Phylogeny of fireflies (Coleoptera : Lampyridae) inferred from mitochondrial 16S ribosomal DNA, with references to morphological and ethological traits

We sequenced partial mitochondrial 16S ribosomal DNA (16S rDNA) of 18 firefly species from Southwest of China. Combined with homologous sequences previously reported, phylogenetic trees including Japanese, Korean and Chinese species were reconstructed by

A survey on relation of morphological, molecular and phylogenetic structure of zoanthids of the islands located in the Hormoz Strait (Hormoz, Qeshm, Larak, Hengam)

The order Zoantharia (Zoanthids) is one of the most neglected orders of cnidarians in the Persian Gulf. The present study aims to investigate the biodiversity of this order with morphological and molecular examination in the Persian Gulf. For this purpose, 123 colonies of zoanthids with variety of shape and colors have been collected from intertidal and shallow water zone of four islands, i. e. Hengam, Qeshm, Larak and Hormoz. After sampling, morphological characteristics of each specimen were recorded based on in situ photographs. Then DNA was extracted using the cetyl trimethyl ammonium bromide (CTAB) method. Both mitochondrial 16S ribosomal DNA (mt 16S rDNA) and cytochrome oxidase subunit I (COI) gene fragments were amplified and sequenced. The results of preliminary morphological identification integrated with two mitochondrial markers sequencing demonstrated the presence of five different species in this region; Zoanthus sansibaricus, Palythoa mutuki, Palythoa cf. mutuki, Palythoa tuberculosa and Neozoanthus persicus?. Although at first sight, morphological properties were not successful to delineate zoanthid species, they become reliable criteria to identify and delineate species in field studies after molecular identification.

Study on some biological and feeding factors of spined loach Cobitis taenia from the Babolrud, Talar and Siahrud Rivers

Spined loach, Cobitis taenia, is a predominant fish in the river systems of the southern Caspian Sea basin. Although there is evidence of the geographical divergence of this taxon, but no information is available on morphological differences within the species populations. This study was designed to evaluate some biological factors including; morphometric and meristic characters, length-weight, age-growth, condition factor, diet, reproduction, variation and differentiation, in the Babolrud, Talar and Siahrud Rivers in south of the Caspian Sea basin. Age, sex ratio, fecundity, ova diameter and gonadosomatic index were estimated. Also, regression analyses was tested the relation between fecundity and fish length, weight, gonad weight, and also age. Totally 858 fish of which 721 were matures, were collected from these rivers by electrofishing. 37 morphometric characters, 9 meristic characters and 78 truss network system characters were estimated. Resulats of DFA analysis based on data of morphometric and meristic showd that these populations are highly (94.5%) varios from each other. In discriminate function analysis, the proportion of individuals correctly classified into their original groups was 61%, 65.4% and 86.5% for upstream and downstream, respectively. Clustering based on Euclidean distances among groups of centroids using an UPGMA and also principal component analysis’ results for morphometric data indicated that these populations from these three rivers were clearly distinct from each other. Regression equations between length and weight in these three populations were significantly different from Folton factor (b=3), that showed the fish has a negative Alometric growth process. Condition factor was estimated between 0.8912 to 1.2736 and 0.8131 to 1.4489 for males and females, respectively. Sex ratio (female: male) in these populations was 1.2816:1. The difference between the number of females and males was significant and females were more than males. The female and male specimens reach maturity by Tl more than 40 and 30 mm and at the age of 2+ and 1+, respectively. The mean of ova diameter was 0.5824±0.2882. The spawning took place from May to late July, at the water temperature from 18.7 to 24.0°C. The GSI values average at the beginning of the reproduction period was about 9%, with ranged from 2 to 26% in ripe mature females. The absolute and relative fecundity were 2109±792 and 579±208 respectively. The absolute fecundity was significantly related to body weight and gonads weight. Based on the pattern of gonado-somatic index, it was concluded that this fish has prolong active reproductive period, which is a type of adaptation by short-lived small fishes to environmental conditions. The macroscopic and histological results showed that the female and male have 5 and 4 stages in their maturation process, respectively. The RLG index was about 0.4732, which showed the fish is a carnivorous species. Significant difference was observed between fishes with different length and diet. The main foods of the fish were Trichoptera, Chironomidae larvae and Ephemeroptera which were their prefered food as well, however it was estimated that the food selection and diet are affected by environmental conditions.

Population diversity studies of pharaoh cuttlefish (Sepia pharaonis) in the Persian Gulf and the Gulf of Oman

The pharaoh Cuttlefish (Sepia Pharaonis) is the most abundant species in the persian gulf and oman sea. The stock patterns of this species was studied conserning biological, morphological and electrophoretical aspects. In addition to measuring the biological patterns; 21 quantitative and qualitative factors were measured or counted. There tissues namely muscle, eye and liver were also used for further polyacrylamide electrophoresis analysis (SDS-Page method). The densitograms of protein bands of each tissue were prepared by Gel-Scanner and also the amount of bands' areas were estimated. The results of LSD test showed that tentacle length (TL), Tentacle club length (TCL) and TCL were indicative factors which they showed significant difference between male TL and female specimen of Bushehr and Balouchestan regions. Regarding to length and weight frequencies data the results indicated that males are always bigger than females and also, the cuttlefishes of the gulf of oman are bigger than persian gulf's samples. There were found a significant sample correlation (95%) between different quantitative parameters and the most correlation (0.963) was found to be between TL and TCL; whereas the less correlation (0.384) was observed between GL and LA3. However the gill length factor illustrated the less correlation with the other factors. The results of Cluster analysis for both sexes showed that the cuttlefishes of both studied regions belongs to seperate stocks. The electrophoretic experiments of proteins showed that the protein bands of the sample tissue of muscle and eye from both sampling areas revealed significant differences; whereas the tissue of liver wasn't recognized as an indicative tissue for population studies. Taking into consideration the findings of the present study including: (1) difference in spawning season, (2) results of dendrograms, (3) observed Significant differences in one-way analysis of variance (ANOVA) for morphometric measurements, (4) differences in body length and weight, (5) ecological variations of the persian gulf and oman sea, (6) as well as the results of electrophoresis of proteins have indicatend that: "The Pharaoh cuttlefishes of Bushehr and Balouchestan waters belong to two seperate stocks. Also, it is believed that each region has propably two different populations and more studies are needed to approve this result.

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.

Immersed Boundary Method for generalised finite volume and finite difference Navier-Stokes solvers

In Immersed Boundary Methods (IBM) the effect of complex geometries is introduced through the forces added in the Navier-Stokes solver at the grid points in the vicinity of the immersed boundaries. Most of the methods in the literature have been used with Cartesian grids. Moreover many of the methods developed in the literature do not satisfy some basic conservation properties (the conservation of torque, for instance) on non-uniform meshes. In this paper we will follow the RKPM method originated by Liu et al. [1] to build locally regularized functions that verify a number of integral conditions. These local approximants will be used both for interpolating the velocity field and for spreading the singular force field in the framework of a pressure correction scheme for the incompressible Navier-Stokes equations. We will also demonstrate the robustness and effectiveness of the scheme through various examples. Copyright © 2010 by ASME.

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.

Temporal difference models describe higher-order learning in humans.

The ability to use environmental stimuli to predict impending harm is critical for survival. Such predictions should be available as early as they are reliable. In pavlovian conditioning, chains of successively earlier predictors are studied in terms of higher-order relationships, and have inspired computational theories such as temporal difference learning. However, there is at present no adequate neurobiological account of how this learning occurs. Here, in a functional magnetic resonance imaging (fMRI) study of higher-order aversive conditioning, we describe a key computational strategy that humans use to learn predictions about pain. We show that neural activity in the ventral striatum and the anterior insula displays a marked correspondence to the signals for sequential learning predicted by temporal difference models. This result reveals a flexible aversive learning process ideally suited to the changing and uncertain nature of real-world environments. Taken with existing data on reward learning, our results suggest a critical role for the ventral striatum in integrating complex appetitive and aversive predictions to coordinate behaviour.

Cabaret finite-difference schemes for the one-dimensional Euler equations

In the present paper we consider second order compact upwind schemes with a space split time derivative (CABARET) applied to one-dimensional compressible gas flows. As opposed to the conventional approach associated with incorporating adjacent space cells we use information from adjacent time layer to improve the solution accuracy. Taking the first order Roe scheme as the basis we develop a few higher (i.e. second within regions of smooth solutions) order accurate difference schemes. One of them (CABARET3) is formulated in a two-time-layer form, which makes it most simple and robust. Supersonic and subsonic shock-tube tests are used to compare the new schemes with several well-known second-order TVD schemes. In particular, it is shown that CABARET3 is notably more accurate than the standard second-order Roe scheme with MUSCL flux splitting.

How neurons migrate: a dynamic in-silico model of neuronal migration in the developing cortex.

BACKGROUND: Neuronal migration, the process by which neurons migrate from their place of origin to their final position in the brain, is a central process for normal brain development and function. Advances in experimental techniques have revealed much about many of the molecular components involved in this process. Notwithstanding these advances, how the molecular machinery works together to govern the migration process has yet to be fully understood. Here we present a computational model of neuronal migration, in which four key molecular entities, Lis1, DCX, Reelin and GABA, form a molecular program that mediates the migration process. RESULTS: The model simulated the dynamic migration process, consistent with in-vivo observations of morphological, cellular and population-level phenomena. Specifically, the model reproduced migration phases, cellular dynamics and population distributions that concur with experimental observations in normal neuronal development. We tested the model under reduced activity of Lis1 and DCX and found an aberrant development similar to observations in Lis1 and DCX silencing expression experiments. Analysis of the model gave rise to unforeseen insights that could guide future experimental study. Specifically: (1) the model revealed the possibility that under conditions of Lis1 reduced expression, neurons experience an oscillatory neuron-glial association prior to the multipolar stage; and (2) we hypothesized that observed morphology variations in rats and mice may be explained by a single difference in the way that Lis1 and DCX stimulate bipolar motility. From this we make the following predictions: (1) under reduced Lis1 and enhanced DCX expression, we predict a reduced bipolar migration in rats, and (2) under enhanced DCX expression in mice we predict a normal or a higher bipolar migration. CONCLUSIONS: We present here a system-wide computational model of neuronal migration that integrates theory and data within a precise, testable framework. Our model accounts for a range of observable behaviors and affords a computational framework to study aspects of neuronal migration as a complex process that is driven by a relatively simple molecular program. Analysis of the model generated new hypotheses and yet unobserved phenomena that may guide future experimental studies. This paper thus reports a first step toward a comprehensive in-silico model of neuronal migration.

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.