A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset.

BACKGROUND: Single-nucleotide polymorphisms (SNPs) are the most widely used form of molecular genetic variation studies. As reference genomes and resequencing data sets expand exponentially, tools must be in place to call SNPs at a similar pace. The genome analysis toolkit (GATK) is one of the most widely used SNP calling software tools publicly available, but unfortunately, high-performance computing versions of this tool have yet to become widely available and affordable. RESULTS: Here we report an open-source high-performance computing genome variant calling workflow (HPC-GVCW) for GATK that can run on multiple computing platforms from supercomputers to desktop machines. We benchmarked HPC-GVCW on multiple crop species for performance and accuracy with comparable results with previously published reports (using GATK alone). Finally, we used HPC-GVCW in production mode to call SNPs on a "subpopulation aware" 16-genome rice reference panel with ~ 3000 resequenced rice accessions. The entire process took ~ 16 weeks and resulted in the identification of an average of 27.3 M SNPs/genome and the discovery of ~ 2.3 million novel SNPs that were not present in the flagship reference genome for rice (i.e., IRGSP RefSeq). CONCLUSIONS: This study developed an open-source pipeline (HPC-GVCW) to run GATK on HPC platforms, which significantly improved the speed at which SNPs can be called. The workflow is widely applicable as demonstrated successfully for four major crop species with genomes ranging in size from 400 Mb to 2.4 Gb. Using HPC-GVCW in production mode to call SNPs on a 25 multi-crop-reference genome data set produced over 1.1 billion SNPs that were publicly released for functional and breeding studies. For rice, many novel SNPs were identified and were found to reside within genes and open chromatin regions that are predicted to have functional consequences. Combined, our results demonstrate the usefulness of combining a high-performance SNP calling architecture solution with a subpopulation-aware reference genome panel for rapid SNP discovery and public deployment.

Remyelination-oriented clemastine treatment attenuates neuropathies of optic nerve and retina in glaucoma.

As one of the top causes of blindness worldwide, glaucoma leads to diverse optic neuropathies such as degeneration of retinal ganglion cells (RGCs). It is widely accepted that the level of intraocular pressure (IOP) is a major risk factor in human glaucoma, and reduction of IOP level is the principally most well-known method to prevent cell death of RGCs. However, clinical studies show that lowering IOP fails to prevent RGC degeneration in the progression of glaucoma. Thus, a comprehensive understanding of glaucoma pathological process is required for developing new therapeutic strategies. In this study, we provide functional and histological evidence showing that optic nerve defects occurred before retina damage in an ocular hypertension glaucoma mouse model, in which oligodendroglial lineage cells were responsible for the subsequent neuropathology. By treatment with clemastine, an Food and Drug Administration (FDA)-approved first-generation antihistamine medicine, we demonstrate that the optic nerve and retina damages were attenuated via promoting oligodendrocyte precursor cell (OPC) differentiation and enhancing remyelination. Taken together, our results reveal the timeline of the optic neuropathies in glaucoma and highlight the potential role of oligodendroglial lineage cells playing in its treatment. Clemastine may be used in future clinical applications for demyelination-associated glaucoma.

A High-Quality Data Set of Protein-Ligand Binding Interactions Via Comparative Complex Structure Modeling.

High-quality protein-ligand complex structures provide the basis for understanding the nature of noncovalent binding interactions at the atomic level and enable structure-based drug design. However, experimentally determined complex structures are scarce compared with the vast chemical space. In this study, we addressed this issue by constructing the BindingNet data set via comparative complex structure modeling, which contains 69,816 modeled high-quality protein-ligand complex structures with experimental binding affinity data. BindingNet provides valuable insights into investigating protein-ligand interactions, allowing visual inspection and interpretation of structural analogues' structure-activity relationships. It can also be used for evaluating machine-learning-based scoring functions. Our results indicate that machine learning models trained on BindingNet could reduce the bias caused by buried solvent-accessible surface area, as we previously found for models trained on the PDBbind data set. We also discussed strategies to improve BindingNet and its potential utilization for benchmarking the molecular docking methods and ligand binding free energy calculation approaches. The BindingNet complements PDBbind in constructing a sufficient and unbiased protein-ligand binding data set and is freely available at http://bindingnet.huanglab.org.cn.

Joint association of weight-adjusted-waist index and physical activity with insulin resistance in adolescents: a cross-sectional study.

BACKGROUND: The weight-adjusted waist index (WWI) is a recently developed obesity metric, and the aim of this study was to investigate the relationship between physical activity (PA) and WWI and the homeostasis model assessment of insulin resistance (HOMA-IR) in adolescents, as well as the joint association of HOMA-IR. METHODS: This study was based on the National Health and Nutrition Survey conducted between 2013 and 2016 and included 1024 adolescents whose median age was 15.4. Multivariate linear regression was used to examine the associations between HOMA-IR and PA and WWI. Using generalized additive models, a potential nonlinear link between WWI and HOMA-IR was evaluated. Subgroup analysis was also carried out. RESULTS: The fully adjusted model revealed a positive association (ß: 0.48, 95% CI: 0.43, 0.53) between the WWI and HOMA-IR. The HOMA-IR was lower in physically active (ß: -0.16, 95% CI: -0.26, -0.05) participants versus inactive participants. Participants who had higher WWI and were not physically active (ß: 0.69; 95% CI: 0.56, 0.82) had the highest levels of HOMA-IR compared to participants who had lower WWI and were physically active. Subgroup analysis revealed that these correlations were similar in males and females. CONCLUSION: Our results demonstrated that higher WWI and PA were associated with a lower HOMA-IR and that WWI and PA had a combined association with HOMA-IR. The findings of this study are informative for the preventing insulin resistance in adolescents.

Co-exposure of butyl benzyl phthalate and TiO2 nanomaterials (anatase) in Metaphire guillelmi: Gut health implications by transcriptomics.

During the COVID-19 pandemic, an abundance of plastic face masks has been consumed and disposed of in the environment. In addition, substantial amounts of plastic mulch film have been used in intensive agriculture with low recovery. Butyl benzyl phthalate (BBP) and TiO2 nanomaterials (nTiO2) are widely applied in plastic products, leading to the inevitable release of BBP and nTiO2 into the soil system. However, the impact of co-exposure of BBP and nTiO2 at low concentrations on earthworms remains understudied. In the present study, transcriptomics was applied to reveal the effects of individual BBP and nTiO2 exposures at a concentration of 1 mg kg-1, along with the combined exposure of BBP and nTiO2 (1 mg kg-1 BBP + 1 mg kg-1 nTiO2 (anatase)) on Metaphire guillelmi. The result showed that BBP and nTiO2 exposures have the potential to induce neurodegeneration through glutamate accumulation, tau protein, and oxidative stress in the endoplasmic reticulum and mitochondria, as well as metabolism dysfunction. The present study contributes to our understanding of the toxic mechanisms of emerging contaminants at environmentally relevant levels and prompts consideration of the management of BBP and nTiO2 within the soil ecosystems.

Screening and identification of 3-aryl-quinolin-2-one derivatives as antiviral agents against influenza A.

Quinolin-2-one represents an important and valuable chemical motif that possesses a wide variety of biological activities; however, the anti-influenza activities of quinolin-2-one-containing compounds were rarely reported. Herein, we describe the screening and identification of 3-aryl-quinolin-2-one derivatives as a novel class of antiviral agents. The 3-aryl-quinolinone derivatives were synthesized via an efficient copper-catalyzed reaction cascade that we previously developed. Using this synthetic method, preliminary structure-activity relationships of this scaffold against the influenza A virus infection were systematically explored. The most potent compound 34 displayed IC50 values of 2.14 and 4.88 µM against the replication of H3N2 (A/HK/8/68) and H1N1 (A/WSN/33) strains, respectively, without apparent cytotoxicity on MDCK cells. We further demonstrated that 27 and 34 potently inhibited the plaque formation of the IAV, rendering this scaffold attractive for pursuing novel anti-influenza agents.

Transcriptome-wide identification of indole glucosinolate dependent flg22-response genes in Arabidopsis.

Indole glucosinolates are known to play essential and diverse roles in Arabidopsis immunity to pathogens. However, a complete understanding of the function of these compounds in plant immunity remains unclear. In this study, we investigated the transcriptome profile in loss-of-function mutant of MYB51, the key transcription factor that controls the biosynthesis of indole glucosinolates. Upon treatment with flg22 (a 22-amino acid peptide derived from bacterial flagellin), the genes that responded in a MYB51-dependent manner were analyzed. The results suggested that MYB51 was possibly implicated in most resistance processes, including pathogen recognition, signal transduction and PR protein activation. Of note, several genes in the ethylene pathway and the WRKY family, including WRKY33, were induced by flg22 in a MYB51-dependent manner. WRKY33 and ethylene were demonstrated to be crucial regulators in plant immunity defense and are functionally upstream of MYB51 during MAMP triggered immunity (MTI). This result suggested a "positive feedback loop" between MYB51 and its upstream regulators.

The deletion of dicer in mature myelinating glial cells causes progressive axonal degeneration but not overt demyelination in adult mice.

Myelinating glial cells (MGCs), oligodendrocytes (OLs) in the central nervous system (CNS) and Schwann cells (SCs) in the peripheral nervous system (PNS), generate myelin sheaths that insulate axons. After myelination is completed in adulthood, MGC functions independent from myelin are required to support axon survival, but the underlying mechanisms are still unclear. Dicer is a key enzyme that is responsible for generating functional micro-RNAs (miRNAs). Despite the importance of Dicer in initiating myelination, the role of Dicer in mature MGCs is still unclear. Here, Dicer was specifically deleted in mature MGCs in 2-month old mice (PLP-CreERT; Dicer fl/fl) by tamoxifen administration. Progressive motor dysfunction was observed in the Dicer conditional knockout mice, which displayed hind limb ataxia at 3 months post recombination that deteriorated into paralysis within 5 months. Massive axonal degeneration/atrophy in peripheral nerves was responsible for this phenomenon, but overt demyelination was not observed in either the CNS or PNS. In contrast to the PNS, signs of axonal degeneration were not observed in the CNS of these animals. We induced a Dicer deletion in oligodendroglia at postnatal day 5 in NG2-CreERT; Dicer fl/fl mice to evaluate whether Dicer expression in OLs is essential for axonal survival. Dicer deletion in oligodendroglia did not cause motor dysfunction at the age of 7 months. Neither axonal atrophy nor demyelination was observed in the CNS. Based on our results, Dicer expression in SCs is required to maintain axon integrity in adult PNS, and Dicer is dispensable for maintaining myelin sheaths in MGCs.

Spatial variability and uncertainty associated with soil moisture content using INLA-SPDE combined with PyMC3 probability programming.

Spatial variability and uncertainty associated with soil volumetric moisture content (SVMC) is crucial in moisture prediction accuracy, this paper sets out to address this point of SVMC by developing data-driven model. Grid samples of SVMC covered approximately a 3-ha field during the jointing growth stage of winter wheat, and SVMC were measured by Time Domain Reflectometry (TDR), located in North China Plain, China. Bayesian inference was performed to explore spatial heterogeneity, robustness, transparency, interpretability and uncertainty related to SVMC using python-based PyMC3 combined with Integrated Nested Laplace Approximation with the Stochastic Partial Differential Equation (INLA-SPDE) model. The results showed that the prediction surface of SVMC, the lower and upper limits of 95% credible intervals quantified uncertainty associated with SVMC, cauchy prior of the flexibility and adaptability to obtain state-of-the-art predictive performance is more robust than gaussian prior for SVMC prediction, the transparency and interpretability of SVMC prediction model were revealed by MCMC (Markov-Chain Monte-Carlo) trace plots, KDE (Kernel density estimates), and rank plots. The uncertainty associated with SVMC can explicitly be described using the highest-posterior density interval, the prediction lower and upper limits.

Synthesis of deuterated S-217622 (Ensitrelvir) with antiviral activity against coronaviruses including SARS-CoV-2.

S-217622 (Ensitrelvir) is a reversible severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) 3-chymotrypsin-like protease (3CLpro) inhibitor which obtained emergency regulatory approval in Japan for the treatment of SARS-CoV-2 infection on Nov 22, 2022. Herein, analogs of S-271622 with deuterium-for-hydrogen replacement were synthesized for comparison of the antiviral activities and pharmacokinetic (PK) profiles. Compared to the parent compound, C11-d2-S-217622 compound YY-278 retained in vitro activity against 3CLpro and SARS-CoV-2. X-ray crystal structural studies showed similar interactions of SARS-CoV-2 3CLpro with YY-278 and S-271622. The PK profiling revealed the relatively favorable bioavailability and plasma exposure of YY-278. In addition, YY-278, as well as S-217622, displayed broadly anti-coronaviral activities against 6 other coronaviruses that infect humans and animals. These results laid the foundation for further research on the therapeutic potential of YY-278 against COVID-19 and other coronaviral diseases.

Astrocyte endfoot formation controls the termination of oligodendrocyte precursor cell perivascular migration during development.

Oligodendrocyte precursor cells (OPCs) undergo an extensive and coordinated migration in the developing CNS, using the pre-formed scaffold of developed blood vessels as their physical substrate for migration. While OPC association with vasculature is critical for dispersal, equally important for permitting differentiation and proper myelination of target axons is their appropriate and timely detachment, but regulation of this process remains unclear. Here we demonstrate a correlation between the developmental formation of astrocytic endfeet on vessels and the termination of OPC perivascular migration. Ex vivo and in vivo live imaging shows that astrocyte endfeet physically displace OPCs from vasculature, and genetic abrogation of endfoot formation hinders both OPC detachment from vessels and subsequent differentiation. Astrocyte-derived semaphorins 3a and 6a act to repel OPCs from blood vessels at the cessation of their perivascular migration and, in so doing, permit subsequent OPC differentiation by insulating them from a maturation inhibitory endothelial niche.

Discovery of BRAF/HDAC Dual Inhibitors Suppressing Proliferation of Human Colorectal Cancer Cells.

The combination of histone deacetylase inhibitor and BRAF inhibitor (BRAFi) has been shown to enhance the antineoplastic effect and reduce the progress of BRAFi resistance. In this study, a series of (thiazol-5-yl)pyrimidin-2-yl)amino)-N-hydroxyalkanamide derivatives were designed and synthesized as novel dual inhibitors of BRAF and HDACs using a pharmacophore hybrid strategy. In particular, compound 14b possessed potent activities against BRAF, HDAC1, and HDAC6 enzymes. It potently suppressed the proliferation of HT-29 cells harboring BRAFV600E mutation as well as HCT116 cells with wild-type BRAF. The dual inhibition against BRAF and HDAC downstream proteins was validated in both cells. Collectively, the results support 14b as a promising lead molecule for further development and a useful tool for studying the effects of BRAF/HDAC dual inhibitors.

Enantioselective semisynthesis of novel cephalotaxine esters with potent antineoplastic activities against leukemia.

Cephalotaxine-type alkaloids (CTAs), represented by homoharringtonine (HHT, 1), display potent efficacy against different types of leukemia cells. In this study, a method for hydrogenation of ß-substituted itaconic acid monoesters with chiral Ru[DTBM-SegPhos](OAc)2 was developed. This metal-catalyzed asymmetric hydrogenation enabled the convenient semisynthesis of novel cephalotaxine derivatives with chiral 2'-substituted-succinic acid 4-mono-methyl esters as side chains. The preliminary structure-activity relationship (SAR) of the compounds' antineoplastic activities was studied. Eventually, we discovered compound 10b with potent antineoplastic activities against leukemia and broadly anticancer activities against a panel of cancer cells. Our study provided a highly enantioselective process enabling the semisynthesis of cephalotaxine derivatives, which are interesting for further study on a scientific basis.

The adenosine analog prodrug ATV006 is orally bioavailable and has preclinical efficacy against parental SARS-CoV-2 and variants.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus driving the ongoing coronavirus disease 2019 (COVID-19) pandemic, continues to rapidly evolve. Because of the limited efficacy of vaccination in prevention of SARS-CoV-2 transmission and continuous emergence of variants of concern (VOCs), orally bioavailable and broadly efficacious antiviral drugs are urgently needed. Previously, we showed that the parent nucleoside of remdesivir, GS-441524, has potent anti-SARS-CoV-2 activity. Here, we report that esterification of the 5'-hydroxyl moieties of GS-441524 markedly improved antiviral potency. This 5'-hydroxyl-isobutyryl prodrug, ATV006, demonstrated excellent oral bioavailability in rats and cynomolgus monkeys and exhibited potent antiviral efficacy against different SARS-CoV-2 VOCs in vitro and in three mouse models. Oral administration of ATV006 reduced viral loads and alleviated lung damage when administered prophylactically and therapeutically to K18-hACE2 mice challenged with the Delta variant of SARS-CoV-2. These data indicate that ATV006 represents a promising oral antiviral drug candidate for SARS-CoV-2.

Chronic Exposure to Hypoxia Inhibits Myelinogenesis and Causes Motor Coordination Deficits in Adult Mice.

Exposure to chronic hypoxia is considered to be a risk factor for deficits in brain function in adults, but the underlying mechanisms remain largely unknown. Since active myelinogenesis persists in the adult central nervous system, here we aimed to investigate the impact of chronic hypoxia on myelination and the related functional consequences in adult mice. Using a transgenic approach to label newly-generated myelin sheaths (NG2-CreERTM; Tau-mGFP), we found that myelinogenesis was highly active in most brain regions, such as the motor cortex and corpus callosum. After exposure to hypoxia (10% oxygen) 12 h per day for 4 weeks, myelinogenesis was largely inhibited in the 4-month old brain and the mice displayed motor coordination deficits revealed by the beam-walking test. To determine the relationship between the inhibited myelination and functional impairment, we induced oligodendroglia-specific deletion of the transcription factor Olig2 by tamoxifen (NG2-CreERTM; Tau-mGFP; Olig2 fl/fl) in adult mice to mimic the decreased myelinogenesis caused by hypoxia. The deletion of Olig2 inhibited myelinogenesis and consequently impaired motor coordination, suggesting that myelinogenesis is required for motor function in adult mice. To understand whether enhancing myelination could protect brain functions against hypoxia, we treated hypoxic mice with the myelination-enhancing drug-clemastine, which resulted in enhanced myelogenesis and improved motor coordination. Taken together, our data indicate that chronic hypoxia inhibits myelinogenesis and causes functional deficits in the brain and that enhancing myelinogenesis protects brain functions against hypoxia-related deficits.

Spatial Variability of Soil Properties and Portable X-Ray Fluorescence-quantified Elements of typical Golf Courses Soils.

Understanding and quantitative delineation of Portable X-Ray Fluorescence (PXRF) -quantified elements and soil properties spatial variability are important for healthy turf development for golf courses. In this study, PXRF-quantified elements and soil properties (except soil acidity and alkalinity (pH), electric conductivity (EC), and textures) of 200 soil samples were measured by PXRF analyzer at different golf courses in Lubbock, Amarillo, and Midland in Texas, and Hobbs in New Mexico. Furthermore, principal component analysis (PCA), empirical bayesian kriging (EBK) and the ordinary least square model (OLSM) were used in the study. Two kinds of components were extracted and interpreted by PCA, the results showed Zn, Ti, Fe, Rb, V, Mn and Zr were associated with the component 1, while Sr was associated with the component 2, the preliminary classification of PXRF-quantified elements was formed by PCA. The EBK approach was used to evaluate the spatial patterns of PXRF-quantified elements and soil properties. The OLSM model quantitatively related pH to EC, silt texture and the PXRF-quantified K, Ca and Sr. The integration of PCA, EBK and OLSM revealed quantitative links between soil pedogenesis and causes, spatial variability and couple relationships of PXRF-quantified elements and soil properties over golf courses.

Mechanisms of TREG cell adaptation to inflammation.

Inflammation is an important defense mechanism. In this complex and dynamic process, drastic changes in the tissue micro-environment play key roles in dictating the nature of the evolving immune response. However, uncontrolled inflammation is detrimental, leading to unwanted cellular damage, loss of physiological functions, and even death. As such, the immune system possesses tools to limit inflammation while ensuring rapid and effective clearance of the inflammatory trigger. Foxp3+ regulatory T (TREG ) cells, a potently immunosuppressive CD4+ T cell subset, play a crucial role in immune tolerance by controlling the extent of the response to self and non-self Ags, all-the-while promoting a quick return to immune homeostasis. TREG cells adapt to changes in the local micro-environment enabling them to migrate, proliferate, survive, differentiate, and tailor their suppressive ability at inflamed sites. Several inflammation-associated factors can impact TREG cell functional adaptation in situ including locally released alarmins, oxygen availability, tissue acidity and osmolarity and nutrient availability. Here, we review some of these key signals and pathways that control the adaptation of TREG cell function in inflammatory settings.

Salt Sensing by Serum/Glucocorticoid-Regulated Kinase 1 Promotes Th17-like Inflammatory Adaptation of Foxp3+ Regulatory T Cells.

Regulatory T (Treg) cells integrate diverse environmental signals to modulate their function for optimal suppression. Translational regulation represents a favorable mechanism for Treg cell environmental sensing and adaptation. In this study, we carry out an unbiased screen of the Treg cell translatome and identify serum/glucocorticoid-regulated kinase 1 (SGK1), a known salt sensor in T cells, as being preferentially translated in activated Treg cells. We show that high salt (HS) drives thymic Treg cells to adopt a T helper type 17 (Th17)-like phenotype and enhances generation of Th17-like induced Treg cells in a SGK1-dependent manner, all the while maintaining suppressive function. Salt-mediated Th17-like differentiation of Treg cells was evident in mice fed with HS diet or injected with HS-preconditioned T cells. Overall, SGK1 enables Treg cells to adapt their function in response to environmental cues. By understanding these environmental-sensing mechanisms, we envision targeted approaches to fine-tune Treg cell function for better control of inflammation.

Enhancing Oligodendrocyte Myelination Rescues Synaptic Loss and Improves Functional Recovery after Chronic Hypoxia.

To address the significance of enhancing myelination for functional recovery after white matter injury (WMI) in preterm infants, we characterized hypomyelination associated with chronic hypoxia and identified structural and functional deficits of excitatory cortical synapses with a prolonged motor deficit. We demonstrate that genetically delaying myelination phenocopies the synaptic and functional deficits observed in mice after hypoxia, suggesting that myelination may possibly facilitate excitatory presynaptic innervation. As a gain-of-function experiment, we specifically ablated the muscarinic receptor 1 (M1R), a negative regulator of oligodendrocyte differentiation in oligodendrocyte precursor cells. Genetically enhancing oligodendrocyte differentiation and myelination rescued the synaptic loss after chronic hypoxia and promoted functional recovery. As a proof of concept, drug-based myelination therapies also resulted in accelerated differentiation and myelination with functional recovery after chronic hypoxia. Together, our data indicate that myelination-enhancing strategies in preterm infants may represent a promising therapeutic approach for structural/functional recovery after hypoxic WMI.

[Heavy metal pollution in street dusts from different functional zones of Luoyang City and its potential ecological risk].

The concentrations of heavy metals (Cu, Zn, Pb, Cr, Cd) in street dusts were investigated in six different functional zones of Luoyang City, i.e., urban-rural continuum, urban artery, industrial district, urban green space, residential district, and business district. The pollution levels and potential ecological risk of heavy metals were assessed by the methods of potential ecological risk index suggested by Håkanson. The results showed that heavy metal concentrations in street dusts from different functional zones of Luoyang City were all higher than soil background values in Henan, with average concentrations of Zn (1019.75 mg x kg(-1)) > Cr (401.63 mg x kg(-1)) > Cu (240.94 mg x kg(-1)) > Pb (176.04 mg x kg(-1)) > Cd (2.33 mg x kg(-1)). Cd was the most seriously polluted metal in all functional zones, and the average pollution index (Cf(i)) reached 35.84, following by Zn (16.32) > Cu (12.05) > Pb (7.90) > Cr (6.36). Heavy metal concentrations and pollution levels varied greatly in different functional zones, and industrial zone had the highest total contents and the heaviest pollution. The integrated potential ecological risk index (RI) in different functional zones all reached very strong levels, with an order of industrial district (1709.51) > urban green space (1581.50) > business district (1 297.45) > residential district (1 111.25) > urban artery (889.97) > urban-rural continuum (641.39). Among the surveyed heavy metals, Cd accounted for the major potential ecological risk, and the average potential ecological risk index (Er(i)) reached 1075.16 (extremely strong risk level) in all six functional zones. The average Er(i) of Cu and Pb reached 60.23 and 40.77 respectively, belonging to moderate risk level, while Zn (16.32) and Cr (12.71) only reached slight risk level. A reduction in industrial and traffic pollution might be the key measure to decrease the heavy metal pollution and potential risk in street dusts.