从专刊论文管窥我国食用菌科学研究动态

1978年以来,我国食用菌产业科学技术研究成果斐然,近年来基础研究和应用基础研究在各个领域迅速展开,科学研究为食用菌产业发展提供了有力的技术支撑。本期《菌物学报》“食用菌专刊”共刊登了27篇论文,其中综述1篇,研究论文26篇。尽管这些论文尚不能代表我国食用菌科学研究的最高水平,但基本上反映了我国食用菌科学研究的最新动态。论文主要以香菇、侧耳类、金针菇、羊肚菌类、草菇等为研究材料,研究课题主要集中在食用菌组学分析、营养及生物活性物质和重要性状遗传等方面。总体而言,我国食用菌基础研究和应用基础研究相对滞后,它亟需学术界凝聚共识,鼎力支持以国家自然科学基金为代表的基础研究项目,提高我国食用菌基础研究水平。     

Lessons learnt on the analysis of large sequence data in animal genomics

The ’omics revolution has made a large amount of sequence data available to researchers and the industry. This has had a profound impact in the field of bioinformatics, stimulating unprecedented advancements in this discipline. Mostly, this is usually looked at from the perspective of human ’omics, in particular human genomics. Plant and animal genomics, however, have also been deeply influenced by next‐generation sequencing technologies, with several genomics applications now popular among researchers and the breeding industry. Genomics tends to generate huge amounts of data, and genomic sequence data account for an increasing proportion of big data in biological sciences, due largely to decreasing sequencing and genotyping costs and to large‐scale sequencing and resequencing projects. The analysis of big data poses a challenge to scientists, as data gathering currently takes place at a faster pace than does data processing and analysis, and the associated computational burden is increasingly taxing, making even simple manipulation, visualization and transferring of data a cumbersome operation. The time consumed by the processing and analysing of huge data sets may be at the expense of data quality assessment and critical interpretation. Additionally, when analysing lots of data, something is likely to go awry—the software may crash or stop—and it can be very frustrating to track the error. We herein review the most relevant issues related to tackling these challenges and problems, from the perspective of animal genomics, and provide researchers that lack extensive computing experience with guidelines that will help when processing large genomic data sets.     

When nature’s robots go rogue: exploring protein homeostasis dysfunction and the implications for understanding human aging disease pathologies

Introduction: Proteins have been historically regarded as ‘nature’s robots’: Molecular machines that are essential to cellular/extracellular physical mechanical properties and catalyze key reactions for cell/system viability. However, these robots are kept in check by other protein-based machinery to preserve proteome integrity and stability. During aging, protein homeostasis is challenged by oxidation, decreased synthesis, and increasingly inefficient mechanisms responsible for repairing or degrading damaged proteins. In addition, disruptions to protein homeostasis are hallmarks of many neurodegenerative diseases and diseases disproportionately affecting the elderly.

Areas covered: Here we summarize age- and disease-related changes to the protein machinery responsible for preserving proteostasis and describe how both aging and disease can each exacerbate damage initiated by the other. We focus on alteration of proteostasis as an etiological or phenomenological factor in neurodegenerative diseases such as Alzheimer’s, Parkinson’s, and Huntington’s, along with Down syndrome, ophthalmic pathologies, and cancer.

Expert commentary: Understanding the mechanisms of proteostasis and their dysregulation in health and disease will represent an essential breakthrough in the treatment of many (senescence-associated) pathologies. Strides in this field are currently underway and largely attributable to the introduction of high-throughput omics technologies and their combination with novel approaches to explore structural and cross-link biochemistry.     

Trait discovery and editing in tomato

Tomato (Solanum lycopersicum), which is used for both processing and fresh markets, is a major crop species that is the top ranked vegetable produced over the world. Tomato is also a model species for research in genetics, fruit development and disease resistance. Genetic resources available in public repositories comprise the 12 wild related species and thousands of landraces, modern cultivars and mutants. In addition, high quality genome sequences are available for cultivated tomato and for several wild relatives, hundreds of accessions have been sequenced, and databases gathering sequence data together with genetic and phenotypic data are accessible to the tomato community. Major breeding goals are productivity, resistance to biotic and abiotic stresses, and fruit sensorial and nutritional quality. New traits, including resistance to various biotic and abiotic stresses and root architecture, are increasingly being studied. Several major mutations and quantitative trait loci (QTLs) underlying traits of interest in tomato have been uncovered to date and, thanks to new populations and advances in sequencing technologies, the pace of trait discovery has considerably accelerated. In recent years, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing (GE) already proved its remarkable efficiency in tomato for engineering favorable alleles and for creating new genetic diversity by gene disruption, gene replacement, and precise base editing. Here, we provide insight into the major tomato traits and underlying causal genetic variations discovered so far and review the existing genetic resources and most recent strategies for trait discovery in tomato. Furthermore, we explore the opportunities offered by CRISPR/Cas9 and their exploitation for trait editing in tomato.     

组学时代的化学生态学：传统交叉学科的现代使命

作为传统的交叉学科,化学生态学在解决农林生产和人类健康的问题中逐步成为内涵越来越丰富的学科领域;同时,技术进步极大推动着化学生态学的发展,使得我们对于生物之间化学通讯规律的认识更加深入和全面。本“昆虫化学生态学”专辑论文全面反映了我国昆虫化学生态学研究的特色,即以农林生产应用为导向,传统和现代技术并用,研究水平逐步和国际同步。在组学的技术背景下,坚持交叉学科特色,加强合作,化学生态学研究在粮食安全、生态保护、应对全球气候变化等方面会发挥更大作用。     

Omics Metadata Management Software (OMMS)

Next-generation sequencing projects have underappreciated information management tasks requiring detailed attention to specimen curation, nucleic acid sample preparation and sequence production methods required for downstream data processing, comparison, interpretation, sharing and reuse. The few existing metadata management tools for genome-based studies provide weak curatorial frameworks for experimentalists to store and manage idiosyncratic, project-specific information, typically offering no automation supporting unified naming and numbering conventions for sequencing production environments that routinely deal with hundreds, if not thousands of samples at a time. Moreover, existing tools are not readily interfaced with bioinformatics executables, (e.g., BLAST, Bowtie2, custom pipelines). Our application, the Omics Metadata Management Software (OMMS), answers both needs, empowering experimentalists to generate intuitive, consistent metadata, and perform analyses and information management tasks via an intuitive web-based interface. Several use cases with short-read sequence datasets are provided to validate installation and integrated function, and suggest possible methodological road maps for prospective users. Provided examples highlight possible OMMS workflows for metadata curation, multistep analyses, and results management and downloading. The OMMS can be implemented as a stand alone-package for individual laboratories, or can be configured for webbased deployment supporting geographically-dispersed projects. The OMMS was developed using an open-source software base, is flexible, extensible and easily installed and executed. The OMMS can be obtained at http://omms.sandia.gov.

Availability

The OMMS can be obtained at http://omms.sandia.gov     

野生大豆耐逆分子调控机制研究进展

野生大豆(Glycine soja)起源于中国,是栽培大豆(G. max)的近缘祖先,逆境适应能力强,是研究耐逆分子机制和挖掘耐逆关键调控基因的优良材料。该文综述了野生大豆耐逆基因组、转录组和蛋白质组等组学研究进展,总结了近年来类受体蛋白激酶、转录因子、离子通道和氧化还原在野生大豆耐逆应答中的调控作用及机制,为耐逆作物...