Differences in gut microbiota between Dutch and South-Asian Surinamese: potential implications for type 2 diabetes mellitus.

Gut microbiota, or the collection of diverse microorganisms in a specific ecological niche, are known to significantly impact human health. Decreased gut microbiota production of short-chain fatty acids (SCFAs) has been implicated in type 2 diabetes mellitus (T2DM) disease progression. Most microbiome studies focus on ethnic majorities.

Microbiome depiction through user-adapted bioinformatic pipelines and parameters.

The role of the microbiome in health and disease continues to be increasingly recognized. However, there is significant variability in the bioinformatic protocols for analysing genomic data. This, in part, has impeded the potential incorporation of microbiomics into the clinical setting and has challenged interstudy reproducibility.

Attention Deficit Hyperactivity Disorder (ADHD) and the gut microbiome: An ecological perspective.

Attention Deficit Hyperactivity Disorder (ADHD) is an increasingly prevalent neuropsychiatric disorder characterized by hyperactivity, inattention, and impulsivity. Symptoms emerge from underlying deficiencies in neurocircuitry, and recent research has suggested a role played by the gut microbiome. The gut microbiome is an ecosystem of interdependent taxa involved in an exponentially complex web of interactions, plus host gene and reaction pathways, some of which involve neurotransmitters with roles in ADHD neurocircuitry.

Lower respiratory tract microbiome composition and community interactions in smokers.

The lung microbiome impacts on lung function, making any smoking-induced changes in the lung microbiome potentially significant. The complex co-occurrence and co-avoidance patterns between the bacterial taxa in the lower respiratory tract (LRT) microbiome were explored for a cohort of active (AS), former (FS) and never (NS) smokers. Bronchoalveolar lavages (BALs) were collected from 55 volunteer subjects (9 NS, 24 FS and 22 AS).

Microbiome Dysbiosis Shows Strong Association of Gut-Derived Altered Metabolomic Profile in Gulf War Chronic Multisymptom Illness Symptom Persistence Following Western Diet Feeding and Development of Obesity.

The pathophysiology of Gulf War Illness (GWI) remains elusive even after three decades. The persistence of multiple complex symptoms along with metabolic disorders such as obesity worsens the health of present Gulf War (GW) Veterans often by the interactions of the host gut microbiome and inflammatory mediators. In this study, we hypothesized that the administration of a Western diet might alter the host metabolomic profile, which is likely associated with the altered bacterial species.

Potential Autoimmunity Resulting from Molecular Mimicry between SARS-CoV-2 Spike and Human Proteins.

Molecular mimicry between viral antigens and host proteins can produce cross-reacting antibodies leading to autoimmunity. The coronavirus SARS-CoV-2 causes COVID-19, a disease curiously resulting in varied symptoms and outcomes, ranging from asymptomatic to fatal. Autoimmunity due to cross-reacting antibodies resulting from molecular mimicry between viral antigens and host proteins may provide an explanation.

Prior exposure to microcystin alters host gut resistome and is associated with dysregulated immune homeostasis in translatable mouse models.

A strong association between exposure to the common harmful algal bloom toxin microcystin and the altered host gut microbiome has been shown. We tested the hypothesis that prior exposure to the cyanotoxin microcystin-LR may alter the host resistome. We show that the mice exposed to microcystin-LR had an altered microbiome signature that harbored antibiotic resistance genes.

Inferring directional relationships in microbial communities using signed Bayesian networks.

Background: Microbe-microbe and host-microbe interactions in a microbiome play a vital role in both health and disease. However, the structure of the microbial community and the colonization patterns are highly complex to infer even under controlled wet laboratory conditions. In this study, we investigate what information, if any, can be provided by a Bayesian Network (BN) about a microbial community.

The gut microbiome and neuropsychiatric disorders: implications for attention deficit hyperactivity disorder (ADHD).

Neuropsychiatric disorders (NPDs) such as depression, anxiety, bipolar disorder, autism spectrum disorder (ASD) and attention deficit hyperactivity disorder (ADHD) all relate to behavioural, cognitive and emotional disturbances that are ultimately rooted in disordered brain function. More specifically, these disorders are linked to various neuromodulators (i.e.

MATria: a unified centrality algorithm.

Background: Computing centrality is a foundational concept in social networking that involves finding the most "central" or important nodes. In some biological networks defining importance is difficult, which then creates challenges in finding an appropriate centrality algorithm.

Results: We instead generalize the results of any k centrality algorithms through our iterative algorithm MATRIA, producing a single ranked and unified set of central nodes.

Constructing lightweight and flexible pipelines using Plugin-Based Microbiome Analysis (PluMA).

Motivation: Software pipelines have become almost standardized tools for microbiome analysis. Currently many pipelines are available, often sharing some of the same algorithms as stages. This is largely because each pipeline has its own source language and file formats, making it typically more economical to reinvent the wheel than to learn and interface to an existing package.

ATria: a novel centrality algorithm applied to biological networks.

Background: The notion of centrality is used to identify "important" nodes in social networks. Importance of nodes is not well-defined, and many different notions exist in the literature. The challenge of defining centrality in meaningful ways when network edges can be positively or negatively weighted has not been adequately addressed in the literature.

Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis.

Microbiomes are ubiquitous and are found in the ocean, the soil, and in/on other living organisms. Changes in the microbiome can impact the health of the environmental niche in which they reside. In order to learn more about these communities, different approaches based on data from multiple omics have been pursued.

GPUDePiCt: A Parallel Implementation of a Clustering Algorithm for Computing Degenerate Primers on Graphics Processing Units.

In order to make multiple copies of a target sequence in the laboratory, the technique of Polymerase Chain Reaction (PCR) requires the design of "primers", which are short fragments of nucleotides complementary to the flanking regions of the target sequence. If the same primer is to amplify multiple closely related target sequences, then it is necessary to make the primers "degenerate", which would allow it to hybridize to target sequences with a limited amount of variability that may have been caused by mutations. However, the PCR technique can only allow a limited amount of degeneracy, and therefore the design of degenerate primers requires the identification of reasonably well-conserved regions in the input sequences.

Long Timestep Molecular Dynamics on the Graphical Processing Unit.

Molecular dynamics (MD) simulations now play a key role in many areas of theoretical chemistry, biology, physics, and materials science. In many cases, such calculations are significantly limited by the massive amount of computer time needed to perform calculations of interest. Herein, we present Long Timestep Molecular Dynamics (LTMD), a method to significantly speed MD simulations.

The mechanisms of microtubule catastrophe and rescue: implications from analysis of a dimer-scale computational model.

Microtubule (MT) dynamic instability is fundamental to many cell functions, but its mechanism remains poorly understood, in part because it is difficult to gain information about the dimer-scale events at the MT tip. To address this issue, we used a dimer-scale computational model of MT assembly that is consistent with tubulin structure and biochemistry, displays dynamic instability, and covers experimentally relevant spans of time. It allows us to correlate macroscopic behaviors (dynamic instability parameters) with microscopic structures (tip conformations) and examine protofilament structure as the tip spontaneously progresses through both catastrophe and rescue.

MDLab: a molecular dynamics simulation prototyping environment.

Molecular dynamics (MD) simulation involves solving Newton's equations of motion for a system of atoms, by calculating forces and updating atomic positions and velocities over a timestep Deltat. Despite the large amount of computing power currently available, the timescale of MD simulations is limited by both the small timestep required for propagation, and the expensive algorithm for computing pairwise forces. These issues are currently addressed through the development of efficient simulation methods, some of which make acceptable approximations and as a result can afford larger timesteps.

From Genes to Organisms Via the Cell A Problem-Solving Environment for Multicellular Development.

To gain performance, developers often build scientific applications in procedural languages, such as C or Fortran, which unfortunately reduces flexibility. To address this imbalance, the authors present CompuCell3D, a multitiered, flexible, and scalable problem-solving environment for morphogenesis simulations that's written in C++ using object-oriented design patterns.

A framework for three-dimensional simulation of morphogenesis.

We present COMPUCELL3D, a software framework for three-dimensional simulation of morphogenesis in different organisms. COMPUCELL3D employs biologically relevant models for cell clustering, growth, and interaction with chemical fields. COMPUCELL3D uses design patterns for speed, efficient memory management, extensibility, and flexibility to allow an almost unlimited variety of simulations.