DNA methylation of Quercus robur L. plumules following cryo-pretreatment and cryopreservation

Pedunculate oak (Quercus robur) is an ecologically and economically important forest tree species which produces seeds that are classified as recalcitrant. Thus, cryopreservation of seed meristems is a method for long-term preservation of this germplasm in gene banks. During cryopreservation, many factors, such as desiccation, cryoprotection and cooling/rewarming, can induce stress in the frozen meristems. In this study, in vitro survival and the global DNA methylation level of plumules after cryoprotection, desiccation and cryostorage was evaluated. Results indicated that both desiccation and storage in liquid nitrogen have negligible influence on DNA methylation status of Q. robur plumules. These findings support the cryopreservation of plumules as an appropriate method for conservation of Q. robur germplasm.     

Cryopreservation of oocyte and ovarian tissue

Cryopreservation of reproductive cells (i.e., oocytes, spermatozoa) and tissues (i.e., ovarian and testicular tissue) is a developing technology that has tremendous implications for rapid advancement of biomedical research in general. Since the early 1980s, advances have been made in establishing optimal conditions for in vitro oocyte maturation, fertilization, and culture of resulting embryos. These in vitro systems have contributed significantly to the utilization of these cells and tissues after thawing and have made it possible to evaluate protocols designed to cryopreserve such biomaterials more effectively. Although cryopreservation of preimplantation embryos from various species including mouse, human, and farm animals has been successful, cryopreservation of oocytes from most mammalian species has been more challenging due to their extreme sensitivity to suboptimal conditions during the cryopreservation process. Cryopreservation on mouse oocytes have been well documented and have resulted in greater success than studies with other mammalian species. Ovarian tissue cryopreservation and transplantation techniques have recently received much scientific and public attention due to their great potential use in human infertility treatment, in safeguarding the reproductive potential of the endangered species, and in genome banking of genetically important lab animal strains. A review of past and current research in the field of oocyte and ovarian tissue cryopreservation and transplantation and discussion of possible strategies for oocyte and ovarian tissue banking are provided.     

我国人类遗传资源采集活动现状分析与对策建议*

人类遗传资源是指含有人体基因组、基因等遗传物质的器官、组织、细胞等遗传材料及其产生的数据等资料。我国人类遗传资源极其丰富,合理利用人类遗传资源对推动我国生命科学、生物医药和临床研究具有重要意义。为有效保护、管理和利用我国人类遗传资源,管理部门严格依法依规开展人类遗传资源行政审批。通过梳理2021年我国人类遗传资源采集活动行政许可情况,结合工作实际,对存在问题进行分析,并提出对策建议。     

黄唇鱼(Bahaba flavolabiata)的全基因组测序和基因组特征研究

黄唇鱼(Bahaba flavolabiata)为国家二级重点保护野生动物、IUCN(世界自然保护联盟)红色名录的极度濒危物种(CR)。基于其样本数量极其有限,全基因组研究可以提供大量与重要性状相关的功能基因和分子标记,从而揭示其重要生命现象的遗传机制。采用二代测序技术于2018年5月完成了黄唇鱼基因组精细图的测序,分析结果表明,测序得到约202 Gb的高质量数据,总测序深度约为317×;组装得到的基因组大小为637.43 Mb,Contig N50约为88 Kb,Scaffold N50约为4.65 Mb;重复序列约142.72 Mb,占比22.39%,预测得到23743个基因、920个t RNA、85个rRNA、176个假基因;98.46%的基因可以注释到NR、GO等数据库中;有67个基因家族是黄唇鱼所特有的。本研究从单碱基错误率、核心基因完整性及二代Reads比对分析3个方面对黄唇鱼基因组精细图的组装结果进行了评估,结果显示所组装的基因区的完整性较好。黄唇鱼基因组序列图谱的绘制完成,对于黄唇鱼自然资源的保护和种质资源挖掘具有极其重要的科学意义。     

间充质干细胞过滤分离器制备人羊膜间充质干细胞的研究

自然存在的间充质干细胞数量少,限制了其研究应用。依靠自主发明的间充质干细胞过滤分离器,分离制备了人羊膜间充质干细胞,并对制备的干细胞进行了三维培养扩增。结果表明,制备的干细胞形态长势良好,并能诱导分化为类胰岛样组织。与常规方法相比,干细胞收获率提高了8倍以上,且细胞活性状态良好。间充质干细胞过滤分离器可以批量制备高质量的各种间充质干细胞,有利于高效率地建设各种间充质干细胞库,以促进间充质干细胞的研究应用。     

European approach to the Human Gene Project

In the history of gene mapping, which extends through most of the present century, Europe has played an important role. This has continued during the evolution of the 10 International Human Gene Mapping Workshops that have been held in seven different countries since 1973. Nationally coordinated programs have been a recent development, and several European countries, including the United Kingdom and Italy, have followed the lead of the United States in investing substantial sums of money in research on the human genome. In addition, the European Community has launched a multinational program of research on Human Genome Analysis to complement the various national initiatives. The particular approach in Europe has been to support those in the field by establishing resource centers for distributing biomaterials and accessing databases, by assisting in the training of scientists, and by funding programs of research directed at present needs in both physical and genetic mapping.     

Cryobanking mammalian embryos: Priorities and the optimal choice of reproductive technologies

This article reviews the main achievements in embryo cryobanking in conservation and preservation of animal strains, breeds, and species. Modern advances in this technology with respect to the main groups of laboratory and farm animals are discussed. Alternative approaches to solving the problems associated with cryobanking are considered and the priorities are substantiated. Special attention is given to discussing the role of cryobanks and respective reproductive technologies in programs aimed at conservation of genetic resources of wild and endangered mammalian species.     

Locating genetic disease: the impact of clinical nosology on biomedical conceptions of the human genome (1966–1990)

The variability of disease expression often complicates clinical classification. Since the 1960s, medical geneticists have sought to address this problem by associating diseases with discrete locations in the human genome. While this nosological approach was quite successful in the 1980s, unanticipated complications arose. In 1987, two historically distinct disorders, Prader-Willi and Angelman syndromes, were unexpectedly associated with the same genomic “address.” Does genomic overlap imply nosological sameness? This paper explores the clinical and biological implications of this finding, and argues that the process by which it was resolved represented new modes of thinking and practice in late-twentieth-century biomedicine. In the decades before the completion of the Human Genome Project, the genome was understood to be, at once, a standardized scientific object and an observable part of the human anatomy. Depicted and analyzed at the level of chromosomes, the genome became an important conceptual space and experimental system for late-twentieth-century biomedicine, producing novel research questions that drew the attention of both clinically oriented physicians and basic laboratory geneticists.     

Genome resource banking for wildlife research, management, and conservation

Cryobiology offers an important opportunity to assist in the management and study of wildlife, including endangered species. The benefits of developing genome resource banks for wildlife are profound, perhaps more so than for traditional uses in terms of livestock and human fertility. In addition to preserving heterozygosity and assisting in the genetic management of rare populations held in captivity, frozen repositories help insure wild populations against natural and human-induced catastrophes. Such banks also are an invaluable source of new knowledge (for basic and applied research) from thousands of species that have yet to be studied. However, it is crucial that genome resource banks for wildlife species be developed in a coordinated fashion that first benefits the conservation of biodiversity. Spurious collections will be of no advantage to genuine conservation. The Conservation Breeding Specialist Group (CBSG; of the International Union for the Conservation of Nature and Natural Resources' Species Survival Commission) has promoted international dialogue on this topic. CBSG working groups have recognized that such repositories be developed according to specific, scientific guidelines consistent with an international standard that ensures practicality, high-quality ethics, and cost-effectiveness. Areas requiring priority attention also are reviewed, including the need for more basic research, advocacy, and support for developing organized repositories of biomaterials representing the world's diverse biota.     

Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes

Application of single nucleotide polymorphisms (SNPs) is revolutionizing human bio-medical research. However, discovery of polymorphisms in low polymorphic species is still a challenging and costly endeavor, despite widespread availability of Sanger sequencing technology. We present CRoPS as a novel approach for polymorphism discovery by combining the power of reproducible genome complexity reduction of AFLP with Genome Sequencer (GS) 20/GS FLX next-generation sequencing technology. With CRoPS, hundreds-of-thousands of sequence reads derived from complexity-reduced genome sequences of two or more samples are processed and mined for SNPs using a fully-automated bioinformatics pipeline. We show that over 75% of putative maize SNPs discovered using CRoPS are successfully converted to SNPWave assays, confirming them to be true SNPs derived from unique (single-copy) genome sequences. By using CRoPS, polymorphism discovery will become affordable in organisms with high levels of repetitive DNA in the genome and/or low levels of polymorphism in the (breeding) germplasm without the need for prior sequence information.     

New Directions in Dipterocarp Biology and Conservation: A Synthesis

The Dipterocarpaceae is an ecologically and economically important tree family in Southeast Asia. In this article, we synthesize the contributions to our understanding of the population genetics, ecology, and conservation of the family presented in this Special Section, and discuss their implications for mechanisms of dipterocarp species coexistence in natural and disturbed forests. We highlight the need for research to address how the processes that give rise to dipterocarp diversity are maintained in landscapes modified by anthropogenic activity.     

Role of nanotopography in the development of tissue engineered 3D organs and tissues using mesenchymal stem cells

Recent regenerative medicine and tissue engineering strategies(using cells, scaffolds, medical devices and gene therapy) have led to fascinating progress of translation of basic research towards clinical applications. In the past decade, great deal of research has focused on developing various three dimensional(3D) organs, such as bone, skin, liver, kidney and ear,using such strategies in order to replace or regenerate damaged organs for the purpose of maintaining or restoring organs’ functions that may have been lost due to aging, accident or disease. The surface properties of a material or a device are key aspects in determining the success of the implant in biomedicine, as the majority of biological reactions in human body occur on surfaces or interfaces. Furthermore, it has been established in the literature that cell adhesion and proliferation are, to a great extent, influenced by the micro- and nanosurface characteristics of biomaterials and devices. In addition, it has been shown that the functions of stem cells, mesenchymal stem cells in particular, could be regulated through physical interaction with specific nanotopographical cues. Therefore, guided stem cell proliferation, differentiation and function are of great importance in the regeneration of 3D tissues and organs using tissue engineering strategies. This review will provide an update on the impact of nanotopography on mesenchymal stem cells for the purpose of developing laboratory-based 3D organs and tissues, as well as the most recent research and case studies on this topic.     

菌寄生属研究进展

菌寄生属通常寄生于其他真菌子实体上,是子囊菌的重要类群之一,在生物医药和工农业等方面具有经济重要性。简述了菌寄生属在资源与分类、系统发育和寄主专化性等方面的研究现状及进展。已有的分子系统学研究表明,菌寄生属是多谱系类群,形成多个分支,各分支与其无性型特征和寄主种类有关。今后需进一步澄清属种概念,建立稳定的有性阶段-无性阶段对应关系,在全面了解其物种多样性和地理分布特点基础上,深入探讨种间系统发育关系。     

基因捕获技术的现状及应用

随着越来越多生物基因组测序的完成,生物医学研究已进入后基因组时代。基因捕获技术由于其在克隆、发现新基因及揭示基因功能方面具有独特的优点,已成为功能基因组时代研究的有力工具,在生物医学研究各个领域的应用日趋广泛。主要对基因捕获技术的原理、分类、一般操作流程、优缺点及基因捕获在发育生物学、新基因鉴定、干细胞分化、肿瘤和生殖医学研究方面的应用作一综述,为相关研究者提供借鉴。     

我国生物种质资源库及其信息化平台建设的科技进展

摘要：生物种质资源是保障国家粮食安全、生态安全、人类健康安全等的战略性资源。本文简述了我国生物种质资源库的建设布局、样本保存、整合汇交以及信息化平台建设支撑的国家科技部署等进展情况,分析了我国生物种质资源库及其信息化平台建设面临的挑战,对未来的发展提出了建议。     

No evidence that sex and transposable elements drive genome size variation in evening primroses

Genome size varies dramatically across species, but despite an abundance of attention there is little agreement on the relative contributions of selective and neutral processes in governing this variation. The rate of sex can potentially play an important role in genome size evolution because of its effect on the efficacy of selection and transmission of transposable elements (TEs). Here, we used a phylogenetic comparative approach and whole genome sequencing to investigate the contribution of sex and TE content to genome size variation in the evening primrose (Oenothera) genus. We determined genome size using flow cytometry for 30 species that vary in genetic system and find that variation in sexual/asexual reproduction cannot explain the almost twofold variation in genome size. Moreover, using whole genome sequences of three species of varying genome sizes and reproductive system, we found that genome size was not associated with TE abundance; instead the larger genomes had a higher abundance of simple sequence repeats. Although it has long been clear that sexual reproduction may affect various aspects of genome evolution in general and TE evolution in particular, it does not appear to have played a major role in genome size evolution in the evening primroses.     

<Emphasis Type="Italic">In vitro</Emphasis> and cryogenic preservation of plant biodiversity in Brazil

The Brazilian biomes (Amazon, Atlantic Forest, Cerrado, Caatinga, Pantanal, and Pampa) comprise one of the highest levels of plant diversity in the world; however, non-sustainable practices, deforestation, and land use have resulted in significant losses and fragmentation of the native forests. These ecosystems are now threatened and protection of their native plants through ex situ conservation is an urgent necessity. Cryopreservation and in vitro conservation are complementary options for securing and protecting Brazil’s native plant species because their potential economic value is critically important to develop strategies that will (1) support their sustainable utilization, (2) protect against the over-exploitation of species growing in natural habitats, and (3) conserve the genetic diversity of germplasm from species of different provenances. Biotechnological approaches will help to address future economic and environmental demands placed upon already at-risk species. Conserving seed germplasm ex situ provides an additional safeguard against the risks (e.g., loss due to disease, climate change) of field conservation. Moreover, seed banks and cryobanks permit the long-term conservation of a wider genetic base; this offsets the labor and space intensive costs of conserving in the active growing state. This paper is a compilation of the current status of strategies applied for conserving Brazilian native plant species.     

What can patterns of differentiation across plant genomes tell us about adaptation and speciation?

Genome scans have become a common approach to identify genomic signatures of natural selection and reproductive isolation, as well as the genomic bases of ecologically relevant phenotypes, based on patterns of polymorphism and differentiation among populations or species. Here, we review the results of studies taking genome scan approaches in plants, consider the patterns of genomic differentiation documented and their possible causes, discuss the results in light of recent models of genomic differentiation during divergent adaptation and speciation, and consider assumptions and caveats in their interpretation. We find that genomic regions of high divergence generally appear quite small in comparisons of both closely and more distantly related populations, and for the most part, these differentiated regions are spread throughout the genome rather than strongly clustered. Thus, the genome scan approach appears well-suited for identifying genomic regions or even candidate genes that underlie adaptive divergence and/or reproductive barriers. We consider other methodologies that may be used in conjunction with genome scan approaches, and suggest further developments that would be valuable. These include broader use of sequence-based markers of known genomic location, greater attention to sampling strategies to make use of parallel environmental or phenotypic transitions, more integration with approaches such as quantitative trait loci mapping and measures of gene flow across the genome, and additional theoretical and simulation work on processes related to divergent adaptation and speciation.     

Overexploitation and anthropogenic disturbances threaten the genetic diversity of an economically important neotropical palm

The Caatinga biome is one of the largest areas of the South American seasonally dry tropical forest that has been severely affected by unsustainable natural resource use. Furthermore, the biome has been identified as an ecologically sensitive region that is particularly susceptible to climate changes. One of the most economically important native palm tree for traditional communities from the semi-arid Caatinga is the carnauba palm, Copernicia prunifera, which offers diverse natural resources, yet its natural populations suffer intense exploitation. To inform conservation and population management strategies, we sought to determine if remaining natural populations of this species in an intensively exploited area in Northeast Brazil displayed evidence of negative genetic impacts because of exploitation and how this might interact with expected environmental changes. Mantel’s test revealed a positive and significant correlation between geographic and genetic distances, suggesting natural populations are structured by isolation by distance, while also experiencing genetic barriers as identified through Monmonier's algorithm. The studied populations showed evidence of genetic bottlenecks, while future climate scenarios suggest that potentially suitable habitats for C. prunifera within its native range will be reduced. Significant genetic differentiation among populations resulted in three distinct genetic groups which are consistent with ecological niche modelling. In addition to the need for in situ conservation of C. prunifera populations to minimize the loss of important alleles, the creation of germplasm banks for ex situ conservation and strategies for developing planted productive forests are urgently required to maintain natural populations and ensure sustainability resources for traditional communities.