WormBase in 2022—data,processes, and tools for analyzing Caenorhabditis elegans

WormBase (www.wormbase.org) is the central repository for the genetics and genomics of the nematode Caenorhabditis elegans. We provide the research community with data and tools to facilitate the use of C. elegans and related nematodes as model organisms for studying human health, development, and many aspects of fundamental biology. Throughout our 22-year history, we have continued to evolve to reflect progress and innovation in the science and technologies involved in the study of C. elegans. We strive to incorporate new data types and richer data sets, and to provide integrated displays and services that avail the knowledge generated by the published nematode genetics literature. Here, we provide a broad overview of the current state of WormBase in terms of data type, curation workflows, analysis, and tools, including exciting new advances for analysis of single-cell data, text mining and visualization, and the new community collaboration forum. Concurrently, we continue the integration and harmonization of infrastructure, processes, and tools with the Alliance of Genome Resources, of which WormBase is a founding member.     

Phosphoproteomics toolbox: computational biology, protein chemistry and mass spectrometry

Protein phosphorylation is important for regulation of most biological functions and up to 50% of all proteins are thought to be modified by protein kinases. Increased knowledge about potential phosphorylation of a protein may increase our understanding of the molecular processes in which it takes part. Despite the importance of protein phosphorylation, identification of phosphoproteins and localization of phosphorylation sites is still a major challenge in proteomics. However, high-throughput methods for identification of phosphoproteins are being developed, in particular within the fields of bioinformatics and mass spectrometry. In this review, we present a toolbox of current technology applied in phosphoproteomics including computational prediction, chemical approaches and mass spectrometry-based analysis, and propose an integrated strategy for experimental phosphoproteomics.     

Platform biochemicals for a biorenewable chemical industry

The chemical industry is currently reliant on a historically inexpensive, petroleum-based carbon feedstock that generates a small collection of platform chemicals from which highly efficient chemical conversions lead to the manufacture of a large variety of chemical products. Recently, a number of factors have coalesced to provide the impetus to explore alternative renewable sources of carbon. Here we discuss the potential impact on the chemical industry of shifting from non-renewable carbon sources to renewable carbon sources. This change to the manufacture of chemicals from biological carbon sources will provide an opportunity for the biological research community to contribute fundamental knowledge concerning carbon metabolism and its regulation. We discuss whether fundamental biological research into metabolic processes at a holistic level, made possible by completed genome sequences and integrated with detailed structural understanding of biocatalysts, can change the chemical industry from being dependent on fossil-carbon feedstocks to using biorenewable feedstocks. We illustrate this potential by discussing the prospect of building a platform technology based upon a concept of combinatorial biosynthesis, which would explore the enzymological flexibilities of polyketide biosynthesis.     

植物DNA条形码与生物多样性数据共享平台构建

DNA条形码基于较短的DNA序列实现物种的快速、准确鉴定, 不仅加快了全球生物物种的鉴定和分类步伐, 也为生物多样性的管理、保护和可持续利用提供了新思路和研究方法。植物DNA条形码标准数据库的不断完善, 将使植物多样性信息的快速获取成为可能; 将不同类型数据资源整合、共享和利用, 构建植物DNA条形码数据共享平台, 是满足公众对物种准确鉴定和快速认知的重要支撑。本文介绍了近年来植物DNA条形码的研究进展; 植物DNA条形码参考数据库的研发现状和存在的问题。结合上述问题, 围绕“大数据”时代背景, 对如何管理和使用好海量的植物信息, 如何构建数据共享平台提出了一些设想: (1)数据共享平台的元数据应尽可能翔实、丰富、准确和多关联; (2)数据标准应统一规范; (3)查询入口方便、迅速、多样, 易于管理, 便于实现更大程度的数据共享和全球化的合作交流。     

结合学科建设的应用型本科院校的微生物学实验教学改革

微生物学实验作为生物学科的重要基础课程,在创新人才培养和素质教育中起着重要作用。提高学生的创新实践能力,培养服务区域经济的创新型应用人才是地方应用型本科高校的办学目标。结合长治学院的学科建设,探讨了普通地方本科院校应用型人才培养中,微生物学实验教学模式的新思路,建立了由基础性实验和综合设计性实验相结合的实验内容,开放学科实验室为学生搭建科研创新实践平台,借助微信平台实现"线上"与"线下"的互动交流学习,构建了科学考核评价体系。改革后的新型教学模式能够切实提高教学质量,对学生的能力培养和综合素质提升起到积极促进作用。     

The effect of plantar flexor muscle fatigue on postural control

Objective

Previous studies have demonstrated that ankle muscle fatigue alters postural sway. Our aim was to better understand postural control mechanisms during upright stance following plantar flexor fatigue.

Method

Ten healthy young volunteers, 25.7 ± 2.2 years old, were recruited. Foot center-of-pressure (CoP) displacement data were collected during narrow base upright stance and eyes closed (i.e. blindfolded) conditions. Subjects were instructed to stand upright and as still as possible on a force platform under five test conditions: (1) non-fatigue standing on firm surface; (2) non-fatigue standing on foam; (3) ankle plantar flexor fatigue, standing on firm surface; (4) ankle plantar flexor fatigue, standing on foam; and (5) upper limb fatigue, standing on firm surface. An average of the ten 30-s trials in each of five test conditions was calculated to assess the mean differences between the trials. Traditional measures of postural stability and stabilogram-diffusion analysis (SDA) parameters were analyzed.

Results

Traditional center of pressure parameters were affected by plantar flexor fatigue, especially in the AP direction. For the SDA parameters, plantar flexor fatigue caused significantly higher short-term diffusion coefficients, and critical displacement in both mediolateral (ML) and anteroposterior (AP) directions. Long-term postural sway was different only in the AP direction.

Conclusions

Localized plantar flexor fatigue caused impairment to postural control mainly in the Sagittal plane. The findings indicate that postural corrections, on average, occurred at a higher threshold of sway during plantar flexor fatigue compared to non-fatigue conditions.     

Development of cell-free protein synthesis platforms for disulfide bonded proteins

The use of cell-free protein synthesis (CFPS) for recombinant protein production is emerging as an important technology. For example, the openness of the cell-free system allows control of the reaction environment to promote folding of disulfide bonded proteins in a rapid and economically feasible format. These advantages make cell-free protein expression systems particularly well suited for producing patient specific therapeutic vaccines or antidotes in response to threats from natural and man-made biological agents and for pharmaceutical proteins that are difficult to produce in living cells. In this work we assess the versatility of modern cell-free methods, optimize expression and folding parameters, and highlight the importance of rationally designed plasmid templates for producing mammalian secreted proteins, fusion proteins, and antibody fragments in our E. coli-based CFPS system. Two unique CFPS platforms were established by developing standardized extract preparation protocols and generic cell-free reaction conditions. Generic reaction conditions enabled all proteins to express well with the best therapeutic protein yield at 710 microg/mL, an antibody fragment at 230 microg/mL, and a vaccine fusion protein at 300 microg/mL; with the majority correctly folded. Better yields were obtained when cell-free reaction conditions were optimized for each protein. Establishing general CFPS platforms enhances the potential for cell-free protein synthesis to reliably produce complex protein products at low production and capital costs with very rapid process development timelines.     

Spatial and temporal variability in early successional patterns of an invertebrate assemblage at an offshore oil platform

The effects of selected physical and biological factors on the early development of a subtidal invertebrate assemblage were examined at an offshore oil platform in the Santa Barbara Channel (California, USA). The effects of date, year, length, and depth of submersion were investigated by replacing sets of ceramic tiles with new tiles at frequencies of 2, 4, 6, 12, and 24 months at three depths (6, 12, and 18 m) over a period of 24 months. The effects of existing colonists and depth were explored in a second experiment by removing selected early colonists from ceramic tiles deployed at the same three depths over a period of 12 months. More than 40 invertebrate taxa from seven phyla colonized the tiles. Colonial tunicates and encrusting bryozoans appeared early in the successional sequence (∼2 months), in cover ranging from <5% to 80% and from <5% to 55%, respectively. Tubiculous amphipods, barnacles, and sponges could also appear early, but in low cover (<20%). Composition of the assemblage changed over time with barnacles, sponges, and mussels becoming the principal space holders on tiles submerged for 24 months. When potential competitors were removed monthly, variation in the cover of dominant taxa (i.e., bryozoans, amphipods, barnacles) was maintained to 12 months, suggesting that other factors, such as larval availability or post-settlement mortality, were responsible for these patterns. Development of this assemblage appeared to fit a pattern of early succession that was largely predictable in terms of the composition and sequence of occurrence of dominant taxa, but variable in rate of development, depending on date of submersion, year, and depth.