Detection of long repeat expansions from PCR-free whole-genome sequence data.

Identifying large expansions of short tandem repeats (STRs), such as those that cause amyotrophic lateral sclerosis (ALS) and fragile X syndrome, is challenging for short-read whole-genome sequencing (WGS) data. A solution to this problem is an important step toward integrating WGS into precision medicine. We developed a software tool called ExpansionHunter that, using PCR-free WGS short-read data, can genotype repeats at the locus of interest, even if the expanded repeat is larger than the read length. We applied our algorithm to WGS data from 3001 ALS patients who have been tested for the presence of the C9orf72 repeat expansion with repeat-primed PCR (RP-PCR). Compared against this truth data, ExpansionHunter correctly classified all (212/212, 95% CI [0.98, 1.00]) of the expanded samples as either expansions (208) or potential expansions (4). Additionally, 99.9% (2786/2789, 95% CI [0.997, 1.00]) of the wild-type samples were correctly classified as wild type by this method with the remaining three samples identified as possible expansions. We further applied our algorithm to a set of 152 samples in which every sample had one of eight different pathogenic repeat expansions, including those associated with fragile X syndrome, Friedreich's ataxia, and Huntington's disease, and correctly flagged all but one of the known repeat expansions. Thus, ExpansionHunter can be used to accurately detect known pathogenic repeat expansions and provides researchers with a tool that can be used to identify new pathogenic repeat expansions.

Biomimetic aorta-gonad-Mesonephros-on-a-Chip to study human developmental hematopoiesis.

A fundamental limitation in the derivation of hematopoietic stem and progenitor cells is the imprecise understanding of human developmental hematopoiesis. Herein we established a multilayer microfluidic Aorta-Gonad-Mesonephros (AGM)-on-a-chip to emulate developmental hematopoiesis from pluripotent stem cells. The device consists of two layers of microchannels separated by a semipermeable membrane, which allows the co-culture of human hemogenic endothelial (HE) cells and stromal cells in a physiological relevant spatial arrangement to replicate the structure of the AGM. HE cells derived from human induced pluripotent stem cells (hiPSCs) were cultured on a layer of mesenchymal stromal cells in the top channel while vascular endothelial cells were co-cultured on the bottom side of the membrane within the microfluidic device. We show that this AGM-on-a-chip efficiently derives endothelial-to-hematopoietic transition (EHT) from hiPSCs compared with regular suspension culture. The presence of mesenchymal stroma and endothelial cells renders functional HPCs in vitro. We propose that the AGM-on-a-chip could serve as a platform to dissect the cellular and molecular mechanisms of human developmental hematopoiesis.

Bimetallic d10 -Metal Complexes of a Bipyridine Substituted N-Heterocyclic Carbene.

The hybrid ligand 3-(2,2'-bipyridine-6-ylmethyl)-1-mesityl-1H-imidazolylidene (NHCBipy ) featuring both carbene and N-donor sites, was selectively complexed with various d10 metal cations in order to examine its coordination behavior with regard to homo and heterometallic structures. Respective silver complexes can be obtained by the silver oxide route and are suitable transmetallation reagents for the synthesis of gold(I) compounds. Starting from the mononuclear complexes [(NHCBipy )AuCl], [(NHCBipy )Au(C6 F5 )] and [(NHCBipy )2 Au][ClO4 ], open-chain as well as cyclic heterobimetallic complexes containing Cu+ , Ag+ , Zn2+ , Cd2+ , and Hg2+ were synthesized. Furthermore, the homobimetallic species [(NHCBipy )2 M2 ][ClO4 ]2 (M=Cu, Ag) were obtained. All bimetallic compounds were fully characterized including single-crystal X-ray analysis. Their photoluminescence (PL) properties were investigated in the solid state at temperatures between 15 and 295 K and compared with those of the mononuclear species. There is a clear difference in PL properties between the open chain and the cyclic heterobimetallic complexes. The latter species show different PL properties, depending on the metals involved. In addition, collision-induced dissociation (CID) experiments were performed on electrosprayed cations of the cyclic heterobimetallic compounds, to compare the metal binding at the carbene and N-donor sites.

Cocoa Flavanol Intake and Biomarkers for Cardiometabolic Health: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.

BACKGROUND: Cocoa flavanols may improve cardiometabolic health. Evidence from small short-term randomized clinical trials (RCTs) remains inconsistent, and large long-term RCTs testing the efficacy of cocoa flavanols are still lacking. OBJECTIVE: We performed a systematic review and meta-analysis of RCTs to quantify the effect of cocoa flavanol intake on cardiometabolic biomarkers. METHODS: We searched PubMed, Web of Science, and the Cochrane Library for RCTs that evaluated the effects of cocoa flavanols on biomarkers relevant to vascular disease pathways among adults. Data were extracted following a standardized protocol. We used DerSimonian and Laird random-effect models to compute the weighted mean differences (WMDs) and 95% CIs. We also examined potential modification by intervention duration, design, age, sex, comorbidities, and the form and amount of cocoa flavanol intake. RESULTS: We included 19 RCTs that comprised 1131 participants, and the number of studies for a specific biomarker varied. The amount of cocoa flavanols ranged from 166 to 2110 mg/d, and intervention duration ranged from 2 to 52 wk. Cocoa flavanol intake significantly improved insulin sensitivity and lipid profile. The WMDs between treatment and placebo were -0.10 mmol/L (95% CI: -0.16, -0.04 mmol/L) for total triglycerides, 0.06 mmol/L (95% CI: 0.02, 0.09 mmol/L) for HDL cholesterol, -2.33 µIU/mL (95% CI: -3.47, -1.19 µIU/mL) for fasting insulin, -0.93 (95% CI: -1.31, -0.55) for the homeostatic model assessment of insulin resistance, 0.03 (95% CI: 0.01, 0.05) for the quantitative insulin sensitivity check index, 2.54 (95% CI: 0.63, 4.44) for the insulin sensitivity index, -0.83 mg/dL (95% CI: -0.88, -0.77 mg/dL) for C-reactive protein, and 85.6 ng/mL (95% CI: 16.0, 155 ng/mL) for vascular cell adhesion molecule 1. No significant associations were found for other biomarkers. None of the modifiers seemed to qualitatively modify the effects of cocoa flavanol intake. CONCLUSIONS: Our study suggests that cocoa flavanol intake has favorable effects on select cardiometabolic biomarkers among adults. These findings support the need for large long-term RCTs to assess whether cocoa flavanol intake reduces the risk of diabetes and cardiovascular events.

Studies of pesticide residues in tomatoes and cucumbers from Kazakhstan and the associated health risks.

The aim of the present study was to assess the level of pesticide residues in vegetables in the Almaty Region of Kazakhstan and to determine the potential health risks associated with the exposures to these pesticides. A total of 82 samples of cucumbers and tomatoes from top agro-based market and greenhouses were analysed using a gas chromatography-micro electron capture detector/nitrogen-phosphorous detector (GC-µECD/NPD), a multiresidue method to analyse 184 different pesticide types. The results indicated that more than half of samples (59 %) contained 29 pesticides, in which 10 are not registered in Kazakhstan, ranging from 0.01 to 0.88 mg kg(-1), and 28 % contained pesticide residues above maximum residue levels (MRLs). The estimated daily intakes (EDIs) ranged from 0.01 % of the acceptable daily intake (ADI) for pyrimethanil to 12.05 % of the ADI for lambda-cyhalothrin. The most critical commodity is triazophos and flusilazole in tomatoes, contributing 70.8 and 42.5 % to the acute hazard index (aHI). The results provided important information on the current pesticide contamination status of two commonly consumed vegetables and pointed an urgent need to control the use of plant protection products applied, especially potentially persistent pesticides, such as endosulfan and dicofol. These results also show that the detected pesticides may be considered a public health problem.

Loss of Ahi1 affects early development by impairing BM88/Cend1-mediated neuronal differentiation.

Mutations in the Abelson helper integration site-1 (AHI1) gene result in N-terminal Ahi1 fragments and cause Joubert syndrome, an autosomal recessive brain malformation disorder associated with delayed development. How AHI1 mutations lead to delayed development remains unclear. Here we report that full-length, but not N-terminal, Ahi1 binds Hap1, a huntingtin-associated protein that is essential for the postnatal survival of mice and that this binding is regulated during neuronal differentiation by nerve growth factor. Nerve growth factor induces dephosphorylation of Hap1A and decreases its association with Ahi1, correlating with increased Hap1A distribution in neurite tips. Consistently, Ahi1 associates with phosphorylated Hap1A in cytosolic, but not in synaptosomal, fractions isolated from mouse brain, suggesting that Ahi1 functions mainly in the soma of neurons. Mass spectrometry analysis of cytosolic Ahi1 immunoprecipitates reveals that Ahi1 also binds Cend1 (cell cycle exit and neuronal differentiation protein 1)/BM88, a neuronal protein that mediates neuronal differentiation and is highly expressed in postnatal mouse brain. Loss of Ahi1 reduces the levels of Cend1 in the hypothalamus of Ahi1 KO mice, which show retarded growth during postnatal days. Overexpressed Ahi1 can stabilize Cend1 in cultured cells. Furthermore, overexpression of Cend1 can rescue the neurite extension defects of hypothalamic neurons from Ahi1 KO mice. Our findings suggest that Cend1 is involved in Ahi1-associated hypothalamic neuronal differentiation in early development, giving us fresh insight into the mechanism behind the delayed development in Joubert syndrome.

FRA1 controls acinar cell plasticity during murine KrasG12D-induced pancreatic acinar to ductal metaplasia.

Acinar cells have been proposed as a cell-of-origin for pancreatic ductal adenocarcinoma (PDAC) after undergoing acinar-to-ductal metaplasia (ADM). ADM can be triggered by pancreatitis, causing acinar cells to de-differentiate to a ductal-like state. We identify FRA1 (gene name Fosl1) as the most active transcription factor during KrasG12D acute pancreatitis-mediated injury, and we have elucidated a functional role of FRA1 by generating an acinar-specific Fosl1 knockout mouse expressing KrasG12D. Using a gene regulatory network and pseudotime trajectory inferred from single-nuclei ATAC-seq and bulk RNA sequencing (RNA-seq), we hypothesized a regulatory model of the acinar-ADM-pancreatic intraepithelial neoplasia (PanIN) continuum and experimentally validated that Fosl1 knockout mice are delayed in the onset of ADM and neoplastic transformation. Our study also identifies that pro-inflammatory cytokines, such as granulocyte colony stimulating factor (G-CSF), can regulate FRA1 activity to modulate ADM. Our findings identify that FRA1 is a mediator of acinar cell plasticity and is critical for acinar cell de-differentiation and transformation.

A network meta-analysis of association between cardiometabolic risk factors and COVID-19 outcome severity.

BACKGROUND: Cardiometabolic comorbidities have been associated with a higher risk of COVID-19 severity and mortality, but more investigations are needed to determine which comorbidity is more detrimental. METHODS: Embase, Emcare, and MEDLINE were searched systematically for prospective and retrospective studies assessing the associations of cardiometabolic risk factors and COVID-19 outcomes of hospitalization, severity, and mortality among COVID-19-diagnosed patients. Literature search was performed from first publication to May 19, 2021. Study quality was assessed by the Newcastle-Ottawa Scale. RESULTS: From the literature search, 301 studies suggested that all included cardiometabolic risk factors were associated with a higher risk of COVID-19 hospitalization, severity, and mortality, except that overweight was associated with a decreased risk of mortality (relative risk [RR] 0.88; 95% CI, 0.80-0.98). Patients with diabetes (RR 1.46; 95% CI, 1.45-1.47) were most likely to be hospitalized; patients with heart failure had the highest risk for severe COVID-19 outcomes (RR 1.89; 95% CI, 1.71-2.09); while patients with stroke were most susceptible to overall mortality (RR 1.99; 95% CI, 1.90-2.08). In the network meta-analysis, cerebrovascular disease had the highest impact (RR 1.69; 95% CI, 1.65-1.73) on COVID-19 outcomes compared to other cardiometabolic risk factors. For different combinations of risk factors, cardiovascular disease and diabetes combined (RR 6.98; 95% CI, 5.28-9.22) was more detrimental than others. CONCLUSIONS: Considering the high prevalence of cardiometabolic comorbidities and risk of all severe outcomes, patients with cardiometabolic comorbidities should be prioritized in vaccination and treatment development of COVID-19.

Protocol for Local On-Site Dialysate Production for Continuous Renal Replacement Therapy during the COVID-19 Pandemic.

AKI frequently occurs in patients with COVID-19, and kidney injury severe enough to require RRT is a common complication among patients who are critically ill. During the surge of the pandemic, there was a high demand for dialysate for continuous RRT, and this increase in demand, coupled with vulnerabilities in the supply chain, necessitated alternative approaches, including internal production of dialysate. Using a standard hemodialysis machine and off-the-shelf supplies, as per Food and Drug Administration guidelines, we developed a method for on-site dialysate production that is adaptable and can be used to fill multiple bags at once. The use of a central reverse osmosis unit, dedicated hemodialysis machine, sterile bags with separate ports for fill and use, and frequent testing will ensure stability, sterility, and-therefore-safety of the produced dialysate. The dialysate made in house was tested and it showed both stability and sterility for at least 30 hours. This detailed description of our process for generating dialysate can serve as a guide for other programs experiencing similar vulnerabilities in the demand versus supply of dialysate.