DIVERSITY AND HABITAT PROFILE OF THE SHALLOW WATER HOLOTHURIANS IN CAMOTES ISLANDS, CENTRAL PHILIPPINES

Species diversity and habitat profile of holothurians in Camotes Islands, Cebu Philippines were studied as baseline data for resource and ecological management. A 150 meter transect was laid in sandy, muddy and rocky substrates of the coastal barangays during the day and night assessments of the four municipalities of Camotes Islands which are San Francisco, Poro, Tudela and Pilar. Physico-chemical instruments and interview guide to the gleaners were used to gather data. Actual collection of specimen and other data was done in every 10 meter distance in the transect where a 1m quadrat was used. Results show that there are 20 species of holothurians belonging to 3 families namely Holothuriidae, Stichopodidae and Synaptidae. There are 2 species found in sandy substrate; 10 in muddy substrate; 2 in pure rocky substrate and 6 found in both rocky and muddy substrates. Results further show that there are 13 common species of Holothurians found in the four municipalities. The most diverse municipality is San Francisco which has 18 species followed by Poro (15); Pilar (14) and Tudela (13). For the distinct species, Holothuria rigida is found only in San Francisco followed by Pearsonothuria graffei (in Tudela and Pilar); Physico-chemical parameters like salinity, range from 23-38 ppt; temperature is 260C-350C, pH 4.5-8.0 both day and night assessments. Substrate grain size analysis shows that 100 microns dominate the amount of substrates in all the barangays, followed by 200 microns and then 400 microns. Keywords: Diversity, Habitat Profile, Holothurians, Camotes Island

Isolation and Characterization of Novel Microsatellite Markers for Yellow Perch (Perca flavescens)

To perform whole genome scanning for complex trait analysis, we isolated and characterized a total of 21 novel genomic-SSRs and EST-SSRs for yellow perch (Perca flavescens), using the methods of construction of SSR-enrichment libraries and EST database mining of a related species P. fluviatilis. Of 16 genomic-SSR primer pairs examined, eight successfully amplified scorable products. The number of alleles at these informative loci varied from 3 – 14 with an average of 8.5 alleles per locus. When tested on wild perch from a population in Pennsylvania, observed and expected heterozygosities ranged from 0.07 – 0.81 and from 0.37 – 0.95, respectively. Of 2,226 EST sequences examined, only 110 (4.93%) contained microsatellites and for those, 13 markers were tested, 12 of which exhibited polymorphism. Compared with genomic-SSRs, EST-SSRs exhibited a lower level of genetic variability with the number of alleles of averaging only 2.6 alleles per locus. Cross-species utility indicated that three of the genomic-SSRs and eight of the EST-SSRs successfully cross-amplified in a related species, the walleye (Sander vitreus)

The catfish genome database cBARBEL: an informatic platform for genome biology of ictalurid catfish

The catfish genome database, cBARBEL (abbreviated from catfish Breeder And Researcher Bioinformatics Entry Location) is an online open-access database for genome biology of ictalurid catfish (Ictalurus spp.). It serves as a comprehensive, integrative platform for all aspects of catfish genetics, genomics and related data resources. cBARBEL provides BLAST-based, fuzzy and specific search functions, visualization of catfish linkage, physical and integrated maps, a catfish EST contig viewer with SNP information overlay, and GBrowse-based organization of catfish genomic data based on sequence similarity with zebrafish chromosomes. Subsections of the database are tightly related, allowing a user with a sequence or search string of interest to navigate seamlessly from one area to another. As catfish genome sequencing proceeds and ongoing quantitative trait loci (QTL) projects bear fruit, cBARBEL will allow rapid data integration and dissemination within the catfish research community and to interested stakeholders. cBARBEL can be accessed at http://catfishgenome.org

Towards the Ictalurid Catfish Transcriptome: Generation and Analysis of 31,215 Catfish ESTs.

Background EST sequencing is one of the most efficient means for gene discovery and molecular marker development, and can be additionally utilized in both comparative genome analysis and evaluation of gene duplications. While much progress has been made in catfish genomics, large-scale EST resources have been lacking. The objectives of this project were to construct primary cDNA libraries, to conduct initial EST sequencing to generate catfish EST resources, and to obtain baseline information about highly expressed genes in various catfish organs to provide a guide for the production of normalized and subtracted cDNA libraries for large-scale transcriptome analysis in catfish. Results A total of 17 cDNA libraries were constructed including 12 from channel catfish (Ictalurus punctatus) and 5 from blue catfish (I. furcatus). A total of 31,215 ESTs, with average length of 778 bp, were generated including 20,451 from the channel catfish and 10,764 from blue catfish. Cluster analysis indicated that 73% of channel catfish and 67% of blue catfish ESTs were unique within the project. Over 53% and 50% of the channel catfish and blue catfish ESTs, respectively, had significant similarities to known genes. All ESTs have been deposited in GenBank. Evaluation of the catfish EST resources demonstrated their potential for molecular marker development, comparative genome analysis, and evaluation of ancient and recent gene duplications. Subtraction of abundantly expressed genes in a variety of catfish tissues, identified here, will allow the production of low-redundancy libraries for in-depth sequencing. Conclusion The sequencing of 31,215 ESTs from channel catfish and blue catfish has significantly increased the EST resources in catfish. The EST resources should provide the potential for microarray development, polymorphic marker identification, mapping, and comparative genome analysis

Characterization of simple sequence repeats (SSRs) from Phlebotomus papatasi (Diptera: Psychodidae) expressed sequence tags (ESTs)

<p>Abstract</p> <p>Background</p> <p><it>Phlebotomus papatasi </it>is a natural vector of <it>Leishmania major</it>, which causes cutaneous leishmaniasis in many countries. Simple sequence repeats (SSRs), or microsatellites, are common in eukaryotic genomes and are short, repeated nucleotide sequence elements arrayed in tandem and flanked by non-repetitive regions. The enrichment methods used previously for finding new microsatellite loci in sand flies remain laborious and time consuming; <it>in silico </it>mining, which includes retrieval and screening of microsatellites from large amounts of sequence data from sequence data bases using microsatellite search tools can yield many new candidate markers.</p> <p>Results</p> <p>Simple sequence repeats (SSRs) were characterized in <it>P. papatasi </it>expressed sequence tags (ESTs) derived from a public database, National Center for Biotechnology Information (NCBI). A total of 42,784 sequences were mined, and 1,499 SSRs were identified with a frequency of 3.5% and an average density of 15.55 kb per SSR. Dinucleotide motifs were the most common SSRs, accounting for 67% followed by tri-, tetra-, and penta-nucleotide repeats, accounting for 31.1%, 1.5%, and 0.1%, respectively. The length of microsatellites varied from 5 to 16 repeats. Dinucleotide types; AG and CT have the highest frequency. Dinucleotide SSR-ESTs are relatively biased toward an excess of (AX)n repeats and a low GC base content. Forty primer pairs were designed based on motif lengths for further experimental validation.</p> <p>Conclusion</p> <p>The first large-scale survey of SSRs derived from <it>P. papatasi </it>is presented; dinucleotide SSRs identified are more frequent than other types. EST data mining is an effective strategy to identify functional microsatellites in <it>P. papatasi</it>.</p

The Role of Inservice Teacher Training (INSET) on Improving Teaching And Learning Process in Public Secondary Schools in Tanzania: A Case of Bukoba Municipal Council in Kagera Region

The study aimed at assessing the role of In-service Teacher Training (INSET) in teachers’ performance in public secondary schools in Bukoba Municipality. Specifically the study sought to: examine the strategies used to conduct INSET; asses the contribution of INSET on teachers’ performance; assess the challenges facing INSET and find out the best practices in human resource training. The study used case study design by applying qualitative approach. Participants involved were 20 secondary school teachers, 4 heads of schools and 1 Education Officer who were purposively and simple randomly selected based on the required characterristics. Data were collected by using semi structured interview and documentary review guides. Based on the study, it was revealed that INSET is promising aspect in teacher education particularly improving the teaching and learning process among teachers who in turn improve students’ performance. The study revealed that INSET in BMC was constrained by serious shortage of teaching and learning materials, lack of programmes inclusiveness, limited time allocation compared to content, limited financial resources, poor record keeping and lack of commitment to some seminar participants. Further, the study revealed existence of lack of fair rotation of seminar attendees as the same person could always attend while limiting access to many participants. Further studies should be conducted to assess on how best should INSET be organized and managed

Fish culture in cages in Lake Danao, Cebu

Lake Danao is a picturesque inland body of water having an area of 685 ha located in the municipality of San Francisco in Pacijan Island, Camotes, Cebu. At the middle of the lake is a circular islet with an area of one acre. This lake is a potential area for cultivation of fishes in pens and cages. To date there are only two agencies which use the lake for fish production, namely; the Department of Agriculture Regional Office No 7 Carmen-Lake Danao Fishery Complex Research Outreach Station and the CSCST-Fishery and Industrial College, San Francisco, Cebu. The following are the ranges of selected water quality parameters: salinity, 0-0.5 ppt; water temperature, 27-29 °C; pH, 8.5-9. The lake has no definite inlet and outlet of water and is free from pollutants. The water is clear with assorted vegetation. The soil is coarse, silty and sandy. The present study has shown the feasibility of growing tilapia in cages in Lake Danao