MMS2plot: An R Package for Visualizing Multiple MS/MS Spectra for Groups of Modified and Non‐Modified Peptides

A large number of post‐translational modifications (PTMs) in proteins are buried in the unassigned mass spectrometric (MS) spectra in shot‐gun proteomics datasets. Because the modified peptide fragments are low in abundance relative to the corresponding non‐modified versions, it is critical to develop tools that allow facile evaluation of assignment of PTMs based on the MS/MS spectra. Such tools will preferably have the ability to allow comparison of fragment ion spectra and retention time between the modified and unmodified peptide pairs or group. Herein, MMS2plot, an R package for visualizing peptide‐spectrum matches (PSMs) for multiple peptides, is described. MMS2plot features a batch mode and generates the output images in vector graphics file format that facilitate evaluation and publication of the PSM assignment. MMS2plot is expected to play an important role in PTM discovery from large‐scale proteomics datasets generated by liquid chromatography‐MS/MS. The MMS2plot package is freely available at https://github.com/lileir/MMS2plot under the GPL‐3 license.     

Applying Pharmacogenomics to Antifungal Selection and Dosing: Are We There Yet?

This review summarizes recent literature for applying pharmacogenomics to antifungal selection and dosing, providing an approach to implementing antifungal pharmacogenomics in clinical practice. The Clinical Pharmacogenetics Implementation Consortium published guidelines on CYP2C19 and voriconazole, with recommendations to use alternative antifungals or adjust voriconazole dose with close therapeutic drug monitoring (TDM). Recent studies demonstrate an association between CYP2C19 phenotype and voriconazole levels, clinical outcomes, and adverse events. Additionally, CYP2C19-guided preemptive dose adjustment demonstrated benefit in two prospective studies for prophylaxis. Pharmacokinetic–pharmacodynamic modeling studies have generated proposed voriconazole treatment doses based on CYP2C19 phenotypes, with further validation studies needed. Sufficient evidence is available for implementing CYP2C19-guided voriconazole selection and dosing among select patients at risk for invasive fungal infections. The institution needs appropriate infrastructure for pharmacogenomic testing, integration of results in the clinical decision process, with TDM confirmation of goal trough achievement, to integrate antifungal pharmacogenomics into routine clinical care.     

Research progress on gut health of farmers teleost fish: a viewpoint concerning the intestinal mucosal barrier and the impact of its damage

Reviews in Fish Biology and Fisheries - The intestinal mucosal barrier plays a critical role in the maintenance of host health. In farmed teleost fish, the intestinal epithelium is challenged by a...     

A biotechnology‐based male‐sterility system for hybrid seed production in tomato

Incorporating male sterility into hybrid seed production reduces its cost and ensures high varietal purity. Despite these advantages, male‐sterile lines have not been widely used to produce tomato (Solanum lycopersicum) hybrid seeds. We describe the development of a biotechnology‐based breeding platform that utilized genic male sterility to produce hybrid seeds. In this platform, we generated a novel male‐sterile tomato line by clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR‐associated protein 9 (Cas9)‐mediated mutagenesis of a stamen‐specific gene SlSTR1 and devised a transgenic maintainer by transforming male‐sterile plants with a fertility‐restoration gene linked to a seedling‐colour gene. Offspring of crosses between a hemizygous maintainer and the homozygous male‐sterile plant segregated into 50% non‐transgenic male‐sterile plants and 50% male‐fertile maintainer plants, which could be easily distinguished by seedling colour. This system has great practical potential for hybrid seed breeding and production as it overcomes the problems intrinsic to other male‐sterility systems and can be easily adapted for a range of tomato cultivars and diverse vegetable crops.     

古DNA捕获新技术与中国南方早期人群遗传研究新格局

古DNA捕获技术目前已获得极大的发展,能够从骨骼和环境沉积物等多种材料中获取到目的DNA片段,而且对于保存环境较差的低纬度地区,同样能够获取有效的内源DNA片段,极大地丰富了古DNA研究的材料来源。本文围绕这一新技术开展总结和讨论,主要分为两个方面：1）总结并介绍该技术应用前景;2）应用这一技术打开了中国南方早期人群研究的新局面,梳理该新技术的应用对史前中国南方人群古基因组研究所获得的新认识,并对中国南方早期人群古基因组深入分析;另外,利用古DNA捕获技术成功获取云南3446~3180 BP的大阴洞遗址4例高质量线粒体基因组信息,并开展了人群遗传历史的研究。     

灌木斑块格局对产流及产沙过程的影响

研究景观斑块盖度和连通方式影响下坡面径流、输沙及其水动力学参量的变化规律,对于揭示坡面土壤侵蚀过程的水动力机制和水文连通性具有重要意义。本研究采用野外人工模拟降雨试验,分析灌木样地不同覆盖度水平(0%、20%、40%、60%、90%)和不同连通方式(竖路径、横路径、S路径、随机斑块路径)下坡面径流、输沙及其水动力学参量的变化。结果表明: 随灌木覆盖度增加,产流量和产沙量均呈指数递减趋势;覆盖度增加到60%以上时,灌木减水减沙能力趋于稳定。随灌木覆盖度增加,流速、径流深、雷诺数、弗劳德数、径流功率和径流剪切力显著降低,曼宁糙率系数和Darcy-Weisbach阻力系数显著增大;但当灌木覆盖度增加到60%以上时,水力学参数特征值变化无显著差异。4种连通方式的产流率大小依次为竖路径>S路径>横路径>随机斑块;产沙率表现为竖路径最大,S路径次之,横路径与随机斑块无显著差异。连通性差的路径(横路径、随机斑块路径)与连通性好的路径(竖路径、S路径)相比,表现出较强的水力传输阻力和较差的水力挟沙能力。研究灌木斑块不同覆盖度和不同组合方式对坡面产流产沙量和水动力参量的作用,阐明植被减水减沙的临界盖度和合理配置方式,可为黄土高原水土流失治理和黄河流域高质量发展提供重要的理论依据。