Identification of larval sea basses (Centropristis spp.) using ribosomal DNA-specific molecular assays

The identification of sea bass (Centropristis) larvae to species is difficult because of similar morphological characters, spawning times, and overlapping species ranges. Black sea bass (Centropristis striata) is an important fishery species and is currently considered to be overfished south of Cape Hatteras, North Carolina. We describe methods for identifying three species of sea bass larvae using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) assays based on species-specific amplification of rDNA internal transcribed spacer regions. The assays were tested against DNA of ten other co-occurring reef fish species to ensure the assay's specificity. Centropristis larvae were collected on three cruises during cross-shelf transects and were used to validate the assays. Seventy-six Centropristis larva were assayed and 69 (91%) were identified successfully. DNA was not amplified from 5% of the larvae and identification was inconclusive for 3% of the larvae. Those assays can be used to identify sea bass eggs and larvae and will help to assess spawning locations, spawning times, and larval dispersal.

Preliminary guide to the identification of the early life history stages of Priacanthid fishes of the Western Central Atlantic

The family Priacanthidae contains four genera and four species that occur in the western central North Atlantic (Starnes, 1988). Pristigenys alta is distributed in the Caribbean, Gulf of Mexico and along the east coast of North America. Although juveniles have been reported from as far north as southern New England waters, adults are not reported north of Cape Hatteras, NC. Priacanthus arenatus is distributed in tropical and tropically influenced areas of the western central North Atlantic in insular and continental shelf waters. Adult P. arenatus are distributed north to North Carolina and Bermuda, juveniles have been collected as far north as Nova Scotia. Cookeolus japonicus and Heteropriacanthus cruentatus are circumglobally distributed species and are both common in insular habitats. In the western central North Atlantic, C. japonicus ranges from New Jersey to Argentina; H. cruentatus from New Jersey and northern Gulf of Mexico to southern Brazil (Starnes, 1988). (PDF contains 6 pages)

Preliminary guide to the identification of the early life history stages of Gerreid fishes of the Western Central Atlantic

The family Gerreidae contains four genera and 13 species that occur in the western central North Atlantic. Adult gerreids are small to medium size fishes that are abundant in coastal waters, bays, and estuaries in tropical and warm temperate regions and sometimes occur in freshwaters. They are generally associate~ with grassy or open bottoms, but not with reefs. Gerreids are silvery fishes, with deeply forked tails, and extremely protrusible mouth that points downward when protracted. They apparently feed on bottom-dwelling organisms and at least one species (Eucinostomus gula) shows a distinct transition, during the juvenile period, from a planktivore (exclusively copepods) to a carnivore that includes a diet of almost solely polychaetes (Carr & Adams, 1973; Robins and Ray, 1987; Murdy et al., 1997). (PDF contains 10 pages)

High-Throughput Sequencing of microRNAs in Peripheral Blood Mononuclear Cells: Identification of Potential Weight Loss Biomarkers

INTRODUCTION: MicroRNAs (miRNAs) are being increasingly studied in relation to energy metabolism and body composition homeostasis. Indeed, the quantitative analysis of miRNAs expression in different adiposity conditions may contribute to understand the intimate mechanisms participating in body weight control and to find new biomarkers with diagnostic or prognostic value in obesity management. OBJECTIVE: The aim of this study was the search for miRNAs in blood cells whose expression could be used as prognostic biomarkers of weight loss. METHODS: Ten Caucasian obese women were selected among the participants in a weight-loss trial that consisted in following an energy-restricted treatment. Weight loss was considered unsuccessful when <5% of initial body weight (non-responders) and successful when >5% (responders). At baseline, total miRNA isolated from peripheral blood mononuclear cells (PBMC) was sequenced with SOLiD v4. The miRNA sequencing data were validated by RT-PCR. RESULTS: Differential baseline expression of several miRNAs was found between responders and non-responders. Two miRNAs were up-regulated in the non-responder group (mir-935 and mir-4772) and three others were down-regulated (mir-223, mir-224 and mir-376b). Both mir-935 and mir-4772 showed relevant associations with the magnitude of weight loss, although the expression of other transcripts (mir-874, mir-199b, mir-766, mir-589 and mir-148b) also correlated with weight loss. CONCLUSIONS: This research addresses the use of high-throughput sequencing technologies in the search for miRNA expression biomarkers in obesity, by determining the miRNA transcriptome of PBMC. Basal expression of different miRNAs, particularly mir-935 and mir-4772, could be prognostic biomarkers and may forecast the response to a hypocaloric diet.

Combined Fluorescent-Chromogenic In Situ Hybridization for Identification and Laser Microdissection of Interphase Chromosomes

Chromosome territories constitute the most conspicuous feature of nuclear architecture, and they exhibit non-random distribution patterns in the interphase nucleus. We observed that in cell nuclei from humans with Down Syndrome two chromosomes 21 frequently localize proximal to one another and distant from the third chromosome. To systematically investigate whether the proximally positioned chromosomes were always the same in all cells, we developed an approach consisting of sequential FISH and CISH combined with laser-microdissection of chromosomes from the interphase nucleus and followed by subsequent chromosome identification by microsatellite allele genotyping. This approach identified proximally positioned chromosomes from cultured cells, and the analysis showed that the identity of the chromosomes proximally positioned varies. However, the data suggest that there may be a tendency of the same chromosomes to be positioned close to each other in the interphase nucleus of trisomic cells. The protocol described here represents a powerful new method for genome analysis

Identification of the egg, early life history and spawning areas if the anchoveta, Cetengraulis mysticetus (Günther), in the Gulf of Panama

ENGLISH: The egg of the anchoveta, Cetengraulis mysticetus (Günther), was identified in the Gulf of Panama by its size, difference in diurnal period of spawning, seasonal occurrence (October to January) and relative abundance. It is pelagic, translucent and oval with mean dimensions of 1.166 mm. and 0.558 mm. for the long and short axes respectively. The egg membrane is unsculptured, the yolk mass is markedly segmented, and no oil globule or pigmentation is present. It was not found in the plankton from mid-January 1957 until the latter part of the following September; during this period the gonads of the anchoveta were immature. Only one other anchovy egg, spawned during the same diurnal period, is sufficiently similar in dimensions to be confused with that of the anchoveta; however, it is slightly smaller. SPANISH: El huevo de la anchoveta, Cetengraulis mysticetus (Günther), fué identificado en el Golfo de Panamá por su tamaño, diferencias en el período diario de desove, su abundancia en la temporada (de octubre a enero) y por su abundancia relativa. El huevo es pelágico, translúcido, oval y con dimensiones promedio de 1.166 mm. y 0.558 mm. para los ejes largo y corto, respectivamente. La membrana es lisa, el vitelo está francamente segmentado y no posee ningún glóbulo graso o pigmentación. El huevo de la anchoveta no se encontró en el plancton en el período comprendido entre mediados de enero y fines de septiembre de 1957; durante este lapso las gónadas estuvieron inactivas.

Genetic and morphological identification of pelagic juvenile rockfish collected from the Gulf of Alaska

Pelagic juvenile rockfish (Sebastes spp.) collected in surveys designed to assess juvenile salmonids and other species in the Gulf of Alaska in 1998 and 2000–2003 provide an opportunity to document the occurrence of the pelagic juveniles of several species of rockfish. Often, species identification of rockfish is difficult or impossible at this stage of development (~20 to 60 mm), and few species indigenous to Alaska waters have been described. Use of mitochondrial DNA markers for rockfish species allowed unequivocal identification of ten species (S. aleutianus, S. alutus, S. borealis, S. entomelas, S. flavidus, S. melanops, S. pinniger, S. proriger, S. reedi, and S. ruberrimus) in subsamples from the collections. Other specimens were genetically assignable to groups of two or three species. Sebastes borealis, S. crameri, and S. reedi were identified using morphological data. Combining genetic and morphological data allowed successful resolution of the other species as S. emphaeus, probably S. ciliatus (although S. polyspinis cannot be totally ruled out), and S. polyspinis. Many specimens were initially morphologically indistinguishable from S. alutus, and several morphological groups included fish genetically identified as S. alutus. This paper details the characteristics of these pelagic juveniles to facilitate morphological identification of these species in future collections. (PDF file contains 32 pages.)

Research Data Management — Activities and Challenges Report on the Knowledge Exchange Workshop

Workshop Research Data Management – Activities and Challenges 14-15 November 2011, Bonn The Knowledge Exchange initiative organised a workshop to highlight current activities and challenges with respect to research data management in the Knowledge Exchange partner countries and beyond. The workshop brought together experts from data centres, libraries, computational centres, funding organisations, publishing services and other institutions in the field of research and higher education who are working to improve research data management and encourage effective reuse of research data. A considerable part of the programme was dedicated to sharing perspectives from these communities, leading to the development of a roadmap of practical actions for the Knowledge Exchange initiative, partner organisations and other stakeholders to progress over the next two years. On the first day, principal investigators and project managers from a great variety of recent projects shared their insights on objectives and methods for improving data management ranging from discipline-specific to more general approaches. A series of short presentations of selected projects was followed by an extensive poster session that functioned as a “trade fair” of current trends and activities in the field of research data management. Moreover, the poster session offered ample network opportunities for participants. The second day was dedicated to intensive group discussions looking at a number of data management challenges. First the most important findings from the "Surfboard for 'Riding the Wave'" report were presented. This included the state of the art on activities and challenges in the field of research data management. The subgroups will concentrate on the following key themes: funding, incentives, training and technical infrastructure. These discussions culminated in the identification of practical recommendations for future cooperation on practical as well as on strategic levels that should be taken forward by the KE partner organisations and beyond. These activities aim to improve the sustainability of services and infrastructures at both national and international levels.

Artificial fertilization of the eggs, and rearing and identification of the larvae of the anchoveta, Cetengraulis mysticetus

ENGLISH: The anchoveta, Cetengraulis mysticetus (Günther), is an important bait fish used to capture tunas in the Eastern Tropical Pacific Ocean. Contributions to the early life history of this species in the Gulf of Panama were made by Simpson (1959), who was able to identify deductively the planktonic egg of the anchoveta from 10 other anchovy eggs concurrently present. He also reared these planktonic eggs in the laboratory and described the resultant larvae to the age of 48 hours after hatching. Because of the lack of differences among the anchovy larvae, this description does not permit the identification of anchoveta larvae from those of other engraulid species. Furthermore, while adult specimens are easily recognized, up to the present it has not been possible to extend the identification of the juvenile anchoveta to specimens smaller than about 25 mm. The purpose of this study, therefore, was to identify anchoveta from the time of hatching to about 25 mm. SPANISH: La anchoveta, Cetengraulis mysticetus (Günther), es un importante pez de carnada que se emplea en la captura de los atunes en el Océano Pacífico Oriental Tropical. Simpson (1959) logró identificar deductivamente el huevo planctónico de la anchoveta al separarlo de otros diez huevos de anchoas que se encuentran al mismo tiempo, contribuyendo de esta manera a conocer los primeros estados de la historia natural de esta especie en el Golfo de Panamá. El también estableció un criadero en el laboratorio con estos huevos planctónicos y describió las larvas resultantes hasta la edad de 48 horas después de la eclosión. Debido a que no hay diferencias entre las larvas de las anchoas, esta descripción no permite identificar las larvas de la anchoveta de las otras especies de engráulidos. Más aun, a pesar de que los especímenes adultos son fácilmente reconocibles, hasta ahora no ha sido posible identificar la anchoveta juvenil de menos de unos 25 mm. Consecuentemente, el propósito del presente estudio ha sido el de identificar al anchoveta desde el momento de la eclosión hasta que tiene unos 25 mm.

Guide to the Identification of Larval and Early Juvenile Poachers (Scorpaeniformes: Agonidae) from the Northeastern Pacific Ocean and Bering Sea

Developmental stages of 22 species representing 16 genera of agonid fishes occurring in the northeastern Pacific Ocean from San Francisco Bay to the Arctic Ocean are presented. Three of these species also occur in the North Atlantic Ocean. Larval stages of nine species are described for the first time. Additional information or illustrations intended to augment original descriptions are provided for eight species. Information on five other species is provided from the literature for comparative purposes. The primary objective of this guide is to present taxonomic characters to help identify the early life history stages of agonid fishes in field collections. Meristic, morphometric, osteological, and pigmentation characters are used to identify agonid larvae. Meristic features include numbers of median-fin elements, pectoral-fin rays, dermal plates, and vertebrae. Eye diameter, body depth at the pectoral-fin origin, snout to first dorsal-fin length, and pectoral-fin length are the most useful morphological characters. Presence, absence, numbers, and/or patterns of dermal plates in lateral rows or on the ventral surface of the gut are also useful. Other important characters are the presence, absence, numbers, and ornamentation of larval head spines. Lastly, distinct pigmentation patterns are often diagnostic. The potential utility of larval characters in phylogenetic analysis of the family Agonidae is discussed. (PDF file contains 92 pages.)