928 resultados para Catalogs and collections


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ENGLISH: One phase of the duties of the Inter-American Tropical Tuna Commission is the gathering and interpretation of data concerning the life history of the commercially important bait species throughout the Eastern Pacific Ocean. During 1958 the Commission established a laboratory in Manta, Ecuador to study tuna. It was subsequently found that this fishery was dependent upon one species of anchovy, Anchoa naso, which was locally referred to as "colorado." During the calendar year 1959 approximately 380,000 scoops of bait were taken by the Manta tuna fleet (Schaefer, 1960), which at that time numbered about 23 vessels. Since then the fleet has increased by about 25 per cent and it is probable that the bait catch has increased also. Virtually nothing has been reported concerning the life history of this species. Hildebrand (1943) reviewed its taxonomy and reported standard lengths ranging from 32 to 135 mm. Peterson (1956) examined specimens from Central America and found them to range from 27 to 66 mm. He also indicated that the species spawned over a long period of time. The present report describes some aspects of the life history of Anchoa naso in Ecuadorian waters. The findings are based on 121 collections taken during the period March 1959 through June 1961. SPANISH: Una fase de las obligaciones de La Comisión Interamericana del Atún Tropical es la obtensión e interpretación de los datos concernientes a la historia natural de las especies de carnada comercialmente importantes en todo el Océano Pacifico Oriental. En el año de 1958 la Comisión estableció un laboratorio en Manta, Ecuador, para estudiar el atún. Se encontró subsecuentemente que esta pesquería dependía de una especie de anchoa, Anchoa naso, conocida localmente con el nombre de colorado. Durante el año calendario de 1959, la flota atunera de Manta, que en ese tiempo alcanzaba a unos 23 barcos, obtuvo aproximadamente 380,000 copas (scoops) de carnada (Schaefer, 1960). Desde entonces la flota ha aumentado en un 25 por ciento, y es probable que la captura de peces-cebo haya aumentado también. Nada se ha informado virtualmente sobre la historia natural de esta especie. Hildebrand (1943) revisó su taxonomia e informó sobre su longitud estándar, que varia entre los 32 y 135 mm. Peterson (1956) examinó especímenes de la América Central, y encontró que variaban entre los 27 y 66 mm. También indicó que la especie desova durante un largo periodo de tiempo. El presente informe describe algunos aspectos de la historia natural de la Anchoa naso en aguas ecuatorianas. Los hallazgos están basados en 121 recolecciones hechas durante el periodo de marzo de 1959 a junio de 1961. (PDF contains 30 pages.)

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The main focus of this thesis is the use of high-throughput sequencing technologies in functional genomics (in particular in the form of ChIP-seq, chromatin immunoprecipitation coupled with sequencing, and RNA-seq) and the study of the structure and regulation of transcriptomes. Some parts of it are of a more methodological nature while others describe the application of these functional genomic tools to address various biological problems. A significant part of the research presented here was conducted as part of the ENCODE (ENCyclopedia Of DNA Elements) Project.

The first part of the thesis focuses on the structure and diversity of the human transcriptome. Chapter 1 contains an analysis of the diversity of the human polyadenylated transcriptome based on RNA-seq data generated for the ENCODE Project. Chapter 2 presents a simulation-based examination of the performance of some of the most popular computational tools used to assemble and quantify transcriptomes. Chapter 3 includes a study of variation in gene expression, alternative splicing and allelic expression bias on the single-cell level and on a genome-wide scale in human lymphoblastoid cells; it also brings forward a number of critical to the practice of single-cell RNA-seq measurements methodological considerations.

The second part presents several studies applying functional genomic tools to the study of the regulatory biology of organellar genomes, primarily in mammals but also in plants. Chapter 5 contains an analysis of the occupancy of the human mitochondrial genome by TFAM, an important structural and regulatory protein in mitochondria, using ChIP-seq. In Chapter 6, the mitochondrial DNA occupancy of the TFB2M transcriptional regulator, the MTERF termination factor, and the mitochondrial RNA and DNA polymerases is characterized. Chapter 7 consists of an investigation into the curious phenomenon of the physical association of nuclear transcription factors with mitochondrial DNA, based on the diverse collections of transcription factor ChIP-seq datasets generated by the ENCODE, mouseENCODE and modENCODE consortia. In Chapter 8 this line of research is further extended to existing publicly available ChIP-seq datasets in plants and their mitochondrial and plastid genomes.

The third part is dedicated to the analytical and experimental practice of ChIP-seq. As part of the ENCODE Project, a set of metrics for assessing the quality of ChIP-seq experiments was developed, and the results of this activity are presented in Chapter 9. These metrics were later used to carry out a global analysis of ChIP-seq quality in the published literature (Chapter 10). In Chapter 11, the development and initial application of an automated robotic ChIP-seq (in which these metrics also played a major role) is presented.

The fourth part presents the results of some additional projects the author has been involved in, including the study of the role of the Piwi protein in the transcriptional regulation of transposon expression in Drosophila (Chapter 12), and the use of single-cell RNA-seq to characterize the heterogeneity of gene expression during cellular reprogramming (Chapter 13).

The last part of the thesis provides a review of the results of the ENCODE Project and the interpretation of the complexity of the biochemical activity exhibited by mammalian genomes that they have revealed (Chapters 15 and 16), an overview of the expected in the near future technical developments and their impact on the field of functional genomics (Chapter 14), and a discussion of some so far insufficiently explored research areas, the future study of which will, in the opinion of the author, provide deep insights into many fundamental but not yet completely answered questions about the transcriptional biology of eukaryotes and its regulation.

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Detailed descriptions of the early development of the striped bass, Roccus saxitilis (Walbaum), with emphasis on variation in size and morphology, sequence of fin formation, changes in body form, and attainment of the full complement of maristic numbers, are presented and illustrated for the first time. The egg is spherical, transparent, non-adhesive and relatively large. It is pelagic and buoyant, although it sinks in quiet fresh water. When unfertilized, it averages 1.3 mm, in diameter, but is 3.4 mm. when fertilized and water-hardened. The granular yolk sac, green when alive and whitish-yellow when preserved, averages 1.2 mm., and the single amber-colored oil globule is about 0.6 mm. in diameter. Newly hatched striped bass prolarvae, which range from 2.9-3.7 mm. in total length, are relatively undeveloped and nearly transparent, with no mouth opening, unpigmented eyes, and a greatly enlarged yolk sac with the large oil globule projecting beyond the head. When 5-6 mm. long the yolk sac and oil globule are assimilated and the postlarvae I show advanced development of the internal anatomy. Although the fish is still transparent, scattered melanophores are found on the head and body and chromatophores in the eyes and the ventro-posterior edge of the body. Postlarvae transform to young between 7 and 10 mm. in length when the finfolds are lost except in the dorsal, anal and caudal regions. The largest fish in this group possess a well-formed skeleton with a full complement of 25 vertebrae. Between 10 and 20 mm. in length all fish are fully transformed, muscular tissue renders most of the internal structure obscure, and the myotomes, which generally correspond in number with the vertebrae, are no longer visible. At fish lengths of 20-30 mm. scales are found on all specimens, and with the exception of the pectoral fin-rays, a full complement of meristic structures is present in all other fins. At this stage the body is pigmented uniformly with small spots. Linear regressions between several dependent variables and the , independent variable of standard length indicate that the rate of development of head, eye. and snout to anus lengths is proportional to the length of the larvae and young. Body depth and standard length are non-linear among newly-hatched larvae. Hatchery-reared striped bass demonstrated a slow rate of growth, and were regarded as "stunted," when compared to growth rates observed in another study and field collections. Observations were also made on abnormal eggs and teratological larvae and young. Blue-sac disease is tentatively identified and described for the first time in larvae and pugnosed larvae and young are also described for the first time in striped bass.

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Amphibian declines and extinctions have been documented around the world, often in protected natural areas. Concern for this alarming trend has focused attention on the need to document all species of amphibians that occur within U.S. National Parks and to search for any signs that amphibians may be declining. This study, an inventory of amphibian species in Virgin Islands National Park, was conducted from 2001 to 2003. The goals of the project were to create a georeferenced inventory of amphibian species, use new analytical techniques to estimate proportion of sites occupied by each species, look for any signs of amphibian decline (missing species, disease, die-offs, etc.), and to establish a protocol that could be used for future monitoring efforts. Several sampling methods were used to accomplish these goals. Visual encounter surveys and anuran vocalization surveys were conducted in all habitats throughout the park to estimate the proportion of sites or proportion of area occupied (PAO) by amphibian species in each habitat. Line transect methods were used to estimate density of some amphibian species and double observer analysis was used to refine counts based on detection probabilities. Opportunistic collections were used to augment the visual encounter methods for rare species. Data were collected during four sampling periods and every major trail system throughout the park was surveyed. All of the amphibian species believed to occur on St. John were detected during these surveys. One species not previously reported, the Cuban treefrog (Osteopilus septentrionalis), was also added to the species list. That species and two others (Eleutherodactylus coqui and Eleutherodactylus lentus) bring the total number of introduced amphibians on St. John to three. We detected most of the reptile species thought to occur on St. John, but our methods were less suitable for reptiles compared to amphibians. No amphibian species appear to be in decline at this time. We found no evidence of disease or of malformations. Our surveys provide a snapshot picture of the status of the amphibian species, so continued monitoring would be necessary to determine long-term trends, but several potential threats to amphibians were identified. Invasive species, especially the Cuban treefrog, have the potential to decrease populations of native amphibians. Introduced mammalian predators are also a potential threat, especially to the reptiles of St. John, and mammalian grazers might have indirect effects on amphibians and reptiles through habitat modification. Finally, loss of habitat to development outside the park boundary could harm some important populations of amphibians and reptiles on the island.

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Amphibian declines and extinctions have been documented around the world, often in protected natural areas. Concern for this trend has prompted the U.S. Geological Survey and the National Park Service to document all species of amphibians that occur within U.S. National Parks and to search for any signs that amphibians may be declining. This study, an inventory of amphibian species in Big Cypress National Preserve, was conducted from 2002 to 2003. The goals of the project were to create a georeferenced inventory of amphibian species, use new analytical techniques to estimate proportion of sites occupied by each species, look for any signs of amphibian decline (missing species, disease, die-offs, and so forth.), and to establish a protocol that could be used for future monitoring efforts. Several sampling methods were used to accomplish these goals. Visual encounter surveys and anuran vocalization surveys were conducted in all habitats throughout the park to estimate the proportion of sites or proportion of area occupied (PAO) by each amphibian species in each habitat. Opportunistic collections, as well as limited drift fence data, were used to augment the visual encounter methods for highly aquatic or cryptic species. A total of 545 visits to 104 sites were conducted for standard sampling alone, and 2,358 individual amphibians and 374 reptiles were encountered. Data analysis was conducted in program PRESENCE to provide PAO estimates for each of the anuran species. All of the amphibian species historically found in Big Cypress National Preserve were detected during this project. At least one individual of each of the four salamander species was captured during sampling. Each of the anuran species in the preserve was adequately sampled using standard herpetological sampling methods, and PAO estimates were produced for each species of anuran by habitat. This information serves as an indicator of habitat associations of the species and relative abundance of sites occupied, but it will also be useful as a comparative baseline for future monitoring efforts. In addition to sampling for amphibians, all encounters with reptiles were documented. The sampling methods used for detecting amphibians are also appropriate for many reptile species. These reptile locations are included in this report, but the number of reptile observations was not sufficient to estimate PAO for reptile species. We encountered 35 of the 46 species of reptiles believed to be present in Big Cypress National Preserve during this study, and evidence exists of the presence of four other reptile species in the Preserve. This study found no evidence of amphibian decline in Big Cypress National Preserve. Although no evidence of decline was observed, several threats to amphibians were identified. Introduced species, especially the Cuban treefrog (Osteopilus septentrionalis), are predators and competitors with several native frog species. The recreational use of off-road vehicles has the potential to affect some amphibian populations, and a study on those potential impacts is currently underway. Also, interference by humans with the natural hydrologic cycle of south Florida has the potential to alter the amphibian community. Continued monitoring of the amphibian species in Big Cypress National Preserve is recommended. The methods used in this study were adequate to produce reliable estimates of the proportion of sites occupied by most anuran species, and are a cost-effective means of determining the status of their populations.

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Otto Kelland was a truly unique individual in Newfoundland. During his long life he had several careers from being a prison superintendant to being an instructor at Marine Institute. During his life Kelland made hundreds of wooden boat models. They are beautifuly hand-crafted and represented the type of watercraft used by fishermen in Newfoundland. The collection of boat models made by Otto Kelland and owned by Marine Institute made an ideal object to be digitalized. In particular the collection of dories was an ideal group to be digitized. They were housed in one cabinet and accompanied by hand-written documents describing each model. The Digital Archives Initiative (DAI) is a “gateway to the learning and research-based cultural resources held by Memorial University of Newfoundland and partnering organizations.” The DAI hosts a variety of collections which together reinforce the importance, past and present, of Newfoundland and Labrador's history and culture. I will give an oral presentation of the project followed by a demonstration of the Otto Kelland Dories exhibit on the Digital Archives Initiative (DAI) at Memorial University of Newfoundland. I will be happy to answer questions following my presentation.

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Pacific herring (Clupea pallasii) from the Gulf of Alaska were screened for temporal and spatial genetic variation with 15 microsatellite loci. Thirteen collections were examined in this study: 11 from Southeast Alaska and 2 from Prince William Sound, Alaska. Although FST values were low, a neighbor-joining tree based on genetic distance, homogeneity, and FST values revealed that collectively, the Berners Bay and Lynn Canal (interior) collections were genetically distinct from Sitka Sound and Prince of Wales Island (outer-coastal) collections. Temporal genetic variation within regions (among three years of Berners Bay spawners and between the two Sitka Sound spawners) was zero, whereas 0.05% was attributable to genetic variation between Berners Bay and Sitka Sound. This divergence may be attributable to environmental differences between interior archipelago waters and outer-coast habitats, such as differences in temperature and salinity. Early spring collections of nonspawning Lynn Canal herring were nearly genetically identical to collections of spawning herring in Berners Bay two months later—an indication that Berners Bay spawners over-winter in Lynn Canal. Southeast Alaskan herring (collectively) were significantly different from those in Prince William Sound. This study illustrates that adequate sample size is needed to detect variation in pelagic fish species with a large effective population size, and microsatellite markers may be useful in detecting low-level genetic divergence in Pacific herring in the Gulf of Alaska.

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Ichthyoplankton surveys were conducted in shelf and slope waters of the northern Gulf of Mexico during the months of May–September in 2005 and 2006 to investigate the potential role of this region as spawning and nursery habitat of sailfish (Istiophorus platypterus). During the two-year study, 2426 sailfish larvae were collected, ranging in size from 2.0 to 24.3 mm standard length. Mean density for all neuston net collections (n=288) combined was 1.5 sailfish per 1000 m2, and maximum density was observed within frontal features created by hydrodynamic convergence (2.3 sailfish per 1000 m2). Sagittal otoliths were extracted from 1330 larvae, and otolith microstructure analysis indicated that the sailfish ranged in age from 4 to 24 days after hatching (mean=10.5 d, standard deviation [SD]=3.2 d). Instantaneous growth coefficients (g) among survey periods (n=5) ranged from 0.113 to 0.127, and growth peaked during July 2005 collections when density within frontal features was highest. Daily instantaneous mortality rates (Z) ranged from 0.228 to 0.381, and Z was indexed to instantaneous weight-specific growth (G) to assess stage-specific production potential of larval cohorts. Ratios of G to Z were greater than 1.0 for all but one cohort examined, indicating that cohorts were gaining biomass during the majority of months investigated. Stage-specific production potential, in combination with catch rates and densities of larvae, indicates that the Gulf of Mexico likely represents important spawning and nursery habitat for sailfish.

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Citharichthys cornutus and C. gymnorhinus, diminutive flatfishes inhabiting continental shelves in the western Atlantic Ocean, are infrequently reported and poorly known. We identified 594 C. cornutus in 56 different field collections (68–287 m; most between 101–200 m) off the eastern United States, Bahamas, and eastern Caribbean Sea. Historical records and recently captured specimens document the northern geographic range of adults on the shelf off New Jersey (40°N, 70°W). Citharichthys cornutus measured 17.2–81.3 mm standard length (SL); males (20.0–79.1 mm SL) and females (28.0–81.3 mm SL) attain similar sizes (sex could not be determined for fish <20 mm SL). Males reach nearly 100% maturity at ≥60 mm SL. The smallest mature females are 41.5 mm SL, and by 55.1 mm SL virtually all are mature. Juveniles are found with adults on the outer shelf. Only 214 C. gymnorhinus were located in 42 different field collections (35–201 m, with 90% between 61 and 120 m) off the east coast of the United States, Bahamas, and eastern Caribbean Sea. Adults are found as far north as the shelf off Cape Hatteras, NC (35°N, 75°W). This diminutive species (to 52.4 mm SL) is among the smallest flatfishes but males (n=131; 20.3–52.4 mm SL) attain a slightly larger maximum size than that of females (n=58; 26.2–48.0 mm SL). Males begin to mature between 29 and 35 mm SL and reach 100% maturity by 35–40 mm SL. Some females are mature at 29 mm SL, and all females >35.1 mm SL are mature. Overlooked specimens in museum collections and literature enabled us to correct long-standing inaccuracies in northern distributional limits that appear in contemporary literature and electronic data bases for these species. Associated locality-data for these specimens allow for proper evaluation of distributional information for these species in relation to hypotheses regarding shifts in species ranges due to climate change effects.

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Ten growth models were fitted to age and growth data for spiny dogfish (Squalus acanthias) in the Gulf of Alaska. Previous studies of spiny dogfish growth have all fitted the t0 formulation of the von Bertalanffy model without examination of alternative models. Among the alternatives, we present a new two-phase von Bertalanffy growth model formulation with a logistically scaled k parameter and which estimates L0. A total of 1602 dogfish were aged from opportunistic collections with longline, rod and reel, set net, and trawling gear in the eastern and central Gulf of Alaska between 2004 and 2007. Ages were estimated from the median band count of three independent readings of the second dorsal spine plus the estimated number of worn bands for worn spines. Owing to a lack of small dogfish in the samples, lengths at age of small individuals were back-calculated from a subsample of 153 dogfish with unworn spines. The von Bertalanffy, two-parameter von Bertalanffy, two-phase von Bertalanffy, Gompertz, two-parameter Gompertz, and logistic models were fitted to length-at-age data for each sex separately, both with and without back-calculated lengths at age. The two-phase von Bertalanffy growth model produced the statistically best fit for both sexes of Gulf of Alaska spiny dogfish, resulting in L∞ = 87.2 and 102.5 cm and k= 0.106 and 0.058 for males and females, respectively.

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Multiyear ichthyoplankton surveys used to monitor larval fish seasonality, abundance, and assemblage structure can provide early indicators of regional ecosystem changes. Numerous ichthyoplankton surveys have been conducted in the northern Gulf of Mexico, but few have had high levels of temporal resolution and sample replication. In this study, ichthyoplankton samples were collected monthly (October 2004–October 2006) at a single station off the coast of Alabama as part of a long-term biological survey. Four seasonal periods were identified from observed and historic water temperatures, including a relatively long (June–October) “summer” period (water temperature >26°C). Fish egg abundance, total larval abundance, and larval taxonomic diversity were significantly related to water temperature (but not salinity), with peaks in the spring, spring–summer, and summer periods, respectively. Larvae collected during the survey represented 58 different families, of which engraulids, sciaenids, carangids, and clupeids were the most prominent. The most abundant taxa collected were unidentified engraulids (50%), sand seatrout (Cynoscion arenarius, 7.5%), Atlantic bumper (Chloroscombrus chrysurus, 5.4%), Atlantic croaker (Micropogonias undulatus, 4.4%), Gulf menhaden (Brevoortia patronus, 3.8%), and unidentified gobiids (3.6%). Larval concentrations for dominant taxa were highly variable between years, but the timing of seasonal occurrence for these taxa was relatively consistent. Documented increases in sea surface temperature on the Alabama shelf may have various implications for larval fish dynamics, as indicated by the presence of tropical larval forms (e.g., fistularids, labrids, scarids, and acanthurids) in our ichthyoplankton collections and in recent juvenile surveys of Alabama and northern Gulf of Mexico seagrass habitats.

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The community structure of fishes associated with pelagic Sargassum spp. and open water lacking Sargassum was examined during summer and fall cruises, 1999–2003, in the Gulf Stream off North Carolina. Significantly more individual fishes (n= 18,799), representing at least 80 species, were collected from samples containing Sargassum habitat, compared to 60 species (n=2706 individuals) collected from openwater habitat. The majority (96%) of fishes collected in both habitats were juveniles, and planehead filefish (Stephanolepis hispidus) dominated both habitats. Regardless of sampling time (day or night), Sargassum habitat yielded significantly higher numbers of individuals and species compared with open-water collections. Overall, fishes collected by neuston net tows from Sargassum habitat were significantly larger in length than fishes collected from open-water habitat with neuston nets. A significant positive, linear relationship existed between numbers of fishes and the quantity of Sargassum collected by neuston net. Underwater video recordings indicated a layered structure of fishes among and below the algae and that smaller fishes were more closely associated with the algae than larger fishes. Observations of schooling behaviors of filefishes (Monacanthidae), dolphinfish (Coryphaena hippurus), and jacks (Carangidae), and fish-jellyfish associations were also recorded with an underwater video camera. Our data indicate that Sargassum provides a substantial nursery habitat for many juvenile fishes off the U.S. southeast coast.

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The findings are presented of a search conducted on traditional fishing gear design and construction using the ASFA database (1971-90) and the ICLARM Library and professional staff collections.

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Morphological development of the larvae and small juveniles of estuary perch (Macquaria colonorum) (17 specimens, 4.8−13.5 mm body length) and Australian bass (M. novemaculeata) (38 specimens, 3.3−14.1 mm) (Family Percichthyidae) is described from channel-net and beach-seine collections of both species, and from reared larvae of M. novemaculeata. The larvae of both are characterized by having 24−25 myomeres, a large triangular gut (54−67% of BL) in postflexion larvae, small spines on the preopercle and interopercle, a smooth supraocular ridge, a small to moderate gap between the anus and the origin of the anal fin, and distinctive pigment patterns. The two species can be distinguished most easily by the different distribution of their melanophores. The adults spawn in estuaries and larvae are presumed to remain in estuaries before migrating to adult freshwater habitat. However, larvae of both species were collected as they entered a central New South Wales estuary from the ocean on flood tides; such transport may have consequences for the dispersal of larvae among estuaries. Larval morphology and published genetic evidence supports a reconsideration of the generic arrangement of the four species currently placed in the genus Macquaria.

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Spencer Fullerton Baird (Fig. 1), a noted systematic zoologist and builder of scientific institutions in 19th century America, persuaded the U.S. Congress to establish the United States Commission of Fish and Fisheries1 in March 1871. At that time, Baird was Assistant Secretary of the Smithsonian Institution. Following the death of Joseph Henry in 1878, he became head of the institution, a position he held until his own demise in 1887. In addition to his many duties as a Smithsonian official, including his prominent role in developing the Smithsonian’s Federally funded National Museum as the repository for governmental scientific collections, Baird directed the Fish Commission from 1871 until 1887. The Fish Commission’s original mission was to determine the reasons and remedies for the apparent decline of American fisheries off southern New England as well as other parts of the United States. In 1872, Congress further directed the Commission to begin a large fish hatching program aimed at increasing the supply of American food f