A user's guide to the bioinformatic analysis of shotgun metagenomic sequence data for bacterial pathogen detection.

Metagenomics, i.e., shotgun sequencing of the total microbial community DNA from a sample, has become a mature technique but its application to pathogen detection in clinical, environmental, and food samples is far from common or standardized.

Buckwheat: an underutilized crop with attractive sensory qualities and health benefits.

The pseudocereal buckwheat is one of the ancient domesticated crops. The aim of the present review was to outline the potential of buckwheat as an agricultural crop and brings studies on buckwheat into a new larger perspective combining current knowledge in agricultural history and practice, nutritional and sensory properties, as well as possible benefits to human health. Historically, buckwheat was an appreciated crop because of its short growth period, moderate requirements for growth conditions, and high adaptability to adverse environments.

RecruitPlotEasy: An Advanced Read Recruitment Plot Tool for Assessing Metagenomic Population Abundance and Genetic Diversity.

Mapping of short metagenomic (or metatranscriptomic) read data to reference isolate or single-cell genomes or metagenome-assembled genomes (MAGs) to assess microbial population relative abundance and/or structure represents an essential task of many studies across environmental and clinical settings. The filtering for the quality of the read match and assessment of read mapping results are frequently performed without visual aids or with the assistance of visualizations produced through ad-hoc, in-house approaches. Here, we introduce RecruitPlotEasy, a fully automated, user-friendly pipeline for these purposes that integrates statistical approaches to quantify intra-population sequence and gene-content diversity and identify co-occurring relative populations in the sample.

Conceptual frameworks and key questions for assessing the contribution of marine protected areas to shark and ray conservation.

Marine protected areas (MPAs) are key tools in addressing the global decline of sharks and rays, and marine parks and shark sanctuaries of various configurations have been established to conserve shark populations. However, assessments of their efficacy are compromised by inconsistent terminology, lack of standardized approaches to assess how MPAs contribute to shark and ray conservation, and ambiguity about how to integrate movement data in assessment processes. We devised a conceptual framework to standardize key terms (e.

MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations.

Background: Microbes and their viruses are hidden engines driving Earth's ecosystems from the oceans and soils to humans and bioreactors. Though gene marker approaches can now be complemented by genome-resolved studies of inter-(macrodiversity) and intra-(microdiversity) population variation, analytical tools to do so remain scattered or under-developed.

Results: Here, we introduce MetaPop, an open-source bioinformatic pipeline that provides a single interface to analyze and visualize microbial and viral community metagenomes at both the macro- and microdiversity levels.

Independent control of mean and noise by convolution of gene expression distributions.

Gene expression noise can reduce cellular fitness or facilitate processes such as alternative metabolism, antibiotic resistance, and differentiation. Unfortunately, efforts to study the impacts of noise have been hampered by a scaling relationship between noise and expression level from individual promoters. Here, we use theory to demonstrate that mean and noise can be controlled independently by expressing two copies of a gene from separate inducible promoters in the same cell.

Salvage Therapy With Polatuzumab Vedotin, Bendamustine, and Rituximab Prior to Allogeneic Hematopoietic Transplantation in Patients With Aggressive Lymphomas Relapsing After Therapy With Chimeric Antigen Receptor T-Cells-Report on Two Cases.

Up to 60% of patients with aggressive B-cell lymphoma who receive chimeric antigen receptor (CAR) T-cell therapy experience treatment failure and subsequently have a poor prognosis. Allogeneic hematopoietic stem cell transplantation (alloHSCT) remains a potentially curative approach for patients in this situation. Induction of a deep response prior to alloHSCT is crucial for long-term outcomes, but the optimal bridging strategy following relapse after CAR T-cell therapy has not yet been established.

Two rare cases of bronchus-associated lymphoid tissue lymphoma successfully treated with rituximab-bendamustine.

BALT lymphoma is a rare B-NHL with a favorable prognosis. We here report on two patients with nonspecific symptoms: one showed as major symptom severe thrombocytopenia and the other dyspnea and dry cough, thereby suggesting an inflammatory focus in the lungs. There is no standard of care established yet.

Production of Phytochromes by High-Cell-Density Fermentation.

Phytochromes are important photoreceptors of plants, bacteria, and fungi responsive to light in the red and far-red spectrum. For increasing applications in basic research, synthetic biology, and materials sciences, it is required to recombinantly produce and purify phytochromes in high amounts. An ideal host organism for this purpose is due to its widespread use, fast growth, and ability for high-cell-density fermentation.

DIY optogenetics: Building, programming, and using the Light Plate Apparatus.

Optogenetic systems enable unmatched precision for controlling molecular biological processes but require the use of specialized electrical and optical hardware. In an effort to make working with optogenetic systems more accessible, we recently described an open-source hardware platform called the Light Plate Apparatus (LPA). The LPA is a device capable of delivering two independent light signals from standard LEDs to wells of a 24-well culture plate.

Rewiring bacterial two-component systems by modular DNA-binding domain swapping.

Two-component systems (TCSs) are the largest family of multi-step signal transduction pathways and valuable sensors for synthetic biology. However, most TCSs remain uncharacterized or difficult to harness for applications. Major challenges are that many TCS output promoters are unknown, subject to cross-regulation, or silent in heterologous hosts.

Opinion: Taking phytoremediation from proven technology to accepted practice.

Phytoremediation is the use of plants to extract, immobilize, contain and/or degrade contaminants from soil, water or air. It can be an effective strategy for on site and/or in situ removal of various contaminants from soils, including petroleum hydrocarbons (PHC), polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), solvents (e.g.

An open-hardware platform for optogenetics and photobiology.

In optogenetics, researchers use light and genetically encoded photoreceptors to control biological processes with unmatched precision. However, outside of neuroscience, the impact of optogenetics has been limited by a lack of user-friendly, flexible, accessible hardware. Here, we engineer the Light Plate Apparatus (LPA), a device that can deliver two independent 310 to 1550 nm light signals to each well of a 24-well plate with intensity control over three orders of magnitude and millisecond resolution.