On the comparison of population-level estimates of haplotype and nucleotide diversity: a case study using the gene cox1 in animals

Estimates of genetic diversity represent a valuable resource for biodiversity assessments and are increasingly used to guide conservation and management programs. The most commonly reported estimates of DNA sequence diversity in animal populations are haplotype diversity (h) and nucleotide diversity (π) for the mitochondrial gene cytochrome c oxidase subunit I (cox1). However, several issues relevant to the comparison of h and π within and between studies remain to be assessed. We used population-level cox1 data from peer-reviewed publications to quantify the extent to which data sets can be re-assembled, to provide a standardized summary of h and π estimates, to explore the relationship between these metrics and to assess their sensitivity to under-sampling. Only 19 out of 42 selected publications had archived data that could be unambiguously re-assembled; this comprised 127 population-level data sets (n ≥ 15) from 23 animal species. Estimates of h and π were calculated using a 456-base region of cox1 that was common to all the data sets (median h=0.70130, median π=0.00356). Non-linear regression methods and Bayesian information criterion analysis revealed that the most parsimonious model describing the relationship between the estimates of h and π was π=0.0081 h(2). Deviations from this model can be used to detect outliers due to biological processes or methodological issues. Subsampling analyses indicated that samples of n>5 were sufficient to discriminate extremes of high from low population-level cox1 diversity, but samples of n ≥ 25 are recommended for greater accuracy.     

Instrumental neutron activation analysis of biological samples

The elemental compositions of 18 biological reference materials have been processed, for 14 stepped combinations of irradiation/decay/counting times, by the INAA Advance Prediction Computer Program. The 18 materials studied include 11 plant materials, 5 animal materials, and 2 other biological materials. Of these 18 materials, 14 are NBS Standard Reference Materials and four are IAEA reference materials. Overall, the results show that a mean of 52% of the input elements can be determined to a relative standard deviation of ±10% or better by reactor flux (thermal plus epithermal) INAA.

     

The state of commercial augmentative biological control: plenty of natural enemies,but a frustrating lack of uptake

Augmentative biological control concerns the periodical release of natural enemies. In commercial augmentative biological control, natural enemies are mass-reared in biofactories for release in large numbers to obtain an immediate control of pests. The history of commercial mass production of natural enemies spans a period of roughly 120 years. It has been a successful, environmentally and economically sound alternative for chemical pest control in crops like fruit orchards, maize, cotton, sugar cane, soybean, vineyards and greenhouses. Currently, augmentative biological control is in a critical phase, even though during the past decades it has moved from a cottage industry to professional production. Many efficient species of natural enemies have been discovered and 230 are commercially available today. The industry developed quality control guidelines, mass production, shipment and release methods as well as adequate guidance for farmers. However, augmentative biological control is applied on a frustratingly small acreage. Trends in research and application are reviewed, causes explaining the limited uptake are discussed and ways to increase application of augmentative biological control are explored.     

A global biological conservation horizon scan of issues for 2023

We present the results of our 14th horizon scan of issues we expect to influence biological conservation in the future. From an initial set of 102 topics, our global panel of 30 scientists and practitioners identified 15 issues we consider most urgent for societies worldwide to address. Issues are novel within biological conservation or represent a substantial positive or negative step change at global or regional scales. Issues such as submerged artificial light fisheries and accelerating upper ocean currents could have profound negative impacts on marine or coastal ecosystems. We also identified potentially positive technological advances, including energy production and storage, improved fertilisation methods, and expansion of biodegradable materials. If effectively managed, these technologies could realise future benefits for biological diversity.     

Bioaerosols associated with animal production operations

Air emissions from animal housing and manure management operations include a complex mixture of biological, microbial, and inorganic particulates along with odorous volatile compounds. This report highlights the state of current issues, technical knowledge, and remaining challenges to be addressed in evaluating the impacts of airborne microorganisms, dusts, and odorants on animals and workers at animal production facilities and nearby communities. Reports documenting bioaerosol measurements illustrate some of the technical issues related to sample collection, analysis, as well as dispersion and transport to off-farm locations. Approaches to analysis, mitigation and modeling transport are discussed in the context of the risk reduction and management of airborne spread of bioaerosols from animal operations. The need for standardization and validation of bioaerosol collection and analytical techniques for indoor as well as outdoor animal agriculture settings is critical to evaluation of health effects from modern animal production systems that are increasingly situated near communities.     

“ISA-Lation” of Single-Stranded Positive-Sense RNA Viruses from Non-Infectious Clinical/Animal Samples

Isolation of viral pathogens from clinical and/or animal samples has traditionally relied on either cell cultures or laboratory animal model systems. However, virus viability is notoriously susceptible to adverse conditions that may include inappropriate procedures for sample collection, storage temperature, support media and transportation. Using our recently described ISA method, we have developed a novel procedure to isolate infectious single-stranded positive-sense RNA viruses from clinical or animal samples. This approach, that we have now called "ISA-lation", exploits the capacity of viral cDNA subgenomic fragments to re-assemble and produce infectious viral RNA in susceptible cells. Here, it was successfully used to rescue enterovirus, Chikungunya and Tick-borne encephalitis viruses from a variety of inactivated animal and human samples. ISA-lation represents an effective option to rescue infectious virus from clinical and/or animal samples that may have deteriorated during the collection and storage period, but also potentially overcomes logistic and administrative difficulties generated when complying with current health and safety and biosecurity guidelines associated with shipment of infectious viral material.     

用生物学方法重建心脏起搏点的研究进展

正常人的心脏节律源于右心房的天然起搏点（pacemaker）——窦房结。窦房结的功能异常或者房室传导阻滞会导致心率异常（如心律缓慢）。治疗严重的心动过缓需要植入在技术上已经相当成熟的电子起搏器,但这种治疗存在一些缺陷和不足。近年来,在动物实验模型中应用基因或细胞来重建心脏的生物起搏点已经取得了进展。超极化活化环核苷酸门控（hyperpolarization-activated cyclic-nucleotide-modulated,HCN）通道（起搏通道）通过超极化活化的阳离子电流（hyperpolarization-activated cation current,It）调制心脏的自律性。利用病毒载体或转染HCN基因的细胞将HCN基因导入动物心脏内可重建生物起搏点。也有导入其它基因或植入自律细胞来探索心脏起搏点的重建。本文总结了重建心脏生物起搏点的一些研究进展。一旦稳定性和寿命等关键问题得到相应解决,遗传工程改造的生物起搏点可用于治疗严重的心动过缓。     

Sharing genomes: an integrated approach to funding, managing and distributing genomic clone resources

National biological resource centres have a vital role in archiving and distributing biological reagents that result from large-scale genome programmes. These reagents are invaluable to the research community as they enable independent validation of results disclosed in peer review and provide tools that facilitate the next steps in discovery science. Here we address the crucial issues of open access, quality of materials, integration with public databases and sustainability of resources.     

A comparative study of distant hybridization in plants and animals

Distant hybridization refers to crosses between two different species, genera, or higher-ranking taxa, which can break species limits, increase genetic variation, and combine the biological characteristics of existing species. It is an important way of creating genetic variation, fertile strains, and excellent characteristics in new strains and populations. Combining analyses and summaries from many inter-related documents in plants and animals, both domestic and international, including examples and long-standing research on distant hybridization in fish from our laboratory, we summarize and compare the similarities and differences in plant and animal distant hybridization. In addition, we analyze and review the biological characteristics of their different ploidy progenies and the possible causes of disparity in survival rates. Mechanisms of sterility in animal and plant distant hybrids are also discussed, and research methods for the study of biological characteristics of hybrids, including morphology, cytology,and molecular cytogenetics are presented. This paper aims to provide comprehensive research materials and to systematically compare the general and specific characteristics of plant and animal hybrids with regards to reproduction, genetics, growth traits,and other biological characteristics. It is hoped that this paper will have great theoretical and practical significance for the study of genetic breeding and biological evolution of plant and animal distant hybridization.     

动物外泌体分离方法的研究进展*

外泌体是一种由细胞分泌的细胞外囊泡,其广泛存在于各类生物液中,是细胞间信息交流的途径之一。由于外泌体内携带的核酸、蛋白质及脂质等功能性物质可作为生物标记用于动物生理诊断,也可作为信息传输载体用于调节动物生理状态以及治疗动物疾病,因而受到广泛的研究,开发潜力巨大。建立成熟稳定且方便快捷的外泌体分离手段是保证外泌体相关研究顺利开展的前提。以下对当前动物外泌体分离的主要方法进行了综述,比较了不同分离手段的特点,以此为相关技术的进一步开发与后续的动物外泌体研究提供方法及理论参考。     

呼肠孤病毒Ⅲ型（Re03）RT—PCR检测方法的建立

目的建立呼肠孤病毒Ⅲ型（Re03）RT—PCR检测方法,应用于实验动物及人用动物源性材料及生物制品外源Re03的检测。方法根据已发表的呼肠孤病毒Ⅲ型（Re03）M1基因序列,设计合成引物。提取Re03细胞毒RNA,以其为模板,进行PCR扩增。优化反应条件,进行特异性、敏感性、重复性试验。结果建立的Re03RT—PCR检测方法特异、敏感、稳定。以Re03RNA逆转录产物为模板,所能检测RNA最小模板浓度为0．42pg／μL,可检测病毒最小滴度为10^-9／mL。结论建立的呼肠孤病毒Ⅲ型（Re03）RT—PCR检测方法可用于实验动物及人用动物源性材料及生物制品外源Re03的检测。     

Virus PCR assay panels: an alternative to the mouse antibody production test

Antibody production tests have traditionally been used to test biological materials for viral contamination. Now molecular biology techniques have emerged as an alternative. The authors compare MAP testing with PCR-based detection methods, focusing on differences in animal use, laboratory requirements, sample size, and limits of detection.     

How Distinctive is Genetic Information?

There is extensive discussion of the ethical, social, economic and political issues associated with the use of technologies based on DNA techniques. Many of these debates are premised on the assumption that DNA, and the genetic information that may be derived from it, have unique features which raise new social and ethical issues. In this paper it is argued that several of the features associated with DNA which are sometimes regarded as unique are shared with other biological materials. Others owe more to the cultural image of DNA and some of the metaphors used to discuss it in biology and in wider debates than to the biological properties of DNA. The paper discusses the concepts of genetic material and genetic information and the social construction of DNA in relation to forensic DNA databases, paternity testing and genetic testing for disease. The paper concludes by suggesting that there are seven areas where issues related to DNA and genetic information are at least relatively distinct.     

Variation in Taxonomic Composition of the Fecal Microbiota in an Inbred Mouse Strain across Individuals and Time

Genetics, diet, and other environmental exposures are thought to be major factors in the development and composition of the intestinal microbiota of animals. However, the relative contributions of these factors in adult animals, as well as variation with time in a variety of important settings, are still not fully understood. We studied a population of inbred, female mice fed the same diet and housed under the same conditions. We collected fecal samples from 46 individual mice over two weeks, sampling four of these mice for periods as long as 236 days for a total of 190 samples, and determined the phylogenetic composition of their microbial communities after analyzing 1,849,990 high-quality pyrosequencing reads of the 16S rRNA gene V3 region. Even under these controlled conditions, we found significant inter-individual variation in community composition, as well as variation within an individual over time, including increases in alpha diversity during the first 2 months of co-habitation. Some variation was explained by mouse membership in different cage and vendor shipment groups. The differences among individual mice from the same shipment group and cage were still significant. Overall, we found that 23% of the variation in intestinal microbiota composition was explained by changes within the fecal microbiota of a mouse over time, 12% was explained by persistent differences among individual mice, 14% by cage, and 18% by shipment group. Our findings suggest that the microbiota of controlled populations of inbred laboratory animals may not be as uniform as previously thought, that animal rearing and handling may account for some variation, and that as yet unidentified factors may explain additional components of variation in the composition of the microbiota within populations and individuals over time. These findings have implications for the design and interpretation of experiments involving laboratory animals.     

Cutaneous acariasis in the African clawed frog (Xenopus laevis)

Increased mortality was observed in a single colony of 50 Xenopus laevis. The frogs were used as oocyte donors in developmental biology studies. Necropsy findings included dermal erythema and petechiation consistent with red leg syndrome; dermal ulcerations and white, filamentous growths on the skin were consistent with Saprolegnia sp. Microscopic evaluation of the skin and fungus revealed an astigmatid mite similar to those of the genus Rhizoglyphus. The mite was also found in the water and the biological filter of the tanks housing the frogs. This mite is considered not to be a parasite of X. laevis; instead, it feeds off moss, fungi, and detritus. Subsequent evaluation of the sphagnum moss used for shipping the frogs from the supplier revealed the same mite in the moss. Our hypothesis is that the mite was introduced into the tank with the shipment of new frogs in sphagnum moss. The mites lived within the biological filter, and were only found after the growth of Saprolegnia sp. attracted the mites to the frogs. Laboratory animal care and veterinary personnel should consider non-pathogenic species of mites in the differential diagnosis of acariasis in Xenopus frogs.     

Evaluation of the GenoCard as a tool for transport and storage of samples for tuberculosis molecular drug susceptibility testing

Early identification and monitoring of the spread of resistant M. tuberculosis strains is essential to control tuberculosis. The paper-based transport device GenoCard enables the safe shipment of inactivated biological material and strains to be used for molecular detection of drug resistance.     

Biobanking

Biobanks, more formally known as biological resource centers (BRCs), form an “unsung” yet critical component of the infrastructures for scientific research, industry and conservation, without which much of the current scientific activity involving microbial cultures and cell-lines would be effectively impossible. BRCs are de facto depositories of “biological standards” holding taxonomic and other reference strains on which much of the associated published science and industrial standards are built and upon which some significant international commercial and ethical issues rely. The establishment and maintenance of BRCs is a knowledge- and skill-rich activity that in particular requires careful attention to the implementation of reliable preservation technologies and appropriate quality assurance to ensure that recovered cultures and other biological materials perform in the same way as the originally isolated culture or material. There are many types of BRC, which vary both in the kinds of material they hold and in their functional role. All BRCs are expected to provide materials and information of an appropriate quality for their intended use and work to standards relevant to those applications. There are important industrial, biomedical, and conservation issues that can only be addressed through effective and efficient operation of BRCs in the long term. This requires a high degree of expertise in the maintenance and management of collections of biological materials at ultra-low temperatures, or as freeze-dried material, to secure their long-term integrity and relevance for future research, development, and conservation.     

The four questions of ethology

Ethology is the biological study of behaviour and concerns itself with questions about the causes, functions, evolution and development of aspects of behaviour. These different questions are illustrated with examples from the study of bird song. This subject has had most impact on understanding of developmental issues, showing the intricate interplay between genes and environment during ontogeny. Work on the evolution of song has involved comparison between closely related species to see how their songs have changed since separation, but also the shorter term cultural evolution that occurs when song is passed from one animal to another by learning. Studies of function, while fraught with difficulties, have revealed that song can have a variety of advantages. As far as causes are concerned, some impressive discoveries have recently been made on the neural basis of song. The need for such work to be complemented by studies of behaviour at the level of the whole animal is stressed, and studies of song sequencing are used to illustrate this.     

WHO technical workshop on stability of reference materials for biological medicines and in vitro diagnostics, Geneva, Switzerland, 28–29 November 2005

In November 2005, the World Health Organization convened an informal technical workshop on the stability of reference materials for biological medicines and in vitro diagnostics. The meeting was attended by experts from WHO collaborating centres in the area of biological standardization, national control laboratories, industries and other relevant organizations. The consultation group discussed current practices and approaches to predicting and monitoring the stability of biological reference materials. The group agreed to the need for establishing a working group (i) to continue dialogue on potential issues encompassing the principles, strategies and practicality for assuring the stability of WHO international reference standards for biological medicines and in vitro diagnostics and (ii) to develop more detailed guidance for assessment of the stability of WHO international biological reference materials.     

Primary cell culture from the nose of a marine organism, the banded houndshark, Triakis scyllium

Animal cells have been widely and continuously studied due to their usefulness in biological researches and production of pharmacological agents as well as food additives. Nevertheless, there are several problems such as the existence of viruses which introduce the possibility of mammalian-infection. In this reason, recently, animal cells derived from marine organisms have emerged to overcome these problems by many researches. However, marine animal-derived cells have not yet been well developed. The banded hound shark occupies an important position in an evolutionary perspective and currently a few biological substances have been used for medicines or food additives such as shark squalene and cartilage extract. In this study, primary cells were cultivated from a banded hound shark nose containing many extracellular matrix (ECM) materials. After successful isolation of one type of primary nasal cell, we optimized culture conditions including coating materials, media composition, serum concentrations and pH. Additionally, these cells demonstrated proliferation ability in vitro, generating secretions of collagen and sulfated polysaccharides. The cultivated primary cells are useful in the study of cellular biology and may be used to create a variety of ECM-originated bioactive substances.