Experimental design trade-offs for gene regulatory network inference: an in silico study of the yeast Saccharomyces cerevisiae cell cycle

Time-series of high throughput gene sequencing data intended for gene regulatory network (GRN) inference are often short due to the high costs of sampling cell systems. Moreover, experimentalists lack a set of quantitative guidelines that prescribe the minimal number of samples required to infer a reliable GRN model. We study the temporal resolution of data vs quality of GRN inference in order to ultimately overcome this deficit. The evolution of a Markovian jump process model for the Ras/cAMP/PKA pathway of proteins and metabolites in the G1 phase of the Saccharomyces cerevisiae cell cycle is sampled at a number of different rates. For each time-series we infer a linear regression model of the GRN using the LASSO method. The inferred network topology is evaluated in terms of the area under the precision-recall curve AUPR. By plotting the AUPR against the number of samples, we show that the trade-off has a, roughly speaking, sigmoid shape. An optimal number of samples corresponds to values on the ridge of the sigmoid

Body mass index and blood pressure in a semi-urban community in Ota, Nigeria

This study was designed to establish the relationship between body mass index (BMI) and blood pressure (BP) in an increasingly industrialised town in Nigeria due to the rising prevalence of hypertension in non-industrialised countries. Factors associated with BMI and BP levels were determined in three hundred adult male and female subjects in Ota community of Ogun State, Nigeria. The levels of the overweight among the male and female subjects were 53.03 % and 47.37 % respectively. The levels of hypertensive male and female subjects were 40.91 % and 35.34 % respectively. The overweight and underweight among the hypertensive male were 54.29 % and 0 % respectively; while the overweight and underweight among the hypertensive female were 42.86 % and 28.57 % respectively. Hypertension among the overweight, and hypotension among the underweight, are major health concern in Ota that requires intensive medical care

VirSorter Curated Dataset genbank file package

This zip package includes the annotated genbank files (affiliation against PFAM and Refseq) of all viral sequences predicted in the VirSorter Curated Dataset, organized in different folders based on the host of the virus (i.e. the taxonomy of the genomic data in which the viral sequence was identified)

Additional file 2 of Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics

Additional file 2: Supplementary Data 1. Genome information of SHIPPO MAGs. Supplementary Data 2. (DOI link: https://doi.org/10.6084/m9.figshare.17161715 ). Genome files of SHIPPO MAGs

Additional file 3 of Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics

Additional file 3: Supplementary Data 3. RM system of MAGs from ocean metagenomic studies

Additional file 4 of Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics

Additional file 4: Supplementary Data 4. Methylation profiles of 5-mer motifs across MAGs and sampling stations

Additional file 1 of Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics

Additional file 1: Supplementary Figure S1. SHIPPO samples in the northwest Pacific Ocean. Supplementary Figure S2. Compositional profile of microbial communities spanning eukaryotes, prokaryotes, and viruses. Supplementary Figure S3. The Cand. P. Giovannoni NP1 genome-wide distribution of methylated fractions. Supplementary Figure S4. The Pelagibacter (SHIPPO PRO 33) genome-wide distribution of methylated fractions. Supplementary Figure S5. GANTC motif density in the SHIPPO_PRO_33 genome. Supplementary Figure S6. Phylogenetic tree of eukaryotic plankton MAGs obtained from SHIPPO. Supplementary Figure S7. The GANTC methylation proportion comparison according to the genome fraction in six species belonging to the Alphaproteobacteria. Supplementary Figure S8. Benchmarking of viral taxonomy classification according to the number and fraction of viral genes. Supplementary Table S1. SHIPPO samples in the northwest Pacific Ocean. Supplementary Table S2. Methylated motifs of SHIPPO MAGs. Supplementary Table S3. Unmethylated GANTC sites across samples

Genomic context and phylogenetic analysis of the Peptidase M15 <i>Microviridae</i> sequences.

<p><b>(</b>A) Organization of the Peptidase M15_3 region in the 11 newly assembled <i>Microviridae</i> genomes. The regions encompassing homologous peptidase genes in three bacterial and two phages (noted with a black circle) genomes are also shown. <i>P2 GpR</i> stands for the P2 phage tail completion protein. (B) Maximum-likelihood tree computed from the multiple alignment of peptidase M15 sequences of the <i>Microvidae</i> and their closest homologues in viral and bacterial genomes. Bootstrap support values are indicated on each node. A fully expanded view of this tree is available as <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040418#pone.0040418.s009" target="_blank">Fig. S9</a>.</p

Major capsid protein (MCP) variation within the <i>Microviridae</i>.

<p> (A) Three-dimensional model of the SpV4 virion (PDB ID:1KVP). Three capsomers donating long insertion loops to form the ‘mushroom-like’ protrusions at the three-fold axes of symmetry of the icosahedral capsid are highlighted in blue, green, and red. (B) A boxplot illustrating the variation of MCP sizes between the four subgroups of the <i>Microviridae</i>. (C) Three-dimensional models of the MCPs from viruses representing the four subgroups of the <i>Microviridae</i>: <i>Microvirus</i> (ΦX174 protein F; PDB ID:1CD3), <i>Gokushovirinae</i> (SpV4 VP1, PDB ID:1KVP), <i>Alpavirinae</i> (<i>Prevotella bucalis</i> prophage BMV5 protein VP1; GI:282877220), <i>Pichovirinae</i> (Pavin_279 protein VP1). The insertions within the VP1 proteins of gokusho-, alpa- and pichoviruses relative to the F protein of ΦX174 are highlighted in green.</p

Assembled_chimeric_viruses_Gb-files

This zip package contains the annotated genbank file for each chimeric virus genome described and analyzed in the manuscript