Application of omics technologies for a deeper insight into quali-quantitative production traits in broiler chickens:A review

The poultry industry is continuously facing substantial and different challenges such as the increasing cost of feed ingredients, the European Union’s ban of antibiotic as growth promoters, the antimicrobial resistance and the high incidence of muscle myopathies and breast meat abnormalities. In the last decade, there has been an extraordinary development of many genomic techniques able to describe global variation of genes, proteins and metabolites expression level. Proper application of these cutting-edge omics technologies(mainly transcriptomics, proteomics and metabolomics) paves the possibility to understand much useful information about the biological processes and pathways behind different complex traits of chickens. The current review aimed to highlight some important knowledge achieved through the application of omics technologies and proteo-genomics data in the field of feed efficiency, nutrition, meat quality and disease resistance in broiler chickens.

Neglected scrub typhus:An updated review with a focus on omics technologies

Scrub typhus is a neglected disease and one of the most serious health problems in the Asia-Pacific region.The disease is caused by an obligate intracellular bacteria Orientia tsutsugamushi,which is transmitted by chigger bites or larval mite bites.Scrub typhus is a threat to billions of people worldwide causing different health complications and acute encephalitis in infants and growing children.The disease causes multiple organ failure and mortality rates may reach up to 70%due to a lack of appropriate healthcare.Currently available genome and proteome databases,and bioinformatics methods are valuable tools to develop novel therapeutics to curb the pathogen.This review discusses the state-of-the-art of information about Orientia tsutsugamushi-mediated scrub typhus and delineates the role of omics technologies to develop drugs against the pathogen.The role of proteome-wide in silico approaches for the identification of therapeutic targets is also highlighted.

Omics Technologies Reveal Abundant Natural Variation in Metabolites and Transcripts among Conventional Maize Hybrids

In this report we have evaluated metabolite and RNA profiling technologies to begin to understand the natural variation in these biomolecules found in commercial-quality, conventional (non-GM) maize hybrids. Our analyses focus on mature grain, the article of commerce that is most typically subjected to the rigorous studies involved in the comparative safety assessment of GM products. We have used a population of conventionally-bred maize hybrids that derive from closely related inbred parents grown under standard field conditions across geographically similar locations. This study highlights the large amount of natural variation in metabolites and transcripts across conventional maize germplasm grown under normal field conditions, and underscores the critical need for further extensive studies before these technologies can be seriously considered for utility in the comparative safety assessment of GM crops.

Integration of multi-omics in investigations on the mechanisms of action of Chinese herbal medicine interventions in metabolic diseases

The rapid development of bioinformatics has provided novel approaches and methods for exploring the mechanisms of disease treatment via Chinese herbal medicines.Compound Chinese herbal medicines formulas have complex compositions and are characterized by their multiple constituents and diverse array of biological targets.Therefore,the mechanisms of action of most compound Chinese herbal medicines formulas cannot be adequately explained using a single pathway.Omics technologies describe high-throughput-based analytical and detection techniques,which include transcriptomics,proteomics,and metabolomics and provide multilayer parameter information that can be integrated to characterize the overall relationships involved in the therapeutic effects of Chinese herbal medicines formulas.Through their combination with network biology and drug effect networks,omics technologies also enable investigations into the mechanisms of disease treatment in traditional Chinese medicine.The integration of multiple omics technologies is in line with the concept of holism in traditional Chinese medicine and provides an approach for combining modern science and technology with traditional Chinese medicine theories.In recent years,omics technologies have been widely used to elucidate the mechanisms of action of Chinese herbal medicines.The latest studies employing multi-omics integration for investigating the mechanisms of action of Chinese herbal medicines interventions in metabolic diseases have devoted greater attention to in-depth explorations of disease pathogenesis.This paper provides a review of the following multi-omics technologies,which are used in research on the treatment of common metabolic diseases(e.g.,type-2 diabetes mellitus,nonalcoholic fatty liver disease):network pharmacology combined with metabolomics,16S rRNA sequencing combined with transcriptomics,16S rRNA sequencing combined with metabolomics,and 16S rRNA sequencing combined with network pharmacology and metabolomics.

Advances in Genomic,Transcriptomic,and Metabolomic Analyses of Fruit Quality in Fruit Crops

Fruit quality is the main factor determining market competitiveness;it represents the combination of fruit flavor,color,size,and the contents of aromatic and bioactive substances.Research on the genetic basis of fruit quality can provide new information about fruit biology,promote genomic-assisted breeding,and provide technological support for the regulation of fruit quality via habitat selection and/or the control of environmental conditions.High-throughput sequencing is a powerful research method for studying fruit quality traits,and reference genome sequences for many important fruit crops have provided vast amounts of genomic data.To study fruit quality,it is important to select appropriate omics strategies and to analyze omics data meaningfully.Here,we summarize genomic mechanisms of fruit quality formation:gene duplication,transposable element insertion,structural variations and genome methylation in functional genes.We review the genomic,transcriptomic,and metabolomic strategies that have been used to study the genetic basis of fruit quality traits.We also describe some of the genes associated with fruit traits;these genes are a valuable resource for genomics-assisted breeding and are useful models for deciphering the mechanisms of agronomic traits,such as fruit color,size,hardness,aroma components,sugar and acid content.Finally,to maximize the application of omics information,we propose some further directions for research using omics strategies.

High-throughput research on superconductivity

As an essential component of the Materials Genome Initiative aiming to shorten the period of materials research and development, combinatorial synthesis and rapid characterization technologies have been playing a more and more important role in exploring new materials and comprehensively understanding materials properties. In this review, we discuss the advantages of high-throughput experimental techniques in researches on superconductors. The evolution of combinatorial thin-film technology and several high-speed screening devices are briefly introduced. We emphasize the necessity to develop new high-throughput research modes such as a combination of high-throughput techniques and conventional methods.

根际化学与生物多样性的表征方法:组学技术的机遇与挑战

根际是联结植物、土壤和微生物的重要界面,是化学与生物过程耦合最活跃的区域.根际环境影响土壤中有机和无机污染物的行为,而研究方法的完善与提升有助于阐释根际中复杂的过程与作用机制.本文从传统的化学和生物学方法到新兴的组学技术对根际科学的方法学研究进展进行了综述,重点讨论了当今组学技术在根际研究中应用机遇与挑战,同时展望了今后需要关注的科学问题.根际化学组分的传统分析方法涵盖了光谱、色谱、质谱和色质联用等技术,主要聚焦于低分子量有机酸等小分子的定性定量测定,导致对根际化学多样性的认知偏差;传统的根际微生物研究依赖于培养技术,对微生物多样性的描述存在很大的局限.揭示根际异质性和复杂性,亟需采用高端的技术,组学方法显示出极大的优势,显著提高了研究者对根际科学的认识.基于靶向和非靶向代谢组学有利于深入研究根际复杂的化学多样性过程;基于宏基因组学、转录组学和蛋白组学等组学工具能够提供微生物组基因和蛋白的表达、功能特性等更详细的信息,可以全面地揭示根际微生物的多样性.应该强调的是,未来多组学整合分析更是表征根际化学与生物多样性的一个强有力工具,但需要更多的模型、框架和计算基础来实现根际基因、蛋白、转录和代谢水平的多层次关联,以助于挖掘根-微生物-土壤界面大量尚未揭示的关键过程、机理及生态环境效应.

组学技术在黄芪质量评价及药理作用机制研究中的应用

黄芪为补气之要药,临床应用广泛。但因各种因素导致黄芪质量参差不齐现象突出,且现行评价方法难以从整体上把控黄芪药材的质量优劣,未能有效的与不同复方中黄芪功效定向关联,严重影响其临床疗效及安全用药。针对上述问题,探索具有整体性和系统性特点的组学技术在中药材黄芪质量优劣性评价中的应用迫在眉睫。鉴于此本文查阅近年文献,对组学(代谢组学、转录组学、基因组学、蛋白组学)技术应用于中药材黄芪质量控制(品种、产地、种植方式、逆境、炮制加工)以及药理作用(抗疲劳、抗心衰、防治内分泌疾病、抗肿瘤)机制方面的研究进行综述,提出未来研究的方向与趋势,旨在为临床合理用药建立其全面系统的质量评价体系提供新的思路及方法。

保活运输应激对水产动物肌肉品质影响的研究进展

【目的】揭示应激对水产动物肌肉品质的影响,以期为水产动物保活运输提供参考。【方法】将保活运输过程中的应激源分为温度、低氧、拥挤、振动、氨氮和空气暴露等,综述各种应激源对不同水产动物肌肉品质的影响;在此基础上,概括加盐、暂养、加抗氧化剂、休眠和冷驯化等减缓应激措施对水产动物肌肉品质的影响,总结组学技术在揭示应激影响水产动物肌肉品质机制的应用。【结果与结论】应激状态下,水产动物的生命活动中,如基因表达、代谢和免疫等都会进行适应性调控,使蛋白质、代谢物组成和细胞形态等发生改变,并最终影响肌肉品质。消除应激可提升水产动物肌肉品质,关于其对提升肌肉品质的机理方面研究是未来的研究方向。

多组学整合策略在中药抗抑郁机制研究中的应用

抑郁症是一种常见的精神和心理疾病,发病机制复杂,中医辨证论治治疗抑郁症具有因人而异、因病而异的独特优势。随着分子生物学技术快速发展,多组学技术在中药有效成分抗抑郁效果的分析中得到广泛应用。文章系统介绍了多组学的核心技术,重点综述了近年来基因组学、蛋白质组学、转录组学、代谢组学和多组学整合技术在中药抗抑郁作用机制研究中的思路、方法和进展,为推进多组学技术在中药治疗抑郁症中的应用提供参考。

Advances and applications in spatial transcriptomics

Spatial transcriptomics is an organizational study done on tissue sections that preserves the spatial information of the sample.Spatial transcriptomics aims to combine spatial information with gene expression data to quantify the mRNA expression of a large number of genes in the spatial context of tissues and cells.As a paradigm shift in biological research,spatial transcriptomics can provide both spatial location information and transcriptome-level cellular gene expression data,elucidating the interactions between cells and the microenvironment.From the understanding of the entire functional life cycle of RNA to the characterization of molecular mechanisms to the mapping of gene expression in various tissue regions,by choosing the appropriate spatial transcriptome technology,researchers can achieve a deeper exploration of biological developmental processes,disease pathogenesis,etc.In recent years,the field of spatial transcriptomics has ushered in several challenges along with its rapid development,such as the dependence on sample types,the resolution of visualized genes,the difficulty of commercialization,and the ability to obtain detailed single-cell information.In this paper,we summarize and review the four major categories of spatial transcriptome technologies and compare and analyze the technical advantages and major challenges of multiple research strategies to assist current experimental design and research analysis.Finally,the importance of spatial transcriptomics in the integration of multi-omics analysis and disease modeling as well as the future development prospects are summarized and outlined.

手足口病患者肠道微生物特征及其对疾病影响的研究进展

手足口病(HFMD)是一种由肠道病毒引起的主要影响儿童的传染性疾病,其与肠道微生物之间的关联特征近年来受到了广泛关注。肠道微生物是指生活在人体消化道中并与人体共生的微生物,这类微生物与人体健康息息相关。多组学技术已被广泛用于肠道微生物和微生物衍生代谢物的鉴定和表征,了解肠道微生物与HFMD之间的相互作用不仅是研究需要,也是HFMD感染预防和治疗措施的发展方向。本综述旨在了解HFMD人群肠道菌群和病毒组,并着重介绍肠道微生物在HFMD中免疫稳态的相关作用,以期为HFMD的诊断和防治提供新思路。

多组学技术在绵羊肉质性状研究中的应用进展

羊肉具有高蛋白、低脂肪、肉质细嫩和风味独特等特点,深受广大消费者喜爱。绵羊的肉质性状受品种、营养、环境、屠宰后加工等多种因素影响,调控机制复杂,传统的肉质评定方法难以阐明肉品质变化的潜在机制和途径。在后基因组时代,基因组、转录组、蛋白质组、微生物组和代谢组等组学技术凭借高通量、高灵敏度和系统性等优势,已成为畜禽肉质性状研究的有力工具,能从分子层面深入研究生物特性形成的根源。本文基于公开发表的文献,重点综述了组学技术及多组学联用方法在绵羊肉质性状中的应用进展,并对其应用的挑战和前景进行了展望,以期为绵羊肉质性状的机理解析提供方法,为绵羊分子育种提供思路。

现代组学技术在中药防治糖脂代谢紊乱机制探索中的应用

糖脂代谢紊乱加速了血管并发症的进展,中药综合调整策略显示出巨大的治疗潜力。然而,中药成分复杂、作用途径多样,严重制约了中药的临床应用及现代化进程。现代组学技术的快速发展为中药治疗糖脂代谢疾病的机制探索创造了有利的条件,使揭示中药治疗糖脂代谢疾病的科学内涵成为可能。近年来研究发现中药可以通过调节肠道菌群、降低炎症因子水平、抑制脂肪生成及脂质累积、减少胰岛β细胞的凋亡、提高胰岛素敏感性、改善胰岛抵抗等多靶点、多途径发挥防治糖脂代谢紊乱的作用。文章通过梳理现代组学技术在中药防治糖脂代谢紊乱机制探索中的应用进展,为精准化、客观化揭示中药防治糖脂代谢紊乱的作用机制提供有益参考,为中药临床应用及开发提供理论支撑。

Application of high-throughput sequencing technology in HIV drug resistance detection

Drug resistance via drug-resistant mutations in the human immunodeficiency virus(HIV)genome is the primary cause of antiviral therapy failure.Consequently,HIV drug resistance genotyping has become a critical approach in HIV prevention and control.Compared to the Sanger sequencing technology,high-throughput sequencing(HTS)technology has superior sensitivity and timeliness,with strong detection capabilities for low-frequency mutations.With the continued advancement of HTS technologies,their prominence in HIV drug resistance detection techniques has increased accordingly.This article will review the latest developments in HTS technology and its applications in HIV drug resistance testing.

组学技术在猪肉品质评价中的应用研究进展

猪肉品质是影响消费者购买欲望的重要因素。随着技术的发展,在肉类研究中开始广泛应用组学技术来提高食品的质量和安全性,保障消费者的健康和需求。本文介绍了用于猪肉品质评价方面的蛋白质组学、代谢组学以及脂质组学3种组学技术,阐述3种组学技术各自的特点及其在肉类品质评价中的实际应用,讨论了组学技术在肉质评价方面未来的方向,为组学技术在猪肉的质量控制和预测上的研究和应用提供参考。

基于质谱的单细胞多组学分析技术研究进展

近年来,随着质谱技术的飞速发展,单细胞质谱技术在生命科学领域发挥着越来越重要的作用.质谱已被广泛用于检测细胞群代谢和蛋白组,单细胞质谱多组学技术结合微观生物学和尖端质谱分析,为在单细胞层面进行深入研究提供了强有力的工具,进一步阐明了细胞微观复杂性.特别是在生物医学应用中,单细胞质谱多组学有助于细胞图谱绘制、生命现象分子机制探究及精准医学的发展等.本文综合评述了近年来基于质谱的单细胞代谢、蛋白组及其整合组学技术研发中面临的挑战与突破,并对其未来的发展趋势进行了展望.

单细胞多组学在灵长类早期胚胎发育中的研究应用

啮齿类是研究胚胎发育的重要模型,然而啮齿类与灵长类在发育过程中存在巨大的种属差异,啮齿类中的研究并不能简单推广到灵长类中,因此灵长类生殖发育研究亟待开展。早期胚胎细胞数量稀少且复杂多样,通常采用单细胞测序技术来揭示其发育过程及调控机制。然而仅依靠单细胞单组学分析并不能有效全面地解析细胞间编码的复杂网络信息。单细胞多组学有效地联合转录组、表观遗传组、蛋白质组、代谢组等进行分析,使研究者能够在同一细胞水平上系统地解码不同细胞类型的异质性及发育轨迹,从多维度去理解灵长类早期胚胎发育的关键事件。本文总结了单细胞RNA治疗发展到多组学过程中关键技术的发展历程,并概述了多组学技术在深入解读灵长类早期胚胎发育研究中的应用及未来潜在的发展方向和挑战。

转基因组学分析技术研究进展

转基因技术备受世人关注,且转基因作物关乎人体健康和生态环境,因此对转基因作物的安全评价地位极其重要,各种评价方法也在不断前进与发展。组学分析技术成为安全评价工作的新思路。本文主要论述了转基因组学分析技术的必要性,组学分析技术的发展,世界主要转基因作物组学评价发展情况及未来转基因组学分析技术的发展趋势,以期对转基因安全评价工作提供新的思路和方向。

酒精发酵过程中酿酒酵母耐受环境胁迫的研究进展

提高酿酒酵母细胞耐受环境胁迫(高渗透压、高浓度酒精和高温)的能力对酒精工业生产具有重要的意义。对提高酿酒酵母耐受性的研究方法和策略的发展历程进行了综述。基因组学、转录组学和蛋白质组学等现代组学技术在这一领域的研究获得了广泛的应用。这些技术将提供期待的信息,去理性改造并获得更加耐受胁迫的工业酵母菌株。