Paired Single-Cell Transcriptome and DNA Barcode Detection in Zebrafish Using ScarTrace.

ScarTrace is a CRISPR/Cas9-based genetic lineage tracing method that allows for uniquely barcoding the DNA of single cells at a target GFP sequence during developing zebrafish embryos. Single cells from barcoded adult zebrafish can be isolated from various tissues (e.g.

Design, creation, and use of the Test Us Bank (TUB) COVID-19 sample biorepository.

Shortly after the first case of SARS-CoV-2 was diagnosed a public health emergency (PHE) was declared and a multi-agency response was initiated within the US federal government to create and propagate testing capacity. As part of this response, an unprecedented program designated Rapid Acceleration of Diagnostics (RADx) Tech was established by the National Institutes of Health (NIH) to facilitate the development of point-of-care tests for the COVID-19. The RADx Tech Clinical Studies Core (CSC), located at the University of Massachusetts Chan Medical School (UMass Chan), with partnering academic, private, and non-governmental organizations around the country, was tasked with developing clinical studies to support this work.

Investigating microstructural changes between in vivo and perfused ex vivo marmoset brains using oscillating gradient and b-tensor encoded diffusion MRI at 9.4 T.

Purpose: To investigate microstructural alterations induced by perfusion fixation in brain tissues using advanced diffusion MRI techniques and estimate their potential impact on the application of ex vivo models to in vivo microstructure.

Methods: We used oscillating gradient spin echo (OGSE) and b-tensor encoding diffusion MRI to examine in vivo and ex vivo microstructural differences in the marmoset brain. OGSE was used to shorten effective diffusion times, whereas b-tensor encoding allowed for the differentiation of isotropic and anisotropic kurtosis.

Alternating between even and odd ploidy levels switches on and off the recombination control, even near the centromeres.

Meiotic recombination is a key biological process in plant evolution and breeding, as it generates genetic diversity in each generation through the formation of crossovers (COs). However, due to their importance in genome stability, COs are highly regulated in frequency and distribution. We previously demonstrated that this strict regulation of COs can be modified, both in terms of CO frequency and distribution, in allotriploid Brassica hybrids (2n = 3x = 29; AAC) resulting from a cross between Brassica napus (2n = 4x = 38; AACC) and Brassica rapa (2n = 2x = 20; AA).

Persisting Hypercalcemia and Hyperparathyroidism after Kidney Transplantation Have a Negative Impact on Graft and Patient Survival.

Hyperparathyroidism (HPT) with hypercalcemia, often deemed irreversible and detrimental to graft survival post-kidney transplantation (KT), prompts pre-transplant parathyroidectomy in hypercalcemic patients. In this retrospective analysis of 1212 kidney transplant recipients (KTRs) between 2006 and 2019, the incidence and effect of persistent HPT and hypercalcemia on graft and patient survival, and risk factors for persistence were analyzed until 60 months of follow up (FU). At KT, 5.

Genomic and phenomic predictions help capture low-effect alleles promoting seed germination in oilseed rape in addition to QTL analyses.

Phenomic prediction implemented on a large diversity set can efficiently predict seed germination, capture low-effect favorable alleles that are not revealed by GWAS and identify promising genetic resources. Oilseed rape faces many challenges, especially at the beginning of its developmental cycle. Achieving rapid and uniform seed germination could help to ensure a successful establishment and therefore enabling the crop to compete with weeds and tolerate stresses during the earliest developmental stages.

Identification of transcriptional modules linked to the drought response of Brassica napus during seed development and their mitigation by early biotic stress.

In order to capture the drought impacts on seed quality acquisition in Brassica napus and its potential interaction with early biotic stress, seeds of the 'Express' genotype of oilseed rape were characterized from late embryogenesis to full maturity from plants submitted to reduced watering (WS) with or without pre-occurring inoculation by the telluric pathogen Plasmodiophora brassicae (Pb + WS or Pb, respectively), and compared to control conditions (C). Drought as a single constraint led to significantly lower accumulation of lipids, higher protein content and reduced longevity of the WS-treated seeds. In contrast, when water shortage was preceded by clubroot infection, these phenotypic differences were completely abolished despite the upregulation of the drought sensor RD20.

Improving the Abrasion Resistance of Nodular Cast Iron Castings by Remelting Their Surfaces by Laser Beam.

This paper presents the results of research conducted in the field of the technology of surface hardening of castings from unalloyed and low-alloy nodular cast iron using the laser remelting method. The range of studies included macro- and microhardness measurements using Rockwell and Vickers methods as well as metallographic microscopic examinations using a scanning electron microscope. Moreover, abrasive wear resistance tests were performed using the pin-on-disk method in the friction pair of nodular cast iron-SiC abrasive paper and the reciprocating method in the friction pair of nodular cast iron-unalloyed steel.

Relevance of Tacrolimus Trough Concentration and Hepatitis E virus Genetic Changes in Kidney Transplant Recipients With Chronic Hepatitis E.

Introduction: Hepatitis E virus (HEV) can cause chronic infection (≥3 months) and cirrhosis in immunocompromised patients, especially kidney transplant recipients. Low alanine aminotransferase (ALT) levels and high HEV intrahost diversity have previously been associated with evolution toward chronicity in these patients. We hypothesized that additional clinical and viral factors could be associated with the risk of chronic HEV infection.

Structure-based design of small molecule inhibitors of the cagT4SS ATPase Cagα of .

We here describe the structure-based design of small molecule inhibitors of the type IV secretion system of . The secretion system is encoded by the  pathogenicity island, and we chose Cagα, a hexameric ATPase and member of the family of VirB11-like proteins, as target for inhibitor design. We first solved the crystal structure of Cagα in a complex with the previously identified small molecule inhibitor 1G2.

Inhibition of the type IV secretion system from antibiotic-resistant clinical isolates supports the potential of Cagα as an anti-virulence target.

resistance to antibiotics is a growing problem and it increasingly leads to treatment failure. While the bacterium is present worldwide, the severity of clinical outcomes is highly dependent on the geographical origin and genetic characteristics of the strains. One of the major virulence factors identified in is the pathogenicity island (PAI), which encodes a type IV secretion system (T4SS) used to translocate effectors into human cells.

Computational model to address lens-based acoustic field aperture in the in vitro ultrasonic cell stimulation.

Low-Intensity Pulsed Ultrasound Stimulation (LIPUS) is a therapeutic modality used for bone tissue regeneration and healing. Its clinical efficacy is still debated, as the underlying physical phenomena remain poorly understood. The interaction between ultrasonic waves and cells, likely to trigger mechanotransduction inducing bone regeneration, is at the center of scientific concerns on the subject.

A correction algorithm for improved magnetic field monitoring with distal field probes.

Purpose: A significant source of artifacts in MRI are field fluctuations. Field monitoring is a new technology that allows measurement of field dynamics during a scan via "field probes," which can be used to improve image reconstruction. Ideally, probes are located within the volume where gradients produce nominally linear field patterns.

O partitioning of sulfur oxidizing bacteria drives acidity and thiosulfate distributions in mining waters.

The acidification of water in mining areas is a global environmental issue primarily catalyzed by sulfur-oxidizing bacteria (SOB). Little is known about microbial sulfur cycling in circumneutral pH mine tailing impoundment waters. Here we investigate biological sulfur oxidation over four years in a mine tailings impoundment water cap, integrating aqueous sulfur geochemistry, genome-resolved metagenomics and metatranscriptomics.

Single-shot spiral diffusion-weighted imaging at 7T using expanded encoding with compressed sensing.

Purpose: The expanded encoding model incorporates spatially- and time-varying field perturbations for correction during reconstruction. To date, these reconstructions have used the conjugate gradient method with early stopping used as implicit regularization. However, this approach is likely suboptimal for low-SNR cases like diffusion or high-resolution MRI.

Estimation of free water-corrected microscopic fractional anisotropy.

Water diffusion anisotropy MRI is sensitive to microstructural changes in the brain that are hallmarks of various neurological conditions. However, conventional metrics like fractional anisotropy are confounded by neuron fiber orientation dispersion, and the relatively low resolution of diffusion-weighted MRI gives rise to significant free water partial volume effects in many brain regions that are adjacent to cerebrospinal fluid. Microscopic fractional anisotropy is a recent metric that can report water diffusion anisotropy independent of neuron fiber orientation dispersion but is still susceptible to free water contamination.

Optimization in the space domain for density compensation with the nonuniform FFT.

The non-uniform Discrete Fourier Transform algorithm has shown great utility for reconstructing images from non-uniformly spaced Fourier samples in several imaging modalities. Due to the non-uniform spacing, some correction for the variable density of the samples must be made. Common methods for generating density compensation values are either sub-optimal or only consider a finite set of points in the optimization.

A longitudinal microstructural MRI dataset in healthy C57Bl/6 mice at 9.4 Tesla.

Multimodal microstructural MRI has shown increased sensitivity and specificity to changes in various brain disease and injury models in the preclinical setting. Here, we present an in vivo longitudinal dataset, including a subset of ex vivo data, acquired as control data and to investigate microstructural changes in the healthy mouse brain. The dataset consists of structural T2-weighted imaging, magnetization transfer ratio and saturation imaging, and advanced quantitative diffusion MRI (dMRI) methods.