Species identification of Chinese sturgeon using acoustic descriptors and ascertaining their spatial distribution in the spawning ground of Gezhouba Dam

This study has developed an improved subjective approach of classification in conjunction with Step wise DFA analysis to discriminate Chinese sturgeon signals from other targets. The results showed that all together 25 Chinese sturgeon echo-signals were detected in the spawning ground of Gezhouba Dam during the last 3 years, and the identification accuracy reached 90.9%. In Stepwise DFA, 24 out of 67 variables were applied in discrimination and identification. PCA combined with DFA was then used to ensure the significance of the 24 variables and detailed the identification pattern. The results indicated that we can discriminate Chinese sturgeon from other fish species and noise using certain descriptors such as the behaviour variables, echo characteristics and acoustic cross-section characteristics. However, identification of Chinese sturgeon from sediments is more difficult and needs a total of 24 variables. This is due to the limited knowledge about the acoustic-scattering properties of the substrate regions. Based on identified Chinese sturgeon individuals, 18 individuals were distributed in the region between the site of Gezhouba Dam and Miaozui reach, with a surface area of about 3.4 km(2). Seven individuals were distributed in the region between Miaozui and Yanshouba reach, with a surface area of about 13 km(2).

Detection of hybridization between two loach species (Paramisgurnus dabryanus and Misgurnus anguillicaudatus) in wild populations

Artificial interspecific hybrids between large scale loach P. dabryanus and tetraploid pond loach M. anguillicaudatus (Cobitidae, Cypriniformes) are viable. To detect the occurrence of possible natural hybridization, genetic analyses by using microsatellite markers were performed for natural populations of large scale loach and pond loach, the reciprocal laboratory hybrids, and "supposed hybrids" with ambiguous morphology. The fertility of the artificial hybrids was also tested. At one diagnostic microsatellite (Mac50), one out of 20 "supposed hybrids" was identified to be F-1 hybrid between the two loach species because it had the same genotype as that of the laboratory hybrids. The triploid hybrids between the two species were confirmed to be female-sterile. The results show that rare hybridization has occurred between diploid large scale loach and tetraploid pond loach in nature although it may have little effect in genetic introgression. This study is helpful for fish conservation and encourages further investigation on natural hybridization and introgression of loaches.

Triplophysa lixianensis, a new nemacheiline loach species (Pisces : Balitoridae) from the upper Yangtze River drainage in Sichuan Province, South China

Triplophysa lixianensis, a new nemacheiline loach species, is described from the Min Jiang of the upper Yangtze River drainage in Sichuan Province, South China. It can be separated from all other species of Triplophysa by having a unique combination of the following characters: posterior chamber of gas bladder greatly reduced or absent; caudal peduncle columnar with a roughly round cross- section at its beginning; anterior edge of lower jaw completely exposed or uncovered by lower lip; intestine short, forming a zigzag loop below stomach; dorsal- fin origin closer to caudal- fin base than to snout tip; pelvic fin inserted anterior to dorsal- fin origin; snout length 50.6 - 57.5 % of head length; eye diameter 12.3 15.4 % of head length; caudal peduncle length 25.1 - 27.1 % of standard length; anal fin with five branched rays; lower lip greatly furrowed with two thick lateral lobes; and body smooth or scaleless.

Cytoplasmic impact on cross-genus cloned fish derived from transgenic common carp (Cyprinus carpio) nuclei and goldfish (Carassius auratus) enucleated eggs

In previous studies of nuclear transplantation, most cloned animals were obtained by intraspecies nuclear transfer and are phenotypically identical to their nuclear donors; furthermore, there was no further report on successful fish cloning since the report of cloned zebrafish. Here we report the production of seven cross-genus cloned fish by transferring nuclei from transgenic common carp into enucleated eggs of goldfish. Nuclear genomes of the cloned fish were exclusively derived from the nuclear donor species, common carp, whereas the mitochondrial DNA from the donor carp gradually disappeared during the development of nuclear transfer (NT) embryos. The somite development process and somite number of nuclear transplants were consistent with the recipient species, goldfish, rather than the nuclear donor species, common carp. This resulted in a long-lasting effect on the vertebral numbers of the cloned fish, which belonged to the range of goldfish. These demonstrate that fish egg cytoplasm not only can support the development driven by transplanted nuclei from a distantly related species at the genus scale but also can modulate development of the nuclear transplants.

RADIATION CROSS-LINKING OF CHLORINATED POLYISOBUTYLENE

The effects of radiation on chlorinated polyisobutylene were studied. It was found that polyisobutylene, which is generally considered to be a typical radiation-degradative polymer, could be crosslinked by gamma-ray irradiation after chlorine had been introduced into its macromolecules. Carbon-chlorine bonds act both as radiation-sensitive groups and reaction species in the radiation process of chlorinated polyisobutylene.

ELECTROCHEMICAL CATALYSIS AT AN ULTRAMICROELECTRODE MODIFIED WITH REDOX SPECIES

General equations of the electrocatalytic reaction at an ultramicroelectrode modified with redox species have been described according to the Andrieux Saveant model. The electrocatalytic kinetic process has been discussed for the whole set of cases, ie (R), (R + S), (SR) (SR + E), (E), (R + E), (ER), (S), (ER + S) and (S + E) limiting situations. The effect of gamma on the catalytic steady state current shows that the higher the value of gamma, the lower the catalytic current. The kinetic process shifts rapidly from R to E with increasing values of gamma. It is favorable for catalysis only when gamma is very low. Therefore, the redox species modified ultramicroelectrode with thin film is utilized for electrocatalysis, and the larger the radius of ultramicroelectrode, the higher the catalytic efficiency.

ELECTROCATALYSIS AT A MICRODISK ELECTRODE MODIFIED WITH A REDOX SPECIES

The current equation of the electrocatalytic reaction at a microdisk electrode modified with redox species has been described and verified experimentally. There exists a linear relationship between plateau limiting current and the radius of the microdisk electrode for a catalytic process. The influence of the dimensions of the microdisk electrode on catalytic efficiency is discussed. The polyvinylferrocene (PVFc)-modified microdisk electrode prepared by the coating method was taken as a typical example, on which the electrocatalytic oxidation of ascorbic acid could be studied. The catalytic reaction rate constants were determined as an average value of 1.5 X 10(-7) cm3/mol s by this method, and are consistent with those obtained at a conventional electrode.

Molecular evidence for the sister relationship of the eastern Asia-North American intercontinental species pair in the Podophyllum group (Berberidaceae)

The presumed pair relationships of intercontinental vicariad species in the Podophyllum group (Sinopodophyllum hexandrum vs. Podophyllum pelatum and Diphylleia grayi vs. D. cymosa) were recently, considered to be paraphyletic. In the present paper, the trnL-F and ITS gene sequences of the representatives were used to examine the sister relationships of these two vicariad species. A heuristic parsimony analysis based on the trnLF data identified Diphylleia as the basal clade of the other three genera, but provided poor resolution of their inter-relationships. High sequence divergence was found in the ITS data. ITS1 region, more variable but parsimonyuninformative. has no phylogenetic value, Sequence divergence of the ITS2 region provided abundant, phylogenetically informative variable characters. Analysis of ITS2 sequences confirmeda sister relationship between the presumable vicariad species, in spite of a low bootstrap support for Sinopodophyllum hexandrum vs. Podophyllum pelatum. The combined ITS2 and trnL-F data enforced a sister relationship between Sinopodophyllum hexandrum and Podophyllum pelatum with an elevated bootstrap support of 100%. Based on molecular phylogeny, the morphological evolution of this group was discussed. The self-pollination might have evolved from cross-fertilization two times in this group. The different pollination and seed dispersal systems of Sinopodophyllum hexandrum and Podophlyllum pelatum resulted from their adaptations to different ecological habitats. The divergence time of Sinopodophyllum hexandrum-Podophyllum pelatum is estimated to be 6.52+/-1.89 myr based on the ITS divergence. The divergence of this species pair predated or co-occurred with the recent uplift of the Himalayas 4-3 myr during the late Miocene and the formation of the alpine habitats. Sinopodophyllum hexandrum developed a host of specialized characters in its subsequent adaptation to the arid alpine surroundings. The present study confirmed the different patterns of species relationship between Asian-North American disjuncts. The isolation of plant elements between North America and eastern Asia must have been a gradual process, resulting in the different phylogenetic patterns and divergence times of the disjuncts.

Mammalian genes induce partially reprogrammed pluripotent stem cells in non-mammalian vertebrate and invertebrate species.

Cells are fundamental units of life, but little is known about evolution of cell states. Induced pluripotent stem cells (iPSCs) are once differentiated cells that have been re-programmed to an embryonic stem cell-like state, providing a powerful platform for biology and medicine. However, they have been limited to a few mammalian species. Here we found that a set of four mammalian transcription factor genes used to generate iPSCs in mouse and humans can induce a partially reprogrammed pluripotent stem cell (PRPSCs) state in vertebrate and invertebrate model organisms, in mammals, birds, fish, and fly, which span 550 million years from a common ancestor. These findings are one of the first to show cross-lineage stem cell-like induction, and to generate pluripotent-like cells for several of these species with in vivo chimeras. We suggest that the stem-cell state may be highly conserved across a wide phylogenetic range. DOI:http://dx.doi.org/10.7554/eLife.00036.001.

The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes.

BACKGROUND: A hierarchical taxonomy of organisms is a prerequisite for semantic integration of biodiversity data. Ideally, there would be a single, expansive, authoritative taxonomy that includes extinct and extant taxa, information on synonyms and common names, and monophyletic supraspecific taxa that reflect our current understanding of phylogenetic relationships. DESCRIPTION: As a step towards development of such a resource, and to enable large-scale integration of phenotypic data across vertebrates, we created the Vertebrate Taxonomy Ontology (VTO), a semantically defined taxonomic resource derived from the integration of existing taxonomic compilations, and freely distributed under a Creative Commons Zero (CC0) public domain waiver. The VTO includes both extant and extinct vertebrates and currently contains 106,947 taxonomic terms, 22 taxonomic ranks, 104,736 synonyms, and 162,400 cross-references to other taxonomic resources. Key challenges in constructing the VTO included (1) extracting and merging names, synonyms, and identifiers from heterogeneous sources; (2) structuring hierarchies of terms based on evolutionary relationships and the principle of monophyly; and (3) automating this process as much as possible to accommodate updates in source taxonomies. CONCLUSIONS: The VTO is the primary source of taxonomic information used by the Phenoscape Knowledgebase (http://phenoscape.org/), which integrates genetic and evolutionary phenotype data across both model and non-model vertebrates. The VTO is useful for inferring phenotypic changes on the vertebrate tree of life, which enables queries for candidate genes for various episodes in vertebrate evolution.

Likelihood, entropy and species diversity; some comparisons in a Sumatran forest

In attempts to conserve the species diversity of trees in tropical forests, monitoring of diversity in inventories is essential. For effective monitoring it is crucial to be able to make meaningful comparisons between different regions, or comparisons of the diversity of a region at different times. Many species diversity measures have been defined, including the well-known abundance and entropy measures. All such measures share a number of problems in their effective practical use. However, probably the most problematic is that they cannot be used to meaningfully assess changes, since thay are only concerned with the number of species or the proportions of the population/sample which they constitute. A natural (though simplistic) model of a species frequency distribution is the multinomial distribution. It is shown that the likelihood analysis of samples from such a distribution are closely related to a number of entropy-type measures of diversity. Hence a comparison of the species distribution on two plots, using the multinomial model and likelihood methods, leads to generalised cross-entropy as the LRT test statistic of the null that the species distributions are the same. Data from 30 contiguous plots in a forest in Sumatra are analysed using these methods. Significance tests between all pairs of plots yield extremely low p-values, indicating strongly that it ought to been "Obvious" that the observed species distributions are different on different plots. In terms of how different the plots are, and how these differences vary over the whole study site, a display of the degrees of freedom of the test, (equivalent to the number of shared species) seems to be the most revealing indicator, as well as the simplest.

Heterospecific mating and species recognition in the planktonic marine copepods Temora stylifera and T. longicornis

Many planktonic copepods use diffusible pheromone or hydromechanical signals to remotely detect the presence of potential mates. To determine whether these mating signals also play a role in species recognition and mate choice, we observed and video recorded (3D) mate-finding and pursuit behaviors in heterospecific and conspecific mating crosses in a pair of congeneric, partially sympatric species (Temora stylifera and T. longicornis) in the laboratory. The species appear to have asymmetrical pre-mating isolation, with T. longicornis males readily pursuing T. stylifera females to mate contact and capture, but with little mate-finding activity observed in the reverse cross. Males of T. longicornis pursuing heterospecific females executed a number of behaviors known to facilitate successful pheromone trail following and mate capture in conspecific mating, including accelerated swimming in a ‘signal-scanning’ mode to recover a lost pheromone trail, reversal of the tracking direction in cases when the male initiated tracking in the incorrect direction, and accelerated swimming speeds when in the presence of a pheromone signal but prior to locating the trail. Detailed analyses of mate-tracking behavior in T. longicornis male × T. stylifera female crosses gave no indication that males were aware they were pursuing heterospecific females prior to mate contact, indicating that diffusible pheromone and hydromechanical signals are not used, either singly or in combination, for species recognition in this mating pair. Heterospecific mating attempts among sympatric, congeneric copepods may commonly proceed to mate capture, and incur fitness costs to either or both mating partners.

Absolute single and multiple charge exchange cross sections for highly charged C, O, and Ne ions on H2O, CO, and CO2

Reported herein are measured absolute single, double, and triple charge exchange (CE) cross sections for the highly charged ions (HCIs) Cq+ (q=5,6), Oq+ (q=6,7,8), and Neq+ (q=7,8) colliding with the molecular species H2O, CO, and CO2. Present data can be applied to interpreting observations of x-ray emissions from comets as they interact with the solar wind. As such, the ion impact energies of 7.0q keV (1.62–3.06 keV/amu) are representative of the fast solar wind, and data at 1.5q keV for O6+ (0.56 keV/amu) on CO and CO2 and 3.5q keV for O5+ (1.09 keV/amu) on CO provide checks of the energy dependence of the cross sections at intermediate and typical slow solar wind velocities. The HCIs are generated within a 14 GHz electron cyclotron resonance ion source. Absolute CE measurements are made using a retarding potential energy analyzer, with measurement of the target gas cell pressure and incident and final ion currents. Trends in the cross sections are discussed in light of the classical overbarrier model (OBM), extended OBM, and with recent results of the classical trajectory Monte Carlo theory.

Measurement of charge exchange and X-ray emission cross sections for solar wind-comet interactions

X-ray emission from a comet was observed for the first time in 1996. One of the mechanisms believed to be contributing to this surprisingly strong emission is the interaction of highly charged solar wind ions with cometary gases. Reported herein are total absolute charge-exchange and normalized line-emission (X-ray) cross sections for collisions of high-charge state (+3 to +10) C, N, O, and Ne ions with the cometary species H2O and CO2. It is found that in several cases the double charge-exchange cross sections can be large, and in the case of C3+ they are equal to those for single charge exchange. Present results are compared to cross section values used in recent comet models. The importance of applying accurate cross sections, including double charge exchange, to obtain absolute line-emission intensities is emphasized.

Characterisation of antibodies to chloramphenicol, produced in different species by enzyme-linked immunosorbent assay and biosensor technologies

Six polyclonal antisera to chloramphenicol (CAP) were successfully raised in camels, donkeys and goats. As a comparison of sensitivity, IC50 values ranged from 0.3 ng mL(-1) to 5.5 ng mL(-1) by enzyme-linked immunosorbent assay (ELISA) and from 0.7 ng mL(-1) to 1.7 ng mL(-1) by biosensor assay. The introduction of bovine milk extract improved the sensitivity of four of the antisera by ELISA and two by biosensor assay; a reduction in sensitivity of the remaining antisera ranged by a factor of 1.1-2.6. Porcine kidney extract reduced the sensitivity of all the antisera by a factor ranging from 1.1 to 7 by ELISA and a factor of 1.5 to 4 by biosensor. A low cross-reactivity with thiamphenicol (TAP) and florfenicol (FF) was displayed by antiserurn G2 (1.2% and 18%, respectively) when a homologous ELISA assay format was employed. No cross-reactivity was displayed by any of the antisera when a homologous biosensor assay format was employed. Switching to a heterologous ELISA format prompted three of the antisera to display more significant cross-reactivity with TAP and FF (53% and 82%, respectively, using Dl). The heterologous biosensor assay also increased the cross-reactivity of D1 for TAP and FF (56% and 129%, respectively) and of one other antiserum (Gl) to a lesser degree. However, unlike the ELISA, the heterologous biosensor assay produced a substantial reduction in sensitivity (by a factor of 6 for D1). (C) 2007 Elsevier B.V. All rights reserved.