Identification and characterization of insect-specific proteins by genome data analysis

Background: Insects constitute the vast majority of known species with their importance including biodiversity, agricultural, and human health concerns. It is likely that the successful adaptation of the Insecta clade depends on specific components in its

Identification of mesopelagic fish (with emphasis on major family) in Iranian water of the Oman Sea

This project was done for identifying the mesopelagic fish of the Iranian waters of Oman Sea, during two year from 2008 to 2010. The specimens were collected using two trawler vessel from nine station. All the specimens were fixed in formalin then in 70% alcohol and carried to the laboratory. In total of 19 species belonged to 14 families of 6 orders identified including: Echinorhinidae, Stomidae, Phosichthyidae, Synodontidae, Paralepididae, Myctophidae, Acropomatidae, Priacanthidae, Pentacerotidae, Champsodontidae, Gempylidae, Trichiuridae, Nomeidae and Congridae. Of which 17 species were identified up to species level including: Echinorhinus brucus, Bathophilus indicus, Chauliodus sloani, Harpadon nehereus, Lestrolepis japonica, Benthosema pterotum, Diaphus garmani, Diaphus effulgens, Bolinichthys photothorax, Acropoma japonicum, Synagrops adeni, Cookeolus boops, Histiopterus typus, Champsodon sagittus, Neoepinnula orientalis, Trichiurus lepturus, Cubiceps baxteri. Vinciguerria was identified up to genus level because only one specimen caught during the survey and one species (Congridae) was identified up to family level because only 3 specimens of this fish in early stage of life were caught and their characters were not suitable for identify up to species level. The highest species belong to Myctophidae family of Myctophiformes order.

Identification of biodiversity and distribution pattern of benthic Foraminifera and Ostracoda in continental shelf sediments of the Oman Sea

Biodiversity and distribution of benthic Foraminifera and Ostracoda in the continental shelf sediments of the Omman Sea was studied in order to indicating of the composition of benthic foraminiferal and ostracodal communities and determining of their relationship with the environmental factors of the Omman Sea. Sediment samples were gathered in winter 2006 from twelve stations ranging in depth from 30 to 103 meters. Environmental factors including depth, temperature, salinity, dissolved Oxygen and pH were measured with a CTD system during sampling time and grain size and total organic matter were measured in laboratory. From the overall 57 benthic foram species, there were 52 identified species belong to 25 genera of 16 families. The cosmopolitan foraminifer, Ammonia beccarii, was common in all sampling stations. The composition of benthic foram communities had a highly positive correlation with depth, salinity and total organic matter. From the overall 30 ostracod species, there were 26 identified species belong to 22 genera of 13 families. Diversity and aboundance of ostracoda of the Oman Sea decreased from east to west and from south to north but increased slightly in the northwest (near the Strait of Hormoz). Ostracoda of the genus Propontocypris were common in all sampling stations but the genera Cyprideis, Paradoxostom and Hemicytheridea were rare in the Oman Sea. Diversity and aboundance of ostracoda in northern regions were less than southern and were less than foraminifera too. The composition of ostracodal communities had a highly positive correlation with dept, salinity and grain size. Biodiversity and distribution pattern of benthic foraminifera and ostracoda were being different in various sampling stations, especially between northern and southern regions. Water depth, salinity and structure of the sediments were the most important abiotic factors controlling the distribution pattern of benthic foraminifera and ostracoda in the Omman Sea. None existence or rare observation of structural abnormalities and oil polluted individuals in the vicinity of all sampling stations, resulted to the "clean" benthic environment of the Omman Sea.

Molecular identification of symbiotic dinoflagellates (Zooxanthellae) of dominant reef-building corals off Kish Island

Scleractinian coral species harbour communities of photosynthetic taxa of the genus Symbiodinium. As many as eight genetic clades (A, B, C, D, E, F, G and H) of Symbiodinium have been discovered using molecular biology. These clades may differ from each other in their physiology, and thus influence the ecological distribution and resilience of their host corals to environmental stresses. Corals of the Persian Gulf are normally subject to extreme environmental conditions including high salinity and seasonal variation in temperature. This study is the first to use molecular techniques to identify the Symbiodinium of the Iranian coral reefs to the level of phylogenetic clades. Samples of eight coral species were collected at two different depths from the eastern part of Kish Island in the northern Persian Gulf. Partial 28S nuclear ribosomal (nr) DNA of Symbiodinium (D1/D2 domains) were amplified by Polymerase Chain Reaction (PCR). PCR products were analyzed using Single Stranded Conformational Polymorphism (SSCP) and phylogenetic analyses of the LSU DNA sequences from a subset of the samples. The results showed that Symbiodinium populations were generally uniform among and within the populations of 8 coral species studied, and there are at least two clades of Symbiodinium from Kish Island. Clade D was detected from 8 of the coral species while clade C90 was found in 2 of species only (one species hosted two clades simultaneously). The dominance of clade D might be explained by high temperatures or the extreme temperature variation, typical of the Persian Gulf.

Chemical ecology fatty acids of mollusks dominant species in intertidal zone of Chabahar Bay

Chemical ecology is the science of study and analysis of natural chemical products in result of biochemical processes in organisms and their reactions to variations of ecological and environmental parameters. In marine chemical ecology the existence of natural products in aquatic organisms and their ecological roles in marine animals and their reactions to environmental parameters variations will be studied. Among them, fatty acids are the most various and abundant ones in natural products which had been extracted from many marine organisms such as mollusks and algae. In this study selected animals were the dominant species of mollusks in intertidal zone of chabahar bay including gastropods, bivalves and polyplacophora classes. Nerita textilis and Turbo coronatus species are among gastropoda, Saccostrea cucullata is from bivalve, and Chiton lamyi is from polyplacophora. After seasonal sampling, separation and identification of natural products of these species, fatty acids had been isolated and identified by GC mass chromatography and their seasonal variations had been identified. In addition environmental factors of the location including pH, salinity temperature, dissolved oxygen, chlorophyll a and nutrients were measured monthly. Then the effect of seasonal variations of environmental factors on fatty acids had been studied by applying statistical analysis. GC/MS resulted thirteen fatty acids, which the most importants were myristic, stearic, oleic, palmitoleic, arachidonic and eicosapentaenoic acids. In majority of species palmitic acid was most abundant than the others and saturatedes had the most percentage levels than unsaturated ones. Although seasonal variations of identified fatty acids was not similar in species, but the majority of unsaturated ones had their maximum during winter, while saturated acids reached their maximum in summer. Statistical Analysis showed the strong correlations between Environmental factors and some fatty acids and temperature, nitrate, silicate and pH had strong correlations in all species. The species was studied from the point of lipid content and the results showed a good quality of lipid content in the selected species in the intertidal zone of Chabahar bay.

Quantative and qualitive identification of the fatty acids in the mullet (Liza aurata), sever juga (Acipenser stellatus) and Persian sturgeon (A. persicus), considering of cold storing effects on them

At the fishing season, in 2000, samples of species persian sturgeon (A. persicus), Severjuga (A. stellatus) and Mullet (L. aurata), were caught from the southern coasts of Caspian Sea and were freezes and preserved in the cold storage for one year They have also become biometery. The tissue's fillet were identified in order to determined the Fatty Acids. This was done during one year, frequently, fresh, two weeks after freezing and then monthly, respectively. So, after the extraction of lipids from the tissues and methylation, was injected to the gas-liquid Chromatography. After calibration, identified Fatty Acids were compared with standards according to their Retention Times. Peroxid value, lipid content and humidity were controlled. The unsaturated Fatty acids had The most amount, and a plenty of Polyunsaturated Fatty acids (PUFA) were observed, so that linoleic (C18:2), a-linolenic (C18:3), Arashidonic (C20:4), EPA (C20:5) and DHA (C22:6) Fatty acids had high amounts. The w-3, PUFA were more in comparison with w-6. The effects of freezing and cold storing on the fish fatty acids , were evaluated by the statistical tests , like SPSS, Tukey, Homogenous and Anova, and showed that in some species, a group of Fatty acids, specially PUFA, had some variation. The peroxide value that indicates the lipid deterioration, increased during toring. So, the best term if preserving in the cold storage, were determined and their Nutrition value and Medical applications due to their consumption were investigated.

Identification of triosephosphate isomerase (TIM) genes from Microcystis (Cyanobacteria : Chroococcales) and theoretical analyses of the potential of cyanobacterial TIM as a target for designing specific inhibitors

The genes encoding triosephosphate isomerase (TIM) in three species of Microcystis (M. aeruginosa, M. viridis and M. wesenbergii) were investigated. Reverse transcriptase-polymerase chain reaction indicated that they were transcribed in the cells. Analyses showed that their DNA and deduced amino acid sequences were highly conserved between all the three species, only a single nonsynonymous substitution was seen at position 31, from an Asp in M. aeruginosa and M. viridis to Glu in M. wesenbergii. Sequence alignment of these with 12 other known cyanobacterial TIM sequences showed that all the cyanobacterial TIMs had a very high level of amino acid identity (over 50% between each two). Comparison of the cyanobacterial TIMs with other reported TIMs (from diverse lineages of the three Domains) showed that they possessed common active-site residues and sequence motifs. All cyanobacterial TIMs have two common cysteine residues (Cys127 and Cys176), and the Cys176 is almost cyanobacteria-specific with only one exception in Streptomyces coelicolor. Both secondary structure alignment and comparative modelling of Synechocystis sp. TIM showed that Cys176 was located at the hinge region of the flexible loop-6 and might therefore be critical to the movement of TIM's loop-6, which is important to the function of the enzyme. Thus, the cyanobacterial TIM-specific Cys176 may be a potential site for the discovery of suitable drugs against cyanobacteria, and such drugs may have utility in controlling water blooms due to cyanobacteria.

Study ectoparasite infestation of 10 common imported freshwater ornamental fish species

In the present study, ectoparasite infestation of common freshwater ornamental fish species imported into Iran including: Dwarf gourami (Colisa lalia), Angelfish (Pterophyllum scalare), Oscar (Astronatus ocellatus), Red eye Tetra ( Moenkhansia Sanctaefilomenae), Barb( Capoeta tetrazona), Arowana (Osteoglossum bicirrhosum), Goldfish(Carassius auratus), Red fin Shark (Lebeo elythrurus, Catfish (Hypostomus plecostomus) and Pangasius sutchi ( Pangasius hypophthalmus) from May until April was investigated.A total of 6 specimens sample of each fish species) randomly were obtained and taken alive to the lab. After observing gill and skin wet smear under the microscope , gill was dissected and examined carefully .Photo and films were taken from the isolated parasites and parasite identification was performed according to Yamaguti AP1), Bychowsky (■Y).From a total of examined fishes 1\ ► sample (YY.V.) were parasitized .Parasite groups that were observed consisting ciliated protozoan myxosporidian , monogenean Digenean metacercaria and crustacean .The only non-parasitized fish was Barb. Monogenea Trianchoratus sp. , Cleidodiscus sp. , Ancylodiscoides sp. , Thaparocleidus sp. , Centrocestus formosanus metacercaria and Myxobolus longisporus report for the first time in ornamental fish which imported from Southeast of Asia to Iran. According to the results, it seems that severe quarantine and sanitary rules are necessary.

Identification and distribution of cartilaginous fishes of the Persian Gulf (Bushehr Province waters)

Class Condrichthyes consist of two sub-classes: Holocehali and. Elasmobranchii, the second one are more divers and has more importance. Selachimorpha (sharkes) and Batidoidimorpha (rays and skates) are two super-order of Elasmobranchii, which they have crucial role in ecological balance in marine ecosystmes. Except few cases, most of sharks and rays (rays and skates) are not well identified, so a lot of works need to be done in this regards. The area of study is located between 49°, 35' and 52°, 33' E and between 27°, 21' and 30°, 02' N in depth of 7 to 78 in. Study were conducted diuring August 1998, September 1999. Samples were taken during 3 sea cruises from 70 bottom trawl net. All sharks and batoid fishes were identified based on biometric specifications (weight, total, length and sexuality for both group and extra biometric specifications, disc width, disc length, and tail length only for, batoid fishes). The 1140 specimens of batoid fishes identified belonged to 6 families, and 18 species. 3 new species were identified, they are Himantura sp.1 and Himantura sp.2 belonged to Dasyatidae family and Rhinobatos sp. belonged to Rhinobatidae Familiy. It needs more works and more adaquate ducuments for cl.earfing scientific names of these species. The 275 specimens of sharks identified belonged to 6 families and 10 species. Chiloscyllium sp. belonged to Hemiscylliidae, family as a new species was identified.

Discovery of a male-biased mutant family and identification of a male-specific SCAR marker in gynogenetic gibel carp Carassius auratus gibelio

Gibel carp ( Carassius auratus gibelio) is a uniquely gynogenetic species with a minor ratio of males in natural habitats, but its male origin and sex determination mechanisms have been unknown. In this study, a male-biased mutant family was discovered from the gynogenetic gibel carp, and a male-specific SCAR marker was identified from the mutant family. Normal spermatogenesis was observed in the male testes by immuno. fluorescence histochemistry. Nearly identical AFLP profiles were observed between males and females, but a male-specific 86 bp AFLP fragment was screened by sex-pool bulked segregant analysis and individual screening. Based on the male-specific AFLP fragment, a total of 579 bp sequences were cloned by genome walking. Subsequently, a male-specific SCAR marker was designed, and the male-specific DNA fragment was confirmed to be steadily transmitted to the next generation and consistently detected only in males. (C) 2009 National Natural Science Foundation of China and Chinese Academy of Sciences. Published by Elsevier Limited and Science in China Press. All rights reserved.

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 Prorocentrum minimum and Takayama pulchella by fluorescence in situ hybridization through epifluorescence microscopy and flow cytometry

Partial rDNA sequences of Prorocentrum minimum and Takayama pulchella were amplified, cloned and sequenced. and these sequence data were deposited in the GenBank. Eight oligonucleotide probes (DNA probes) were designed based on the sequence analysis. The probes were employed to detect and identify P. minimum and T. pulchella in unialgal and mixed algal samples with a fluorescence in situ hybridization method using flow cytometry. Epifluorescence micrographs showed that these specific probes labeled with fluorescein isothiocyanate entered the algal cells and bound to target sequences, and the fluorescence signal resulting from whole-cell hybridization varied from probe to probe. These DNA probes and the hybridization protocol we developed were specific and effective for P. minimum and T. pulchella, without any specific binding to other algal species. The hybridization efficiency of different probes specific to P. minimum was in the order: PM18S02 > PM28S02 > PM28S01 > PM18S01, and that of the probes specific to T. pulchella was TP18S02 > TP28S01 > TP28S02 > TP18S01. The different hybridization efficiency of the DNA probes could also be shown in the fluorescent signals between the labeled and unlabeled cells demonstrated using flow cytometry. The DNA probes PM18S02, PM28S02; TP18S02 and TP28S01, and the protocol, were also useful for the detection of algae in natural samples.

First description of a novel Weissella species as an opportunistic pathogen for rainbow trout Oncorhynchus mykiss (Walbaum) in China

Six strains of Gram-positive, catalase-negative, non-motile, irregular short rod-shaped Weissella bacteria, with width and length of 0.5-0.6 and 1.2-2.7 mu m were isolated from diseased rainbow trout Oncorhynchus mykiss (Walbaum) in winter of 2007 at a commercial fishery in Jingmen, Hubei province, China. The diseased rainbow trout exhibited hemorrhage in eyes, anal region, intestine and abdomen wall, petechia of liver, some fish with hydrocele in stomach. Six isolates had identical biochemical reactions, phylogenetic analysis of 16S rDNA sequences, amplified ribosomal DNA restriction analysis (ARDRA), enzymatic profile analysis and antimicrobial susceptibility results, indicating as a single clonal outbreak. But all were different from any other validated twelve Weissella species in the term of physiological and biochemical characters. It is indicated that isolates are phylogenetically closer to Weissella halotolerans, Weissella viridescens and Weissella minor on 16S rDNA phylogenetic analysis result, than to W halotolerans and W viridescens on the result of ARDRA study and enzymatic profile analysis. Antimicrobial susceptibility testing was used to scan effective drugs for the therapy of this disease. Experimental infection assays with one isolate were conducted and pathogenicity (by intraperitoneal injection) was demonstrated in rainbow trout O. mykiss (Walbaum) and crucian carp (Carassius auratus gibelio) fingerlings. Because no Weissella was detected in fish feedstuffs and pond water, the source of this pathogen remains unknown, and Weissella isolates were regarded as an opportunistic pathogen for rainbow trout. This is the first report of Weissella strains which can cause disease of cultured fish in the world. (C) 2009 Elsevier B.V. All rights reserved.

Identification of an additional two-cysteine containing type I interferon in rainbow trout Oncorhynchus mykiss provides evidence of a major gene duplication event within this gene family in teleosts

Multiple type I interferons (IFNs) have recently been identified in salmonids, containing two or four conserved cysteines. In this work, a novel two-cysteine containing (2C) IFN gene was identified in rainbow trout. This novel trout IFN gene (termed IFN5) formed a phylogenetic group that is distinct from the other three salmonid IFN groups sequenced to date and had a close evolutionary relationship with IFNs from advanced fish species. Our data demonstrate that two subgroups are apparent within each of the 2C and 4C type I IFNs, an evolutionary outcome possibly due to two rounds of genome duplication events that have occurred within teleosts. We have examined gene expression of the trout 2C type I IFN in cultured cells following stimulation with lipopolysaccharide, phytohaemagglutinin, polyI:C or recombinant IFN, or after transfection with polyI:C. The kinetics of gene expression was also studied after viral infection. Analysis of the regulatory elements in the IFN promoter region predicted several binding sites for key transcription factors that potentially play an important role in mediating IFN5 gene expression.

Identification and characterization of hypoxia-induced genes in Carassius auratus blastulae embryonic cells using suppression subtractive hybridization

Organisms living in water are inevitably exposed to periods of hypoxia. Environmental hypoxia has been an important stressor having manifold effects on aquatic life. Many fish species have evolved behavioral, physiological, biochemical and molecular adaptations that enable them to cope with hypoxia. However, the molecular mechanisms of hypoxia tolerance in fish, remain unknown. in this study, we used suppression subtractive hybridization to examine the differential gene expression in CAB cells (Carassius auratus blastulae embryonic cells) exposed to hypoxia for 24 h. We isolated 2100 clones and identified 211 differentially expressed genes (e-value <= 5e-3; Identity > 45%). Among the genes whose expression is modified in cells, a vast majority involved in metabolism, signal transduction, cell defense, angiogenesis, cell growth and proliferation. Twelve genes encoding for ERO1-L, p53, CPO, HO-1, MKP2, PFK-2, cystatin B, GLUT1, BTG1, TGF beta 1, PGAM1, hypothetical protein F1508, were selected and identified to be hypoxia-induced using semi-quantitive RT-PCR and real-time PCR. Among the identified genes, two open reading frames (ORFs) encoding for CaBTG1 and Cacystatin B were obtained. The deduced amino acid sequence of CaBTG1 had 94.1%, 72.8%, 72.8%, 72.8%, 68.6% identity with that of DrBTG1, HsBTG1, BtBTG1, MmBTG1 and XIBTG1. Comparison of Cacystatin B with known cystatin B, the molecules exhibited 49.5 to 76.0% identity overall. These results may provide significant information for further understanding of the adaptive mechanism by which C. auratus responds to hypoxia. (c) 2008 Elsevier Inc. All rights reserved.