A compiled key to the recent Stomatopoda of the Indo-West Pacific region

A taxonomic key is presented of the Stomatopoda (family Gonodactylidae) of the IndoWest Pacific Region.

Distribution of decapod larvae in the Bombay Harbour-Thana-Bassein Creek regions

Variations in the abundance and composition of larval decapods were studied from 90 km stretch of the Bombay Harbour-Thana Creek-Bassein Creek (BHTCBC) system for a period of 15 months. The larvae belonged to Penacidea, Caridea, Anomura and Brachyura. Among these, brachyurans were the most abundant in the entire study area indicating good potential for crab fishery. Penaeus, Metapenaeus and Parapenaeopsis were the genera recorded in the family Penaeidae of which Metapenaeus spp. were the most common. Generally there was a higher abundance of Penaeus and Metapenaeus during monsoon probably indicating intense breeding. A few genera of decapods showed patchy occurrence in this system. Results of this first investigation were quantitatively and qualitatively evaluated with comments on fishery potential of the commercially important groups of decapods.

The study of biological characteristics and determination of population dynamic parameters of sawtooth barracuda (Sphyraena putnamae) in the Persian Gulf (Hormozgun Province waters)

The biological characteristics and population dynamisms of Sphyraena putnamae, were studied in the northern Persian Gulf and Oman Sea restricted to Hormuzgan province waters within 13 months period, from November 2006 up to November 2007. Biometrical and anatomical measurements were carried out, and biological surveys were conducted on 486 specimens. On the other hand, the growth and mortality parameters were estimated by using 3096 samples. These samples were collected from 3 landings, namely Bandar Abbas, Bandar Lengeh and Bandar Jask. The measurements of the minimum and maximum Fork lengths and weights were 11.7 to 8.03 cm and 135.0 to 4140.0 g, respectively. The results indicated that this species, having the Relative Length of Gut, RLG=0.34±0.002, is strongly carnivorous (often fish-eater), proven by the fact that more than 98% of its stomach contents were fish pieces. Examining the changes in the index of stomach emptiness by the percentage of CV = 0.47% indicates that this fish is Moderate feeder. The level of feeding increased in March, before spawning and decreased in June and September, simultaneously with the spawning season. There are 2 peaks of reproduction or spawning seasons during the months of April-May and September, of which the prior is assumed as the main spawning. The sex ratio (M:F) was calculated 0.5:1.0(X2 =2.11), which did not show a significant difference with expected level of 1:1 (P>0.05). The average absolute and relative reproduction rates of Sphyraena putnamae is respectively as follows: 1866827.1±255448.9 and 1097.7±94.3. The highest and the lowest diameter of matured egg are from 200 to 750 μ, and its average diameter is 402.10 ± 0.190 μ. A parameter for Saw-tooth barracuda length measurement, Lm50, based on the Fork-length, was calculated as 54.01 cm. In other words, as far as the fisheries management is concerned, the fish whose lengths are less than 54.01 cm should not be caught. The calculated level of (R2) (correlations of total length & weight), indicated strong correlations between length and weight of this fish, and the obtained formula included W =0.007100 FL 2.9295 and reinforced this assumption. The “K” Index for this fish in 3 above mentioned landings (Jask, Bandar-Abbas and Bandar-Length) were 1.24, 0.37 and 0.46 per year, respectively and the FL index for the same landings were estimated as 129, 110 and 134 cm, respectively. The growth coefficient (MONRO) for the above mentioned regions were calculated as 3.601, 3.647 and 3.917, respectively; and in the surveyed regions there were no significant differences in populations. The Total mortality coefficient (Z) was calculated 0.76, 1.12 and 1.07 per year, the Natural mortality coefficient was 0.46, 0.63 and 0.70, and the Fishing mortality coefficient (rate) (F) was found to be 0.30, 0.49 and 0.37 per year. The value of the exploitation rate (E) is equal to 0.39 per year, indicating that this species is an under-exploited resource, and there is no excessive fishing pressure on the fish supply of this species in the afore-said regions. The highest level of exploitation was found for ‘Bandar Abbas’ fishing region and the lowest level of exploitation is in ‘Bandar Lengeh’ waters.

On the structure of state-feedback LQG controllers for distributed systems with communication delays

This paper presents explicit solutions for a few distributed LQG problems in which players communicate their states with delays. The resulting control structure is reminiscent of a simple management hierarchy, in which a top level input is modified by newer, more localized information as it gets passed down the chain of command. It is hoped that the controller forms arising through optimization may lend insight into the control strategies of biological and social systems with communication delays. © 2011 IEEE.

Genome-wide identification and characterization of cytochrome P450 monooxygenase genes in the ciliate Tetrahymena thermophila

Background: Cytochrome P450 monooxygenases play key roles in the metabolism of a wide variety of substrates and they are closely associated with endocellular physiological processes or detoxification metabolism under environmental exposure. To date, however, none has been systematically characterized in the phylum Ciliophora. T. thermophila possess many advantages as a eukaryotic model organism and it exhibits rapid and sensitive responses to xenobiotics, making it an ideal model system to study the evolutionary and functional diversity of the P450 monooxygenase gene family. Results: A total of 44 putative functional cytochrome P450 genes were identified and could be classified into 13 families and 21 sub-families according to standard nomenclature. The characteristics of both the conserved intron-exon organization and scaffold localization of tandem repeats within each P450 family clade suggested that the enlargement of T. thermophila P450 families probably resulted from recent separate small duplication events. Gene expression patterns of all T. thermophila P450s during three important cell physiological stages (vegetative growth, starvation and conjugation) were analyzed based on EST and microarray data, and three main categories of expression patterns were postulated. Evolutionary analysis including codon usage preference, sit-especific selection and gene-expression evolution patterns were investigated and the results indicated remarkable divergences among the T. thermophila P450 genes. Conclusion: The characterization, expression and evolutionary analysis of T. thermophila P450 monooxygenase genes in the current study provides useful information for understanding the characteristics and diversities of the P450 genes in the Ciliophora, and provides the baseline for functional analyses of individual P450 isoforms in this model ciliate species.

Identification of Differentially Expressed Genes Between Cloned and Zygote-Developing Zebrafish (Danio rerio) Embryos at the Dome Stage Using Suppression Subtractive Hybridization

Comparative analyses of differentially expressed genes between somatic cell nuclear transfer (SCNT) embryos and zygote-developing (ZD) embryos are important for understanding the molecular mechanism underlying the reprogramming processes. Herein, we used the suppression subtractive hybridization approach and from more than 2900 clones identified 96 differentially expressed genes between the SCNT and ZD embryos at the dome stage in zebrafish. We report the first database of differentially expressed genes in zebrafish SCNT embryos. Collectively, our findings demonstrate that zebrafish SCNT embryos undergo significant reprogramming processes during the dome stage. However, most differentially expressed genes are down-regulated in SCNT embryos, indicating failure of reprogramming. Based on Ensembl description and Gene Ontology Consortium annotation, the problems of reprogramming at the dome stage may occur during nuclear remodeling, translation initiation, and regulation of the cell cycle. The importance of regulation from recipient oocytes in cloning should not be underestimated in zebrafish.

Cloning and expression of medaka dazl during ernbryogenesis and gametogenesis

The Deleted in azoospermia family consists of RNA-binding proteins Bottle, Daz, and Daz-like (Dazl) that are expressed in the germline. Here, we report the cloning and expression of the medakafish (Oryzias latipes) dazl gene (odazl). Interestingly, although the predicted medaka Dazl protein (oDazl) contains a RRM motif and a DAZ repeat characteristic of its mammalian homologs, it lacks 80 aa at the C-terminus. By RT-PCR, RNA in situ hybridization, Western blotting and fluorescent immunohistochemistry using a rabbit anti-DazI antibody (alpha Oazl), we analyzed the expression patterns of odazl and its protein. The odazl transcript persists throughout embryogenesis and delineates with primordial germ cells. In adults, the expression of odazl RNA and its protein is restricted to germ cells of both the testis and ovary. We observed differential expression of RNA and protein at critical stages of gametogenesis. In the testis, the odazl RNA is low at premeiotic stages, abundant at meiotic stages, but absent in postmeiotic stages; whereas the oDazl protein is rich in premeiotic stages, reduced at meiotic stages, becomes barely detectable or absent in postmeiotic round spermatids or sperm, respectively. This is in sharp mature spermatozoa. In the ovary, the odazl RNA contrast to the human situation where the Dazl transcript and protein are present in and protein persist throughout oogenesis and also show differential expression at premeiotic, meiotic and postmeiotic stages. Thus, the odazl or its protein is a marker for germ cells during embryogenesis and at critical stages of gametogenesis in both sexes of medaka. (c) 2006 Elsevier B.V. All rights reserved.

Reproductive effects of prenatal exposure to nonylphenol on zebrafish (Danio rerio)

Mature female and male zebrafish were separated and exposed to nonylphenol (NP) at 0.1, 1, 10, 50, 100 and 500 mu g/L, respectively, for 3 weeks. Gonadosomatic index (GSI) in both sexes and vitellogenin (VTG) induction in males was measured as the bioindicators for the impairment to the parents. The results indicated that 50 mu g/L of NP was the non-observed effect concentration (NOEC) for GSI and VTG induction. Afterwards, the 50 mu g/L NP exposed females and males, and the control females and males were cross-wise pair-bred in the control water for one week to examine the reproductive effects. The embryonic cathepsin D (CAT D) activity, eggshell thickness, fecundity, hatching rate and malformation (vertebral column flexure) rate of offspring were determined in the four pair-bred groups. While endpoints remained unchanged in the groups with exposed males, prenatal exposure of females to 50 mu g/L of NP resulted in the impairment of reproduction in groups with exposed females including inhibition of CAT D activity (P < 0.05), decrease of eggshell thickness (by 23.6%) and elevation of malformation rate (P < 0.001). These results suggested NP could induce reproductive damage to zebrafish at NOEC for parents. The results also imply that alterations of CAT D activity and eggshell thickness may be more sensitive biomarkers to indicate the reproductive effects caused by endocrine disrupting chemicals. (c) 2005 Elsevier Inc. All rights is reserved.

Characterization of transgene integration pattern in F4 hGH-transgenic common carp (Cyprinus carpio L.)

The integration pattern and adjacent host sequences of the inserted pMThGH-transgene in the F4 hGH-transgenic common carp were extensively studied. Here we show that each F4 transgenic fish contained about 200 copies of the pMThGH-transgene and the transgenes were integrated into the host genome generally with concatemers in a head-to-tail arrangement at 4-5 insertion sites. By using a method of plasmid rescue, four hundred copies of transgenes from two individuals of F4 transgenic fish, A and B, were recovered and clarified into 6 classes. All classes of recovered transgenes contained either complete or partial pMThGH sequences. The class I, which comprised 83% and 84.5% respectively of the recovered transgene copies from fish A and B, had maintained the original configuration, indicating that most transgenes were faithfully inherited during the four generations of reproduction. The other five classes were different from the original configuration in both molecular weight and restriction map, indicating that a few transgenes had undergone mutation, rearrangement or deletion during integration and germline transmission. In the five types of aberrant transgenes, three flanking sequences of the host genome were analyzed. These sequences were common carp beta-actin gene, common carp DNA sequences homologous to mouse phosphoglycerate kinase-1 and human epidermal keratin 14, respectively.

Phylogeny of the Amphiliidae (Teleostei : Siluriformes)

The freshwater African catfish family Amphiliidae had been reviewed based on the 73 osteological characters with Diplomystidae, dagger Hypsidoridae, Amblycipitidae, Sisoridae, and Bagridae as out-groups. Because the family position of Leptoglanis (Bagridae/Amphiliidae) is under debate, this genus has been taken as an out-group too. Results of the study indicate that: 1) the Amphiliidae is not a monophyletic group and must now be restricted to the genera Amphilius and Paramphilius; the two subfamilies Amphiliinae and Doumeinae are separated by the sisorids Euchiloglanis (with most of the glyptosternid fishes) and Glyptothorax (with most of the non-glyptosternid fishes); 2) no synapomorphies were found for the subfamily Amphiliinae. 3) The five genera of subfamily Doumeinae constitute a monophyletic group, Andersonia being the sister-group of the four other genera; subfamily Doumeinae + Leptoglanis form the family Doumeidae. The glyptosternids no longer belong to the Sisoridae (family restricted to the non-glyptosternids) and represent the new family Glyptosternidae. (C) 1999 Editions scientifiques et medicales Elsevier SAS.

科尔沁沙地西部草甸植物繁殖对策

本文以科尔沁沙地西部草甸植物为研究对象，从草甸植物的繁殖体形态学、种子萌发特征、花期和果期、结种量和土壤种子库等方面分析了草甸植物的繁殖对策，探讨了草甸植物的繁殖对策与放牧、割草等干扰的关系。研究结果表明：（1）在科尔沁沙地西部草甸植被中，开花早，结果早的植物能够更好的适应自由放牧和秋季割草；（2）科尔沁沙地西部草甸割草草地极小粒种子的植物密度比大粒种子和小粒种子的植物密度小；在放牧草地小粒种子植物密度远远大于大粒种子和极小粒种子的植物密度；（3）在实验室条件下，64种草甸植物种子萌发能力的差异明显；小粒种子、长形或圆锥形种子、具芒和冠毛的繁殖体一般具有高的萌发能力；放牧草地一般由高萌发能力的一年生植物和低萌发能力的多年生植物组成；割草草地一般由低萌发能力的一年生植物和高萌发能力的多年生植物组成；（4）自由放牧草地土壤种子库密度小于秋季割草地，放牧草地种子库密度与地上植物出现频率和多度相关不显著，而割草地种子库物种与地上植物多度具有显著的相关性（r＝0.76，P＜0.01）；〔5）在科尔沁沙地西部草甸植被中，20种草甸植物具有持久种子库，其中豆科植物和一年生植物占据较大的比例。

Phycobilisomes linker family in cyanobacterial genomes: divergence and evolution

Cyanobacteria are the oldest life form making important contributions to global CO2 fixation on the Earth. Phycobilisomes (PBSs) are the major light harvesting systems of most cyanobacteria species. Recent availability of the whole genome database of cyanobacteria provides us a global and further view on the complex structural PBSs. A PBSs linker family is crucial in structure and function of major light-harvesting PBSs complexes. Linker polypeptides are considered to have the same ancestor with other phycobiliproteins (PBPs), and might have been diverged and evolved under particularly selective forces together. In this paper, a total of 192 putative linkers including 167 putative PBSs-associated linker genes and 25 Ferredoxin-NADP oxidoreductase (FNR) genes were detected through whole genome analysis of all 25 cyanobacterial genomes (20 finished and 5 in draft state). We compared the PBSs linker family of cyanobacteria in terms of gene structure, chromosome location, conservation domain, and polymorphic variants, and discussed the features and functions of the PBSs linker family. Most of PBSs-associated linkers in PBSs linker family are assembled into gene clusters with PBPs. A phylogenetic analysis based on protein data demonstrates a possibility of six classes of the linker family in cyanobacteria. Emergence, divergence, and disappearance of PBSs linkers among cyanobacterial species were due to speciation, gene duplication, gene transfer, or gene loss, and acclimation to various environmental selective pressures especially light.

Characterization and mapping of expressed sequence tags isolated from a subtracted cDNA library of Litopenaeus vannamei injected with white spot syndrome virus

A large number of polymorphic simple sequence repeats (SSRs) or microsatellites are needed to develop a genetic map for shrimp. However, developing an SSR map is very time-consuming, expensive, and most SSRs are not specifically linked to gene loci of immediate interest. We report here on our strategy to develop polymorphic markers using expressed sequence tags (ESTs) by designing primers flanking single or multiple SSRs with three or more repeats. A subtracted cDNA library was prepared using RNA from specific pathogen-free (SPF) Litopenaeus vannamei juveniles (similar to 1 g) collected before (0) and after (48 h) inoculation with the China isolate of white spot syndrome virus (WSSV). A total of 224 clones were sequenced, 194 of which were useful for homology comparisons against annotated genes in NCBI nonredundant (nr) and protein databases, providing 179 sequences encoded by nuclear DNA, 4 mitochondrial DNA, and 11 were similar to portions of WSSV genome. The nuclear sequences clustered in 43 groups, 11 of which were homologous to various ESTs of unknown function, 4 had no homology to any sequence, and 28 showed similarities to known genes of invertebrates and vertebrates, representatives of cellular metabolic processes such as calcium ion balance, cytoskeleton mRNAs, and protein synthesis. A few sequences were homologous to immune system-related (allergens) genes and two were similar to motifs of the sex-lethal gene of Drosophila. A large number of EST sequences were similar to domains of the EF-hand superfamily (Ca2+ binding motif and FRQ protein domain of myosin light chains). Single or multiple SSRs with three or more repeats were found in approximately 61 % of the 179 nuclear sequences. Primer sets were designed from 28 sequences representing 19 known or putative genes and tested for polymorphism (EST-SSR marker) in a small test panel containing 16 individuals. Ten (53%) of the 19 putative or unknown function genes were polymorphic, 4 monomorphic, and 3 either failed to satisfactorily amplify genomic DNA or the allele amplification conditions need to be further optimized. Five polymorphic ESTs were genotyped with the entire reference mapping family, two of them (actin, accession #CX535973 and shrimp allergen arginine kinase, accession #CX535999) did not amplify with all offspring of the IRMF panel suggesting presence of null alleles, and three of them amplified in most of the IRM F offspring and were used for linkage analysis. EF-hand motif of myosin light chain (accession #CX535935) was placed in ShrimpMap's linkage group 7, whereas ribosomal protein S5 (accession #CX535957) and troponin I (accession #CX535976) remained unassigned. Results indicate that (a) a large number of ESTs isolated from this cDNA library are similar to cytoskeleton mRNAs and may reflect a normal pathway of the cellular response after im infection with WSSV, and (b) primers flanking single or multiple SSRs with three or more repeats from shrimp ESTs could be an efficient approach to develop polymorphic markers useful for linkage mapping. Work is underway to map additional SSR-containing ESTs from this and other cDNA libraries as a plausible strategy to increase marker density in ShrimpMap.

高寒草甸矮嵩草种群繁殖对策的研究

This paper studied the reproductive strategies of Kobresia humilis in alpine meadow about its sexual reproduction ,vegetative reproduction and reproductive efforts respectively. The results show that the seed output of Kobresia humilis is 715. 5per unit (m2) . The germination is above 60 % in fit condition ,while only about 3 % in field. There is only 16. 13 % seed which get into seed bank and remain vitality till grass greening. So the seedling is only 3. 46 per unit (m2) in field.But the new ramets of Kobresia humilis are 711. 34 unit (m2 ) from vegetative reproduction. In addition ,vegetative reproductive effort is more than sexual reproductive effort . It constitutes 93. 5 % of all reproductive efforts. Therefore ,the main reproductive strategy of Kobresia humilis is vegetative reproduction ,and sexual reproduction is secondary in alpine condition.

Reproductive biology of great cormorant (Phalacrocorax carbo sinensis) in the qinghai-tibet plateau

There have been no detailed studies on reproductive biology of the Great Cormorant (Phalacrocorax carbo sinensis) in Qinghai-Tibet Plateau. We conducted such investigations during the breeding seasons of 1999 and 2000 in Qinghai-Lake Bird Isle, China. Great Cormorants began to migrate to Qinghai-Lake for reproduction from the middle of March and left from early October at the end of reproduction. Nesting periods were from early April to mid June and took 50 days. Egg-laying occurred during the three weeks from the end of April to 20 May. Females typically laid an egg every 1-2 days until clutch completion. Mean clutch size in the study area over two years was 3.3 (SE +/- 0.13, N = 68, range 1-5) and most (66.18%) fell within the range 3-4 eggs. Length of eggs averaged 61.01 mm and breadth averaged 34.13 mm. Fresh egg weight averaged 57.34 g (SE +/- 0.36, range 46.0-73.7 g, N = 179). Hatching success was 48.7% and fledging success was 64.9% over two years. Decline of available fish resources in Qinghai-Lake might be one of main causes of lower reproductive success. The causes of chick loss were possibly high altitude, high winds and prolonged rain.