Molecular and morphological analysis of endangered species Gymnodiptychus integrigymnatus (Teleostei: Cyprinidae)

Gymnodiptychus integrigymnatus is a critically endangered species endemic to the Gaoligongshan Mountains. It was thought to be only distributed in several headwater-streams of the Longchuanjiang River (west slope of the Gaoligongshan Mountains, belonging to the Irrawaddy River drainage). In recent years, dozens of G. integrigymnatus specimens have been collected in some streams on the east slope of the Gaoligongshan Mountains (the Salween drainage). We performed a morphological and genetic analyses (based on cytochrome b and D-loop) of the newly discovered populations of G. integrigymnatus to determine whether the degree of separation of these populations warrants species status. Our analysis from the cytochrome b gene revealed that nine individuals from the Irrawaddy drainage area and seven individuals from the Salween drainage area each have only one unique haplotype. The genetic distance between the two haplotypes is 1.97%. Our phylogenetic analysis revealed that G. integrigymnatus is closely related to highly specialized schizothoracine fishes. Analysis from the mitochondrial control region revealed that G. integrigymnatus has relatively high genetic diversity (pi was 0.00891 and h was 0.8714), and individuals from different river drainages do not share the same haplotypes. The AMOVA results indicated 87.27% genetic variability between the Salween and Irrawaddy populations. Phylogenetic trees show two major geographic groups corresponding to the river systems. We recommend that G. integrigymnatus should be considered as a high priority for protected species status in the Gaoligongshan Mountains National Nature Reserve, and that the area of the Gaoligongshan Mountains National Nature Reserve should be expanded to cover the entire distribution of G. integrigymnatus. Populations of G. integrigymnatus from different river systems should be treated as evolutionarily significant units.

Morphological Phylogeny of the Water Snake Subfamily Homalopsinae (Serpent: Colubridae)

水蛇亚科属于游蛇科,包含10个属。其中7个属为单型属。选取水蛇亚科14个形态学特征进行支序分析,并利用计算机软件Hennig86对水蛇亚科中8个属之间的系统发育关系进行初步探讨,结果显示水蛇亚科分为两支Gerarda和Fordonia两个属构成姊妹群,Cerberus、Erpeton和Homalopsis三个属也构成单系群,与Vorisetal(2002)的分子系统树相同,但Cantoria属的地位则与Vorisetal(2002)的明显不同。

Morphological decomposition in Arabic ASR systems

In recent years, the use of morphological decomposition strategies for Arabic Automatic Speech Recognition (ASR) has become increasingly popular. Systems trained on morphologically decomposed data are often used in combination with standard word-based approaches, and they have been found to yield consistent performance improvements. The present article contributes to this ongoing research endeavour by exploring the use of the 'Morphological Analysis and Disambiguation for Arabic' (MADA) tools for this purpose. System integration issues concerning language modelling and dictionary construction, as well as the estimation of pronunciation probabilities, are discussed. In particular, a novel solution for morpheme-to-word conversion is presented which makes use of an N-gram Statistical Machine Translation (SMT) approach. System performance is investigated within a multi-pass adaptation/combination framework. All the systems described in this paper are evaluated on an Arabic large vocabulary speech recognition task which includes both Broadcast News and Broadcast Conversation test data. It is shown that the use of MADA-based systems, in combination with word-based systems, can reduce the Word Error Rates by up to 8.1 relative. © 2012 Elsevier Ltd. All rights reserved.

Morphological and ultrastructural changes in tobacco BY-2 cells exposed to microcystin-RR

Tobacco BY-2 cells were exposed to microcystin-RR (MC-RR) at two concentrations, 60 mu g mL(-1) and 120 mu g mL(-1), to study the changes in morphology and ultrastructure of cells as a result of the exposure. Exposure to the lower concentration for 5 d led to typical apoptotic morphological changes including condensation of nuclear chromatin, creation of a characteristic 'half moon' structure, and cytoplasm shrinkage and decreased cell volume, as revealed through light microscopy. fluorescence microscopy, and transmission electron microscopy, respectively. Exposure to the higher concentration, on the other hand, led to morphological and ultrastructural changes typical of necrosis, such as rupture of the plasma membrane and the nuclear membrane and a marked swelling of cells. The presence of many vacuoles containing unusual deposits points to the involvement of vacuoles in detoxifying MC-RR. Results of the present study indicate that exposure of tobacco BY-2 cells to MC-RR at a lower concentration (60 mu g mL(-1)) results in apoptosis and that to a higher concentration (120 mu g mL(-1)), in necrosis. (C) 2009 Elsevier Ltd. All rights reserved.

Morphological and molecular phylogenetic analysis of two Saprolegnia sp (Oomycetes) isolated from silver crucian carp and zebra fish

Two Saprolegnia isolates, JY isolated from silver crucian carp (Carassius auratus gibelio Bloch) and BMY isolated from zebra fish (Brachydanio rerio Hamilton) came from infections occurring concurrently in different locations in China. To confirm whether the two isolates were from the same Saprolegnia clone, comparative studies have been carried out based on their morphological, physiological and molecular characteristics. Observations showed that morphologically (both asexual and sexual organs) the two isolates were broadly similar and both isolates under-went repeated zoospore emergence. Comparing 704 base pairs of internal transcribed spacer (ITS) region and the 5.8S rDNA, we found isolates JY and BMY shared an identical ITS sequence with a minor variation (99.6 % similarity). Forty available sequences for representatives Saprolegnia spp. belonged to four phylogenetically separate clades. The two studied isolates fell within clade I that comprised a group of isolates which showed almost an identical ITS sequence but had been identified as a number of different morphological species. our findings suggest that isolates JY and BMY appear to belong to the S. ferax clade and this clade (1) contains a number of closely related phylogenetic species. This is distinct from the more common fish pathogenic isolates, which belong to the S. parasitica clade (III) and are characterized by having cysts decorated by bundles of long hooked hairs and two further clades (II and IV) containing largely saprotrophic or soil born species. (C) 2009 Published by Elsevier Ltd on behalf of The British Mycological Society.

Reduced swimming abilities in fast-growing transgenic common carp Cyprinus carpio associated with their morphological variations

Critical swimming speeds (U-crit) and morphological characters were compared between the F-4 generation of GH-transgenic common carp Cyprinus carpio and the non-transgenic controls. Transgenic fish displayed a mean absolute U-crit value 22.3% lower than the controls. Principal component analysis identified variations in body shape, with transgenic fish having significantly deeper head, longer caudal length of the dorsal region, longer standard length (L-S) and shallower body and caudal region, and shorter caudal length of the ventral region. Swimming speeds were related to the combination of deeper body and caudal region, longer caudal length of the ventral region, shallower head depth, shorter caudal length of dorsal region and L-S. These findings suggest that morphological variations which are poorly suited to produce maximum thrust and minimum drag in GH-transgenic C. carpio may be responsible for their lower swimming abilities in comparison with non-transgenic controls.

Morphological characteristics and phylogenetic relationship of Anabaena species from Lakes Dianchi and Erhai, China

Although Anabaena is one of the most prevalent planktonic freshwater genus in China, there are few taxonomic reports of Anabaena strains by morphology and genetics. In this study, morphological characteristics and phylogenetic relationships of seven Anabaena strains isolated from two plateau lakes, Lakes Dianchi and Erhai, were investigated. Morphological characteristics such as morphology of filament, cellular shapes and sizes, relative position of heterocytes and akinetes, and presence or absence of aerotopes, were described for these seven strains. Phylogenetic relationships were determined by constructing 16S rRNA gene tree using the neighbor-joining algorithm. The seven strains were morphologically identified as three groups, and phylogenetic analysis based on 16S rRNA gene sequences also showed that these seven strains were in three groups. Strains EH-2, EH-3, and EH-4 were in group A belonging to the Anabaena circinalis and A. crassa group, and strains DC-1, DC-2, and EH-1 were in group B and identified as A. flos-aquae. Strain DC-3 without aerotopes was significantly different from the other isolated strains and was determined as A. cylindrica.

Morphological variability between wild populations and inbred stocks of a Chinese minnow, Gobiocypris rarus

Gobiocypris rarus, a small, native cyprinid fish, is currently widely used in research on fish pathology, genetics, toxicology, embryology, and physiology in China. To develop this species as a model laboratory animal, inbred strains have been successfully created. In this study, to explore a method to discriminate inbred strains and evaluate inbreeding effects, morphological variation among three wild populations and three inbred stocks of G. rarus was investigated by the multivariate analysis of eight meristic and 30 morphometric characters. Tiny intraspecific variations in meristic characters were found, but these were not effective for population distinction. Stepwise discriminant analysis and cluster analysis of conventional measures and truss network data showed considerabe divergence among populations, especially between wild populations and inbred stocks. The average discriminant accuracy for all populations was 82.1% based on conventional measures and 86.4% based on truss data, whereas the discriminant accuracy for inbred strains was much higher. These results suggested that multivariate analyses of morphometric characters are an effective method for discriminating inbred strains of G. rarus. Morphological differences between wild populations and inbred strains appear to result from both genetic differences and environmental factors. Thirteen characters, extracted from stepwise discriminant analysis, played important roles in morphological differentiation. These characters were mainly measures related to body depth and head size.

Morphological description of two bucephalid trematodes collected from freshwater fishes in the Uji River, Kyoto, Japan

The morphology of two species of bucephalids (Bucephalidae; Digenea; Trematoda), which since 1999 has caused a fish disease at the Uji River, Kyoto Prefecture, Japan, is described. Parabucephalopsis parasiluri Wang, 1985 was first recorded in the Uji River in 2000, and Prosorhynchoides ozakii (Nagaty, 1937) in 2005. The definitive host of both species is the Lake Biwa catfish (Silurus biwaensis), and the second intermediate hosts include many fish species from several families. P. parasiluri is an introduced parasite that invaded with its first intermediate host, golden mussels (Limnoperna fortunei), from the Asian continent. P ozakii may also be an introduced species, although its first intermediate host has not been identified. (C) 2007 Elsevier Ireland Ltd. All rights reserved.

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.

Morphological and genetic differences of Trypanosoma in some Chinese freshwater fishes: difficulties of species identification

Blood smears and purified trypanosome from freshwater fishes yellow catfish (Pseudobagras fulvidraco) and common carp (Cyprinus carpio) captured from Niushan Lake, Hubei Province were examined to determine whether all of their trypanosomes were Trypanosoma pseudobagri, a species of supposed host specificity and widespread existence across China. Trypanosomes occurred in 16/16 blood smears, and morphometric character analysis of trypanosomes from these smears showed that there were three morphospecies, Trypanosoma sp Carpio, T. sp Pseudobagri, and T. sp. 18S rDNA sequences of trypanosomes from 16 samples revealed three genetic groups among these fish trypanosomes. Group 1 was from C. carpio containing T. sp Carpio; groups 2 and 3 were from P. fulvidraco containing T. sp Pseudobagri and T. sp, respectively. The high similarity of morphometric characters and 18S rDNA sequences showed that T. sp Carpio and T. siniperca probably were the same species. T. sp Pseudobagri was the first occurrence in China. Sequence comparison showed that T. sp Pseudobagri sequence was most similar to that of clone Marv, whereas T. sp sequence differ from those of T. sp Carpio and T. sp Pseudobagri by 5.4 and 5.8%, respectively, and tentatively identified as T. pseudobagri. It was concluded that three species of trypanosomes, at least three genotypes occur in Niushan Lake fishes, and P. fulvidraco in this region appear to contain both types, although the identification of T. pseudobagri remains a problem.

Redescription of Trypanosoma siniperca Chang 1964 from freshwater fish of China based on morphological and molecular data

During the parasite fauna investigation within 2005, the freshwater fish trypanosome Trypanosoma siniperca Chang 1964 was isolated from the blood of Mandarin carp (Siniperca chuatsi) from Niushan Lake, Hubei Province, central China. Blood trypomastigotes were observed only, and the density of infection was low. Light microscopy examinations of this material made it possible to study in detail the morphology of this parasite and redescribe it according to current standards. T. siniperca is characterized also on the molecular level using the sequences of SSU rRNA gene. Phylogenetic analyses based on these sequences allowed clearer phylogenetic relationships to be established with other fish trypanosomes sequenced to date.

Molecular and morphological data suggest that Spinibarbus caldwelli (Nichols) (Teleostei : Cyprinidae) is a valid species

The taxonomic problem of the cyprinid species of genus Spinibarbus, occurring in southern China and northern Vietnam, was resolved on the basis of molecular and morphological analyses. Spinibarbus caldwelli and Spinibarbus hollandi have a smooth posterior edge of the last unbranched dorsal fin ray among species in the genus. Spinibarbus caldwelli is currently regarded as a junior synonym of S. hollandi because of ambiguities in diagnostic characters. In this article, 11 mtDNA cytochrome b sequences of Spinibarbus specimens were analyzed together with Barbodes gonionotus and Puntius conchonius as outgroups. Our results showed that specimens identified as S. hollandi from Taiwan were different from those from the Asian mainland at a high level of genetic divergence (0.097-0.112), which is higher than that between the two valid species, S. sinensis and S. yunnanensis ( 0.089), and suggested that Taiwan specimens should be considered as a different species from the Asian mainland one. In a molecular phylogenetic analysis, the sister-group relationship between Taiwan specimens and the Asian mainland specimens was supported strongly by a high confidence level ( 100% in bootstrap value). Further analysis of morphological characters showed that overlap of diagnostic characters is much weaker than previously suggested. Taiwan specimens had 8 branched rays in the dorsal fin, whereas those from the mainland had almost 9-10. The molecular and morphological differences suggest S. caldwelli to be valid. The molecular divergence shows the genetic speciation of S. hollandi and S. caldwelli might have occurred 5.6-4.9 million years ago; the former could be a relict species in Taiwan, and the latter dispersed in the Asian mainland.

Morphological computation of multi-gaited robot locomotion based on free vibration.

In recent years, there has been increasing interest in the study of gait patterns in both animals and robots, because it allows us to systematically investigate the underlying mechanisms of energetics, dexterity, and autonomy of adaptive systems. In particular, for morphological computation research, the control of dynamic legged robots and their gait transitions provides additional insights into the guiding principles from a synthetic viewpoint for the emergence of sensible self-organizing behaviors in more-degrees-of-freedom systems. This article presents a novel approach to the study of gait patterns, which makes use of the intrinsic mechanical dynamics of robotic systems. Each of the robots consists of a U-shaped elastic beam and exploits free vibration to generate different locomotion patterns. We developed a simplified physics model of these robots, and through experiments in simulation and real-world robotic platforms, we show three distinctive mechanisms for generating different gait patterns in these robots.