基因表达系列分析技术在真菌功能基因组学中的应用

基因表达系列分析( SAGE)是一种在mRNA水平上高通量、快速、灵敏分析细胞或组织基因表达信息,并在基因组学研究中广泛应用的技术.该技术不仅能够全面地分析特定组织或细胞表达的基因,比较不同时空条件下基因表达的差异,还可以在全基因组范围内获得基因的表达谱,从而发现新基因.综述基因表达系列分析技术在材料用量、标签长度、技术流程和标签测序等方面的研究进展及该技术在病原真菌、工业真菌和食用真菌功能基因组学中的应用.     

Transcriptomic analysis of skin pigmentation variation in the Virginia opossum (Didelphis virginiana)

Skin pigmentation and coat pigmentation are two of the best‐studied examples of traits under natural selection given their quantifiable fitness interactions with the environment (e.g., camouflage) and signalling with other organisms (e.g., warning coloration). Previous morphological studies have found that skin pigmentation variation in the Virginia opossum (Didelphis virginiana) is associated with variation in precipitation and temperatures across its distribution range following Gloger's rule (lighter pigmentation in temperate environments). To investigate the molecular mechanism associated with skin pigmentation variation, we used RNA‐Seq and quantified gene expression of wild opossums from tropical and temperate populations. Using differential expression analysis and a co‐expression network approach, we found that expression variation in genes with melanocytic and immune functions is significantly associated with the degree of skin pigmentation variation and may be underlying this phenotypic difference. We also found evidence suggesting that the Wnt/β‐catenin signalling pathway might be regulating the depigmentation observed in temperate populations. Based on our study results, we present several alternative hypotheses that may explain Gloger's rule pattern of skin pigmentation variation in opossum, including changes in pathogen diversity supporting a pathogen‐resistant hypothesis, thermal stress associated with temperate environments, and pleiotropic and epistatic interactions between melanocytic and immune genes.     

Global richness patterns of venomous snakes reveal contrasting influences of ecology and history in two different clades

Recent studies addressing broad-scale species richness gradients have proposed two main primary drivers: contemporary climate and evolutionary processes (differential balance between speciation and extinction). Here, we analyze the global richness patterns of two venomous snake clades, Viperidae and Elapidae. We used ordinary least squares multiple regression (OLS) and partial regression analysis to investigate to what extent actual evapotranspiration (AET; summarizing current environmental conditions) and biogeographical regions (representing evolutionary effects) were associated with species richness. For viperids, AET explained 45.6% of the variance in richness whereas the effect of this variable for elapids was almost null (0.5%). On the other hand, biogeographic regions were the best predictors of elapid richness (56.5%), against its relatively small effect (25.9%) in viperid richness. Partial regressions also revealed similar patterns for independent effects of climate and history in both clades. However, the independent historical effect in Elapidae decreased from 45.2 to 17.8% when we excluded Australia from the analyses, indicating that the strong historical effect that had emerged for the global richness pattern was reflecting the historical process of elapid radiation into Australia. Even after excluding Australia, the historical signal in elapid richness in the rest of the globe was still significant and much higher than that observed in viperid richness at a global scale (2.7% after controlling for AET effects). Differences in the evolutionary age of these two clades can be invoked to explain these contrasting results, in that viperids probably had more time for diversification, generating richness responses to environmental gradients, whereas the pattern of distribution of elapid richness can be more directly interpreted in an evolutionary context. Moreover, these results show the importance of starting to adopt deconstructive approaches to species richness, since the driving factors of these patterns may vary from group to group according to their evolutionary history. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

超大容量人源性抗体库的构建

构建大容量抗体库是获得高亲和力抗体的重要基础和保障,如何构建大容量抗体库一直是被关注的热点。本对比分析了天然库、半合成库及全合成库基因多样性的特点,指出获得多样的功能性抗体基因是建库的关键。构建大容量抗体库要从提高连接和转化效率、利用体内重组系统提高抗体基因组合多样性以及提高包装和呈现的效率等多个环节进行条件优化,提高库容量和多样性。     

The effects of owl predation on the foraging behavior of heteromyid rodents

Summary Researchers have documented microhabitat partitioning among the heteromyid rodents of the deserts of North America that may result from microhabitat specific predation rates; large/bipedal species predominate in the open/risky microhabitat and small/quadrupedal species predominate in the bush/safer microhabitat. Here, we provide direct experimental evidence on the role of predatory risk in affecting the foraging behavior of three species of heteromyid rodents: Arizona pocket mouse (Perognathus amplus; small/quadrupedal), Bailey's pocket mouse (P. baileyi; large/quadrupedal), and Merriam's kangaroo rat (Dipodomys merriami; large/bipedal). Both kangaroo rats and pocket mice are behaviorally flexible and able to adjust their foraging behavior to nightly changes in predatory risk. Under low levels of perceived predatory risk the kangaroo rat foraged relatively more in the open microhabitat than the two pocket mouse species. In response to the presence of barn owls, however, all three species shifted their habitat use towards the bush microhabitat. In response to direct measures of predatory risk, i.e. the actual presence of owls, all three species reduced foraging and left resource patches at higher giving up densities of seeds. In response to indirect indicators of predatory risk, i.e. illumination, there was a tendency for all three species to reduce foraging. The differences in morphology between pocket mice and kangaroo rats do appear to influence their behavioral responses to predatory risk.     

Latitudinal patterns of mammalian species richness in the New World: the effects of sampling method and faunal group

Abstract. Although the latitudinal gradient of species richness for mammals in North America is well documented, few investigators have quantified the relationship in South America. We examined the pattern in North and South America, at two spatial scales (2.5° and 5°) for each of two sampling methods (quadrats and latitudinal bands). A scale effect was evident for quadrats but not for bands. Significant linear relationships between species richness and latitude were found for three faunal groups: all mammals, nonvolant species, and bats. Effects of area confound the latitudinal relationship. By statistically removing such effects, we found that the latitudinal gradient is not an artifact of the species-area relationship, and that the latitudinal gradients for North and South America were statistically indistinguishable. Our data suggest that both faunal subgroups, nonvolant species and bats, contributed substantially to the overall mammalian pattern. Further, multiple regression analyses showed that only latitude is a necessary variable to explain bat richness; for nonvolant species, in addition to latitude, area and longitude may be important.     

Global biodiversity and biogeography of mangrove crabs: Temperature,the key driver of latitudinal gradients of species richness

Mangroves are ideal habitat for a variety of marine species especially brachyuran crabs as the dominant macrofauna. However, the global distribution, endemicity, and latitudinal gradients of species richness in mangrove crabs remains poorly understood. Here, we assessed whether species richness of mangrove crabs decreases towards the higher latitudes and tested the importance of environmental factors such as Sea Surface Temperature (SST) in creating the latitudinal gradients in species richness of mangrove crabs. A total of 8262 distribution records of 481 species belonging to six families of mangrove crabs including Camptandriidae, Dotillidae, Macrophthalmidae, Ocypodidae, Sesarmidae, and Oziidae were extracted from open-access databases or collected by the authors, quality controlled, cleaned, and analyzed. Species richness was plotted against 5° latitudinal bands in relation to environmental factors. The R software and ArcGIS 10.6.1 were used to analyze the species latitudinal range and richness as well as to map the distribution of mangrove forest, endemic species, species geographical distribution records, and biogeographic regions. The Indo-West Pacific showed the highest species richness of mangrove crabs where more than 65% of species were found in the Indian Ocean and along the western Pacific Ocean. Our results showed that there are 11 significantly different biogeographic regions of mangrove crabs. The highest endemicity rate was observed in the NW Pacific Ocean (29%). Latitudinal patterns of species richness in Macrophthalmidae, Ocypodidae, and Sesarmidae showed an increasing trend from the poles toward the intermediate latitudes including one dip near the equator. However, latitudinal gradients in Camptandriidae, Dotillidae, and Oziidae were unimodal increasing from the higher latitudes towards the equator. Species richness per 5° latitudinal bands significantly increased following mean SST mean (°C), calcite, euphotic depth (m), and mangrove area (km²) across all latitudes, and tide average within each hemisphere. Species richness significantly decreased with dissolved O₂ (ml l⁻¹) and nitrate (μmol l⁻¹) over all latitudes and in the southern hemisphere. The climax of global latitudinal species richness for some mangrove was observed along latitudes 20° N and 15°–25° S, not at the equator. This can suggest that temperature is probably the key driver of latitudinal gradients of mangrove crabs’ species richness. Species richness and mangrove area were also highly correlated.     

A New System for Comparative Functional Genomics of Saccharomyces Yeasts

Whole-genome sequencing, particularly in fungi, has progressed at a tremendous rate. More difficult, however, is experimental testing of the inferences about gene function that can be drawn from comparative sequence analysis alone. We present a genome-wide functional characterization of a sequenced but experimentally understudied budding yeast, Saccharomyces bayanus var. uvarum (henceforth referred to as S. bayanus), allowing us to map changes over the 20 million years that separate this organism from S. cerevisiae. We first created a suite of genetic tools to facilitate work in S. bayanus. Next, we measured the gene-expression response of S. bayanus to a diverse set of perturbations optimized using a computational approach to cover a diverse array of functionally relevant biological responses. The resulting data set reveals that gene-expression patterns are largely conserved, but significant changes may exist in regulatory networks such as carbohydrate utilization and meiosis. In addition to regulatory changes, our approach identified gene functions that have diverged. The functions of genes in core pathways are highly conserved, but we observed many changes in which genes are involved in osmotic stress, peroxisome biogenesis, and autophagy. A surprising number of genes specific to S. bayanus respond to oxidative stress, suggesting the organism may have evolved under different selection pressures than S. cerevisiae. This work expands the scope of genome-scale evolutionary studies from sequence-based analysis to rapid experimental characterization and could be adopted for functional mapping in any lineage of interest. Furthermore, our detailed characterization of S. bayanus provides a valuable resource for comparative functional genomics studies in yeast.     

Cloning and characterisation of mmc-1, a microfilarial-specific gene, from Brugia pahangi

Nine differentially expressed genes were cloned from Brugia pahangi in a screen which sought to identify cDNAs that were differentially expressed between the microfilariae from the mammalian host and the mosquito vector. One gene (mmc-1), that was up-regulated in mammalian-derived microfilariae, was characterised in detail. RT-PCR analysis demonstrated that mmc-1 was specific to the microfilarial stage of the life cycle and was not transcribed by developing microfilariae in utero, but only following the release of the microfilariae from the adult female. Analysis of DNA from other filarial worms suggested that mmc-1 may be a Brugia-specific gene. Using serum samples from individuals exposed to Brugia malayi infection, it was shown that MMC-1 was specifically recognised by antibodies of the IgG3 subclass. mmc-1 has no homologues in the data bases and its function in the parasite is unknown.     

Some inconvenient truths about sex chromosome dosage compensation and the potential role of sexual conflict

Sex chromosome dosage compensation was once thought to be required to balance gene expression levels between sex-linked and autosomal genes in the heterogametic sex. Recent evidence from a range of animals has indicated that although sex chromosome dosage compensation exists in some clades, it is far from a necessary companion to sex chromosome evolution, and is in fact rather rare in animals. This raises questions about why complex dosage compensation mechanisms arise in some clades when they are not strictly needed, and suggests that the role of sex-specific selection in sex chromosome gene regulation should be reassessed. We show there exists a tremendous diversity in the mechanisms that regulate gene dosage and argue that sexual conflict may be an overlooked agent responsible for some of the variation seen in sex chromosome gene dose regulation.