mtDNA "nomenclutter" and its consequences on the interpretation of genetic data.

Population-based studies of human mitochondrial genetic diversity often require the classification of mitochondrial DNA (mtDNA) haplotypes into more than 5400 described haplogroups, and further grouping those into hierarchically higher haplogroups. Such secondary haplogroup groupings (e.g.

Assessing patterns of metazoans in the global ocean using environmental DNA.

Documenting large-scale patterns of animals in the ocean and determining the drivers of these patterns is needed for conservation efforts given the unprecedented rates of change occurring within marine ecosystems. We used existing datasets from two global expeditions, and , that circumnavigated the oceans and sampled down to 4000 m to assess metazoans from environmental DNA (eDNA) extracted from seawater. We describe patterns of taxonomic richness within metazoan phyla and orders based on metabarcoding and infer the relative abundance of phyla using metagenome datasets, and relate these data to environmental variables.

DES-Amyloidoses "Amyloidoses through the looking-glass": A knowledgebase developed for exploring and linking information related to human amyloid-related diseases.

More than 30 types of amyloids are linked to close to 50 diseases in humans, the most prominent being Alzheimer's disease (AD). AD is brain-related local amyloidosis, while another amyloidosis, such as AA amyloidosis, tends to be more systemic. Therefore, we need to know more about the biological entities' influencing these amyloidosis processes.

A cautionary signal from the Red Sea on the impact of increased dust activity on marine microbiota.

Background: Global climate change together with growing desertification is leading to increased dust emissions to the atmosphere, drawing attention to possible impacts on marine ecosystems receiving dust deposition. Since microorganisms play important roles in maintaining marine homeostasis through nutrient cycling and carbon flow, detrimental changes in the composition of marine microbiota in response to increased dust input could negatively impact marine health, particularly so in seas located within the Global Dust Belt. Due to its strategic location between two deserts and unique characteristics, the Red Sea provides an attractive semi-enclosed "megacosm" to examine the impacts of large dust deposition on the vastly diverse microbiota in its exceptionally warm oligotrophic waters.

DTi2Vec: Drug-target interaction prediction using network embedding and ensemble learning.

Drug-target interaction (DTI) prediction is a crucial step in drug discovery and repositioning as it reduces experimental validation costs if done right. Thus, developing in-silico methods to predict potential DTI has become a competitive research niche, with one of its main focuses being improving the prediction accuracy. Using machine learning (ML) models for this task, specifically network-based approaches, is effective and has shown great advantages over the other computational methods.

Splice2Deep: An ensemble of deep convolutional neural networks for improved splice site prediction in genomic DNA.

Background: The accurate identification of the exon/intron boundaries is critical for the correct annotation of genes with multiple exons. Donor and acceptor splice sites (SS) demarcate these boundaries. Therefore, deriving accurate computational models to predict the SS are useful for functional annotation of genes and genomes, and for finding alternative SS associated with different diseases.

DES-Tcell is a knowledgebase for exploring immunology-related literature.

T-cells are a subtype of white blood cells circulating throughout the body, searching for infected and abnormal cells. They have multifaceted functions that include scanning for and directly killing cells infected with intracellular pathogens, eradicating abnormal cells, orchestrating immune response by activating and helping other immune cells, memorizing encountered pathogens, and providing long-lasting protection upon recurrent infections. However, T-cells are also involved in immune responses that result in organ transplant rejection, autoimmune diseases, and some allergic diseases.

KAUST Metagenomic Analysis Platform (KMAP), enabling access to massive analytics of re-annotated metagenomic data.

Exponential rise of metagenomics sequencing is delivering massive functional environmental genomics data. However, this also generates a procedural bottleneck for on-going re-analysis as reference databases grow and methods improve, and analyses need be updated for consistency, which require acceess to increasingly demanding bioinformatic and computational resources. Here, we present the KAUST Metagenomic Analysis Platform (KMAP), a new integrated open web-based tool for the comprehensive exploration of shotgun metagenomic data.

DTiGEMS+: drug-target interaction prediction using graph embedding, graph mining, and similarity-based techniques.

In silico prediction of drug-target interactions is a critical phase in the sustainable drug development process, especially when the research focus is to capitalize on the repositioning of existing drugs. However, developing such computational methods is not an easy task, but is much needed, as current methods that predict potential drug-target interactions suffer from high false-positive rates. Here we introduce DTiGEMS+, a computational method that predicts Drug-Target interactions using Graph Embedding, graph Mining, and Similarity-based techniques.

PATH: A Tool That Facilitates the Searching for Heterologous Biosynthetic Routes.

Developing computational tools that can facilitate the rational design of cell factories producing desired products at increased yields is challenging, as the tool needs to take into account that the preferred host organism usually has compounds that are consumed by competing reactions that reduce the yield of the desired product. On the other hand, the preferred host organisms may not have the native metabolic reactions needed to produce the compound of interest; thus, the computational tool needs to identify the metabolic reactions that will most efficiently produce the desired product. In this regard, we developed the generic tool PATH to facilitate an optimized search for heterologous biosynthetic pathway routes.

Sequencing effort dictates gene discovery in marine microbial metagenomes.

Massive metagenomic sequencing combined with gene prediction methods were previously used to compile the gene catalogue of the ocean and host-associated microbes. Global expeditions conducted over the past 15 years have sampled the ocean to build a catalogue of genes from pelagic microbes. Here we undertook a large sequencing effort of a perturbed Red Sea plankton community to uncover that the rate of gene discovery increases continuously with sequencing effort, with no indication that the retrieved 2.

Splice2Deep: An ensemble of deep convolutional neural networks for improved splice site prediction in genomic DNA.

Background: The accurate identification of the exon/intron boundaries is critical for the correct annotation of genes with multiple exons. Donor and acceptor splice sites (SS) demarcate these boundaries. Therefore, deriving accurate computational models to predict the SS are useful for functional annotation of genes and genomes, and for finding alternative SS associated with different diseases.

Genome Insights of the Plant-Growth Promoting Bacterium JZ38 With Volatile-Mediated Antagonistic Activity Against .

Salinity stress is a major challenge to agricultural productivity and global food security in light of a dramatic increase of human population and climate change. Plant growth promoting bacteria can be used as an additional solution to traditional crop breeding and genetic engineering. In the present work, the induction of plant salt tolerance by the desert plant endophyte sp.

Author Correction: Bioprospecting desert plant Bacillus endophytic strains for their potential to enhance plant stress tolerance.

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

The X Files: "The Mystery of X Chromosome Instability in Alzheimer's Disease".

Alzheimer's disease (AD) is a neurodegenerative disease that affects millions of individuals worldwide and can occur relatively early or later in life. It is well known that genetic components, such as the amyloid precursor protein gene on chromosome 21, are fundamental in early-onset AD (EOAD). To date, however, only the apolipoprotein E4 (ApoE4) gene has been proved to be a genetic risk factor for late-onset AD (LOAD).

Regulation of nitric oxide production in hypothyroidism.

Hypothyroidism is a common endocrine disorder that predominantly occurs in females. It is associated with an increased risk of cardiovascular diseases (CVD), but the molecular mechanism is not known. Disturbance in lipid metabolism, the regulation of oxidative stress, and inflammation characterize the progression of subclinical hypothyroidism.

Comparison Study of Computational Prediction Tools for Drug-Target Binding Affinities.

The drug development is generally arduous, costly, and success rates are low. Thus, the identification of drug-target interactions (DTIs) has become a crucial step in early stages of drug discovery. Consequently, developing computational approaches capable of identifying potential DTIs with minimum error rate are increasingly being pursued.

Bioprospecting desert plant Bacillus endophytic strains for their potential to enhance plant stress tolerance.

Plant growth-promoting bacteria (PGPB) are known to increase plant tolerance to several abiotic stresses, specifically those from dry and salty environments. In this study, we examined the endophyte bacterial community of five plant species growing in the Thar desert of Pakistan. Among a total of 368 culturable isolates, 58 Bacillus strains were identified from which the 16 most divergent strains were characterized for salt and heat stress resilience as well as antimicrobial and plant growth-promoting (PGP) activities.

HbA1C as a marker of retrograde glycaemic control in diabetes patient with co-existed beta-thalassaemia: A case report and a literature review.

What Is Known And Objective: The HbA1C marker used in assessing diabetes control quality is not sufficient in diabetes patients with thalassaemia.

Case Description: A male diabetic patient with thalassaemia was hospitalized due to distal neuropathic pain, right toe trophic ulcer, unacceptable five-point glycaemic profile and recommended HbA1C value. After simultaneously initiated insulin therapy and management of ulcer by hyperbaric oxygen, the patient showed improved glycaemic control and ulcer healing, which led to the patient's discharge.

Antioxidant enzymes expression in lymphocytes of patients undergoing carotid endarterectomy.

To remedy carotid artery stenosis and prevent stroke surgical intervention is commonly used, and the gold standard being carotid endarterectomy (CEA). During CEA cerebrovascular hemoglobin oxygen saturation decreases and when this decrease reaches critical levels it leads to cerebral hypoxia that causes neuronal damage. One of the proposed mechanism that affects changes during CEA and contribute to acute brain ischemia (ABI) is oxidative stress.

Proteome-level assessment of origin, prevalence and function of leucine-aspartic acid (LD) motifs.

Motivation: Leucine-aspartic acid (LD) motifs are short linear interaction motifs (SLiMs) that link paxillin family proteins to factors controlling cell adhesion, motility and survival. The existence and importance of LD motifs beyond the paxillin family is poorly understood.

Results: To enable a proteome-wide assessment of LD motifs, we developed an active learning based framework (LD motif finder; LDMF) that iteratively integrates computational predictions with experimental validation.

Redox control of vascular biology.

Redox control is lost when the antioxidant defense system cannot remove abnormally high concentrations of signaling molecules, such as reactive oxygen species (ROS). Chronically elevated levels of ROS cause oxidative stress that may eventually lead to cancer and cardiovascular and neurodegenerative diseases. In this review, we focus on redox effects in the vascular system.