Comparative study of sequence aligners for detecting antibiotic resistance in bacterial metagenomes

We aim to compare the performance of Bowtie2 , bwa‐mem , blastn and blastx when aligning bacterial metagenomes against the Comprehensive Antibiotic Resistance Database (CARD). Simulated reads were used to evaluate the performance of each aligner under the following four performance criteria: correctly mapped, false positives, multi‐reads and partials. The optimal alignment approach was applied to samples from two wastewater treatment plants to detect antibiotic resistance genes using next generation sequencing. blastn mapped with greater accuracy among the four sequence alignment approaches considered followed by Bowtie2 . blastx generated the greatest number of false positives and multi‐reads when aligned against the CARD. The performance of each alignment tool was also investigated using error‐free reads. Although each aligner mapped a greater number of error‐free reads as compared to Illumina‐error reads, in general, the introduction of sequencing errors had little effect on alignment results when aligning against the CARD. Given each performance criteria, blastn was found to be the most favourable alignment tool and was therefore used to assess resistance genes in sewage samples. Beta‐lactam and aminoglycoside were found to be the most abundant classes of antibiotic resistance genes in each sample.

Significance and Impact of the Study

Antibiotic resistance genes (ARGs) are pollutants known to persist in wastewater treatment plants among other environments, thus methods for detecting these genes have become increasingly relevant. Next generation sequencing has brought about a host of sequence alignment tools that provide a comprehensive look into antimicrobial resistance in environmental samples. However, standardizing practices in ARG metagenomic studies is challenging since results produced from alignment tools can vary significantly. Our study provides sequence alignment results of synthetic, and authentic bacterial metagenomes mapped against an ARG database using multiple alignment tools, and the best practice for detecting ARGs in environmental samples.     

SC-formation in someAllium species,and a discussion of the significance of SC-associated structures and of the mechanisms for presynaptic alignment

Earlier observations on synaptonemal complex (SC) formation inAllium are supplemented by data from diploidA. sphaerocephalon, pentaploidA. oleraceum and allotetraploidA. senescens. Accumulating information about structures like lateral element thickenings and -doublings allows to draw conclusions about their nature. The occurrence of discrete intercalary and terminal homologous associations prior to synapsis is confirmed for a range ofAllium species and it is argued that they are a general phenomenon. Several hypotheses on homologous recognition and/or attraction are discussed in the light of the observations on homologous alignment inAllium. Gratefully dedicated to my highly respected mentor, Prof. DrElisabeth Tschermak-Woess, on the occasion of her 70th birthday.     

FaBox: an online toolbox for fasta sequences

FaBox is a collection of simple and intuitive web services that enable biologists and medical researchers to quickly perform typical task with sequence data. The services makes it easy to extract, edit, and replace sequence headers and join or divide data sets based on header information. Other services include collapsing a set of sequences into haplotypes and automated formatting of input files for a number of population genetics programs, such as arlequin , tcs and mrbayes . The toolbox is expected to grow on the basis of requests for particular services and converters in the future. FaBox is freely available at http://www.birc.au.dk/fabox .     

Two "unrelated" families of ATP-dependent enzymes share extensive structural similarities about their cofactor binding sites.

Two proteins, D-alanine:D-alanine ligase and cAMP-dependent protein kinase, share a remarkable degree of structural convergence despite having different three-dimensional folds and different enzymatic functions. Here we report that as many as 103 residues from 10 segments form two identical super-secondary structures between which the cofactor ATP is bound. The cofactor, two bound metal cations, and several water molecules form a large network of electrostatic and hydrophobic interactions common to both enzymes, and these are mediated by the similar placement of equivalent amino acids within the common supersecondary structures.     

Resident multipotent vascular stem cells exhibit amplitude dependent strain avoidance similar to that of vascular smooth muscle cells

Atherosclerosis is one of the leading causes of mortality worldwide, and presents as a narrowing or occlusion of the arterial lumen. Interventions to re-open the arterial lumen can result in re-occlusion through intimal hyperplasia. Historically only de-differentiated vascular smooth muscle cells were thought to contribute to intimal hyperplasia. However recent significant evidence suggests that resident medial multipotent vascular stem cells (MVSC) may also play a role. We therefore investigated the strain response of MVSC since these resident cells are also subjected to strain within their native environment. Accordingly, we applied uniaxial 1 Hz cyclic uniaxial tensile strain at three amplitudes around a mean strain of 5%, (4–6%, 2–8% and 0–10%) to either rat MVSC or rat VSMC before their strain response was evaluated. While both cell types strain avoid, the strain avoidant response was greater for MVSC after 24 h, while VSMC strain avoid to a greater degree after 72 h. Additionally, both cell types increase strain avoidance as strain amplitude is increased. Moreover, MVSC and VSMC both demonstrate a strain-induced decrease in cell number, an effect more pronounced for MVSC. These experiments demonstrate for the first time the mechano-sensitivity of MVSC that may influence intimal thickening, and emphasizes the importance of strain amplitude in controlling the response of vascular cells in tissue engineering applications.     

Conformational Study Based on Simulated Annealing and 1H NMR of Peptides Comprising the Consensus Sequence Arg5-Asp-Val-Arg-Gly9: Effects of the Substitution Ser 12 by Ala 12 or of 3 Residues Deletion at the N-Terminus

Summary

A conformational search by simulated annealing has been performed on two peptides derivated from the tetradecapeptide used to isolate the Xenopus laevis skin maturation RXVRG-endoprotease. The Ala 12 derivative, obtained by substitution in the hydrophobic C terminal fragment and the undecapeptide 4–14, obtained by deletion of an acidic rich tripeptide, were studied. No unique structure has been found for the tetradecapeptide Ala 12. This structural disorganization could explain the loss of activity of the endoprotease towards the subsituted peptide. For the undecapeptide, two different models in accordance with the NMR data were found. The conformational differences between these two models are locat ed in the consensus sequence and in each case an hairpin-like conformation is observed. These results could be related to the enhanced cleavage activity of the maturation enzyme. The obtained structures are also compared with those of the original tetradecapeptide.     

Protein structure modeling in the proteomics era

Structural proteomics aims to understand the structural basis of protein interactions and functions. A prerequisite for this is the availability of 3D protein structures that mediate the biochemical interactions. The explosion in the number of available gene sequences set the stage for the next step in genome-scale projects – to obtain 3D structures for each protein. To achieve this ambitious goal, the slow and costly structure determination experiments are supplemented with theoretical approaches. The current state and recent advances in structure modeling approaches are reviewed here, with special emphasis on comparative protein structure modeling techniques.     

Surgeon variability in total knee arthroplasty component alignment: a Monte Carlo analysis

Component mal-alignment in total knee arthroplasty has been associated with increased revision rates and poor clinical outcomes. A significant source of variability in traditional, jig-based total knee arthroplasty is the performance of the surgeon. The purpose of this study was to determine the most sensitive steps in the femoral and tibia arthroplasty procedures. A computational model of the total knee arthroplasty procedure was created, and Monte Carlo simulations were performed that included surgeon variability in each step of the procedure. The proportion of well-aligned components from the model agrees with clinical literature in most planes. When components must be aligned within ±3° in all planes, component alignment was most sensitive to the accuracy of identifying the lateral epicondyle for the femoral component, and to the precision of the transverse plane alignment of the extramedullary guide for the tibial component. This model can be used as a tool for evaluating different procedural approaches or sources of variability to improve the quality of the total knee arthroplasty procedure.     

Halonatronomonas betaini gen. nov., sp. nov., a haloalkaliphilic isolate from soda lake capable of betaine degradation and proposal of Halarsenatibacteraceae fam. nov. and Halothermotrichaceae fam. nov. within the order Halanaerobiales

A search for the organisms responsible for anaerobic betaine degradation in soda lakes resulted in isolation of a novel bacterial strain, designated Z-7014^T. The cells were Gram-stain-negative, non-endospore-forming rods. Growth occurred at 8–52 °C (optimum 40–45 °C), pH 7.1–10.1 (optimum pH 8.1–8.8) and 1.0–3.5 M Na⁺ (optimum 1.8 M), i.e. it can be regarded as a haloalkaliphile. The strain utilized a limited range of substrates, mostly peptonaceous but not amino acids, and was able to degrade betaine. Growth on betaine occurred only in the presence of peptonaceous substances which could not be replaced by vitamins. The G + C content of the genomic DNA of strain Z-7014^T was 36.1 mol%. The major cellular fatty acids (>5% of the total) were C_16:0 DMA, C_{18: 0} DMA, C_16:1ω8, C_16:0, C_18:1 DMA, C_16:1 DMA, C_18:1ω9, and C_18:0. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain Z-7014^T formed a distinct evolutionary lineage in the order Halanaerobiales with the highest similarity to Halarsenitibacter silvermanii SLAS-1^T (83.6%), Halothermothrix orenii H168^T (85.6%), and Halocella cellulosilytica DSM 7362^T (85.6%). AAI and POCP values between strain Z-7014^T and type strains of the order Halanaerobiales were 51.7–57.8%, and 33.8–58.3%, respectively. Based on polyphasic results including phylogenomic data, the novel strain could be distinguished from other genera, which suggests that strain Z-7014^T represents a novel species of a new genus, for which the name Halonatronomonas betaini gen. nov., sp. nov. is proposed. The type strain is Z-7014^T (=KCTC 25237^T = VKM B-3506^T). On the basis of phylogenomic data, it is also proposed to evolve two novel families Halarsenitibacteraceae fam. nov. and Halothermotrichaceae fam. nov. within the current order Halanaerobiales.