抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

The Theory of Island Biogeography

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.

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Bioconductor: open software development for computational biology and bioinformatics

Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.

/pdf/the-fair-guiding-principles-for-scientific-data-management-1tg0qbz9se.pdf

The FAIR Guiding Principles for scientific data management and stewardship

Caecilians:: Mysterious amphibians of the Eastern Arc Mountains

We present genome sequences for the caecilians Geotrypetes seraphini (3.8Gb) and Microcaecilia unicolor (4.7Gb), representatives of a limbless, mostly soil-dwelling amphibian clade with reduced eyes, and unique putatively chemosensory tentacles. More than 69% of both genomes are composed of repeats, with retrotransposons the most abundant. We identify 1,150 orthogroups which are unique to caecilians and enriched for functions in olfaction and detection of chemical signals. There are 379 orthogroups with signatures of positive selection on caecilian lineages with roles in organ development and morphogenesis, sensory perception and immunity amongst others. We discover that caecilian genomes are missing the ZRS enhancer of Sonic Hedgehog which is also mutated in snakes. In vivo deletions have shown ZRS is required for limb development in mice, thus revealing a shared molecular target implicated in the independent evolution of limblessness in snakes and caecilians.

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Caecilian Genomes Reveal the Molecular Basis of Adaptation and Convergent Evolution of Limblessness in Snakes and Caecilians

Identifying individual animals is important for studying populations and for the optimal management of individual animals in captivity. In the absence of natural markings that discriminate individuals, such identification may require animals to be marked by researchers. Amphibians are challenging subjects to mark due to their small size and sensitive, permeable and frequently shed skin. Visible Implant Elastomer (VIE) has been widely used to mark amphibians, but no long-term study has validated this technique in caecilian amphibians. We anaesthetised and attempted to VIE mark seven Herpele squalostoma and one Microcaecilia unicolor held at ZSL London Zoo. No specimens suffered ill effects of anaesthesia or VIE injection, but mean persistence of marks was 191 days in H. squalostoma suggesting that this marking technique is not suitable for identifying individuals of this species in the long-term. We were unable to inject VIE into the M. unicolor and/or the elastomer was not visible through the darkly pigmented skin. Further research is required to develop methods for long-term marking of a diversity

/pdf/the-use-of-visible-implant-elastomer-to-permanently-identify-37x0dgc6fg.pdf

The use of visible implant elastomer to permanently identify caecilians (Amphibia: Gymnophiona)

/pdf/first-record-of-predation-on-the-caecilian-microcaecilia-obkljbtwwx.pdf

First record of predation on the caecilian Microcaecilia unicolor (Duméril, 1863)

Gene expression profiles can provide insights into the molecular machinery behind tissue functions and, in turn, can further our understanding of environmental responses, and developmental and evolutionary processes. During vertebrate evolution, the skin has played a crucial role, displaying a wide diversity of essential functions. To unravel the molecular basis of skin specialisations and adaptations, we compared gene expression in the skin with eight other tissues in a phylogenetically and ecologically diverse species sample of one of the most neglected vertebrate groups, the caecilian amphibians (order Gymnophiona). The skin of the five studied caecilian species showed a distinct gene expression profile reflecting its developmental origin and showing similarities to other epithelial tissues. We identified 59 sequences with conserved enhanced expression in the skin that might be associated with caecilian dermal specialisations. Some of the up-regulated genes shared expression patterns with human skin and potentially are involved in skin functions across vertebrates. Variation trends in gene expression were detected between mid and posterior body skin suggesting different functions between body regions. Several candidate biologically active peptides were also annotated. Our study provides the first atlas of differentially expressed sequences in caecilian tissues and a baseline to explore the molecular basis of the skin functions in caecilian amphibians, and more broadly in vertebrates.

/pdf/insights-into-the-skin-of-caecilian-amphibians-from-gene-1ql9gjgkvg.pdf

Mark Wilkinson

Papers

Caecilians:: Mysterious amphibians of the Eastern Arc Mountains

Caecilian Genomes Reveal the Molecular Basis of Adaptation and Convergent Evolution of Limblessness in Snakes and Caecilians

The use of visible implant elastomer to permanently identify caecilians (Amphibia: Gymnophiona)

First record of predation on the caecilian Microcaecilia unicolor (Duméril, 1863)

Insights into the skin of caecilian amphibians from gene expression profiles