Takshan/R1 huggingface dataset:
Adaptive evolution of rhizobial symbiotic compatibility mediated by co-evolved insertion sequences.

Mutualism between bacteria and eukaryotes has essential roles in the history of life, but the evolution of their compatibility is poorly understood. Here we show that different Sinorhizobium strains can form either nitrogen-fixing nodules or uninfected pseudonodules on certain cultivated soybeans, while being all effective microsymbionts of some wild soybeans. However, a few well-infected nodules can be found on a commercial soybean using inocula containing a mixed pool of Tn5 insertion mutants derived from an incompatible strain. Reverse genetics and genome sequencing of compatible mutants demonstrated that inactivation of T3SS (type three secretion system) accounted for this phenotypic change. These mutations in the T3SS gene cluster were dominated by parallel transpositions of insertion sequences (ISs) other than the introduced Tn5. This genetic and phenotypic change can also be achieved in an experimental evolution scenario on a laboratory time scale using incompatible wild-type strains as inocula. The ISs acting in the adaptive evolution of Sinorhizobium strains exhibit broader phyletic and replicon distributions than other ISs, and prefer target sequences of low GC% content, a characteristic feature of symbiosis plasmid where T3SS genes are located. These findings suggest an important role of co-evolved ISs in the adaptive evolution of rhizobial compatibility. The ISME Journal advance online publication, 11 August 2017; doi:10.1038/ismej.2017.136.
Influence of silver nanoparticles on growth and health of broiler chickens after infection with Campylobacter jejuni.

BACKGROUND: Silver nanoparticles (AgNP) have gained much attention in recent years due to their biomedical applications, especially as antimicrobial agents. AgNP may be used in poultry production as an alternative to the use of antibiotic growth promoter. However, little is known about the impact of oral administration of AgNP on the gut microbiota and the immune system. The aim of the present study was to investigate the effects of AgNP on growth, hematological and immunological profile as well as intestinal microbial composition in broilers challenged with Campylobacter jejuni (C. jejuni). RESULTS: AgNP did not affect the intestinal microbial profile of birds. The body weight gain and the relative weights of bursa and spleen were reduced when supplemented with AgNP. There was no difference with respect to packed cell volume. However, the plasma concentrations of IgG and IgM were lower in birds receiving AgNP compared to the non-supplemented control group. The expression of TNF-α and NF-kB at mRNA level was significantly higher in birds receiving AgNP. CONCLUSIONS: The application of AgNP via the drinking water in the concentration of 50 ppm reduced broiler growth, impaired immune functions and had no antibacterial effect on different intestinal bacterial groups, which may limit the applicability of AgNP against C. jejuni in broiler chickens.
Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses.

BACKGROUND: Movile Cave (Mangalia, Romania) is a unique ecosystem where the food web is sustained by microbial primary production, analogous to deep-sea hydrothermal vents. Specifically, chemoautotrophic microbes deriving energy from the oxidation of hydrogen sulphide and methane form the basis of the food web. RESULTS: Here, we report the isolation of the first methane-oxidizing bacterium from the Movile Cave ecosystem, Candidatus Methylomonas sp. LWB, a new species and representative of Movile Cave microbial mat samples. While previous research has suggested a prevalence of anoxic conditions in deeper lake water and sediment, using small-scale shotgun metagenome sequencing, we show that metabolic genes encoding enzymes for aerobic methylotrophy are prevalent in sediment metagenomes possibly indicating the presence of microoxic conditions. Moreover, this study also indicates that members within the family Gallionellaceae (Sideroxydans and Gallionella) were the dominant taxa within the sediment microbial community, thus suggesting a major role for microaerophilic iron-oxidising bacteria in nutrient cycling within the Movile Cave sediments. CONCLUSIONS: In this study, based on phylogenetic and metabolic gene surveys of metagenome sequences, the possibility of aerobic microbial processes (i.e., methylotrophy and iron oxidation) within the sediment is indicated. We also highlight significant gaps in our knowledge on biogeochemical cycles within the Movile Cave ecosystem, and the need to further investigate potential feedback mechanisms between microbial communities in both lake sediment and lake water.
Discovery of a proteolytic flagellin family in diverse bacterial phyla that assembles enzymatically active flagella.

Bacterial flagella are cell locomotion and occasional adhesion organelles composed primarily of the polymeric protein flagellin, but to date have not been associated with any enzymatic function. Here, we report the bioinformatics-driven discovery of a class of enzymatic flagellins that assemble to form proteolytically active flagella. Originating by a metallopeptidase insertion into the central flagellin hypervariable region, this flagellin family has expanded to at least 74 bacterial species. In the pathogen, Clostridium haemolyticum, metallopeptidase-containing flagellin (which we termed flagellinolysin) is the second most abundant protein in the flagella and is localized to the extracellular flagellar surface. Purified flagellar filaments and recombinant flagellin exhibit proteolytic activity, cleaving nearly 1000 different peptides. With ~ 20,000 flagellin copies per  ~ 10-μm flagella this assembles the largest proteolytic complex known. Flagellum-mediated extracellular proteolysis expands our understanding of the functional plasticity of bacterial flagella, revealing this family as enzymatic biopolymers that mediate interactions with diverse peptide substrates. So far no enzymatic activity has been attributed to flagellin, the major component of bacterial flagella. Here the authors use bioinformatic analysis and identify a metallopeptidase insertion in flagellins from 74 bacterial species and show that recombinant flagellin and flagellar filaments have proteolytic activity.
Prediction of sensitivity to gefitinib/erlotinib for EGFR mutations in NSCLC based on structural interaction fingerprints and multilinear principal component analysis.

BACKGROUND: Non-small cell lung cancer (NSCLC) with activating EGFR mutations, especially exon 19 deletions and the L858R point mutation, is particularly responsive to gefitinib and erlotinib. However, the sensitivity varies for less common and rare EGFR mutations. There are various explanations for the low sensitivity of EGFR exon 20 insertions and the exon 20 T790 M point mutation to gefitinib/erlotinib. However, few studies discuss, from a structural perspective, why less common mutations, like G719X and L861Q, have moderate sensitivity to gefitinib/erlotinib. RESULTS: To decode the drug sensitivity/selectivity of EGFR mutants, it is important to analyze the interaction between EGFR mutants and EGFR inhibitors. In this paper, the 30 most common EGFR mutants were selected and the technique of protein-ligand interaction fingerprint (IFP) was applied to analyze and compare the binding modes of EGFR mutant-gefitinib/erlotinib complexes. Molecular dynamics simulations were employed to obtain the dynamic trajectory and a matrix of IFPs for each EGFR mutant-inhibitor complex. Multilinear Principal Component Analysis (MPCA) was applied for dimensionality reduction and feature selection. The selected features were further analyzed for use as a drug sensitivity predictor. The results showed that the accuracy of prediction of drug sensitivity was very high for both gefitinib and erlotinib. Targeted Projection Pursuit (TPP) was used to show that the data points can be easily separated based on their sensitivities to gefetinib/erlotinib. CONCLUSIONS: We can conclude that the IFP features of EGFR mutant-TKI complexes and the MPCA-based tensor object feature extraction are useful to predict the drug sensitivity of EGFR mutants. The findings provide new insights for studying and predicting drug resistance/sensitivity of EGFR mutations in NSCLC and can be beneficial to the design of future targeted therapies and innovative drug discovery.
Mutations in the gene of the Gα subunit of the heterotrimeric G protein are the cause for the brachytic1 semi-dwarf phenotype in barley and applicable for practical breeding.

BACKGROUND: Short-culm mutants have been widely used in breeding programs to increase lodging resistance. In barley (Hordeum vulgare L.), several hundreds of short-culm mutants have been isolated over the years. The objective of the present study was to identify the Brachytic1 (Brh1) semi-dwarfing gene and to test its effect on yield and malting quality. RESULTS: Double-haploid lines generated through a cross between a brh1.a mutant and the European elite malting cultivar Quench, showed good malting quality but a decrease in yield. Especially the activities of the starch degrading enzymes β-amylase and free limit dextrinase were high. A syntenic approach comparing markers in barley to those in rice (Oryza sativa L.), sorghum (Sorghum bicolor Moench) and brachypodium (Brachypodium distachyon P. Beauv) helped us to identify Brh1 as an orthologue of rice D1 encoding the Gα subunit of a heterotrimeric G protein. We demonstrated that Brh1 is allelic to Ari-m. Sixteen different mutant alleles were described at the DNA level. CONCLUSIONS: Mutants in the Brh1 locus are deficient in the Gα subunit of a heterotrimeric G protein, which shows that heterotrimeric G proteins are important regulators of culm length in barley. Mutant alleles do not have any major negative effects on malting quality.
A novel esterase subfamily with α/β-hydrolase fold suggested by structures of two bacterial enzymes homologous to l-homoserine O-acetyl transferases.

MekB from Pseudomonas veronii and CgHle from Corynebacteriumglutamicum belong to the superfamily of α/β-hydrolase fold proteins. Based on sequence comparisons, they are annotated as homoserine transacetylases in popular databases like UNIPROT, PFAM or ESTHER. However, experimentally, MekB and CgHle were shown to be esterases that hydrolyse preferentially acetic acid esters. We describe the x-ray structures of these enzymes solved to high resolution. The overall structures confirm the close relatedness to experimentally validated homoserine acetyl transferases, but simultaneously the structures exclude the ability of MekB and CgHle to bind homoserine and acetyl-CoA. Insofar the MekB and CgHle structures suggest dividing the homoserine transacetylase family into subfamilies, namely genuine acetyl transferases and acetyl esterases with MekB and CgHle as constituting members of the latter.
Identity of Fasciola spp. in sheep in Egypt.

BACKGROUND: In Egypt, liver flukes, Fasciola spp. ( Digenea: Fasciolidae), have a serious impact on the farming industry and public health. Both Fasciola hepatica and Fasciola gigantica are known to occur in cattle, providing the opportunity for genetic recombination. Little is known on the identity and genetic variability of Fasciola populations in sheep. METHODS: This study was performed to determine the prevalence of liver flukes in sheep in Menofia Province as a representative area of the delta region in Egypt, as measured by postmortem examination of slaughtered animals at three abattoirs. The identity and genetic variability of Fasciola spp. in slaughtered animals were determined by PCR-sequence analysis of the nuclear ribosomal internal transcribed spacer 1 (ITS1) and the mitochondrial NADH dehydrogenase subunit 1 (nad1) genes. RESULTS: Physical inspection of the liver indicated that 302 of 2058 (14.7%) slaughtered sheep were infected with Fasciola spp. Sequence analysis of the ITS1 and nad1 genes of liver flukes from 17 animals revealed that 11 animals were infected with F. hepatica, four with F. gigantica, and two with both species. Seventy eight of 103 flukes genetically characterized from these animals were F. hepatica, 23 were F. gigantica, and two had ITS1 sequences identical to F. hepatica but nad1 sequences identical to F. gigantica. nad1 sequences of Egyptian isolates of F. gigantica showed pronounced differences from those in the GenBank database. Egyptian F. gigantica haplotypes formed haplogroup D, which clustered in a sister clade with haplogroups A, B and C circulating in Asia, indicating the existence of geographic isolation in the species. CONCLUSIONS: Both F. hepatica and F. gigantica are prevalent in sheep in Egypt and an introgressed form of the two occurs as the result of genetic recombination. In addition, a geographically isolated F. gigantica population is present in the country. The importance of these observations in epidemiology of fascioliasis needs to be examined in future studies.
Fluorescence in situ hybridization karyotyping reveals the presence of two distinct genomes in the taxon Aegilops tauschii.

BACKGROUND: Aegilops tauschii is the donor of the bread wheat D genome. Based on spike morphology, the taxon has conventionally been subdivided into ssp. tauschii and ssp. strangulata. The present study was intended to address the poor match between this whole plant morphology-based subdivision and genetic relationships inferred from genotyping by fluorescence in situ hybridization karyotyping a set of 31 Ae. tauschii accessions. RESULTS: The distribution of sites hybridizing to the two probes oligo-pTa-535 and (CTT)10 split the Ae. tauschii accessions into two clades, designated Dt and Ds, which corresponded perfectly with a previously assembled phylogeny based on marker genotype. The Dt cluster was populated exclusively by ssp. tauschii accessions, while the Ds cluster harbored both ssp. strangulata and morphologically intermediate accessions. As a result, it is proposed that Ae. tauschii ssp. tauschii is restricted to carriers of the Dt karyotype: their spikelets are regularly spaced along the rachis, at least in the central portion of their spike. Accessions classified as Ae. tauschii ssp. strangulata carry the Ds karyotype; their spikelets are irregularly spaced. Based on this criterion, forms formerly classified as ssp. tauschii var. meyeri have been re-designated ssp. strangulata var. meyeri. CONCLUSIONS: According to the reworking of the taxon, the bread wheat D genome was most probably donated by ssp. strangulata var. meyeri. Chromosomal differentiation reveals intra-species taxon of Ae. tauschii. Ae. tauschii ssp. tauschii has more distant relationship with breed wheat than ssp. strangulata and can be used for breeding improving effectively.
Anesthetic Management of Narcolepsy Patients During Surgery: A Systematic Review.

BACKGROUND: Narcolepsy is a rare sleep disorder characterized by excessive daytime sleepiness, sleep paralysis, and/or hypnagogic/hypnopompic hallucinations, and in some cases cataplexy. The response to anesthetic medications and possible interactions in narcolepsy patients is unclear in the perioperative period. In this systematic review, we aim to evaluate the current evidence on the perioperative outcomes and anesthetic considerations in narcolepsy patients. METHODS: Electronic literature search of Medline, Medline in-process, Embase, Cochrane Database of Systematic Reviews databases, international conference proceedings, and abstracts was conducted in November 2015 according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis Protocols guideline. A total of 3757 articles were screened using a 2-stage strategy (title-abstract followed by full text). We included case studies/series, cohort studies, and randomized controlled trials of narcolepsy patients undergoing surgical procedures under anesthesia or sedation. Preoperative narcolepsy symptoms and sleep study data, anesthetic technique, and perioperative complications were extracted. Screening of articles, data extraction, and compilation were conducted by 2 independent reviewers and any conflict was resolved by the senior author. RESULTS: A total of 19 studies including 16 case reports and 3 case series were included and evaluated. The majority of these patients received general anesthesia, whereas a small percentage of patients received regional anesthesia. Reported complications of narcolepsy patients undergoing surgeries were mainly related to autonomic dysregulation, or worsening of narcolepsy symptoms intra/postoperatively. Narcolepsy symptoms worsened only in those patient populations where the preoperative medications were either discontinued or reduced (mainly in obstetric patients). In narcolepsy patients, use of depth of anesthesia monitoring and total intravenous technique may have some advantage in terms of safety profile. Several patients undergoing neurosurgery involving the hypothalamus or third or four ventricles developed new-onset narcolepsy. CONCLUSIONS: We found a paucity of prospective clinical trials in this patient population, as most of the studies were case reports or observational studies. Continuation of preoperative medications, depth of anesthesia monitoring, use of multimodal analgesia with short-acting agents and regional anesthesia techniques were associated with favorable outcomes. Obstetric patients may be at greater risk for worsening narcolepsy symptoms, possibly related to a reduction or discontinuation of medications. For neurosurgical procedures involving the hypothalamus or third and fourth ventricle, postoperative considerations should include monitoring for symptoms of narcolepsy. Future studies are needed to better define perioperative risks associated with anesthesia and surgery in this population of patients.
Improved Prediction of Michaelis Constants in CYP450-Mediated Reactions by Resilient Back Propagation Algorithm.

BACKGROUND: In drug metabolism reactions, it has become increasingly important to measure Michaelis constants (Km), which are used for a variety of purposes, including identification of enzymes involved in drug metabolism, prediction of drug-drug interactions, etc. Cytochrome P450s (CYPs) comprise a super family of major human enzymes responsible for drug metabolism. Hence, computational prediction of Km in CYP-mediated reactions facilitates drug development in an efficient and economical way. METHODS: In this study, we firstly constructed a large dataset of ten CYP isoforms associated with 169 binding substrates, and 210 experimental Km values in CYP-mediated reactions. To predict Km of substrates metabolized by various CYP isoforms, we developed a general prediction model by using resilient back-propagation neutral network algorithm, based on the structural and physicochemical properties of the substrates and the metabolic specificity of the enzymes. RESULTS: The predictive Km values achieve a squared cross-validation correlation coefficients (Q2) of 0.73 with the experimental values, which is better than that of the existing models. Moreover, our model can predict Kmvalues of the compounds metabolized by a wide range of CYP isoforms. CONCLUSION: This tool will be useful in large-scale drug screening studies for CYP enzymes and helpful in the drug design and development.
Effectiveness and safety of ferric carboxymaltose compared to iron sucrose in women with iron deficiency anemia: phase IV clinical trials.

BACKGROUND: Iron deficiency anemia (IDA) is a significant problem worldwide particularly in women. The aim of the study was to evaluate the effectiveness and safety of intravenous ferric carboxymaltose (FCM) in comparison to iron sucrose (IS) in women with IDA. METHOD: Two hundred patients at Department of Obstetrics and Gynaecology, Sher-i-Kashmir Institute of Medical Sciences Medical College and Hospital, Jammu & Kashmir, India identified with IDA were enrolled for the study. Intravenous FCM and IS were both given as per the protocol. Change in the laboratory parameters such as hemoglobin (Hb), mean corpuscular value, and serum ferritin levels at two weeks and four weeks interval after the treatment was recorded. RESULT: A significant increase in the mean Hb was observed from 7.76 ± 0.709 to 13.25 ± 0.606 in patients treated with FCM and 7.64 ± 0.710 to 11.59 ± 0.733 g/dL (P < 0.001) in patients treated with IS after four weeks of therapy. The rise in mean corpuscular volume was from 66.82 ± 5.24 to 86.76 ± 3.765 and 68.05 ± 5.56 to 93.80 ± 3.80 and rise in serum ferritin levels were from 8.32 ± 1.787 to 38.94 ± 6.095 μg/L and 8.16 ± 1.540 to 27 ± 8.175 μg/L in patients treated with FCM and IS respectively after four weeks of therapy. No serious adverse effects were reported. CONCLUSION: Parenteral therapy is effective in IDA, but FCM elevates hemoglobin level and restored iron stores faster than IS with minimum adverse drug reactions. TRIAL REGISTRATION NUMBER: ISRCTN14484575 Dated: 15-12-2017 retrospectively registered. https://doi.org/10.1186/ISRCTN14484575.
Fast GPU-based Monte Carlo code for SPECT/CT reconstructions generates improved 177Lu images.

BACKGROUND: Full Monte Carlo (MC)-based SPECT reconstructions have a strong potential for correcting for image degrading factors, but the reconstruction times are long. The objective of this study was to develop a highly parallel Monte Carlo code for fast, ordered subset expectation maximum (OSEM) reconstructions of SPECT/CT images. The MC code was written in the Compute Unified Device Architecture language for a computer with four graphics processing units (GPUs) (GeForce GTX Titan X, Nvidia, USA). This enabled simulations of parallel photon emissions from the voxels matrix (1283 or 2563). Each computed tomography (CT) number was converted to attenuation coefficients for photo absorption, coherent scattering, and incoherent scattering. For photon scattering, the deflection angle was determined by the differential scattering cross sections. An angular response function was developed and used to model the accepted angles for photon interaction with the crystal, and a detector scattering kernel was used for modeling the photon scattering in the detector. Predefined energy and spatial resolution kernels for the crystal were used. The MC code was implemented in the OSEM reconstruction of clinical and phantom 177Lu SPECT/CT images. The Jaszczak image quality phantom was used to evaluate the performance of the MC reconstruction in comparison with attenuated corrected (AC) OSEM reconstructions and attenuated corrected OSEM reconstructions with resolution recovery corrections (RRC). RESULT: The performance of the MC code was 3200 million photons/s. The required number of photons emitted per voxel to obtain a sufficiently low noise level in the simulated image was 200 for a 1283 voxel matrix. With this number of emitted photons/voxel, the MC-based OSEM reconstruction with ten subsets was performed within 20 s/iteration. The images converged after around six iterations. Therefore, the reconstruction time was around 3 min. The activity recovery for the spheres in the Jaszczak phantom was clearly improved with MC-based OSEM reconstruction, e.g., the activity recovery was 88% for the largest sphere, while it was 66% for AC-OSEM and 79% for RRC-OSEM. CONCLUSION: The GPU-based MC code generated an MC-based SPECT/CT reconstruction within a few minutes, and reconstructed patient images of 177Lu-DOTATATE treatments revealed clearly improved resolution and contrast.