of infected fish. Apparent lower mortality rates were correlated well with both decrescent bacterial burden and significant down-regulated transcripts of representative genes in the treated groups with clove oil, followed by ciprofloxacin as a prophylactic use for 15 days (P < 0.0001); however, the essential oil apart from ciprofloxacin significantly enhanced different hematological parameters (P < 0.05). In addition, administration of antibiotic may be considered as a pronounced stress factor in the fish even when it used in the prophylactic dose. In conclusion, medicinal plants-derived essential oils provide a virtually safer alternative to chemotherapeutics on fish, consumers and ecosystems.

Quercetin mitigates fenitrothion-induced testicular toxicity in rats.

Fenitrothion (FNT) is a widely used organophosphorus pesticide in agriculture. Quercetin (QR), a plant-derived flavonoid, has a free radical scavenging property. This study investigated the protective effect of QR on FNT-induced testicular toxicity in rats. Twenty-four male rats were divided into four groups. Group I (control) received normal saline. Group II was administered QR at the dose of 50 mg kg(-1) b.wt. Group III was orally administered FNT (20 mg kg(-1) b.wt). Group IV was gavaged FNT and QR together at the same doses. All administrations were performed daily by gavage and maintained for 70 days. Sperm parameters and histopathological changes in testes were investigated. Serum testosterone and luteinising hormone were estimated using radioimmunoassay kits. In testes, expressions of steroidogenic genes (3ß-hydroxysteroid dehydrogenase type 6, 17 ß-hydroxysteroid dehydrogenase type 3 and steroidogenic factor-1) and oxidative stress genes (catalase and superoxide dismutase) were determined using real-time PCR. FNT administration caused significant decreases in sperm count, motility and hormonal levels, a significant increase in abnormal sperm morphology and a significant down-regulation of steroidogenic and antioxidant genes in the testis. However, QR administration ameliorated FNT-induced toxic effects. Our results concluded that QR effectively mitigated testicular damage induced by FNT in rats.

A Pilot Randomized Control Cross over Study Evaluating the Effectiveness and Safety of Mechanical Percussor Compared with Conventional Chest Physiotherapy in Adults with Productive Cough.

INTRODUCTION: Conventional Chest Physiotherapy (CCPT) remains the mainstay of treatment for sputum mobilization in patients with productive cough such as bronchiectasis and "Chronic Obstructive Airway Disease" (COPD). However CCPT is time consuming requires the assistance of a physiotherapist and limits the independence of the patient. Mechanical percussors which are electrical devices used to provide percussion to the external chest wall might provide autonomy and greater compliance. We compared safety and efficacy of a mechanical chest percusser devised by Formedic Technology with conventional chest percussion. METHODS: Twenty patients (mean age 64years) were randomly assigned to receive either CCPT or mechanical percussor on the first day and crossed over by "Latin square randomisation" to alternative treatment for 6 consecutive days and the amount of sputum expectorated was compared by dry and wet weight. Adverse events and willingness to use was assessed by a home diary and a questionnaire. RESULTS: There were 13 males and 7 females, eight diagnosed as bronchiectasis and 12 COPD. The mean dry weight of sputum induced by CCPT (0.54g ± 0.32) was significantly more compared with MP (0.40g + 0.11); p-value = 0.002. The mean wet weight of sputum with CCPT (10.71g ± 8.70) was also significantly more compared with MP (5.99g ± 4.5); p-value < 0.001. There were no significant difference in adverse events and majority of patients were willing to use the device by themselves. CONCLUSION: The mechanical percussor although produces less sputum is well tolerated and can be a useful adjunct to CCPT.

Deciphering the functional and structural complexity of the Solar Lake flat mat microbial benthic communities.

The Solar Lake in Taba, Egypt, encompasses one of the few modern-day microbial mats' systems metabolically analogous to Precambrian stromatolites. Solar Lake benthic communities and their adaptation to the Lake's unique limnological cycle have not been described for over two decades. In this study, we revisit the flat mat and describe the summer's shallow water versus exposed microbial community; the latter occurs in response to the seasonal partial receding of water. We employed metagenomic NovaSeq-6000 shotgun sequencing and 16S rRNA, mcrA, and dsrB quantitative PCR. A total of 292 medium-to-high-quality metagenome-assembled genomes (MAGs) were reconstructed. At the structural level, Candidatus Aenigmatarchaeota, Micrarchaeota, and Omnitrophota MAGs were exclusively detected in the shallow-water mats, whereas Halobacteria and Myxococcota MAGs were specific to the exposed microbial mat. Functionally, genes involved in reactive oxygen species (ROS) detoxification and osmotic pressure were more abundant in the exposed than in the shallow-water microbial mats, whereas genes involved in sulfate reduction/oxidation and nitrogen fixation were ubiquitously detected. Genes involved in the utilization of methylated amines for methane production were predominant when compared with genes associated with alternative methanogenesis pathways. Solar Lake methanogen MAGs belonged to Methanosarcinia, Bathyarchaeia, Candidatus Methanofastidiosales, and Archaeoglobales. The latter had the genetic capacity for anaerobic methane oxidation. Moreover, Coleofasciculus chthonoplastes, previously reported to dominate the winter shallow-water flat mat, had a substantial presence in the summer. These findings reveal the taxonomic and biochemical microbial zonation of the exposed and shallow-water Solar Lake flat mat benthic community and their capacity to ecologically adapt to the summer water recession. IMPORTANCE: Fifty-five years ago, the extremophilic "Solar Lake" was discovered on the Red Sea shores, garnering microbiologists' interest worldwide from the 1970s to 1990s. Nevertheless, research on the lake paused at the turn of the millennium. In our study, we revisited the Solar Lake benthic community using a genome-centric approach and described the distinct microbial communities in the exposed versus shallow-water mat unveiling microbial zonation in the benthic communities surrounding the Solar Lake. Our findings highlighted the unique structural and functional adaptations employed by these microbial mat communities. Moreover, we report new methanogens and phototrophs, including an intriguing methanogen from the Archaeoglobales family. We describe how the Solar Lake's flat mat microbial community adapts to stressors like oxygen intrusion and drought due to summer water level changes, which provides insights into the genomic strategies of microbial communities to cope with altered and extreme environmental conditions.

Cost of Cholera for Households and Health Facilities, Somalia.

INTRODUCTION: Cholera remains a substantial public health challenge in Somalia. Ongoing droughts in the country have caused significant outbreaks which have negatively affected the lives of many individuals and overwhelmed health facilities. We aimed to estimate the costs associated with cholera cases for households and health facilities in Somalia. METHODS: This cost-of-illness study was conducted in five cholera treatment centres in Somalia and 400 patients treated in these facilities. Data collection took place during October and November 2023. Given that a significant portion of the patients were children, we interviewed their caregivers to gather cost data. We interviewed staff at the centres and the patients. The data obtained from the household questionnaire covered direct (medical and non-medical) and indirect (lost wages) costs, while direct costs were estimated for the health facility (personnel salaries, drugs and consumables used to treat a patient, and utility expenses). All costs were calculated in US dollars (USD), using 2023 as the base year for the estimation. RESULTS: The average total cost of a cholera episode for a household was US$ 33.94 (2023 USD), with 50.4% (US$ 17.12) being direct costs and 49.6% (US$ 16.82) indirect costs. The average total cost for a health facility to treat an episode of cholera was US$ 82.65. The overall average cost to households and health facilities was US$ 116.59. The average length of stay for a patient was 3.08 days. In the households, patients aged 41 years and older incurred the highest mean total cost (US$ 73.90) while patients younger than 5 years had the lowest cost (US$ 21.02). Additionally, 61.8% of households had to use family savings to cover the cost of the cholera episode, while 14.5% had to borrow money. Most patients (71.8%) were younger than 16 years- 45.3% were 5 years or younger- and 94.0% had never received a cholera vaccine. CONCLUSION: Our study suggests that preventing one cholera episode in Somalia could avert substantial losses for both the households and cholera treatment centres. The findings shed light on the expenses associated with cholera that extend beyond healthcare, including substantial direct and indirect costs borne by households. Preventing cholera cases could lead to a decrease in this economic burden, consequently our study supports the need for preventive measures.

Evaluation of knowledge about osteoporosis risk factors among adults above 40 years of age in Qassim region, Saudi Arabia.

OBJECTIVE: Osteoporosis is a bone disease that develops when bone mineral density and bone mass decrease, or when the quality of bone changes. It is the most common bone disease, representing a major public health problem. This study aimed to assess the knowledge of risk factors for osteoporosis among adults above 40 in the Qassim region, Saudi Arabia. SUBJECTS AND METHODS: This is a cross-sectional study conducted among adults who were above 40 years of age and living in the Qassim region, Saudi Arabia. A survey questionnaire was distributed to respondents while they attended primary health care as well as online via social media. RESULTS: 390 participants responded to our survey (65.6% females vs. 34.4% males). The most common age group was 41 to 50 years (59.7%). The prevalence of participants who were having information about osteoporosis was 59%. Overall, the knowledge of participants about osteoporosis was good (63.1%), 33.3% had moderate knowledge and only 3.6% were assumed to have a poor knowledge level. Factors associated with increased knowledge was being a female and being an employee. CONCLUSIONS: Although the knowledge of the adult population aged above 40 years old seems adequate, there is still room for improvement. Female participants who were currently employed demonstrated a better understanding of osteoporosis than other adults. Further research is warranted to establish the effect of advanced age on their level of understanding regarding osteoporosis and its risk factors.

Quality Estimates for 3D Protein Models.

Protein structure modeling is one of the most advanced and complex processes in computational biology. One of the major problems for the protein structure prediction field has been how to estimate the accuracy of the predicted 3D models, on both a local and global level, in the absence of known structures. We must be able to accurately measure the confidence that we have in the quality predicted 3D models of proteins for them to become widely adopted by the general bioscience community. To address this major issue, it was necessary to develop new model quality assessment (MQA) methods and integrate them into our pipelines for building 3D protein models. Our MQA method, called ModFOLD, has been ranked as one of the most accurate MQA tools in independent blind evaluations. This chapter discusses model quality assessment in the protein modeling field, demonstrating both its strengths and limitations. We also present some of the best methods according to independent benchmarking data, which has been gathered in recent years.

Design configuration and operational parameters of bi-fluid PVT collectors: an updated review.

The bi-fluid photovoltaic thermal (PVT) collector was introduced to provide more heating options along with improved cooling capabilities for the PV module. Since its introduction, this type of PVT system has been investigated thoroughly in various original works. In this review paper, we intend to put the concept and applications of this technology into question and revise the main achievements and discoveries through research and development with a focus on climatic and operational parameters. The paper encompasses a critical review of the discussed research and future directions for PVT collectors. The main utilized operational modes are discussed in detail, which are (i) water used in both channels, (ii) water in one channel and air in the other, and (iii) air in both channels. The modes were found to lead to different enhancement and performance effects for the utilized photovoltaic modules. The impact of mass flow rate was also taken by keeping one working fluid constant while varying the other to obtain its impact on the energy and exergy efficiency of the collector. In some cases, the fluids were run simultaneously and, in other cases, independently.

Cooling of a PVT System Using an Underground Heat Exchanger: An Experimental Study.

In the recent decades, the researchers have been focused on the use of photovoltaic thermal (PVT) systems that provide the best performance and cooling for the photovoltaic panels. In this study, a PVT system consisting of a monocrystalline PV panel and a spiral heat exchanger was connected to an underground heat exchanger that is buried at a depth of 4 m below the surface of the earth. The procedure of the current study can be considered the first of its kind in the Middle East and North Africa region (based on the researchers' knowledge). The study was carried out on agricultural land in Baghdad-Iraq during months of July and August-2022, which are considered the harshest weather conditions for this city. The heat exchanger consists of a copper tube with a length of 21 m and formed in the shape of 3U, and it was buried in the earth and connected with a PVT system. The results of the study showed that the site chosen to bury the heat exchanger (4 m deep) has a stable soil temperature at 22.5 °C. From various volumetric flow rates, a flow rate of 0.18 l/s was selected which is considered the highest flow rate that can show vibration in the PVT system which may harm the system. The practical measurements showed that the largest difference in the surface temperatures of standalone PV and PVT was around 20 °C in favor of the latter. The electrical efficiency of the studied PVT system also increased to outperform the standalone PV system by 127.3%. By comparing the results of the current study with studies of water-cooled PVT systems from the literature, it is clear that the proposed system is feasible and has an acceptable efficiency in such harsh weather conditions tested during the experiment.

Optimizing MWCNT-Based Nanofluids for Photovoltaic/Thermal Cooling through Preparation Parameters.

Multiwalled carbon nanotubes (MWCNTs) were employed as added particles for nanofluids in this practical investigation. To identify the most appropriate nanofluid for cooling PVT systems that are functional in the extreme summer environment of Baghdad, the parameters of base fluid, surfactant, and sonication time used for mixing were examined. Water was chosen as the base fluid instead of other potential candidates such as ethylene glycol (EG), propylene glycol (PG), and heat transfer oil (HTO). Thermal conductivity and stability were important thermophysical qualities that were impacted by the chosen parameters. The nanofluid tested in Baghdad city (consisting of 0.5% MWCNTs, water, and CTAB with a sonication period of three and a quarter hours) resulted in a 119.5, 308, and 210% enhancement of thermal conductivity (TC) for water compared with EG, PG, and oil, respectively. In addition, the nanofluid-cooled PVT system had an electrical efficiency that was 88.85% higher than standalone PV technology and 44% higher than water-cooled PVT systems. Moreover, the thermal efficiency of the nanofluid-cooled PVT system was 20% higher than the water-cooled PVT system. Finally, the nanofluid-cooled PVT system displayed the least decrease in electrical efficiency and a greater thermal efficiency even when the PV panel was at its hottest at noon.

Insights into the global freshwater virome.

Viruses are by far the most abundant life forms on this planet. Yet, the full viral diversity remains mostly unknown, especially in environments like freshwater. Therefore, we aimed to study freshwater viruses in a global context. To this end, we downloaded 380 publicly available viral metagenomes (>1 TB). More than 60% of these metagenomes were discarded based on their levels of cellular contamination assessed by ribosomal DNA content. For the remaining metagenomes, assembled contigs were decontaminated using two consecutive steps, eventually yielding 273,365 viral contigs longer than 1,000 bp. Long enough contigs (≥ 10 kb) were clustered to identify novel genomes/genome fragments. We could recover 549 complete circular and high-quality draft genomes, out of which 10 were recognized as being novel. Functional annotation of these genomes showed that most of the annotated coding sequences are DNA metabolic genes or phage structural genes. On the other hand, taxonomic analysis of viral contigs showed that most of the assigned contigs belonged to the order Caudovirales, particularly the families of Siphoviridae, Myoviridae, and Podoviridae. The recovered viral contigs contained several auxiliary metabolic genes belonging to several metabolic pathways, especially carbohydrate and amino acid metabolism in addition to photosynthesis as well as hydrocarbon degradation and antibiotic resistance. Overall, we present here a set of prudently chosen viral contigs, which should not only help better understanding of freshwater viruses but also be a valuable resource for future virome studies.