IBM PC Data Acquisition and Processing Software Evaluation

Commercially available software packages for IBM PC-compatibles are evaluated to use for data acquisition and processing work. Moss Landing Marine Laboratories (MLML) acquired computers since 1978 to use on shipboard data acquisition (Le. CTD, radiometric, etc.) and data processing. First Hewlett-Packard desktops were used then a transition to the DEC VAXstations, with software developed mostly by the author and others at MLML (Broenkow and Reaves, 1993; Feinholz and Broenkow, 1993; Broenkow et al, 1993). IBM PC were at first very slow and limited in available software, so they were not used in the early days. Improved technology such as higher speed microprocessors and a wide range of commercially available software made use of PC more reasonable today. MLML is making a transition towards using the PC for data acquisition and processing. Advantages are portability and available outside support.

Dividing population genetic distance data with the software Partitioning Optimization with Restricted Growth Strings (PORGS): an application for Chinook salmon (Oncorhynchus tshawytscha), Vancouver Island, British Columbia

A new method of finding the optimal group membership and number of groupings to partition population genetic distance data is presented. The software program Partitioning Optimization with Restricted Growth Strings (PORGS), visits all possible set partitions and deems acceptable partitions to be those that reduce mean intracluster distance. The optimal number of groups is determined with the gap statistic which compares PORGS results with a reference distribution. The PORGS method was validated by a simulated data set with a known distribution. For efficiency, where values of n were larger, restricted growth strings (RGS) were used to bipartition populations during a nested search (bi-PORGS). Bi-PORGS was applied to a set of genetic data from 18 Chinook salmon (Oncorhynchus tshawytscha) populations from the west coast of Vancouver Island. The optimal grouping of these populations corresponded to four geographic locations: 1) Quatsino Sound, 2) Nootka Sound, 3) Clayoquot +Barkley sounds, and 4) southwest Vancouver Island. However, assignment of populations to groups did not strictly reflect the geographical divisions; fish of Barkley Sound origin that had strayed into the Gold River and close genetic similarity between transferred and donor populations meant groupings crossed geographic boundaries. Overall, stock structure determined by this partitioning method was similar to that determined by the unweighted pair-group method with arithmetic averages (UPGMA), an agglomerative clustering algorithm.

The ECOPATH II software

Problems involved in the development of ecosystem models are discussed, considering in particular the use of the ECOPATH II software and the approach used at ICLARM in the project Global comparisons of trophic aquatic ecosystem models designed to support modelling efforts of research groups throughout the world.

ICLARM software projects: back to the future

The different computer softwares developed by the International Center for Living Aquatic Resources (ICLARM) and its functions and uses in fisheries science are presented.

A computer software package for assessing and managing risks posed by experiments with genetically modified fish and shellfish

Assessment and management of risk is needed for sustainable use of genetically modified aquatic organisms (aquatic GMOs). A computer software package for safely conducting research with genetically modified fish and shellfish is described. By answering a series of questions about the organism and the accessible aquatic ecosystem, a researcher or oversight authority can either identify specific risks or conclude that there is a specific reason for safety of the experiment. Risk assessment protocols with examples involving transgenic coho salmon, triploid grass carp and hybrid tilapia are described. In case a specific risk is identified, the user is led to consider risk management measures, involving culture methods, facilities design and operations management, to minimize the risk. Key features of the software are its user-friendly organization; easy access to explanatory text, literature citations and glossary; and automated completion of a worksheet. Documented completion of the Performance Standards can facilitate approval of a well designed experiment by oversight authorities.

Isolation, purification, and full NMR assignments of cyclopamine from Veratrum californicum

The Hedgehog signaling pathway is essential for embryogenesis and for tissue homeostasis in the adult. However, it may induce malignancies in a number of tissues when constitutively activated, and it may also have a role in other forms of normal and maladaptive growth. Cyclopamine, a naturally occurring steroidal alkaloid, specifically inhibits the Hedgehog pathway by binding directly to Smoothened, an important Hedgehog response element. To use cyclopamine as a tool to explore and/or inhibit the Hedgehog pathway in vivo, a substantial quantity is required, and as a practical matter cyclopamine has been effectively unavailable for usage in animals larger than mice.

Isolation of Salmonella larochelle for the first time in India

The isolation of a new serotype, S. larochelle (6, 7: eh:1, 2), is reported in this communication. This serotype has not so far been reported from any source in this country. The serotype was isolated on November 27th, 1979 at Bombay from a market sample of frozen frog legs intended for domestic consumption.

The software for oceanographic data management: VODC for PC 2.0

To manage and process a large amount of oceanographic data, users must have powerful tools that simplify these tasks. The VODC for PC is software designed to assist in managing oceanographic data. It based on 32 bits Windows operation system and used Microsoft Access database management system. With VODC for PC users can update data simply, convert to some international data formats, combine some VODC databases to one, calculate average, min, max fields for some types of data, check for valid data…

Studies on isolation of salmonella from sea foods 1. Comparison of enrichment and selective media for recovery of salmonellae from fish

Three enrichment broths and six plating media were compared for efficiency of detection Salmonella in the presence of numbers of Coliforms (10super(5)/ml) and proteus (10super(3)/ml) from artificially inoculated fish samples. Recovery experiments Salmonella anatum, S. typhimurium and S. enteritidis indicated that the two enrichment broths Dulcitol Selinite (DSE) and Selinite Cystine (SC) were equally efficient. Further, the viability of Salmonella, inoculated into fish muscle and kept at 4°C for 48 hours, was found to be not affected by the low temperature storage. Selective plating media like Xylose Lysine Deoxycholate agar (XLD), Brilliant Green Sulphadiazine agar (BGS) and Brilliant Green agar (BG) were found to be superior in performance to Salmonella-Shigella agar: (SS) and Bismuth Sui phite agar (BiS).

Utilization of prawn waste: isolation of chitin and its conversion to chitosan

process is described for the preparation of chitosan from prawn waste. The process involves extraction of protein using 0.5% sodium hydroxide solution, bleaching the protein free mass with bleach liquor containing 0.3-0.5% available chlorine followed by demineralisation with 1.25 N hydrochloric acid in the cold and deacetylation using 1:1 (w/w) sodium hydroxide solution at 100°C for 2 hours.

Chemical control of psychrophilic bacterial spoilage of fish 1. Isolation and identification of psychrophilic bacteria from marine fish

Making use of the streak plate technique and low temperature incubation, 28 cultures belonging to six genera namely, Achromobacter, Flavobacterium, Pseudomonas, Micrococcus, Vibrio and Alcaligenes were isolated from different varieties of marine fish. The growth studies indicated that all of them were able to grow between -5 and +5°C within a week's time and none of them showed growth at 37°C. The optimum temperature of growth for all these cultures was in the range 25-28°C. Among these only one, i.e., a Vibrio sp., was found to be an obligate psychrophile.

Isolation of Salmonella roan for the first time in India

The isolation of Salmonella roan for the first time in India is reported.

Isolation of bile from fish and identification by thin layer chromatography

The paper deals with the collection of gall bladders, isolation of bile and identification of the constituents of the bile salts from different fishes. The yield of bile contents from fresh water fishes rohu, mrigal and catla was compared with that from marine fishes seer, tuna, shark and sardine. Considerable variation in yield was showed between marine and fresh water fish as well as between the species in both groups. It ranged from 0.04 to 0.06% of the body weight of fish in calla, mrigal and rohu. The bile constituents from rohu and mrigal were analysed by thin layer chromatography. The result showed that bile of rohu and mrigal contains mainly taurine derivative of lithocholic acid.

Isolation of Salmonella braenderup (6, 7:e, h:e, n, z (sub15)) from Mussel meat

A brief account is given of the morphology, biochemistry and serology of Salmonella braenderup isolated from mussel meat, obtained from fish markets in Calicut, India. Possible implications regarding human salmonellosis are also considered.