Exploring the Diversity of Bacillus Whole Genome Sequencing Projects Using Peasant, the Prokaryotic Assembly and Annotation Tool

The persistent decrease in cost and difficulty of whole genome sequencing of microbial organisms has led to a dramatic increase in the number of species and strains characterized from a wide variety of environments. Microbial genome sequencing can now be conducted by small laboratories and as part of undergraduate curriculum. While sequencing is routine in microbiology, assembly, annotation and downstream analyses still require computational resources and expertise, often necessitating familiarity with programming languages. To address this problem, we have created a light-weight, user-friendly tool for the assembly and annotation of microbial sequencing projects. The Prokaryotic Assembly and Annotation Tool, Peasant, automates the processes of read quality control, genome assembly, and annotation for microbial sequencing projects. High-quality assemblies and annotations can be generated by Peasant without the need of programming expertise or high-performance computing resources. Furthermore, statistics are calculated so that users can evaluate their sequencing project. To illustrate the computational speed and accuracy of Peasant, the SRA records of 322 Illumina platform whole genome sequencing assays for Bacillus species were retrieved from NCBI, assembled and annotated on a single desktop computer. From the assemblies and annotations produced, a comprehensive analysis of the diversity of over 200 high-quality samples was conducted, looking at both the 16S rRNA phylogenetic marker as well as the Bacillus core genome. Peasant provides an intuitive solution for high-quality whole genome sequence assembly and annotation for users with limited programing experience and/or computational resources. The analysis of the Bacillus whole genome sequencing projects exemplifies the utility of this tool. Furthermore, the study conducted here provides insight into the diversity of the species, the largest such comparison conducted to date

S-plot2: Rapid Visual and Statistical Analysis of Genomic Sequences

With the daily release of data from whole genome sequencing projects, tools to facilitate comparative studies are hard-pressed to keep pace. Graphical software solutions can readily recognize synteny by measuring similarities between sequences. Nevertheless, regions of dissimilarity can prove to be equally informative; these regions may harbor genes acquired via lateral gene transfer (LGT), signify gene loss or gain, or include coding regions under strong selection. Previously, we developed the software S-plot. This tool employed an alignment-free approach for comparing bacterial genomes and generated a heatmap representing the genomes’ similarities and dissimilarities in nucleotide usage. In prior studies, this tool proved valuable in identifying genome rearrangements as well as exogenous sequences acquired via LGT in several bacterial species. Herein, we present the next generation of this tool, S-plot2. Similar to its predecessor, S-plot2 creates an interactive, 2-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). This new version, however, includes additional metrics for analysis, new reporting options, and integrated BLAST query functionality for the user to interrogate regions of interest. Furthermore, S-plot2 can evaluate larger sequences, including whole eukaryotic chromosomes. To illustrate some of the applications of the tool, 2 case studies are presented. The first examines strain-specific variation across the Pseudomonas aeruginosa genome and strain-specific LGT events. In the second case study, corresponding human, chimpanzee, and rhesus macaque autosomes were studied and lineage specific contributions to divergence were estimated. S-plot2 provides a means to both visually and quantitatively compare nucleotide sequences, from microbial genomes to eukaryotic chromosomes. The case studies presented illustrate just 2 potential applications of the tool, highlighting its capability to identify and investigate the variation in molecular divergence rates across sequences. S-plot2 is freely available through https://bitbucket.org/lkalesinskas/splot and is supported on the Linux and MS Windows operating systems

Mokytojų teikiamo grįžtamojo ryšio ir mokinių ketinimų palikti mokyklą sąsajos: esminių psichologinių poreikių vaidmuo

Teacher’s feedback is one of the most important factors in educational domain and is crucial in students’ academic motivation, performance and well-being at school. Students’ dropout from school is a common problem in many educational settings. Students who form dropout intentions can in the future act on these intentions. Self-determination theory is useful in explaining the ways how teacher’s feedback can influence the dropout intentions through satisfaction and thwarting of basic psychological needs for autonomy, competence, and relatedness. The goal of this study is to analyze the mediating role of basic psychological needs satisfaction and frustration in the relationships between positive and negative teacher’s feedback and student’s dropout intentions. The participants were 682 (aged 14–18; 49.1% females) students of I–III gymnasium grades from 7 schools. The results showed that only negative teacher’s feedback and the frustration of need for relatedness predicted dropout intentions. When teachers provide negative feedback, the students’ need for relatedness is frustrated and they are more likely to form dropout intentions. Even though the positive teacher’s feedback increases the satisfaction of students’ needs for autonomy, competence and relatedness, it does not predict dropout intentions. Finally, the results provided support for the assumed meditational role of one of the basic psychological need thwarting in teachers’ behavior as social factor to negative educational outcomes.Remiantis savideterminacijos teorija, straipsnyje analizuojamos mokytojų teikiamo teigiamo ir neigiamojo grįžtamojo ryšio bei mokinių ketinimų palikti mokyklą, atsižvelgiant į mokinių esminių psichologinių poreikių patenkinimą, sąsajos. Tyrime dalyvavo 682 I–III gimnazijos klasių mokiniai. Rezultatai parodė, kad tik suvoktas mokytojų teikiamas neigiamas grįžtamasis ryšys prognozuoja mokinių ketinimus palikti mokyklą tiek tiesiogiai, tiek per mokinių sąryšingumo poreikio frustraciją

Draft Genome Sequence of Micrococcus luteus (Schroeter) Cohn (ATCC 12698)

The actinobacterium Micrococcus luteus can be found in a wide variety of habitats. Here, we report the 2,411,958-bp draft genome sequence of the type strain M. leuteus (Schroeter) Cohn (ATCC 12698). Characteristic of this taxa, the genome sequence has a high G+C content, 73.14%

Draft Genome Sequences of Two ATCC Staphylococcus aureus subsp. aureus Strains

Draft genome sequences for Staphylococcus aureus subsp. aureus Rosenbach ATCC 14458 and ATCC 27217 strains were investigated. The genome sizes were 2,880,761 bp and 2,759,100 bp, respectively. Strain ATCC 14458 was assembled into 39 contigs, including 3 plasmids, and strain ATCC 27217 was assembled into 25 contigs, including 2 plasmids

Draft Genome Sequence of Enterococcus faecalis ATCC BAA-2128

While a part of the native gut microflora, the Gram-positive bacterium Enterococcus faecalis can lead to serious infections elsewhere in the body. The draft genome of E. faecalis strain ATCC BAA-2128, isolated from piglet feces, was examined. This draft genome consists of 42 contigs, 12 of which exhibit homology to annotated plasmids

Genome Sequences and Annotation of Two Urinary Isolates of E. Coli

The genus Escherichia includes pathogens and commensals. Bladder infections (cystitis) result most often from colonization of the bladder by uropathogenic E. coli strains. In contrast, a poorly defined condition called asymptomatic bacteriuria results from colonization of the bladder with E. coli strains without symptoms. As part of an on-going attempt to identify and characterize the newly discovered female urinary microbiota, we report the genome sequences and annotation of two urinary isolates of E. coli: one (E78) was isolated from a female patient who self-reported cystitis; the other (E75) was isolated from a female patient who reported that she did not have symptoms of cystitis. Whereas strain E75 is most closely related to an avian extraintestinal pathogen, strain E78 is a member of a clade that includes extraintestinal strains often found in the human bladder. Both genomes are uncommonly rich in prophages

Draft Genome for a Urinary Isolate of Lactobacillus crispatus

While Lactobacillus crispatus contributes to the stability of normal vaginal microbiota, its role in urinary health remains unclear. As part of an on-going attempt to characterize the female urinary microbiota, we report the genome sequence of an L. crispatus strain isolated from a woman displaying no lower urinary tract symptoms

Increasing reproducibility, robustness, and generalizability of biomarker selection from meta-analysis using Bayesian methodology.

A major limitation of gene expression biomarker studies is that they are not reproducible as they simply do not generalize to larger, real-world, heterogeneous populations. Frequentist multi-cohort gene expression meta-analysis has been frequently used as a solution to this problem to identify biomarkers that are truly differentially expressed. However, the frequentist meta-analysis framework has its limitations-it needs at least 4-5 datasets with hundreds of samples, is prone to confounding from outliers and relies on multiple-hypothesis corrected p-values. To address these shortcomings, we have created a Bayesian meta-analysis framework for the analysis of gene expression data. Using real-world data from three different diseases, we show that the Bayesian method is more robust to outliers, creates more informative estimates of between-study heterogeneity, reduces the number of false positive and false negative biomarkers and selects more generalizable biomarkers with less data. We have compared the Bayesian framework to a previously published frequentist framework and have developed a publicly available R package for use