Updating the East Asian mtDNA phylogeny: a prerequisite for the identification of pathogenic mutations

Knowledge about the world phylogeny of human mitochondrial DNA (mtDNA) is essential not only for evaluating the pathogenic role of specific mtDNA mutations but also for performing reliable association studies between mtDNA haplogroups and complex disorder

Identification and culture of common diatoms as possible feed for Penaeus monodon

Diatoms were collected from Buyuan Bay, and from the hatchery tanks at Tigbauan, to determine the commonly occurring species, the feasibility of culturing these species, and the potential of these selected species as food for larval P. monodon. The commonly occurring diatoms were identified as Chaetoceros calcitrans, Navicula grimmei, Nitzchia seriata, Nitzchia closterium and Amphiprora sp. These diatoms were isolated and unialgal cultures prepared. Protein content analysis using the micro-Kjildahl method gave the following result: C. calcitrans, 11 . 78%; Nitzchia seriata, 25%; Nitzchia closterium, 30 . 5%; Navicula grimmei, 9 . 06% and Amphiprora sp. 8 . 96%. Feeding experiments were conducted to determine acceptability of the different diatom species and percentage survival of larval stages Z SUB-1 -M SUB-2 . Larvae were placed in 4-l capacity plastic containers with a stocking density of 10/l. The results of several feeding trials using the different mass-produced diatoms are summarized. From the data gathered, C. calcitrans appears to be the most promising candidate as feed for zoea and mysis stages of P. monodon. The average percentage survival of C. calcitrans was 63 . 76% for the 3 trials, and as high as 82 . 22% in the third trial. Comparatively high percentage survival of larvae was also recorded when Nitzchia seriata (48 . 17%) and Nitzchia closterium (67 . 6%) were given as feed, while both Amphiprora sp. and Navicula grimmei gave 0% survival. The poor results with Amphiprora sp. and Navicula grimmei may be due to their low protein content (8 . 96% and 9 . 06%, respectively) and the inability of the larvae to ingest them. Navicula and Amphiprora were observed to cling to the appendages of the larvae and to settle down in the medium making them unavailable to the larvae. Low survival was also noted when frozen C. calcitrans was used (14 . 25%). This may be due partly to the effect of the floculating agent (ALSO SUB-4 . 25 g/l) used in concentrating the diatoms. When protein contents of C. calcitrans, N. seriata and N. closterium are compared, the 2 Nitzchia species have relatively higher protein contents than C. calcitrans and, therefore, could be the more desirable feed candidates. However, few feeding trials were made using Nitzchia so that additional investigations will have to be done on this aspect.

Identification of protein superfamily from structure-based sequence motif

The structure-based sequence motif of the distant proteins in evolution, protein tyrosine phosphatases (PTP) I and II superfamilies, as an example, has been defined by the structural comparison, structure-based sequence alignment and analyses on substitut

Identification and molecular evolution of cow CENP-A gene family

The centromere protein A (CENP-A), a histone H3-like protein, provides an essential role for chromosomal segregation during mitosis and meiosis. In this study we identified ten new CENP-A-like genes (excluding the original CENP-A gene) in cow by searching

Identification of the postlarval Penaeus (Crustacea, Decapoda, Penaeidae) appearing along shore waters

Diagnostic characters for the identification of postlarval Penaeus appearing along the coastal waters of the Philippines are reviewed and categorized, based on materials from the wild and laboratory. Presently there are 7 adult known species belonging to the genus Penaeus around Panay Island and its adjacent waters, namely: P. monodon, P. semisulcatus, P. merguiensis, P. indicus, P. japonicus , P. canaliculatus, and P. latisulcatus.

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 major histocompatibility complex class I alleles in Chinese rhesus macaques

Major histocompatibility complex (MHC) class I information is vital for understanding variance of immune responses in HIV vaccination and biomedical models. In this study, 9 Mamu-A and 13 Mamu-B alleles were identified from the cDNA products of 10 Chinese

Species identification of family Lutjanidae and separation of populations of John’s snapper (Lutjanus johnii) in Persian Gulf and Oman Sea based on otolith shape analysis

The anatomical and morphometric (shape indices, contour descriptors and otolith weight) characterizations of sagittal otoliths were investigated in 13 species of Lutjanus spp. inhabiting the Persian Gulf. This is the first study that compares the efficiency of three different image analysis techniques for discriminating species based on the shape of the outer otolith contour, including elliptical Fourier descriptors (EFD), fast Fourier transform (FFT) and wavelet transform (WT). Sagittal otoliths of snappers are morphologically similar with some small specific variations. The use of otolith contour based on wavelets (WT) provided the best results in comparison with the two other methods based on Fourier descriptors, but only the combination of the all three methods (EFD, FFT and WT) was useful to obtain a robust classification of species. The species prediction improved when otolith weight was included. In relation to the shape indices, only the aspect ratio provided a clear grouping of species. Also, another study was carried on to test the possibility of application of shape analysis and comparing otolith contour of otoliths of Lutjanus johnii from Persian Gulf and Oman Sea to identify potential stocks. The results showed the otoliths have differences in contour shape and can be contribute to two different stocks.

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.

Species identification and authentication of some of the most important seafood products in Iranian markets using biotechnological methods based on DNA

This study describes the molecular identification of sixteen fish species present in processed products imported into Iran for human consumption. DNA barcoding using direct sequencing of about 650 bp of the mitochondrial Cytochrome Oxidase subunit I gene revealed incorrect labeling (31.25%). Substitution of fish species constitutes serious economic fraud, and our results increase concern regarding the trading of processed fish products in Iran from both health and conservation points of view.

Identification and determination of muscle's fatty acids and amino acids in Cobia and Indian squid

The present study aims to find the effect of freezing Time on the quality of Cobia (Rastrelliger kanagurta) and Indian Squid in commercial scale during freezing and subsequent frozen storage (−18◦C). Total time for freezing was significantly different (P<0.05) between the Cobia and Indian squid samples. The difference in the freezing time could be attributed to the varied quality of the 2 samples. Upon freezing, the moisture content decreased in Indian Squide samples compared to Cobia freezer where protein content decreased in both the samples. Upon freezing and during frozen storage, lipid oxidation products (peroxide value, and free fatty acid value) and volatile bases (total volatile base nitrogen) showed an increasing trend in both the samples with values slightly higher in Indian squid samples compared to cobia frozen samples. The total plate counts showed a significantly (P<0.05) decreasing trend in both the samples. K value did not show any significant (P<0.05) difference between the samples whereas the histamine formation was significantly (P<0.05) increased in Indian squid frozen samples compared to cobia samples. The taste and overall acceptability was significantly different (P<0.05) in cobia samples compared to Indian squid frozen samples on 5th month. Both samples were in acceptable condition up to 5 month but the Cobia frozen samples quality was slightly better than the air blast frozen samples.

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.