Mitochondrial gene sequences useful for species identification of western North Atlantic Ocean sharks

Molecular-based approaches for shark species identification have been driven largely by issues specific to the fishery. In an effort to establish a more comprehensive identification data set, we investigated DNA sequence variation of a 1.4-kb region from the mitochondrial genome covering partial sequences from the 12S rDNA, 16S rDNA, and the complete valine tRNA from 35 shark species from the Atlantic fishery. Generally, within-species variability was low in relation to interspecific divergence because species haloptypes formed monophyletic groups. Phylogenetic analyses resolved ordinal relationships among Carcharhiniformes and Lamniformes, and revealed support for the families Sphyrnidae and Triakidae (within Carcharhiniformes) and Lamnidae and Alopidae (within Lamniformes). The combination of limited intraspecific variability and sufficient between-species divergence indicates that this locus is suitable for species identification.

PCR-based assay for detection of four coral pathogens

Several microorganisms have been identified as pathogenic agents responsible for various outbreaks of coral disease. Little has been learned about the exclusivity of a pathogen to given disease signs. Most pathogens have only been implicated within a subset of corals, leaving gaps in our knowledge of the host range and geographic extent of a given pathogen. PCR-based assays provide a rapid and inexpensive route for detection of pathogens. Pathogen-specific 16S rDNA primer sets were designed to target four identified coral pathogens: Aurantimonas coralicida, Serratia marcescens, Vibrio shilonii, and Vibrio coralliilyticus. Assays detected the presence of targets at concentrations of less than one cell per microliter. The assay was applied to 142 coral samples from the Florida Keys, Puerto Rico, and U.S. Virgin Islands as an in situ specificity test. Assays displayed a high-level of specificity, seemingly limited only by the resolution of the 16S rDNA.

A survey on relation of morphological, molecular and phylogenetic structure of zoanthids of the islands located in the Hormoz Strait (Hormoz, Qeshm, Larak, Hengam)

The order Zoantharia (Zoanthids) is one of the most neglected orders of cnidarians in the Persian Gulf. The present study aims to investigate the biodiversity of this order with morphological and molecular examination in the Persian Gulf. For this purpose, 123 colonies of zoanthids with variety of shape and colors have been collected from intertidal and shallow water zone of four islands, i. e. Hengam, Qeshm, Larak and Hormoz. After sampling, morphological characteristics of each specimen were recorded based on in situ photographs. Then DNA was extracted using the cetyl trimethyl ammonium bromide (CTAB) method. Both mitochondrial 16S ribosomal DNA (mt 16S rDNA) and cytochrome oxidase subunit I (COI) gene fragments were amplified and sequenced. The results of preliminary morphological identification integrated with two mitochondrial markers sequencing demonstrated the presence of five different species in this region; Zoanthus sansibaricus, Palythoa mutuki, Palythoa cf. mutuki, Palythoa tuberculosa and Neozoanthus persicus?. Although at first sight, morphological properties were not successful to delineate zoanthid species, they become reliable criteria to identify and delineate species in field studies after molecular identification.

Bacterial and pathological study of caudal fin rot in brood stocks of Salmo trutta caspius from the propagation and breeding center of Shahid Bahonar of Kelardasht region

In order to study caudal fin rot with emphasis on Aeromonas hydrophila and Pseudomonas fluorescens in Salmo trutta caspius from the salmonids propagation and breeding center of Shahid Bahonar of kelardasht region, One hundred and eighty brood stocks having fin damage symptoms were chosen. Two bacterial samples from each fish were cultured on Aeromonas and Pseudomonas specific media. Biochemical tests, API2OE identification system and antibiogram test using six antibiotic disks were performed for diagnosing isolates bacteria and finding suitable antibiotic. Thirty samples from caudal fin of damaged fishes were fixed in 10% formalin and 51.tm microscopic sections were prepared using standard scatological methods and then stained by Haematoxylin-Eosin staining method to observe the pathological changes and also Maccallum-Goodpasture staining method to observe the bacterial colonies. In second stage of the study, bacterial samples were taken from thirty brood stocks using similar method at the first stage of sampling. For isolation and biochemical diagnosis of Aeromonas and Pseudormonas genus, the samples were analyzed by molecular research included PCR amplification (using 16S rDNA genes of the genus pseudomonas and 16S-23S rDNA intergenic spacer of the genus Aeromonas) and restriction analysis by four restriction enzymes for each genus. The results of biochemical tests showed that isolated bacteria were belonged to Aeromonas caviae and Aeromonas hydrophila (subspecies anaerogenes), Pseudomonas fluorescens, Pseudomonas putida and Pseudomonas alcaligenes while the results of API2OE identification system showed that the isolated bacteria belonged to Aeromonas hydrophila, Pseudomonas fluorescens, Pseudomonas putida and Pseudomonas aeruginosa. Restriction analysis of Aeromonas samples with Hin6l, Csp6I, Taql, and Tasl revealed three samples were different from others while restriction analysis of Pseudomonas samples with Alul, Hinfl, Rsal, and Trull showed at least five species or biovars. The results of antibiogram test showed all Aeromonas samples were sensitive to Trimethoprim, Chloramphenicol and Nitrofurazone, mostly to Nalidixic acid and Chloramphenicol, while most of samples were resistant to Erythromycin and Oxytetracycline. Pseudomonas samples were only sensitive to Nitrofurazone and mostly resistant to Oxytetracycline, Nalidixic acid, Erythromycin, Trimethoprim and Chloramphenicol. The results of light microscope study showed hyperplasia and spongiosis of the malpigian cells of epidermis, increasing of melanin pigments underlying epidermis; sever necrosis in both epidermis and dermis and also sloughing the epidermis in some cases. Occurrence of clefts through the epithelium, neovascularization, hyperemia and mild inflammatory response in dermis and separation of the fin rays also were observed. No bacterial colonies were found in the sections.

Metrics of monograph use in the Marston Science Library

As academic libraries are increasingly supported by a matrix of databases functions, the use of data mining and visualization techniques offer significant potential for future collection development and service initiatives based on quantifiable data. While data collection techniques are still not standardized and results may be skewed because of granularity problems, faulty algorithms, and a host of other factors, useful baseline data is extractable and broad trends can be identified. The purpose of the current study is to provide an initial assessment of data associated with science monograph collection at the Marston Science Library (MSL), University of Florida. These sciences fall within the major Library of Congress Classification schedules of Q, S, and T, excluding R, TN, TR, and TT. Overall strategy of this project is to look at the potential science audiences within the university community and analyze data related to purchasing and circulation patterns, e-book usage, and interlibrary loan statistics. While a longitudinal study from 2004 to the present would be ideal, this paper presents the results from the academic year July 1, 2008 to June 30, 2009 which was chosen as the pilot period because all data reservoirs identified above were available.

Measuring Learning Outcomes in Library Instruction

The author uses clicker technology to incorporate polling and multiple choice question techniques into library instruction classes. Clickers can be used to give a keener understanding of how many students grasp the concepts presented in a specific class session. Typically, a student that aces a definition-type question will fail to answer an application-type question correctly. Immediate, electronic feedback helps to calibrate teaching approaches and gather data about learning outcomes. This presentation will analyze learning outcomes specific to scientific disciplines, and demonstrate the usefulness of clickers to engage and sustain student learning.

Data management plans - the role of the library

Planning the management of data at proposal time and throughout its lifecycle is becoming increasingly important to funding agencies and is essential to ensure its current usability and long term preservation and access. This presentation will describe the work being done at the Woods Hole Oceanographic Institution (WHOI) to assist PIs with the preparation of data management plans and the role the Library has in this process. Data management does not mean simply storing information. The emphasis is now on sharing data and making research accessible. Topics to be covered include educating staff about the NSF data policy implementation, a data management survey, resources for proposal preparation, collaborating with other librarians, and next steps.

Could the library be dismantled/role of unique holdings in modern times

I have been asked by administration, how much of our collection could go into storage. They optimistically hoping for a room or two for faculty/staff offices, as some buildings need renovation or need to be closed due to safety issues. Clearly, much of the population believes that all/most library materials are available on-line – free. I will present the results of our survey’s of material held and available on-line and space “freed” thanks to archiving. How little space is freed.

The Marine Science Library, Resource Center : poster presentation

The first concept of a new library was introduced in 2001 by a faculty member at the University of Texas Marine Science Institute. The suggestion for the construction of a new library was based on two specific reasons: existing library is located in one of the most vulnerable buildings to hurricane damage and the library has outgrown its current space. This presentation provides a general overview of the current status and changing needs of the Marine Science Library and how the idea of a new library finally became a reality

Creating a collection development model for a marine science library

The purpose of this article is to update and build on the approximate 10,000 item collection of the Harbor Branch Oceanographic Institute Library. This article will present a history of Harbor Branch and its library, and a literature review, outlining the collection development methods of other marine science libraries and academic libraries. The article will relate brief histories of three marine science libraries. A comparative table is constructed to compare Harbor Branch Library with three marine science libraries. The methodology, or how the table was created, is explained. The comparative table will be shown and analyzed, and the results of the table discussed. Finally, some recommendations for improvement of the Harbor Branch Library will be presented.