落叶栎树在中国的地理替代分布及其气候制约

栎属（Quercus L.）按落叶习性可自然分为落叶类型和常绿类型，我国落叶栎类共有20个种和9个变种。落叶栎是栎属中较为进化的一个类群，源于横断山区和云贵高原;除新疆外，全国各省都有落叶栎的天然分布，一些亲缘关系密切的树种之间呈现出较为明显的地理替代分布格局。本研究的目的在于：（1）应用BIOCLIM模型模拟预测落叶栎类植物的潜在分布区，分析其目前的分布格局以及下一步的发展趋势;（2）分析造成落叶栎树地理替代分布格局的主导气候因子，探讨气候因子对不同落叶栎树种地理分布格局的制约作用。 本文以16个在中国具有成片天然分布区的落叶栎树种（包括变种）为研究对象，利用已核对的标本数据以及13个栅格化环境变量图层（分辨率为1km×1km），按照分类（全国广布型、南方广布型、南方狭域型和北方狭域型）和不分类（全部16种）两种处理方式，通过BIOCLIM模型模拟得出了它们的潜在核心分布区和潜在边缘分布区。在运行模型之前，除必选的海拔高程图层外，采用了主成分分析（PCA）的方法从30个候选的气候变量图层中筛选出对相应落叶栎树种的地理分布格局有较大影响的12个图层作为输入图层。然后，本文通过比较两种处理所得模拟结果的ROC（Receiver Operator Characteristic）曲线下方面积AUC（Area Under the Curve），同时结合文献分析来推测不同落叶栎树种地理分布格局的稳定性及发展趋势。结果表明，在无人类活动干扰且种源传播不受阻碍的情况下，全国广布型和南方广布型落叶栎目前的分布格局在维持稳定的基础上有向周边地区扩展的趋势;南方狭域型和北方狭域型落叶栎的分布格局则基本保持稳定，短期内发生扩散的可能很小。 论文中计算了每个落叶栎树种所在分布范围的气候指标（共11个），以便进行下一步的研究。以蒙古栎（Q. mongolica）、辽东栎（Q. wutaishanica）与槲栎（Q. aliena）、锐齿槲栎（Q. aliena var. acuteserrata）、北京槲栎（Q. aliena var. pekingensis）这两组地理替代系列为研究对象，分别采用独立样本t检验和单因素方差分析的方法，分析了气候因子对其地理替代分布格局的主导作用。结果表明，冬季的低温、较高的气温年较差和大陆度是蒙古栎向东北替代辽东栎的主要原因;槲栎向北被北京槲栎和锐齿槲栎替代的主要原因是生长季高温和冬季高温对其分布的双重制约;除最暖月（7月）最高温外，北京槲栎的各项水热指标与另两种槲栎均存在极显著差异，对冬季低温和较大的年较差的适应可能是限制其向南分布的主要原因。 本研究最后部分的内容是对不同类型落叶栎分布区的气候参数进行的主成分分析。结果表明，生长季温度是制约落叶栎分布的最主要的气候因子;寒冷程度和冬季的低温则对其在大尺度范围的扩散有较大影响;另外，降水、年较差与大陆度对落叶栎的向北分布也起着重要的作用。

Evolutionary trends of the mitochondrial lineage differentiation in species of genera Martes and Mustela

We compared partial sequences (402 bp) of the mitochondrial cytochrome b gene in 68 individuals of martens (Martes), weasels (Mustela) and their relatives from the Northern Hemisphere to identify the modes of geographic differentiation in each species. We then compared complete sequences (1140 bp) of the gene in 17 species of the family Mustelidae to know the spatial and temporal modes of speciation, constructing linearized trees with transversional substitutions for deeper lineage divergences and with transversions and transitions for younger lineages. Our data suggested that these lineages of Martes and Mustela differentiated in a stepwise fashion with five radiation stages from the generic divergences (stage I) to the intraspecific divergences (stage V), during the last 10 or 20 million years as the fossil evidence suggests. In the lineage of Martes, the first offshoots are of Martes flavigula, M. pennanti, and Gulo gulo (stage II), the second is M. foina (stage III), and the third are M. americana, M. martes, M. melampus, and M. zibellina (stage IV). The divergence of the lineages of Mustela is likely to have taken place concurrently with the radiations of the Martes. These divergence processes are attributable in part to the geographic allocation along the two continents, North America and Eurasia, as well as among peripheral insular domains, such as Taiwan and the Japanese Islands. In addition, the Eurasian continent itself was shown to have been involved in the species diversification in the martens and weasels.

Revealing the History of Sheep Domestication Using Retrovirus Integrations

The domestication of livestock represented a crucial step in human history. By using endogenous retroviruses as genetic markers, we found that sheep differentiated on the basis of their "retrotype" and morphological traits dispersed across Eurasia and Afr

A New Odorrana (Amphibia: Ranidae) from Vietnam and China

Eastern and western populations of the ranid frog Odorrano chapaensis from Vietnam and China are readily differentiated by morphology and mtDNA, and weakly differentiated by morphometrics. The western population contains the type localities of O. chopoens

Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication

Background: Various evolutionary models have been proposed to interpret the fate of paralogous duplicates, which provides substrates on which evolution selection could act. In particular, domestication, as a special selection, has played important role in crop cultivation with divergence of many genes controlling important agronomic traits. Recent studies have indicated that a pair of duplicate genes was often sub-functionalized from their ancestral functions held by the parental genes. We previously demonstrated that the rice cell-wall invertase (CWI) gene GIF1 that plays an important role in the grain-filling process was most likely subjected to domestication selection in the promoter region. Here, we report that GIF1 and another CWI gene OsCIN1 constitute a pair of duplicate genes with differentiated expression and function through independent selection. Results: Through synteny analysis, we show that GIF1 and another cell-wall invertase gene OsCIN1 were paralogues derived from a segmental duplication originated during genome duplication of grasses. Results based on analyses of population genetics and gene phylogenetic tree of 25 cultivars and 25 wild rice sequences demonstrated that OsCIN1 was also artificially selected during rice domestication with a fixed mutation in the coding region, in contrast to GIF1 that was selected in the promoter region. GIF1 and OsCIN1 have evolved into different expression patterns and probable different kinetics parameters of enzymatic activity with the latter displaying less enzymatic activity. Overexpression of GIF1 and OsCIN1 also resulted in different phenotypes, suggesting that OsCIN1 might regulate other unrecognized biological process. Conclusion: How gene duplication and divergence contribute to genetic novelty and morphological adaptation has been an interesting issue to geneticists and biologists. Our discovery that the duplicated pair of GIF1 and OsCIN1 has experiencedsub-functionalization implies that selection could act independently on each duplicate towards different functional specificity, which provides a vivid example for evolution of genetic novelties in a model crop. Our results also further support the established hypothesis that gene duplication with sub-functionalization could be one solution for genetic adaptive conflict.

Transplantable neural progenitor populations derived from Rhesus monkey embryonic stem cells

Cell-based therapies using embryonic stem cells (ESCs) in the treatment of neural disease will require the generation of homogenous donor neural progenitor (NP) populations. Here we describe an efficient culture system containing hepatocyte growth factor (HGF) and G5 supplement for the production of highly enriched (88.3% +/- 8.1%)populations of NPs from rhesus monkey ESCs. Additional purification resulted in NP preparations that were 98% nestin positive. Moreover, NPs, as monolayers or neurospheres, could be maintained for prolonged periods of time in media containing HGF+G5 or G5 alone. In vitro differentiation and in vivo transplantation assays showed that NPs could differentiate into neurons, astrocytes, and oligodendrocytes. The kinds and quantities of differentiated cells derived from NPs were closely correlated with their niches in vivo. Glial differentiation was predominant in periventricular areas, whereas cells migrating into the cortex were mostly neurons. Cell counts showed that 2 months after transplantation, approximately 25% of transplanted NPs survived and 65% - 80% of the surviving transplanted cells migrated along the ventricular wall or in a radial fashion. Subcloning demonstrated that several clonal lines derived from NPs expressed nestin and differentiated into three neural lineages in vitro and in rat brains in vivo. In contrast, some subcloned lines showed restricted differentiation both in vitro and in vivo in rat brains. These observations set the stage for obtaining highly enriched NPs and evaluating the efficacy of NP-based transplantation therapy in the nonhuman primate and will provide a platform for probing the molecular mechanisms that control neural induction.

Homologous feeder cells support undifferentiated growth and pluripotency in monkey embryonic stem cells

In the present study, five homologous feeder cell lines were developed for the culture and maintenance of rhesus monkey embryonic stem cells (rESCs). Monkey ear skin fibroblasts (MESFs), monkey oviductal fibroblasts (MOFs), monkey follicular granulosa fibroblast-like (MFG) cells, monkey follicular granulosa epithelium-like (MFGE) cells, and clonally derived fibroblasts from MESF (CMESFs) were established and compared with the ability of mouse embryonic fibroblasts (MEFs) to support rESC growth. MESF, MOF, MFG, and CMESF cells, but not MFGE cells, were as good as or better than MEFs in supporting undifferentiated growth while maintaining the differentiation potential of the rESCs. In an effort to understand the unique properties of supportive feeder cells, expression levels for a number of candidate genes were examined. MOF, MESF, and MEF cells highly expressed leukemia inhibitory factor, ciliary neurotrophic factor, basic fibroblast growth factor, stem cell factor, transforming growth factor PI, bone morphogenetic protein 4, and WNT3A, whereas WNT2, WNT4, and WNT5A were downregulated, compared with MFGE cells. Additionally, all monkey feeder cell lines expressed Dkk1 and LRP6, antagonists of the WNT signaling pathway, but not WNT1, WNT8B, or Dkk2. rESCs grown on homologous feeders maintained normal karyotypes, displayed the characteristics of ESCs, including morphology, alkaline phosphatase, Oct4, the cell surface markers stage-specific embryonic antigen (SSEA)-3, SSEA-4, tumor-related antigen (TRA)-1-60, and TRA-1-81, and formed cystic embryoid bodies in vitro that included differentiated cells representing the three major germ layers. These results indicate that the four homologous feeder cell lines can be used to support the undifferentiated growth and maintenance of pluripotency in rESCs.

Paracobitis nanpanjiangensis, a new loach (Balitoridae: Nemacheilinae) from Yunnan, China

A new species of the genus Paracobitis, Paracobitis nanpanjiangensis is described from tributaries of the Nanpanjiang River drainage in China. It is distinguished from its congeners, except P. oligolepis and P. wujiangensis, by body scaleless or with rudimentary scales (caudal peduncle with several deeply embedded scales). It can be differentiated from P. wujiangensis by the complete lateral line (vs. incomplete), lower dorsal crest reaching the vertical of origin of anal fin (vs. shorter and higher dorsal crest not reaching the base of anal fin). It is distinguished from P. oligolepis by the following characters: branched dorsal fin with 81/2 (a few 91/2) rays (vs. 91/2), interspaces between bars in front of dorsal fin conspicuously thinner than those behind (vs. vermiform markings), dorsal head without vermiform markings or obscure (vs. clearly vermiform markings on dorsal head), vertebrae 4 + 36-38 (vs. 4 + 39-41).

Molecular phylogeography and population structure of a mid-elevation montane frog Leptobrachium ailaonicum in a fragmented habitat of southwest China

Leptobrachium ailaonicum is a vulnerable anuran restricted to a patchy distribution associated with small mountain streams surrounded by forested slopes at mid-elevations (approximately 2000-2600 m) in the subtropical Mount Wuliang and Mount Ailao ranges in southwest China (Yunnan Province) and northern Vietnam. Given high habitat specificity and lack of suitable habitat in lower elevations between these ranges, we hypothesized limited gene flow between populations throughout its range. We used two mitochondrial genes to construct a phylogeographic pattern within this species in order to test our hypothesis. We also examined whether this phylogeographic pattern is a response to past geological events and/or climatic oscillations. A total of 1989 base pairs were obtained from 81 individuals of nine populations yielding 51 unique haplotypes. Both Bayesian and maximum parsimony phylogenetic analyses revealed four deeply divergent and reciprocally monophyletic mtDNA lineages that approximately correspond to four geographical regions separated by deep river valleys. These results suggest a long history of allopatric separation by vicariance. The distinct geographic distributions of four major clades and the estimated divergence time suggest spatial and temporal separations that coincide with climatic and paleogeographic changes following the orogeny and uplift of Mount Ailao during the late Miocene to mid Pliocene in southwest China. At the southern distribution, the presence of two sympatric yet differentiated clades in two areas are interpreted as a result of secondary contact between previously allopatric populations during cooler Pleistocene glacial cycles. Analysis of molecular variance indicates that most of the observed genetic variation occurs among the four regions implying long-term interruption of maternal gene flow, suggesting that L ailaonicum may represent more than one distinct species and should at least be separated into four management units corresponding to these four geographic lineages for conservation. (C) 2009 Elsevier Inc. All rights reserved.

Phylogeography of Schizothorax o'connori (Cyprinidae: Schizothoracinae) in the Yarlung Tsangpo River, Tibet

Schizothorax o'connori is endemic to the Yarlung Tsangpo River on the Tibetan Plateau. We assessed the relative impacts of historical and contemporary factors in organizing genetic variation in S. o'connori populations using mitochondrial cytochrome b sequences. We analyzed 191 samples from 11 populations and identified 78 haplotypes. The phylogenetic analyses and analysis of molecular variance all supported the same conclusions of two well-differentiated east-west phylogroups, separated by the Tsangpo Great Gorge. The split between the two clades accounted for 58% of the genetic variance observed among the examined samples. Waterfalls as effective barriers played an important role in shaping the phylogeographical structure of this species. Analyses of migration rates revealed that upstream dispersal was limited crossing waterfalls. Our study revealed substantial spatial and temporal variation in the influence of landscape features on contemporary patterns of genetic structure in S. o'connori. Interglacial range expansions clearly left their mark on contemporary populations above the Tsangpo Great Gorge.

Pseudobagrus fui Miao, a valid bagrid species from the Yangtze River drainage, South China (Teleostei: Bagridae)

Pseudobagrus fui Miao is a valid bagrid species that can be separated from all its congeners in having 27-33 anal-fin rays. Among the species of Pseudobagrus, it forms part of a group of approximately 20 species putatively characterized by having a smooth anterior margin of the pectoral-fin spine and short maxillary barbels not extending to the base of the pectoral-fin spine. Pseudobagrus fui, together with P. nitidus and P. vachelli, can be differentiated from all other fork-tailed species of this group by having no fewer than 20 branched anal-fin rays, the posterior end of the anal-fin base posterior to the vertical through the posterior end of the adipose-fin base, and anal-fin base longer than the adipose-fin base. It further differs from P. nitidus in having a gas bladder without beaded lateral and posterior margins, and from P. vachelli in having short maxillary barbels not extending to the base of the pectoral-fin spine. Pseudobagrus fui is currently known from the main stream of the upper Yangtze River and its tributaries, the Min River, Jialing River, Tuo River, Wu River and Chishui River in Sichuan Province, Guizhou Province, and the Chongqing City. The identity and nomenclature of Pseudobagrus nitidus is also discussed.

Colony development and physiological characterization of the edible blue-green alga, Nostoc sphaeroides (Nostocaceae, Cyanophyta)

The edible blue-green alga, Nostoc sphaeroides Kutzing, is able to form microcolonies and spherical macrocolonies. It has been used as a potent herbal medicine and dietary supplement for centuries because of its nutraceutical and pharmacological benefits. However, limited information is available on the development of the spherical macrocolonies and the environmental factors that affect their structure. This report described the morphogenesis of N. sphaeroides from single trichomes to macrocolonies. During the process, most structural features of macrocolonies of various sizes were dense maculas, rings, the compact core and the formation of liquid core; and the. laments within the macrocolonies showed different lengths and arrays depending on the sizes of macrocolonies. Meanwhile temperature and light intensity also strongly affected the internal structure of macrocolonies. As microcolonies further increased in size to form 30 mm macrocolonies, the colonies differentiated into distinct outer, middle and inner layers. The. laments of the outer layer showed higher maximum photosynthetic rates, higher light saturation point, and higher photosynthetic effciency than those of the inner layer; whereas the. laments of the inner layer had a higher content of chlorophyll a and phycobiliproteins than those of the outer layer. The results obtained in this study were important for the mass cultivation of N. sphaeroides as a nutraceutical product. (c) 2008 National Natural Science Foundation of China and Chinese Academy of Sciences. Published by Elsevier Limited and Science in China Press. All rights reserved.

Application of methyl parathion hydrolase (MPH) as a labeling enzyme

Methyl parathion hydrolase (MPH) is an enzyme that catalyzes the degradation of methyl parathion, generating a yellow product with specific absorption at 405 nm. The application of MPH as a new labeling enzyme was illustrated in this study. The key advantages of using MPH as a labeling enzyme are as follows: (1) unlike alkaline phosphatase (AP), horseradish peroxidase (HRP), and glucose oxidase (GOD), MPH is rarely found in animal cells, and it therefore produces less background noise; (2) its active form in solution is the monomer, with a molecular weight of 37 kDa; (3) its turnover number is 114.70 +/- 13.19 s(-1), which is sufficiently high to yield a significant signal for sensitive detection; and (4) its 3D structure is known and its C-terminal that is exposed to the surface can be easily subjected to the construction of genetic engineering monocloning antibody-enzyme fusion for enzyme-linked immunosorbent assay (ELISA). To demonstrate its utility, MPH was ligated to an single-chain variable fragment (scFv), known as A1E, against a white spot syndrome virus (WSSV) with the insertion of a [-(Gly-Ser)(5)-] linker peptide. The resulting fusion protein MPH-A1E possessed both the binding specificity of the scFv segment and the catalytic activity of the MPH segment. When MPH-A1E was used as an ELISA reagent, 25 ng purified WSSV was detected; this was similar to the detection sensitivity obtained using A1E scFv and the HRP/Anti-E Tag Conjugate protocol. The fusion protein also recognized the WSSV in 1 mu L hemolymph from an infected shrimp and differentiated it from a healthy shrimp.

Genetic diversity of plankton community as depicted by PCR-DGGE fingerprinting and its relation to morphological composition and environmental factors in lake donghu

To collect information about the genetic diversity of the plankton community and to study how plankton respond to environmental conditions, plankton samples were collected from five stations representing different trophic levels in a shallow, eutrophic lake (Lake Donghu), and investigated by PCR-DGGE fingerprinting. A total of 100 bands (61 of 16S rDNA bands and 39 of 18S rDNA bands) were detected. The DGGE bands unique to any single station accounted for 38% of the total bands, whereas common bands detected at all five stations accounted for only 11%. Using UPGMA clustering and MDS ordination of DGGE fingerprints, stations I and II were found to initially group together into one cluster, which was later joined by station V. Stations III and IV were isolated into two separate groups of one station each. Some differences in grouping relationships were found when analysis was completed on the basis of chemical characteristics and morphological composition, with zooplankton composition showing the greatest variability. However, the most similar stations (I and II) were always initially grouped into one cluster. Moreover, stations that exhibited the same or similar trophic level (stations III and IV), but different concentrations of heavy metals, were further differentiated by the DGGE method. Results of the present study indicated that PCR-DGGE fingerprinting was more sensitive than the traditional methods, as other studies suggested. Additionally, PCR-DGGE appears to be more appropriate for diversity characterization of the plankton community, as it is more canonical, systematic, and effective. Most importantly, fingerprinting results are more convenient for the comparative analyses between different studies. Therefore, the use of the described fingerprinting analysis may provide an operable and sensitive biomonitoring approach to identify critical, and potentially negative, stress within an aquatic ecosystem.