RNA Sequencing Experimental Analysis Workflow Using Caenorhabditis elegans.

RNA sequencing is an approach to transcriptomic profiling that enables the detection of differentially expressed genes in response to genetic mutation or experimental treatment, among other uses. Here we describe a method for the use of a customizable, user-friendly bioinformatic pipeline to identify differentially expressed genes in RNA sequencing data obtained from C. elegans, with attention to the improvement in reproducibility and accuracy of results.

Benchmarking RNA-Seq Aligners at Base-Level and Junction Base-Level Resolution Using the Genome.

The utmost goal of selecting an RNA-Seq alignment software is to perform accurate alignments with a robust algorithm, which is capable of detecting the various intricacies underlying read-mapping procedures and beyond. Most alignment software tools are typically pre-tuned with human or prokaryotic data, and therefore may not be suitable for applications to other organisms, such as plants. The rapidly growing plant RNA-Seq databases call for the assessment of the alignment tools on curated plant data, which will aid the calibration of these tools for applications to plant transcriptomic data.

The OsTIL1 lipocalin protects cell membranes from reactive oxygen species damage and maintains the 18:3-containing glycerolipid biosynthesis under cold stress in rice.

Lipocalins constitute a conserved protein family that binds to and transports a variety of lipids while fatty acid desaturases (FADs) are required for maintaining the cell membrane fluidity under cold stress. Nevertheless, it remains unclear whether plant lipocalins promote FADs for the cell membrane integrity under cold stress. Here, we identified the role of OsTIL1 lipocalin in FADs-mediated glycerolipid remodeling under cold stress.

Deciphering the sex bias in housekeeping gene expression in adipose tissue: a comprehensive meta-analysis of transcriptomic studies.

Background: As the housekeeping genes (HKG) generally involved in maintaining essential cell functions are typically assumed to exhibit constant expression levels across cell types, they are commonly employed as internal controls in gene expression studies. Nevertheless, HKG may vary gene expression profile according to different variables introducing systematic errors into experimental results. Sex bias can indeed affect expression display, however, up to date, sex has not been typically considered as a biological variable.

POSMM: an efficient alignment-free metagenomic profiler that complements alignment-based profiling.

We present here POSMM (pronounced 'Possum'), Python-Optimized Standard Markov Model classifier, which is a new incarnation of the Markov model approach to metagenomic sequence analysis. Built on the top of a rapid Markov model based classification algorithm SMM, POSMM reintroduces high sensitivity associated with alignment-free taxonomic classifiers to probe whole genome or metagenome datasets of increasingly prohibitive sizes. Logistic regression models generated and optimized using the Python sklearn library, transform Markov model probabilities to scores suitable for thresholding.

Evaluation of pathways to the -glycosyl isoflavone puerarin in roots of kudzu ().

Kudzu () is used as a traditional medicine in China and Southeast Asia but is a noxious weed in the Southeastern United States. It produces both - and glycosylated isoflavones, with puerarin (-glucosyl daidzein) as an important bioactive compound. Currently, the stage of the isoflavone pathway at which the glycosyl unit is added remains unclear, with a recent report of direct glycosylation of daidzein contradicting earlier labeling studies supporting glycosylation at the level of chalcone.

Mutational and splicing landscape in a cohort of 43,000 patients tested for hereditary cancer.

DNA germline genetic testing can identify individuals with cancer susceptibility. However, DNA sequencing alone is limited in its detection and classification of mRNA splicing variants, particularly those located far from coding sequences. Here we address the limitations of splicing variant identification and interpretation by pairing DNA and RNA sequencing and describe the mutational and splicing landscape in a clinical cohort of 43,524 individuals undergoing genetic testing for hereditary cancer predisposition.

Mapping Strengths and Weaknesses of Different Clustering Approaches to Deciphering Bacterial Chimerism.

Bacterial genomes are chimeras of DNA of different ancestries. Deconstructing chimeric genomes is central to understanding the evolutionary trajectories of their disparate components and thus the organisms as a whole in the light of their evolutionary contexts. Of specific interest is to delineate and quantify native (vertically inherited) and alien (horizontally acquired) components of bacterial genomes and also specify genomic fractions that represent different donor sources.

The gene co-expression network.

Identifying genes that interact to confer a biological function to an organism is one of the main goals of functional genomics. High-throughput technologies for assessment and quantification of genome-wide gene expression patterns have enabled systems-level analyses to infer pathways or networks of genes involved in different functions under many different conditions. Here, we leveraged the publicly available, information-rich RNA-Seq datasets of the model plant to construct a gene co-expression network, which was partitioned into clusters or modules that harbor genes correlated by expression.

Analysis of transcribed sequences from young and mature zebrafish thrombocytes.

The zebrafish is an excellent model system to study thrombocyte function and development. Due to the difficulties in separating young and mature thrombocytes, comparative transcriptomics between these two cell types has not been performed. It is important to study these differences in order to understand the mechanism of thrombocyte maturation.

RNA-Seq Data Analysis Pipeline for Plants: Transcriptome Assembly, Alignment, and Differential Expression Analysis.

In this chapter, we describe methods for analyzing RNA-Seq data, presented as a flow along a pipeline beginning with raw data from a sequencer and ending with an output of differentially expressed genes and their functional characterization. The first section covers de novo transcriptome assembly for organisms lacking reference genomes or for those interested in probing against the background of organism-specific transcriptomes assembled from RNA-Seq data. Section 2 covers both gene- and transcript-level quantifications, leading to the third and final section on differential expression analysis between two or more conditions.

Role of ribosomal RNA released from red cells in blood coagulation in zebrafish and humans.

Hemolytic disorders are characterized by hemolysis and are prone to thrombosis. It has previously been shown that the RNA released from damaged blood cells activates clotting. However, the nature of the RNA released from hemolysis is still elusive.

Dapagliflozin Does Not Modulate Atherosclerosis in Mice with Insulin Resistance.

Type 2 diabetes mellitus (T2DM) increases morbimortality in humans via enhanced susceptibility to cardiovascular disease (CVD). Sodium-glucose co-transporter 2 inhibitors (SGLT2i) are drugs designed for T2DM treatment to diminish hyperglycaemia by reducing up to 90% of renal tube glucose reabsorption. Clinical studies also suggest a beneficial action of SGLT2i in heart failure and CVD independent of its hypoglycaemiant effect.

Lipophilic signals lead to organ-specific gene expression changes in seedlings.

In plants, -acylethanolamines (NAEs) are most abundant in desiccated seeds and their levels decline during germination and early seedling establishment. However, endogenous NAE levels rise in seedlings when ABA or environmental stress is applied, and this results in an inhibition of further seedling development. When the most abundant, polyunsaturated NAEs of linoleic acid (18:2) and linolenic acid (18:3) were exogenously applied, seedling development was affected in an organ-specific manner.

MYB30 Orchestrates Systemic Reactive Oxygen Signaling and Plant Acclimation.

Systemic acquired acclimation (SAA) is a key biological process essential for plant survival under conditions of abiotic stress. SAA was recently shown to be controlled by a rapid systemic signaling mechanism termed the reactive oxygen species (ROS) wave in Arabidopsis (). MYB30 is a key transcriptional regulator mediating many different biological processes.

Higher-order Markov models for metagenomic sequence classification.

Motivation: Alignment-free, stochastic models derived from k-mer distributions representing reference genome sequences have a rich history in the classification of DNA sequences. In particular, the variants of Markov models have previously been used extensively. Higher-order Markov models have been used with caution, perhaps sparingly, primarily because of the lack of enough training data and computational power.

A High-Throughput In Situ Method for Estimation of Hepatocyte Nuclear Ploidy in Mice.

When the liver is injured, hepatocyte numbers decrease, while cell size, nuclear size and ploidy increase. The expansion of non-parenchymal cells such as cholangiocytes, myofibroblasts, progenitors and inflammatory cells also indicate chronic liver damage, tissue remodeling and disease progression. In this protocol, we describe a simple high-throughput approach for calculating changes in the cellular composition of the liver that are associated with injury, chronic disease and cancer.

Proactive interference apraxic agraphia: a writing and drawing disorder associated with corticobasal syndrome.

Proactive interference is when a previously performed task impairs performance on a current task. It is often associated with memory tasks and has not been reported to interfere with writing or drawing. We evaluated a left-handed man diagnosed with corticobasal syndrome who had a two-year history of progressive agraphia.

The genome of jojoba (): A taxonomically isolated species that directs wax ester accumulation in its seeds.

Seeds of the desert shrub, jojoba (), are an abundant, renewable source of liquid wax esters, which are valued additives in cosmetic products and industrial lubricants. Jojoba is relegated to its own taxonomic family, and there is little genetic information available to elucidate its phylogeny. Here, we report the high-quality, 887-Mb genome of jojoba assembled into 26 chromosomes with 23,490 protein-coding genes.

Molecular analysis of the effects of steroid hormones on mouse meiotic prophase I progression.

Background: Infertility is linked to depletion of the primordial follicle pool consisting of individual oocytes arrested at the diplotene stage of meiotic prophase I surrounded by granulosa cells. Primordial germ cells, the oocyte precursors, begin to differentiate during embryonic development. These cells migrate to the genital ridge and begin mitotic divisions, remaining connected, through incomplete cytokinesis, in clusters of synchronously dividing oogonia known as germ cell cysts.

Expression of a dominant-negative AtNEET-H89C protein disrupts iron-sulfur metabolism and iron homeostasis in Arabidopsis.

Iron-sulfur (Fe-S) clusters play an essential role in plants as protein cofactors mediating diverse electron transfer reactions. Because they can react with oxygen to form reactive oxygen species (ROS) and inflict cellular damage, the biogenesis of Fe-S clusters is highly regulated. A recently discovered group of 2Fe-2S proteins, termed NEET proteins, was proposed to coordinate Fe-S, Fe and ROS homeostasis in mammalian cells.

Vertical and Radial Attentional Neglect in Corticobasal Syndrome.

Corticobasal degeneration (CBD), a tau-related neurodegenerative disease, is characterized by limb rigidity, dystonia, myoclonus, apraxia, and cognitive deficits. We report a patient with probable corticobasal syndrome, a major phenotype of CBD, who revealed both lower vertical and proximal radial attentional neglect on line bisection tests. Brain imaging revealed bilateral parietal atrophy with hypometabolism in the bilateral parietal, dorsolateral prefrontal, and premotor cortices.

Type 1 diabetic mellitus patients with increased atherosclerosis risk display decreased CDKN2A/2B/2BAS gene expression in leukocytes.

Background: Type 1 diabetes mellitus (T1DM) patients display increased risk of cardiovascular disease (CVD) and are characterized by a diminished regulatory T (Treg) cell content or function. Previous studies have shown an association between decreased CDKN2A/2B/2BAS gene expression and enhanced CVD. In the present study the potential relationship between CDKN2A/2B/2BAS gene expression, immune cell dysfunction and increased cardiovascular risk in T1DM patients was explored.