A Retrospective Review of Reclassification of Variants of Uncertain Significance in a Pediatric Epilepsy Cohort Undergoing Genetic Panel Testing.

Background: The interpretation and communication of variant of uncertain significance (VUS) genetic results often present a challenge in clinical practice. VUSs can be reclassified over time into benign/likely benign (B/LB) or pathogenic/likely pathogenic (P/LP) based on the availability of updated data. We evaluate the frequency of VUS reclassification in our tertiary care epilepsy cohort undergoing epilepsy genetic panel (EGP) testing.

Requirement of a Wnt5A-microbiota axis in the maintenance of gut B-cell repertoire and protection from infection.

We investigated the influence of a Wnt5A-gut microbiota axis on gut B-cell repertoire and protection from infection, having previously demonstrated that Wnt5A in association with gut commensals helps shape gut T-cell repertoire. Accordingly, Wnt5A heterozygous mice, which express less than wild-type level of Wnt5A, and their isolated Peyer's patches (PPs) were studied in comparison with the wild-type counterparts. The percentages of IgM- and IgA-expressing B cells were quite similar in the PP of both sets of mice.

An RNA-Seq Data Analysis Pipeline.

In this chapter, we present an established pipeline for analyzing RNA-Seq data, which involves a step-by-step flow starting from raw data obtained from a sequencer and culminating in the identification of differentially expressed genes with their functional characterization. The pipeline is divided into three sections, each addressing crucial stages of the analysis process. The first section covers the initial steps of the pipeline, including downloading of the data of interest and performing quality control assessment.

WRKY48 negatively regulates plant acclimation to a combination of high light and heat stress.

Plants growing under natural conditions experience high light (HL) intensities that are often accompanied by elevated temperatures. These conditions could affect photosynthesis, reduce yield, and negatively impact agricultural productivity. The combination of different abiotic challenges creates a new type of stress for plants by generating complex environmental conditions that often exceed the impact of their individual parts.

Therapeutic potential of rWnt5A in curbing infection.

In view of the antagonism of Wnt5A signaling toward microbial pathogens, we were interested in evaluating the therapeutic potential of recombinant Wnt5A (rWnt5A) in curbing infection. Initially, using -infected RAW 264.7 and peritoneal macrophages, we demonstrated that application of rWnt5A as opposed to the vehicle control to the infected cells significantly dampens infection.

Leveraging comparative genomics to uncover alien genes in bacterial genomes.

A significant challenge in bacterial genomics is to catalogue genes acquired through the evolutionary process of horizontal gene transfer (HGT). Both comparative genomics and sequence composition-based methods have often been invoked to quantify horizontally acquired genes in bacterial genomes. Comparative genomics methods rely on completely sequenced genomes and therefore the confidence in their predictions increases as the databases become more enriched in completely sequenced genomes.

Wnt5A Signaling Regulates Gut Bacterial Survival and T Cell Homeostasis.

In light of the demonstrated antagonism of Wnt5A signaling toward the growth of several bacterial pathogens, it was important to study the influence of Wnt5A on gut-resident bacteria and its outcome. Here, we demonstrate that in contrast to inhibiting the survival of the established gut pathogen Salmonella enterica, Wnt5A clearly promotes the survival of the common gut commensals Enterococcus faecalis and Lactobacillus rhamnosus within macrophages through a self-perpetuating Wnt5A-actin axis. A Wnt5A-actin axis furthermore regulates the subsistence of the natural bacterial population of the Peyer's patches, as is evident from the diminution in the countable bacterial CFU therein through the application of Wnt5A signaling and actin assembly inhibitors.

Reconstructing horizontal gene flow network to understand prokaryotic evolution.

Horizontal gene transfer (HGT) is a major source of phenotypic innovation and a mechanism of niche adaptation in prokaryotes. Quantification of HGT is critical to decipher its myriad roles in microbial evolution and adaptation. Advances in genome sequencing and bioinformatics have augmented our ability to understand the microbial world, particularly the direct or indirect influence of HGT on diverse life forms.

Phytochrome B regulates reactive oxygen signaling during abiotic and biotic stress in plants.

Reactive oxygen species (ROS) and the photoreceptor protein phytochrome B (phyB) play a key role in plant acclimation to stress. However, how phyB that primarily functions in the nuclei impacts ROS signaling mediated by respiratory burst oxidase homolog (RBOH) proteins that reside on the plasma membrane, during stress, is unknown. Arabidopsis thaliana and Oryza sativa mutants, RNA-Seq, bioinformatics, biochemistry, molecular biology, and whole-plant ROS imaging were used to address this question.

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.

A Protocol for Phylogenetic Reconstruction.

The similarity of biological functions and molecular mechanisms in living organisms suggests their common origin. The inference of evolutionary relationships among the extant organisms is primarily based on structural, functional, and sequence data of biomolecules, such as DNA, RNA, and protein, and their relative changes over the course of time. To decipher evolutionary relationships, a variety of data can be used.

Wnt5A-Mediated Actin Organization Regulates Host Response to Bacterial Pathogens and Non-Pathogens.

Wnt5A signaling facilitates the killing of several bacterial pathogens, but not the non-pathogen DH5α. The basis of such pathogen vs. non-pathogen distinction is unclear.

The impact of multifactorial stress combination on plant growth and survival.

Climate change-driven extreme weather events, combined with increasing temperatures, harsh soil conditions, low water availability and quality, and the introduction of many man-made pollutants, pose a unique challenge to plants. Although our knowledge of the response of plants to each of these individual conditions is vast, we know very little about how a combination of many of these factors, occurring simultaneously, that is multifactorial stress combination, impacts plants. Seedlings of wild-type and different mutants of Arabidopsis thaliana plants were subjected to a multifactorial stress combination of six different stresses, each applied at a low level, and their survival, physiological and molecular responses determined.

The impact of water deficit and heat stress combination on the molecular response, physiology, and seed production of soybean.

A combination of drought and heat stress, occurring at the vegetative or reproductive growth phase of many different crops can have a devastating impact on yield. In soybean (Glycine max), a considerable effort has been made to develop genotypes with enhanced yield production under conditions of drought or heat stress. However, how these genotypes perform in terms of growth, physiological responses, and most importantly seed production, under conditions of drought and heat combination is mostly unknown.

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.

Systemic signaling during abiotic stress combination in plants.

Extreme environmental conditions, such as heat, salinity, and decreased water availability, can have a devastating impact on plant growth and productivity, potentially resulting in the collapse of entire ecosystems. Stress-induced systemic signaling and systemic acquired acclimation play canonical roles in plant survival during episodes of environmental stress. Recent studies revealed that in response to a single abiotic stress, applied to a single leaf, plants mount a comprehensive stress-specific systemic response that includes the accumulation of many different stress-specific transcripts and metabolites, as well as a coordinated stress-specific whole-plant stomatal response.

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.

Jasmonic Acid Is Required for Plant Acclimation to a Combination of High Light and Heat Stress.

In the field, plants experience high light (HL) intensities that are often accompanied by elevated temperatures. Such conditions are a serious threat to agriculture production, because photosynthesis is highly sensitive to both HL intensities and high-temperature stress. One of the potential cellular targets of HL and heat stress (HS) combination is PSII because its degree of photoinhibition depends on the balance between the rate of PSII damage (induced by light stress), and the rate of PSII repair (impaired under HS).

Identification and characterization of a core set of ROS wave-associated transcripts involved in the systemic acquired acclimation response of Arabidopsis to excess light.

Systemic acquired acclimation (SAA) plays a key role in optimizing growth and preventing damage associated with fluctuating or abrupt changes in the plant environment. To be effective, SAA has to occur at a rapid rate and depend on rapid signaling pathways that transmit signals from affected tissues to all parts of the plant. Although recent studies have identified several different rapid systemic signaling pathways that could mediate SAA, very little information is known about the extent of their involvement in mediating transcriptomic responses.

Rapid Responses to Abiotic Stress: Priming the Landscape for the Signal Transduction Network.

Plants grow and reproduce within a highly dynamic environment that can see abrupt changes in conditions, such as light intensity, temperature, humidity, or interactions with biotic agents. Recent studies revealed that plants can respond within seconds to some of these conditions, engaging many different metabolic and molecular networks, as well as rapidly altering their stomatal aperture. Some of these rapid responses were further shown to propagate throughout the entire plant via waves of reactive oxygen species (ROS) and Ca that are possibly mediated through the plant vascular system.

Phylogenetic analysis of the CDGSH iron-sulfur binding domain reveals its ancient origin.

The iron-sulfur (2Fe-2S) binding motif CDGSH appears in many important plant and animal proteins that regulate iron and reactive oxygen metabolism. In human it is found in CISD1-3 proteins involved in diabetes, obesity, cancer, aging, cardiovascular disease and neurodegeneration. Despite the important biological role of the CDGSH domain, its origin, evolution and diversification, are largely unknown.

Deciphering pathogenicity and antibiotic resistance islands in methicillin-resistant genomes.

is a versatile pathogen that is capable of causing infections in both humans and animals. It can cause furuncles, septicaemia, pneumonia and endocarditis. Adaptation of to the modern hospital environment has been facilitated, in part, by the horizontal acquisition of drug resistance genes, such as gene that imparts resistance to methicillin.

Mobile Health Application and e-Health Literacy: Opportunities and Concerns for Cancer Patients and Caregivers.

Health literacy is critical for cancer patients as they must understand complex procedures or treatment options. Caregivers' health literacy also plays a crucial role in caring for cancer patients. Low health literacy is associated with low adherence to medications, poor health status, and increased health care costs.