Construction and characterization of bacterial artificial chromosome library of black-handed spider monkey (Ateles geoffroyi)

The large-insert genomic DNA library is a critical resource for genome-wide genetic dissection of target species. We constructed a high-redundancy bacterial artificial chromosome (BAC) library of a New World monkey species, the black-handed spider monkey

Game Vertebrate Densities in Hunted and Nonhunted Forest Sites in Manu National Park, Peru

Manu National Park of southern Peru is one of the most renowned protected areas in the world, yet large-bodied vertebrate surveys conducted to date have been restricted to Cocha Cashu Biological Station, a research station covering <0.06 percent of the 1.7Mha park. Manu Park is occupied by >460 settled Matsigenka Amerindians, 300-400 isolated Matsigenka, and several, little-known groups of isolated hunter-gatherers, yet the impact of these native Amazonians on game vertebrate populations within the park remains poorly understood. On the basis of 1495 km of standardized line-transect censuses, we present density and biomass estimates for 23 mammal, bird, and reptile species for seven lowland and upland forest sites in Manu Park, including Cocha Cashu. We compare these estimates between hunted and nonhunted sites within Manu Park, and with other Neotropical forest sites. Manu Park safeguards some of the most species-rich and highest biomass assemblages of arboreal and terrestrial mammals ever recorded in Neotropical forests, most likely because of its direct Andean influence and high levels of soil fertility. Relative to Barro Colorado Island, seed predators and arboreal folivores in Manu are rare, and generalist frugivores specializing on mature fruit pulp are abundant. The impact of such a qualitative shift in the vertebrate community on the dynamics of plant regeneration, and therefore, on our understanding of tropical plant ecology, must be profound. Despite a number of external threats, Manu Park continues to serve as a baseline against which other Neotropical forests can be gauged.

Extraction, PCR amplification, and sequencing of mitochondrial DNA from scent mark and feces in the giant panda

To expand the feasibility of applying simple, efficient, non-invasive DNA preparation methods using samples that can be obtained from giant pandas living in the wild, we investigated the use of scent markings and fecal samples. Giant panda-specific oligonucleotide primers were used to amplify a portion of the mitochondrial DNA control region as well as a portion of the mitochondrial DNA cytochrome b gene and tRNA(Thr) gene region. A 196 base pair (bp) fragment in the control region and a 449 bp fragment in the cytochrome b gene and tRNA(Thr) gene were successfully amplified. Sequencing of polymerase chain reaction (PCR) products demonstrated that the two fragments are giant panda sequences. Furthermore, under simulated field conditions we found that DNA can be extracted from fecal samples aged as long as 3 months. Our results suggest that the scent mark and fecal samples are simple, efficient, and easily prepared DNA sources. (C) 1998 Wiley-Liss, Inc.

Mitochondrial cytochrome b gene sequence diversity in the Korean hare, Lepus coreanus Thomas (Mammalia, Lagomorpha)

Partial sequences of the mitochondrial cytochrome b gene of the Korean hare (Lepus coreanus) were analyzed to determine the degree of genetic diversity. Nine haPlotyes were observed, and the maximum Tamura-Nei nucleotide distance among them was 2.8%, indicating that genetic diversity of L. coreanus is moderate. In order to clarify the Korean hare's taxonomic status and relationship with the Manchurian hare (L. mandshuricus) and the Chinese hare (L. sinensis), these nine haplotypes of the Korean hare were compared with 13 haplotypes from five other species of eastern Asian Lepus including L. mandshwicus and L. sinensis. The Korean hare was distinct in its cytochrome b gene, and it is confirmed that L. coreanus is a valid species, as noted by Jones and Johnson (1965, Univ. Kansas Publ. (Mus. Nat. Hist.) 16:357). Further analyses of mtDNA cytochrome b gene with additional specimens of L. coreanus from North Korea and other species of Lepus from eastern Asia are needed to clarify the taxonomic status of the divergent mtDNA clades of L. mandshuricus and L. sinensis.

Tracing the Origins of Hakka and Chaoshanese by Mitochondrial DNA Analysis

Hakka and Chaoshanese are two unique Han populations residing in southern China but with northern Han (NH) cultural traditions and linguistic influences. Although most of historical records indicate that both populations migrated from northern China in the last two thousand years, no consensus on their origins has been reached so far. To shed more light on the origins of Hakka and Chaoshanese, mitochondrial DNAs (mtDNAs) of 170 Hakka from Meizhou and 102 Chaoshanese from Chaoshan area, Guangdong Province, were analyzed. Our results show that some southern Chinese predominant haplogroups, e.g. B, F, and M7, have relatively high frequencies in both populations. Although median network analyses show that Hakka/Chaoshanese share some haplotypes with NH, interpopulation comparison reveals that both populations show closer affinity with southern Han (SH) populations than with NH. In consideration of previous results from nuclear gene (including Y chromosome) research, it is likely that matrilineal landscapes of both Hakka and Chaoshanese have largely been shaped by the local people during their migration southward and/or later colonization in southern China, and factors such as cultural assimilation, patrilocality, and even sex-bias in the immigrants might have played important roles during the process. Am J Phys Anthropol 141:124-130, 2010. (C) 2009 Wiley-Liss, Inc.

Evolutionary Conservation of Dazl Genomic Organization and its Continuous and Dynamic Distribution Throughout Germline Development in Gynogenetic Gibel Carp

To investigate germline development and germ cell specification, we identified a Dazl homolog (CagDazl) from gynogenetic gibel carp (Carassius auratus gibelio). Its cDNA sequence and BAC clone sequence analyses revealed the genomic organization conservation and conserved synteny of the Dazl family members and their neighborhood genes among vertebrates, especially in fish. Moreover, a polyclonal antibody specific to CagDazl was produced and used to examine its expression and distribution throughout germline development at protein level. Firstly, ovary-specific expression pattern of CagDazl was confirmed in adult tissues by RT-PCR and Western blot. In addition, in situ hybridization and immunofluorescence localization demonstrated its specific expression in germ cells, and both its transcript and protein were localized to germ plasm. Then, co-localization of CagDazl and mitochondrial cloud was found, confirming that CagDazl transcript and its protein are germ plasm component and move via METRO pathway during oogenesis. Furthermore, the CagDazl is abundant and continuous throughout germline development and germ cell specification including primordial germ cell (PGC) formation, oogonium differentiation, oocyte development, and embryogenesis, and the dynamic distribution occurs at different development stages. The data suggest that maternal CagDazl might play an important role in gibel carp PGC formation. Therefore, CagDazl is a useful and specific marker for tracing germ plasm and germ cell development in the gynogenetic gibel carp. In addition, in comparison with previous studies in sexual reproduction species, the continuous and dynamic distribution of CagDazl protein in the germ plasm throughout the life cycle seems to have significant implication in sex evolution of vertebrates. J. Exp. Zool. (Mol. Deu. Euol.) 312B:855-871, 2009. (C) 2009 Wiley-Liss, Inc.

Field and experimental studies on the combined impacts of cyanobacterial blooms and small algae on crustacean zooplankton in a large, eutrophic, subtropical, Chinese lake

Field and experimental studies were conducted to evaluate the combined impacts of cyanobacterial blooms and small algae on seasonal and long-term changes in the abundance and community structure of crustacean zooplankton in a large, eutrophic, Chinese lake, Lake Chaohu. Seasonal changes of the crustacean zooplankton from 22 sampling stations were investigated during September 2002 and August 2003, and 23 species belonging to 20 genera were recorded. Daphnia spp. dominated in spring but disappeared in mid-summer, while Bosmina coregoni and Ceriodaphnia cornuta dominated in summer and autumn. Both maximum cladoceran density (310 ind. l(-1)) and biomass (5.2 mg l(-1)) appeared in autumn. Limnoithona sinensis, Sinocalanus dorrii and Schmackeria inopinus were the main species of copepods. Microcystis spp. were the dominant phytoplankton species and formed dense blooms in the warm seasons. In the laboratory, inhibitory effects of small colonial Microcystis on growth and reproduction of Daphnia carinata were more remarkable than those of large ones, and population size of D. carinata was negatively correlated with density of fresh large colonial Microcystis within a density range of 0-100 mg l(-1) (r = -0.82, P < 0.05). Both field and experimental results suggested that seasonal and long-term changes in the community structure of crustacean zooplankton in the lake were shaped by cyanobacterial blooms and biomass of the small algae, respectively, i.e., colonial and filamentous cyanobacteria contributed to the summer replacement of dominant crustacean zooplankton from large Daphnia spp. to small B. coregoni and C. cornuta, while increased small algae might be responsible for the increased abundance of crustacean zooplankton during the past decades.

Bibarba bibarba: A new genus and species of Cobitinae (Pisces : Cypriniformes : Cobitidae) from Guangxi Province (China)

A new genus of Cobitinae, Bibarba gen. n., and a new species, B. bibarba sp. n., were discovered and are described for the Chengjiang River, a tributary of the Hongshuihe River in Guangxi Province of southern China. This river region is characterized by a Karst landscape, and the river that is inhabited by the new genus is a slowly moving stream with arenaceous and cobblestone beds. The new genus resembles Cobitis Linnaeus, 1758 (subfamily Cobitinae) in the shape and pigmentation pattern of their body, the absence of scales on their head, and the presence of a suborbital spine, but differs from it by a single Lamina circularis on the third pectoral fin ray instead of on the base of the second pectoral fin ray; two pairs of barbels (one rostral pair and one maxillo-mandibular pair) instead of three pairs of barbels (one rostral pair, one maxillary pair, and one maxillo-mandibular pair); a relatively thick and short suborbital spine with a strong medio-lateral process instead of a suborbital spine without or with a weakly formed medio-lateral process as in Cobitis; and the lack of a black stripe extending from the occiput through the eye to the insertion of the rostral barbel. The first two characters have not been reported in any other genus of the subfamily Cobitinae. A morphometric character analysis based on PCA reveals differences between B. bibarba and C. sinensis in body size, barbel length, interorbital width, pectoral fin length in males, and the position of the dorsal and ventral fins. Type specimens of the new species are kept in the Freshwater Fishes Museum of the Institute of Hydrobiology at the Chinese Academy of Sciences in Wuhan, Hubei Province. (c) 2007 Elsevier GmbH. All rights reserved.

Phylogenetic relationships of Danio within the order cypriniformes: A framework for comparative and evolutionary studies of a model species

The evolutionary relationships of species of Danio and the monophyly and phylogenetic placement of the genus within the family Cyprinidae and subfamily Rasborinae provide fundamentally important phyloinformatics necessary for direct evaluations of an array of pertinent questions in modern comparative biology. Although the genus Danio is not one of the most diverse within the family, Danio rerio is one of the most important model species in biology. Many investigations have used this species or presumed close relatives to address specific questions that have lasting impact on the hypothesis and theory of development in vertebrates. Largely lacking from this approach has been a holistic picture of the exact phylogenetic or evolutionary relationships of this species and its close relatives. One thing that has been learned over the previous century is that many organismal attributes (e.g., developmental pathways, ecologies, behaviors, speciation) are historically constrained and their origins and functions are best explained via a phylogenetic approach. Herein, we provide a molecular evaluation of the phylogenetic placement of the model species Danio rerio within the genus Danio and among hypothesized closely related species and genera. Our analysis is derived from data using two nuclear genes (RAG1, rhodopsin) and five mitochondrial genes (ND4, ND4L, ND5, COI, cyt b) evaluated using parsimony, maximum likelihood, and Bayesian analyses. The family Cyprinidae is resolved as monophyletic but the subfamily Rasborinae (priority over Danioinae) is an unnatural assemblage. Danio is identified as a monophyletic group sister to a clade inclusive of the genera Chela, Microrasbora, Devario, and Inlecypris, not Devario nor Esomus as hypothesized in previous studies. Danio rerio is sister to D. kyathit among the species of Danio evaluated in this analysis. Microrasbora and Rasbora are non-monophyletic assemblages; however, Boraras is monophyletic.

Primary cultured cells as sensitive in vitro model for assessment of toxicants-comparison to hepatocytes and gill epithelia

In an effort to develop cultured cell models for toxicity screening and environmental biomonitoring, we compared primary cultured gill epithelia and hepatocytes from freshwater tilapia (Oreochromis niloticus) to assess their sensitivity to AhR agonist toxicants. Epithelia were cultured on permeable supports (terephthalate membranes, "filters") and bathed on the apical with waterborne toxicants (pseudo in vivo asymmetrical culture conditions). Hepatocytes were cultured in multi-well plates and exposed to toxicants in culture medium. Cytochrome P4501A (measured as 7-Ethoxyresorufin-O-deethylase, EROD) was selected as a biomarker. For cultured gill epithelia, the integrity of the epithelia remained unchanged on exposure to model toxicants, such as 1,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), benzo(a)pyrene B[a]P, polychlorinated biphenyl (PCB) mixture (Aroclor 1254), and polybrominated diphenyl ether (PBDE) mixture (DE71). A good concentration-dependent response of EROD activity was clearly observed in both cultured gill epithelia and hepatocytes. The time-course response of EROD was measured as early as 3 h, and was maximal after 6 h of exposure to TCDD, B [alp and Aroclor 1254. The estimated 6 h EC50 for TCDD, B [a]P, and Aroclor 1254 was 1.2x10(-9), 5.7x10(-8) and 6.6x10(-6) M. For the cultured hepatocytes, time-course study showed that a significant induction of EROD took place at 18 h, and the maximal induction of EROD was observed at 24 h after exposure. The estimated 24 It EC50 for TCDD, B[a]P, and Aroclor 1254 was 1.4x10(-9), 8.1x10(-8) and 7.3x10(-6) M. There was no induction or inhibition of EROD in DE71 exposure to both gill epithelia and hepatocytes. The results show that cultured gill epithelia more rapidly induce EROD and are slightly more sensitive than cultured hepatocytes, and could be used as a rapid and sensitive tool for screening chemicals and monitoring environmental AhR agonist toxicants. (c) 2006 Elsevier B.V. All rights reserved.

Revised diagnosis of the genus Bangana Hamilton, 1822 (Pisces : Cyprinidae), with taxonomic and nomenclatural notes on the Chinese species

Most morphological characters diagnostic of the 13 Chinese species of the cyprinid genus Sinilabeo Rendahl, 1932, are identical to those of the genus Bangana Hamilton, 1822. Consequently, these 13 species are transferred to Bangana. A revised diagnosis is provided for the now-expanded genus Bangana, and a dichotomous key and taxonomic and nomenclatural notes are included for the following valid Chinese species: B. decora, B. dero, B. devdevi, B. discognathoides, B. lemassoni, B. lippa, B. rendahli, B. tonkinensis, B. tungting, B. wui, B. xanthogenys, B. yunnanensis, and B. zhui. Literature reports, by Chinese authors, of Sinilabeo dero from the upper Irrawady River basin, in Yunnan, are based on misidentifcations of B. devdevi. Sinilabeo cirrhinoides Wu and Lin in Wu, Lin, Chen, Chen and He, 1977, and S. laticeps Wu and Lin in Wu, Lin, Chen, Chen and He, 1977, are junior subjective synonyms of B. devdevi and B. lippa, respectively. Sinilabeo yunnanensis Wu, Lin, Chen, Chen and He, 1977, is an available name, and a lectotype is designated for the species. Bangana zhui ( Zheng and Chen, 1983) is a valid species distinct from B. yunnanensis.

Identification and characterization of Bacillus anthracis by multiplex PCR on DNA chip

Bacillus anthracis can be identified by detecting virulence factor genes located on two plasmids, pXO1 and pXO2. Combining multiplex PCR with arrayed anchored primer PCR and biotin-avidin alkaline phosphatase indicator system, we developed a qualitative DNA chip method for characterization of B. anthracis, and simultaneous confirmation of the species identity independent of plasmid contents. The assay amplifies pag gene (in pXO1), cap gene (in pXO2) and Ba813 gene (a B. anthracis specific chromosomal marker), and the results were indicated by an easy-to-read profile based on the color reaction of alkaline phosphatase. About 1 pg of specific DNA fragments on the chip wells could be detected after PCR. With the proposed method, the avirulent (pXO1(+)/2(-), pXO1(-)/2(+) and pXO1(-)/2(-)) strains of B. anthracis and distinguished 'anthrax-like' strains from other B. cereus group bacteria were unambiguously identified, while the genera other than Bacillus gave no positive signal. (C) 2004 Elsevier B.V. All rights reserved.

Effects of salinity on food intake, growth, and survival of pufferfish (Fugu obscurus)

The food intake, growth, food conversion ratio and survival of yearling pufferfish, Fugu obscurus Abe, were investigated under different water salinity conditions over a 54-day period. Within the salinity regimes of 0 (freshwater), 8, 18, and 35parts per thousand, the food intake levels were 0.97%, 1.43%, 1.19% and 1.01%, respectively; food conversion ratios were 1.31, 1.93, 1.61 and 1.36, respectively; and specific growth rates were 0.41%, 1.15%, 0.84%, and 0.35%, respectively. The three data series were reduced with increasing salinity. However, the survival rates did not show the same tendencies, which were 80%, 100%, 100%, and 67%, respectively. There were significant differences among the treatments. In conclusion, the yearling pufferfish optimum culture salinity condition was about 8parts per thousand.

Quantitative relationship between chromatographic retentions and molecular structures of polychlorinated dibenzo-p-dioxins (PCDDs)

A new approach to study the quantitative relationships between chromatographic retentions and molecular structures of polychlorinated dibenzo-p-dioxins (PCDDs) is described. The retention equations of PCDDs log k' = A + B/T in gas chromatography (GC) are used to evaluate the properties of the regression coefficients A and B, which have been widely accepted as highly reliable chromatographic retentions. The quantitative relationships between the A, B values and the molecular structures are found. The molecular descriptors given for the first time in this article are very effective. As a result, the regression equations are derived with correlation coefficients greater than 0.9995. The A, B values of PCDDs with no standards available have been predicted according to these relationships. They are very useful in chromatographic identification. The retention times of all PCDDs can be conveniently predicted at any temperature program. Compared with the data obtained from the relevant experiments, the results of prediction are very accurate. (C) 2000 Elsevier Science Ltd. All rights reserved.

Analog-digital and digital-analog converters using single-electron and MOS transistors

This paper proposes two kinds of novel single-electron analog-digital conversion (ADC) and digital-analog conversion (DAC) circuits that consist of single-electron transistors (SETs) and metal-oxide-semiconductor (MOS) transistors. The SET/MOS hybrid ADC and DAC circuits possess the merits of the SET circuit and the MOS circuit. We obtain the SPICE macro-modeling code of the SET transistor by studying and fitting the characteristics of the SET with SPICE simulation and Monte Carlo simulation methods. The SPICE macro-modeling code is used for the simulation of the SET/MOS hybrid ADC and DAC circuits. We simulate the performances of the SET/MOS hybrid 3-b ADC and 2-b DAC circuits by using the H-SPICE simulator. The simulation results demonstrate that the hybrid circuits can perform analog-digital and digital-analog data conversion well at room temperature. The hybrid ADC and DAC circuits have advantages as-follows: 1) compared with conventional circuits, the architectures of the circuits are simpler; 2) compared with single electron transistor circuits, the circuits have much larger load capability; 3) the power dissipation of the circuits are lower than uW; 4) the data conversion rate of the circuits can exceed 100 MHz; and 5) the resolution of the ADC and DAC circuits can be increased by the pipeline architectures.