Comparison of four quick and reliable methods of assessing body fat appropriate for clinical settings among young, middle-age, and older healthy male and female adults.

[Purpose] Compare four quick (approximately 60 s), reliable methods of assessing %body-fat (%BF) among young (Y, 18-34 years), middle-age (M, 35-59 years), and older (O, 60-88 years) healthy-adults. [Participants and Methods] One-hundred-eighty healthy males-and-females were equally (n=30) divided into Y, M, and O age groups to assess %BF. The %BF methods were: 1) Bioelectrical-impedance-Inbody770 (IB)-criterion reference; 2) Body-mass-index (BMI); 3) Abdominal-and-hip circumferences (CIR); and 4) Skinfold (SF).

Effects of Ankle Position While Performing One- and Two-Leg Floor Bridging Exercises on Core and Lower Extremity Muscle Recruitment.

Given there are no known studies which have examined multiple lower extremity muscles between different ankle positions during bridging activities, the objective was to assess how employing two different ankle positions (PF versus DF) while performing five common bridging exercises (three bipedal and two unipedal) used in rehabilitation and athletic performance affect core and select lower extremity muscle EMG recruitment. Twenty healthy subjects performed a 5 s isometric hold during five two- and one-leg bridge exercises: (1) on right leg with left knee to chest (1LB-LFlex); (2) on right leg with left knee extended (1LB-LExt); (3) standard two-leg bridge (2LB); (4) two-leg bridge with resistance band around knees (2LB-ABD); and (5) two-leg bridge with ball between knees (2LB-ADD). Surface electromyographic (EMG) data were collected using a Noraxon Telemyo Direct Transmission System from fourteen muscles: (1) three superficial quadriceps (VM, VL, and RF); (2) three hip abductors (TFL, GMED, and GMAX); (3) medial hamstrings (ST) and lateral hamstrings (BF); (4) hip adductors (ADD); (5) erector spinae (ES); (6) latissimus dorsi (LATS); (7) upper rectus abdominis (RA); and (8) external oblique (EO) and internal oblique (IO).

Publisher Correction: The calcium-permeable channel OSCA1.3 regulates plant stomatal immunity.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The calcium-permeable channel OSCA1.3 regulates plant stomatal immunity.

Perception of biotic and abiotic stresses often leads to stomatal closure in plants. Rapid influx of calcium ions (Ca) across the plasma membrane has an important role in this response, but the identity of the Ca channels involved has remained elusive. Here we report that the Arabidopsis thaliana Ca-permeable channel OSCA1.

Rapid fine mapping of causative mutations from sets of unordered, contig-sized fragments of genome sequence.

Background: Traditional Map based Cloning approaches, used for the identification of desirable alleles, are extremely labour intensive and years can elapse between the mutagenesis and the detection of the polymorphism. High throughput sequencing based Mapping-by-sequencing approach requires an ordered genome assembly and cannot be used with fragmented, un-scaffolded draft genomes, limiting its application to model species and precluding many important organisms.

Results: We addressed this gap in resource and presented a computational method and software implementations called CHERIPIC (Computing Homozygosity Enriched Regions In genomes to Prioritise Identification of Candidate variants).

Arabidopsis downy mildew effector HaRxL106 suppresses plant immunity by binding to RADICAL-INDUCED CELL DEATH1.

The oomycete pathogen Hyaloperonospora arabidopsidis (Hpa) causes downy mildew disease on Arabidopsis. To colonize its host, Hpa translocates effector proteins that suppress plant immunity into infected host cells. Here, we investigate the relevance of the interaction between one of these effectors, HaRxL106, and Arabidopsis RADICAL-INDUCED CELL DEATH1 (RCD1).

Plant immune and growth receptors share common signalling components but localise to distinct plasma membrane nanodomains.

Cell surface receptors govern a multitude of signalling pathways in multicellular organisms. In plants, prominent examples are the receptor kinases FLS2 and BRI1, which activate immunity and steroid-mediated growth, respectively. Intriguingly, despite inducing distinct signalling outputs, both receptors employ common downstream signalling components, which exist in plasma membrane (PM)-localised protein complexes.

The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers.

Summary: Rapid technological advances have led to an explosion of biomedical data in recent years. The pace of change has inspired new collaborative approaches for sharing materials and resources to help train life scientists both in the use of cutting-edge bioinformatics tools and databases and in how to analyse and interpret large datasets. A prototype platform for sharing such training resources was recently created by the Bioinformatics Training Network (BTN).

EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics.

Background: Next Generation Sequencing technologies have facilitated differential gene expression analysis through RNA-seq and Tag-seq methods. RNA-seq has biases associated with transcript lengths, lacks uniform coverage of regions in mRNA and requires 10-20 times more reads than a typical Tag-seq. Most existing Tag-seq methods either have biases or not high throughput due to use of restriction enzymes or enzymatic manipulation of 5' ends of mRNA or use of RNA ligations.

Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.

Accurate identification of DNA polymorphisms using next-generation sequencing technology is challenging because of a high rate of sequencing error and incorrect mapping of reads to reference genomes. Currently available short read aligners and DNA variant callers suffer from these problems. We developed the Coval software to improve the quality of short read alignments.

SVGenes: a library for rendering genomic features in scalable vector graphic format.

Motivation: Drawing genomic features in attractive and informative ways is a key task in visualization of genomics data. Scalable Vector Graphics (SVG) format is a modern and flexible open standard that provides advanced features including modular graphic design, advanced web interactivity and animation within a suitable client. SVGs do not suffer from loss of image quality on re-scaling and provide the ability to edit individual elements of a graphic on the whole object level independent of the whole image.

Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors.

Background: Wheat yellow (stripe) rust caused by Puccinia striiformis f. sp. tritici (PST) is one of the most devastating diseases of wheat worldwide.

Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.

Single Nucleotide Polymorphisms are invaluable markers for tracing the genetic basis of inheritable traits and the ability to create marker libraries quickly is vital for timely identification of target genes. Next-generation sequencing makes it possible to sample a genome rapidly, but polymorphism detection relies on having a reference genome to which reads can be aligned and variants detected. We present Bubbleparse, a method for detecting variants directly from next-generation reads without a reference sequence.

Spatio-temporal cellular dynamics of the Arabidopsis flagellin receptor reveal activation status-dependent endosomal sorting.

The activity of surface receptors is location specific, dependent upon the dynamic membrane trafficking network and receptor-mediated endocytosis (RME). Therefore, the spatio-temporal dynamics of RME are critical to receptor function. The plasma membrane receptor flagellin sensing2 (FLS2) confers immunity against bacterial infection through perception of flagellin (flg22).

Genome analyses of an aggressive and invasive lineage of the Irish potato famine pathogen.

Pest and pathogen losses jeopardise global food security and ever since the 19(th) century Irish famine, potato late blight has exemplified this threat. The causal oomycete pathogen, Phytophthora infestans, undergoes major population shifts in agricultural systems via the successive emergence and migration of asexual lineages. The phenotypic and genotypic bases of these selective sweeps are largely unknown but management strategies need to adapt to reflect the changing pathogen population.

Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments.

Background: The SAMtools utilities comprise a very useful and widely used suite of software for manipulating files and alignments in the SAM and BAM format, used in a wide range of genetic analyses. The SAMtools utilities are implemented in C and provide an API for programmatic access, to help make this functionality available to programmers wishing to develop in the high level Ruby language we have developed bio-samtools, a Ruby binding to the SAMtools library.

Results: The utility of SAMtools is encapsulated in 3 main classes, Bio::DB::Sam, representing the alignment files and providing access to the data in them, Bio::DB::Alignment, representing the individual read alignments inside the files and Bio::DB::Pileup, representing the summarised nucleotides of reads over a single point in the nucleotide sequence to which the reads are aligned.

Gee Fu: a sequence version and web-services database tool for genomic assembly, genome feature and NGS data.

Summary: Scientists now use high-throughput sequencing technologies and short-read assembly methods to create draft genome assemblies in just days. Tools and pipelines like the assembler, and the workflow management environments make it easy for a non-specialist to implement complicated pipelines to produce genome assemblies and annotations very quickly. Such accessibility results in a proliferation of assemblies and associated files, often for many organisms.

The hyphal tip structure of Basidiobolus sp.: a zygomycete fungus of uncertain phylogeny.

To date, among the zygomycete fungi that have been examined, a Spitzenkörper has not been reported. In this paper, the cytoplasmic order of hyphal tip cells of Basidiobolus sp., a zygomycete genus of uncertain phylogeny, has been examined using light microscopy and transmission electron microscopy methods.

Genome evolution following host jumps in the Irish potato famine pathogen lineage.

Many plant pathogens, including those in the lineage of the Irish potato famine organism Phytophthora infestans, evolve by host jumps followed by specialization. However, how host jumps affect genome evolution remains largely unknown. To determine the patterns of sequence variation in the P.

Genome-wide sequencing data reveals virulence factors implicated in banana Xanthomonas wilt.

Banana Xanthomonas wilt is a newly emerging disease that is currently threatening the livelihoods of millions of farmers in East Africa. The causative agent is Xanthomonas campestris pathovar musacearum (Xcm), but previous work suggests that this pathogen is much more closely related to species Xanthomonas vasicola than to X. campestris.

Disruption of two defensive signaling pathways by a viral RNA silencing suppressor.

The Cucumber mosaic virus (CMV) 2b counter-defense protein disrupts plant antiviral mechanisms mediated by RNA silencing and salicylic acid (SA). We used microarrays to investigate defensive gene expression in 2b-transgenic Arabidopsis thaliana plants. Surprisingly, 2b inhibited expression of few SA-regulated genes and, in some instances, enhanced the effect of SA on certain genes.

Evidence for large complex networks of plant short silencing RNAs.

Background: In plants and animals there are many classes of short RNAs that carry out a wide range of functions within the cell; short silencing RNAs (ssRNAs) of 21-25 nucleotides in length are produced from double-stranded RNA precursors by the protein Dicer and guide nucleases and other proteins to their RNA targets through base pairing interactions. The consequence of this process is degradation of the targeted RNA, suppression of its translation or initiation of secondary ssRNA production. The secondary ssRNAs in turn could then initiate further layers of ssRNA production to form extensive cascades and networks of interacting RNA [1].

A Boolean model of the Pseudomonas syringae hrp regulon predicts a tightly regulated system.

The Type III secretion system (TTSS) is a protein secretion machinery used by certain gram-negative bacterial pathogens of plants and animals to deliver effector molecules to the host and is at the core of the ability to cause disease. Extensive molecular and biochemical study has revealed the components and their interactions within this system but reductive approaches do not consider the dynamical properties of the system as a whole. In order to gain a better understanding of these dynamical behaviours and to create a basis for the refinement of the experimentally derived knowledge we created a Boolean model of the regulatory interactions within the hrp regulon of Pseudomonas syringae pathovar tomato strain DC3000 Pseudomonas syringae.

Finding sRNA generative locales from high-throughput sequencing data with NiBLS.

Background: Next-generation sequencing technologies allow researchers to obtain millions of sequence reads in a single experiment. One important use of the technology is the sequencing of small non-coding regulatory RNAs and the identification of the genomic locales from which they originate. Currently, there is a paucity of methods for finding small RNA generative locales.