characterization and homology modeling of Nile tilapia () Hsp70cBi and Hsp70cBc proteins.

The molecular chaperone heat shock proteins 70 (Hsp70) play a pivotal role in preserving cellular integrity and managing stress. This study extensively examined two Hsp70 proteins, -Hsp70cBi, inducible, and -Hsp70cBc, constitutively expressed, in Nile tilapia () utilizing in silico analysis, homology modeling, and functional annotation. Employing the SWISS-MODEL program for homology modeling, the proposed models underwent thorough reliability assessment via ProSA, Verify 3D, PROVE, ERRAT, and Ramachandran plot analyses.

Identifying priority sites for whale shark ship collision management globally.

The expansion of the world's merchant fleet poses a great threat to the ocean's biodiversity. Collisions between ships and marine megafauna can have population-level consequences for vulnerable species. The Endangered whale shark (Rhincodon typus) shares a circumglobal distribution with this expanding fleet and tracking of movement pathways has shown that large vessel collisions pose a major threat to the species.

New species of redbait from the Philippines (Teleostei, Emmelichthyidae, ).

We describe a new species of redbait in the genus collected from fish markets on Panay and Cebu islands in the Visayas region of the Philippines. The species is externally similar to but is diagnosable by two prominent fleshy papillae associated with the cleithrum and fewer pectoral-fin rays (18-19 vs. 19-21) and gill rakers (30-33 vs.

The Complete Genome Sequences of 5 Species of Sardinella (Clupeidae, Clupeiformes).

We present the complete genome sequences of 5 species of . Illumina sequencing was performed on genetic material from wild-caught specimens. The reads were assembled using a method followed by a finishing step.

The Complete Genome Sequence of (Portunidae, Decapoda), the Blue Swimming Crab.

is a large crab found in the Indo-Pacific. We present the whole genome sequence of this species. Illumina paired-end reads were assembled by a de novo method followed by a finishing step.

Biodiversity of Philippine marine fishes: A DNA barcode reference library based on voucher specimens.

Accurate identification of fishes is essential for understanding their biology and to ensure food safety for consumers. DNA barcoding is an important tool because it can verify identifications of both whole and processed fishes that have had key morphological characters removed (e.g.

Testing the Utility of Alternative Metrics of Branch Support to Address the Ancient Evolutionary Radiation of Tunas, Stromateoids, and Allies (Teleostei: Pelagiaria).

The use of high-throughput sequencing technologies to produce genome-scale data sets was expected to settle some long-standing controversies across the Tree of Life, particularly in areas where short branches occur at deep timescales. Instead, these data sets have often yielded many well-supported but conflicting topologies, and highly variable gene-tree distributions. A variety of branch-support metrics beyond the nonparametric bootstrap are now available to assess how robust a phylogenetic hypothesis may be, as well as new methods to quantify gene-tree discordance.

DNA barcoding cannot discriminate between and (Clupeiformes: Clupeidae).

, the only known freshwater sardinella in the world, is endemic to Taal Lake, Philippines. Previous studies found the Taiwan sardinella, , to be morphologically very similar to and identified it as the marine sister species of . In this study, DNA barcoding using the mitochondrial cytochrome oxidase I (COI) gene was carried out to analyze species demarcation in the genus, focusing primarily on the relationship between and .

Molecular cloning and expression of chitin deacetylase 1 gene from the gills of Penaeus monodon (black tiger shrimp).

Chitin deacetylases have been identified and studied in several fungi and insects but not in crustaceans. These glycoproteins function in catalyzing the conversion of chitin to chitosan by the hydrolysis of N-acetamido bonds of chitin. Here, for the first time, the full length cDNA of chitin deacetylase (CDA) gene from crustaceans was fully cloned using a partial fragment obtained from a transcriptome database of the gills of black tiger shrimp Penaeus monodon that survived White Spot Syndrome Virus (WSSV) infection employing Rapid Amplification of cDNA Ends (RACE) PCR.

Maternal mismatches in farmed tilapia strains (Oreochromis spp.) in the Philippines as revealed by mitochondrial COI gene.

The introduction of genetically enhanced tilapia has significantly boosted the performance of Philippine aquaculture industry. While enhanced strains contribute to the increase in tilapia production, genetic characterization of present tilapia stocks is critical to maintain their quality and to ensure the genetic gains are sustained. To understand and determine the genetic relationship of the genetically enhanced strains produced in the Philippines, mitochondrial cytochrome oxidase subunit I (COI) gene using DNA barcoding approach was analyzed.

Distinct Yellowfin Tuna (Thunnus albacares) Stocks Detected in Western and Central Pacific Ocean (WCPO) Using DNA Microsatellites.

The yellowfin tuna, Thunnus albacares (Bonnaterre, 1788), covers majority of the Philippines' tuna catch, one of the major fisheries commodities in the country. Due to its high economic importance sustainable management of these tunas has become an imperative measure to prevent stock depletion. Currently, the Philippine yellowfin tuna is believed to be part of a single stock of the greater WCPO though some reports suggest otherwise.

Species composition of by-catch from milkfish (Chanos chanos) fry fishery in selected sites in the Philippines as determined by DNA barcodes.

Milkfish fry fishery, an important industry in the Philippines, uses non-selective fishing gears and push nets in coastal areas which lead to the capture of other non-targeted juvenile aquatic species. Unfortunately, information on the amount and the identity of by-catch species is lacking thus the extent of impact of the fry fishery is not known. In this study, the species composition of milkfish fry fishery by-catch sampled from selected coastal areas that are known to be fry collection sites in the country were identified and assessed through the use of DNA barcoding.

Illegal trade of regulated and protected aquatic species in the Philippines detected by DNA barcoding.

Illegal trade has greatly affected marine fish stocks, decreasing fish populations worldwide. Despite having a number of aquatic species being regulated, illegal trade still persists through the transport of dried or processed products and juvenile species trafficking. In this regard, accurate species identification of illegally traded marine fish stocks by DNA barcoding is deemed to be a more efficient method in regulating and monitoring trade than by morphological means which is very difficult due to the absence of key morphological characters in juveniles and processed products.

Hidden diversity in sardines: genetic and morphological evidence for cryptic species in the goldstripe sardinella, Sardinella gibbosa (Bleeker, 1849).

Cryptic species continue to be uncovered in many fish taxa, posing challenges for fisheries conservation and management. In Sardinella gibbosa, previous investigations revealed subtle intra-species variations, resulting in numerous synonyms and a controversial taxonomy for this sardine. Here, we tested for cryptic diversity within S.

Anisakis species (Nematoda: Anisakidae) of Dwarf Sperm Whale Kogia sima (Owen, 1866) stranded off the Pacific coast of southern Philippine archipelago.

Anisakid nematodes in the Pacific region of the Philippine archipelago still remain unexplored. This study was carried out to identify anisakid species from one of their final hosts, the Kogiid whale (Dwarf Sperm Whale, Kogia sima) stranded off the southern part (Davao Gulf) of the Philippine archipelago. Anisakid worms were initially identified morphologically using light and scanning electron microscopy, whereas identification to species level was carried out molecularly using PCR-RFLP and sequencing of the ITS (ITS1-5.

Discrimination of juvenile yellowfin (Thunnus albacares) and bigeye (T. obesus) Tunas using mitochondrial DNA control region and liver morphology.

Yellowfin tuna, Thunnus albacares (Bonnaterre, 1788) and bigeye tuna, Thunnus obesus (Lowe, 1839) are two of the most economically important tuna species in the world. However, identification of their juveniles, especially at sizes less than 40 cm, is very difficult, often leading to misidentification and miscalculation of their catch estimates. Here, we applied the mitochondrial DNA control region D-loop, a recently validated genetic marker used for identifying tuna species (Genus Thunnus), to discriminate juvenile tunas caught by purse seine and ringnet sets around fish aggregating devices (FADs) off the Southern Iloilo Peninsula in Central Philippines.

RNA aptamers inhibit the growth of the fish pathogen viral hemorrhagic septicemia virus (VHSV).

Viral hemorrhagic septicemia virus (VHSV) is a serious disease impacting wild and cultured fish worldwide. Hence, an effective therapeutic method against VHSV infection needs to be developed. Aptamer technology is a new and promising method for diagnostics and therapeutics.

Molecular characterization, expression and functional analysis of a nuclear oligomerization domain proteins subfamily C (NLRC) in Japanese flounder (Paralichthys olivaceus).

Pattern recognition receptors (PRRs) are involved in the effective innate defense against several microbes. Here, we identified a nucleotide-oligomerization domain (NOD)-like receptor subfamily C (NLRC) from Japanese flounder (Paralichthys olivaceus). Full-length transcript of JfNLRC is composed of 3976 bp encoding a protein of 1175 deduced amino acid residues.

Microarray analyses of shrimp immune responses.

Shrimp aquaculture is one of the major foodproducing industries in the world. However, it is being impacted by several problems including diseases, antibiotic use, and environmental factors. The extent of the effects of these problems in the immune system of the shrimp at the molecular level is just beginning to be understood.

Hyper-expansion of large DNA segments in the genome of kuruma shrimp, Marsupenaeus japonicus.

Background: Higher crustaceans (class Malacostraca) represent the most species-rich and morphologically diverse group of non-insect arthropods and many of its members are commercially important. Although the crustacean DNA sequence information is growing exponentially, little is known about the genome organization of Malacostraca. Here, we constructed a bacterial artificial chromosome (BAC) library and performed BAC-end sequencing to provide genomic information for kuruma shrimp (Marsupenaeus japonicus), one of the most widely cultured species among crustaceans, and found the presence of a redundant sequence in the BAC library.

Differential gene expression in black tiger shrimp, Penaeus monodon, following administration of oxytetracycline and oxolinic acid.

The intensification of shrimp farming systems has led to the spreading of a variety of bacterial and viral diseases that continue to plague the shrimp industry worldwide. Efforts to combat these pathogenic organisms include the use of immunostimulants, probiotics, vaccines and antibiotics. Although a few studies have already reported on the effects of various stimuli on shrimp, the effect of antibiotics, particularly on the changes in the shrimp transcriptomic profile have yet to be reported.

Characterization of polyclonal antibodies against Japanese flounder IgM derived from recombinant IgM constant region proteins.

Cell and determinant markers are important in fish immunology and have vast applications in aquaculture but the availability of such markers are quite limited. Hence, there is a need to identify and also further improve existing markers in fish. Here, we developed effective polyclonal antibodies (pAbs) targeting specific parts of the Japanese flounder (Paralichthys olivaceus) IgM constant (C) region.