Estimating age of spotted and spinner dolphins (Stenella attenuata and Stenella longirostris) from teeth

This paper is an account of preparation and examination techniques and criteria used to estimate age in decalcified and stained tooth thin sections from spinner and spotted dolphins. A dentinal growth layer group (GLG), composed of two thin light and two thicker dark-stained layers, is deposited annually. The GLG component layers are variably visible, but the "ideal" pattern and successive thinning of dentinal GLGs are used as a guide to determine GLG limits. Age-specific thicknesses of dentinal GLGs found in Hawaiian spinner dolphin teeth seem to be applicable to teeth of spotted dolphins and can be used as an aid in locating GLG boundaries. Cementa1 GLGs are composed of a dark-stained and alightly stained layer and usually are deposited at a rate of one per year, but may be deposited every other year or two or three times per year. Two slightly different methods of counting dentinal GLGs are presented, along with guidelines for determining whether dentinal or cementa1 GLG counts provide the best estimate of age for a specimen. (PDF contains 23 pages.)

An increment technique for estimating growth parameters of tropical tunas, as applied to yellowfin tuna (Thunnus albacares)

ENGLISH: The rate of growth of tropical tunas has been studied by various investigators using diverse methods. Hayashi (1957) examined methods to determine the age of tunas by interpreting growth patterns on the bony or hard parts, but the results proved unreliable. Moore (1951), Hennemuth (1961), and Davidoff (1963) studied the age and growth of yellowfin tuna by the analysis of size frequency distributions. Schaefer, Chatwin and Broadhead (1961), and Fink (ms.), estimated the rate of growth of yellowfin tuna from tagging data; their estimates gave a somewhat slower rate of growth than that obtained by the study of length-frequency distributions. For the yellowfin tuna, modal groups representing age groups can be identified and followed for relatively long periods of time in length-frequency graphs. This may not be possible, however, for other tropical tunas where the modal groups may not represent identifiable age groups; this appears to be the case for skipjack tuna (Schaefer, 1962). It is necessary, therefore, to devise a method of estimating the growth rates of such species without identifying the year classes. The technique described in this study, hereafter called the "increment technique", employs the measurement of the change in length per unit of time, with respect to mean body length, without the identification of year classes. This technique is applied here as a method of estimating the growth rate of yellowfin tuna from the entire Eastern Tropical Pacific, and from the Commission's northern statistical areas (Areas 01-04 and 08) as shown in Figure 1. The growth rates of yellowfin tuna from Area 02 (Hennemuth, 1961) and from the northern areas (Davidoff, 1963) have been described by the technique of tracing modal progressions of year classes, hereafter termed the "year class technique". The growth rate analyses performed by both techniques apply to the segment of the population which is captured by tuna fishing vessels. The results obtained by both methods are compared in this report. SPANISH: La tasa del crecimiento de los atunes tropicales ha sido estudiada por varios investigadores quienes usaron diversos métodos. Hayashi (1957) examinó los métodos para determinar la edad de los atunes interpretando las marcas del crecimiento de las partes óseas o duras, pero los resultados no han demostrado eficacia. Moore (1951), Hennemuth (1961) y Davidoff (1963) estudiaron la edad y el crecimiento del atún aleta amarilla por medio del análisis de las distribuciones de la frecuencia de tamaños. Schaefer, Chatwin y Broadhead (1961) y Fink (Ms.), estimaron la tasa del crecimiento del atún aleta amarilla valiéndose de los datos de la marcación de los peces; ambos estimaron una tasa del crecimiento algo más lenta que la que se obtiene mediante el estudio de las distribuciones de la frecuencia de longitudes. Para el atún aleta amarilla, los grupos modales que representan grupos de edad pueden ser identificados y seguidos durante períodos de tiempo relativamente largos en los gráficos de la frecuencia de longitudes. Sin embargo, ésto puede no ser posible para otros atunes tropicales para los cuales los grupos modales posiblemente no representan grupos de edad identificables; este parece ser el caso para el barrilete (Schaefer, 1962). Consecuentemente, es necesario idear un método para estimar las tasas del crecimiento de las mencionadas especies sin necesidad de identificar las clases anuales. La técnica descrita en este estudio, en adelante llamada la "técnica incremental", emplea la medida del cambio en la longitud por unidad de tiempo, con respecto al promedio de la longitud corporal, sin tener que identificar las clases anuales. Esta técnica se aplica aquí como un método para estimar la tasa del crecimiento del atún aleta amarilla de todo el Pacífico Oriental Tropical, y de las áreas estadísticas norteñas de la Comisión (Areas 01-04 y 08), como se muestra en la Figura 1. Las tasas del crecimiento del atún aleta amarilla del Area 02 (Hennemuth, 1961) y de las áreas del norte (Davidoff, 1963), han sido descritas por medio de una técnica que consiste en delinear las progresiones modales de las clases anuales, en adelante llamada la "técnica de la clase anual". Los análisis de la tasa del crecimiento llevados a cabo por ambas técnicas se refieren al segmento de la población capturada por embarcaciones pesqueras de atún. Los resultados obtenidos por ambos métodos se comparan en este informe.

A method for estimating the rate of shedding of tags from yellowfin tuna

ENGLISH: The present paper describes a new method for estimating the shedding rate of tags. The method utilizes not only data on tagging and recovery of fish marked with two tags but also data from those marked with one. One important advantage of the new technique is that the estimates of the shedding rates are free from distortion caused by variations in fishing intensity during the total recovery period. The idea of this method appears to be implicit in a short note by Gulland (1963). This technique has been applied to the data obtained by the Inter-American Tropical Tuna Commission in a tagging cruise off the west coast of southern Baja California, during June 1963, at which time both single and double-tagged yellowfin tuna were released. Details of the tagging procedure and equipment have been described by Fink (1965b). The results presented in the present paper are for yellowfin tuna tagged with dart tags. Estimates of shedding should be made separately for each species investigated and also for each type of tag used, since these rates may be variable and often unexpectedly high (Springer and McErlean 1961, Chadwick 1963). SPANISH: El presente estudio describe un nuevo método para estimar las tasas del desprendimiento de marcas. El método emplea no solamente los datos sobre la marcación y recobro de peces marcados con dos marcas, pero también datos de los peces marcados con una marca. Una ventaja importante de la nueva técnica, es que las estimaciones de las tasas de desprendimiento son libres de alteración, causada por las variaciones en la intensidad de pesca durante el período total de recobro. La idea de este método parece ser implícita en un breve apunte por Gulland (1963). Esta técnica se ha aplicado a los datos obtenidos por la Comisión Interamericana del Atún Tropical, en un crucero de marcación efectuado frente a la costa occidental al sur de Baja California, en junio de 1963, tiempo en el cual fueron liberados atunes aleta amarilla marcados tanto con una como con dos marcas. Los detalles del procedimiento de la marcación y del equipo usado han sido descritos por Fink (1965b). Los resultados presentados en este estudio, pertenecen al atún aleta amarilla marcado con marcas de dardo. Las estimaciones del desprendimiento deben efectuarse separadamente para cada especie que ha sido investigada y también para cada tipo de marca usado, ya que estas tasas pueden ser vaiables, y a menudo inesperadamente altas (Springer y McErlean 1961, Chadwick 1963). (PDF contains 20 pages.)

Effects of the Cessation of Sewage Sludge Dumping at the 12-Mile Site: Proceedings of the 12-Mile Dumpsite Symposium, Ocean Place Hilton Hotel, Long Branch, New Jersey, 18-19 June 1991

This study owes its inception to the wisdom and experience of the staff of the Northeast Fisheries Science Center who, after several decades of surveys in the New York Bight, recognized a unique opportunity to capitalize on the decision to stop ocean dumping of sewage sludge and designed an innovative field study to evaluate effects on living marine resources and their habitats. For decades ocean dumping was viewed as a cheap and effective means for disposal of wastes generated by urbanized coastal areas. Even after the 12-mile site was closed, sewage sludge continued to be dumped at Deepwater Dumpsite 106. The 6-mile site off the NewJersey coast is still used as a dumpsite for dredged material from New York Harbor areas. Discussions continue on the propriety of using the deep ocean spaces for disposal of a variety of material including low level radioactive wastes. Consequently, managers are still faced with critical decisions in this area. It is to be hoped that the results from the 12-mile study will provide the necessary information on which these managers can evaluate future risks associated with ocean waste disposal. (PDF file contains 270 pages.)

An egg production method for estimating spawning biomass of pelagic fish: Application to the northern anchovy, Engraulis mordax

Fishery scientists engaged in estimating the size of free-swimming populations have never had a technique available to them whereby all the parameters could be estimated from a resource survey and where no parameter values need to be assumed. Recognizing the need for a technique of this kind, the staff of the Coastal Fisheries Resources Division of the Southwest Fisheries Center (SWFC) devised an egg production method for anchovy biomass assessment. Previously, anchovy biomass was estimated by approximate methods derived from a long-time series and anchovy larval abundance, which required about 5 ma of shiptime each year to integrate the area under a seasonal spawning curve. One major assumption used in the larval abundance census method is that there is constant proportionality between larval numbers and spawning biomass. This has now proved to be erroneous. (PDF file contains 105 pages.)

The lowland dry zone of Sri Lanka: site for study of aquaculture development within farmer-managed irrigation systems and methodology for participatory situation appraisal

The aims of this paper are twofold. Firstly to characterise rural poverty and to give a broad overview of the agro-ecological, climatic and socio-economic conditions in Sri Lanka which shape poverty. Secondly to present the methodology employed to screen suitable field research areas and the techniques subsequently used to carry out Rapid Rural Appraisal in two upper-watersheds villages. Also presented are details of a concurrent stakeholder analysis that aimed to investigate the capacity of secondary stakeholders to promote sustainable aquatic resource development and to invite their participation in the formulation of a participatory research agenda.[PDF contains 58 pages]

Valuing a Natura 2000 network site to inform land use options using a discrete choice experiment: An illustration from the Basque Country

One of the main problems that public institutions face in the management of protected areas, such as the European Natura 2000 network, is determining how to design and implement sustainable management plans that account for the wide range of marketed and non-marketed benefits they provide to society. This paper presents an application of a stated preference valuation approach aimed at evaluating the social preferences of the population of the Basque Country, Spain, for the key attributes of a regional Natura 2000 network site. According to our results, individuals’ willingness-to-pay (WTP) is higher for attributes associated with non-use values (native tree species and biodiversity conservation) than for attributes associated with use values (agricultural development and commercial forestry). The paper concludes that management policies related to Natura 2000 network sites should account for both for the importance of non-use values and the heterogeneity of the population's preferences in order to minimize potential land use conflicts.

The use of aerial photographs for estimating school sizes of cetaceans

ENGLISH: The accuracy and precision of dolphin school size estimates based on aerial photograph counts were examined using data collected on recent aerial and ship surveys. These estimates were found to be accurate during a 1979research cruise aboard a tuna purse-seiner; dolphin schools were photographed from the ship’s helicopter, encircled with the purse-seine, and then counted as the dolphins were released from the net. A comparison of photographic estimates with these counts indicated that the relationship was fairly close and gave no indication of significantly differing from 1:1. During a 1980 aerial study, photographic estimates from different schools, passes, and camera formats were compared and were found to be quite precise with a standard deviation of approximately 60/0 of school size. Photographic estimates were also compared with estimates made by aerial observers. Most observers tended to underestimate school size, particularly for large schools. The variability among observers was high, indicating that observers should be individually calibrated. SPANISH: Se examinó la exactitud y la precisión de las estimaciones de la magnitud de los cardúmenes de delfines basadas en el cálculo de las fotografías aéreas, usando los datos obtenidos en los últimos reconocimientos aéreos y de los barcos. En 1979, durante un crucero de investigación en un cerquero atunero, se encontró que estas estimaciones eran acertadas; se fotografiaron los cardúmenes de delfines desde un helicóptero del barco, cercados con la red y luego se contaron a medida que se libraban los delfines de la red. Una comparación de las estimaciones fotográficas con estos cálculos indicó que la relación era bastante aproximada y no hubo indicación que se diferenció significativamente de la razón 1:1. Durante un estudio aéreo en 1980, se compararon las estimaciones fotográficas de diferentes del cardúmenes, en los pases y los formatos de las cámaras y se encontró que eran bastante precisos, con una desviación normal de cerca del 60/0 de la magnitud cardumen. Se compararon también las estimaciones fotográficas con las estimaciones realizadas por los observadores aéreos. La mayoría de los observadores tienden a subestimar la magnitud de los cardúmenes, especialmente los cardúmenes grandes. La variabilidad entre los observadores fue elevada, lo que indica que se deben calibrar individualmente los datos de observadores. (PDF contains 39 pages.)

Report on estimating the size of dolphin schools, based on data obtained during a charter cruise of the M/V Gina Anne, October 11 -November 25, 1979

Estimates of dolphin school sizes made by observers and crew members aboard tuna seiners or by observers on ship or aerial surveys are important components of population estimates of dolphins which are involved in the yellowfin tuna fishery in the eastern Pacific. Differences in past estimates made from tuna seiners and research ships and aircraft have been noted by Brazier (1978). To compare various methods of estimating dolphin school sizes a research cruise was undertaken with the following major objectives: 1) compare estimates made by observers aboard a tuna seiner and in the ship's helicopter, from aerial photographs, and from counts made at the backdown channel, 2) compare estimates of observers who are told the count of the school size after making their estimate to the observer who is not aware of the count to determine if observers can learn to estimate more accurately, and 3) obtain movie and still photographs of dolphin schools of known size at various stages of chase, capture and release to be used for observer training. The secondary objectives of the cruise were to: 1) obtain life history specimens and data from any dolphins that were killed incidental to purse seining. These specimens and data were to be analyzed by the U.S. National Marine Fisheries Service ( NMFS ) , 2) record evasion tactics of dolphin schools by observing them from the helicopter while the seiner approached the school, 3) examine alternative methods for estimating the distance and bearing of schools where they were first sighted, 4) collect the Commission's standard cetacean sighting, set log and daily activity data and expendable bathythermograph data. (PDF contains 31 pages.)

Shoal manipulation as an effective solution to site specific beach management, examples from three South Carolina beaches

Soft engineering solutions are the current standard for addressing coastal erosion in the US. In South Carolina, beach nourishment from offshore sand deposits and navigation channels has mostly replaced construction of seawalls and groins, which were common occurrences in earlier decades. Soft engineering solutions typically provide a more natural product than hard solutions, and also eliminate negative impacts to adjacent areas which are often associated with hard solutions. A soft engineering solution which may be underutilized in certain areas is shoal manipulation. (PDF contains 4 pages)

The development of the South Carolina Coastal Information Network and portal site: Bringing training opportunities and educational resources to coastal community officials and the public

The South Carolina Coastal Information Network (SCCIN) emerged as a result of a number of coastal outreach institutions working in partnership to enhance coordination of the coastal community outreach efforts in South Carolina. This organized effort, led by the S.C. Sea Grant Consortium and its Extension Program, includes partners from federal and state agencies, regional government agencies, and private organizations seeking to coordinate and/or jointly deliver outreach programs that target coastal community constituents. The Network was officially formed in 2006 with the original intention of fostering intra-and inter- agency communication, coordination, and cooperation. Network partners include the S.C. Sea Grant Consortium, S.C. Department of Health and Environmental Control – Office of Ocean and Coastal Resource Management and Bureau of Water, S.C. Department of Natural Resources – ACE Basin National Estuarine Research Reserve, North Inlet-Winyah Bay National Estuarine Research Reserve, Clemson University Cooperative Extension Service and Carolina Clear, Berkeley-Charleston-Dorchester Council of Governments, Waccamaw Regional Council of Governments, Urban Land Institute of South Carolina, S.C. Department of Archives and History, the National Oceanic and Atmospheric Administration – Coastal Services Center and Hollings Marine Laboratory, Michaux Conservancy, Ashley-Cooper Stormwater Education Consortium, the Coastal Waccamaw Stormwater Education Consortium, the S.C. Chapter of the U.S. Green Building Council, and the Lowcountry Council of Governments. (PDF contains 3 pages)

Binding site size limitations of imidazole-pyrrole polyamides for recognition in the minor groove of DNA

The discovery that the three ring polyamide Im-Py-Py-Dp containing imidazole (Im) and pyrrole (Py) carboxamides binds the DNA sequence 5'-(A,T)G(A,T)C(A,T)-3' as an antiparallel dimer offers a new model for the design of ligands for specific recognition of sequences in the minor groove containing both G,C and A,T base pairs. In Chapter 2, experiments are described in which the sequential addition of five N- methylpyrrolecarboxamides to the imidazole-pyrrole polyamide Im-Py-Py-Dp affords a series of six homologous polyamides, Im-(Py)_2-7-Dp, that differ in the size of their binding site, apparent first order binding affinity, and sequence specificity. These results demonstrate that DNA sequences up to nine base pairs in length can be specifically recognized by imidazole-pyrrole polyamides containing three to seven rings by 2:1 polyamide-DNA complex formation in the minor groove. Recognition of a nine base pair site defines the new lower limit of the binding site size that can be recognized by polyamides containing exclusively imidazole and pyrrolecarboxamides. The results of this study should provide useful guidelines for the design of new polyamides that bind longer DNA sites with enhanced affinity and specificity.

In Chapter 3 the design and synthesis of the hairpin polyamide Im-Py-Im-Py-γ-Im- Py-Im-Py-Dp is described. Quantitative DNase I footprint titration experiments reveal that Im-Py-Im-Py-γ-Im-Py-Im-Py-Dp binds six base pair 5'-(A,T)GCGC(A,T)-3' sequences with 30-fold higher affinity than the unlinked polyamide Im-Py-Im-Py-Dp. The hairpin polyamide does not discriminate between A•T and T•A at the first and sixth positions of the binding site as three sites 5'-TGCGCT-3', 5'-TGCGCA-3', and 5 'AGCGCT- 3' are bound with similar affinity. However, Im-Py-Im-Py-γ-Im-Py-Im-PyDp is specific for and discriminates between G•C and C•G base pairs in the 5'-GCGC-3' core as evidenced by lower affinities for the mismatched sites 5'-AACGCA-3', 5'- TGCGTT-3', 5'-TGCGGT-3', and 5'-ACCGCT-3'.

In Chapter 4, experiments are described in which a kinetically stable hexa-aza Schiff base La³⁺ complex is covalently attached to a Tat(49-72) peptide which has been shown to bind the HIV-1 TAR RNA sequence. Although these metallo-peptides cleave TAR site-specifically in the hexanucleotide loop to afford products consistent with hydrolysis, a series of control experiments suggests that the observed cleavage is not caused by a sequence-specifically bound Tat(49-72)-La(L)³⁺ peptide.

Characterizing the regulation of mitochondrial nucleoids

Mitochondria contain a 16.6 kb circular genome encoding 13 proteins as well as mitochondrial tRNAs and rRNAs. Copies of the genome are organized into nucleoids containing both DNA and proteins, including the machinery required for mtDNA replication and transcription. Although mtDNA integrity is essential for cellular and organismal viability, regulation of proliferation of the mitochondrial genome is poorly understood. To elucidate the mechanisms behind this, we chose to study the interplay between mtDNA copy number and the proteins involved in mitochondrial fusion, another required function in cells. Strikingly, we found that mouse embryonic fibroblasts lacking fusion also had a mtDNA copy number deficit. To understand this phenomenon further, we analyzed the binding of mitochondrial transcription factor A, whose role in transcription, replication, and packaging of the genome is well-established and crucial for cellular maintenance. Using ChIP-seq, we were able to detect largely uniform, non-specific binding across the genome, with no occupancy in the known specific binding sites in the regulatory region. We did detect a single binding site directly upstream of a known origin of replication, suggesting that TFAM may play a direct role in replication. Finally, although TFAM has been previously shown to localize to the nuclear genome, we found no evidence for such binding sites in our system.

To further understand the regulation of mtDNA by other proteins, we analyzed publicly available ChIP-seq datasets from ENCODE, modENCODE, and mouseENCODE for evidence of nuclear transcription factor binding to the mitochondrial genome. We identified eight human transcription factors and three mouse transcription factors that demonstrated binding events with the classical strand asymmetrical morphology of classical binding sites. ChIP-seq is a powerful tool for understanding the interactions between proteins and the mitochondrial genome, and future studies promise to further the understanding of how mtDNA is regulated within the nucleoid.