Underwater Passive Acoustic Monitoring for Remote Regions, Hawaii Institute of Marine Biology, Coconut Island, Hawaii, February 7-9, 2007: workshop proceedings

The Alliance for Coastal Technologies (ACT) convened a workshop, sponsored by the Hawaii-Pacific and Alaska Regional Partners, entitled Underwater Passive Acoustic Monitoring for Remote Regions at the Hawaii Institute of Marine Biology from February 7-9, 2007. The workshop was designed to summarize existing passive acoustic technologies and their uses, as well as to make strategic recommendations for future development and collaborative programs that use passive acoustic tools for scientific investigation and resource management. The workshop was attended by 29 people representing three sectors: research scientists, resource managers, and technology developers. The majority of passive acoustic tools are being developed by individual scientists for specific applications and few tools are available commercially. Most scientists are developing hydrophone-based systems to listen for species-specific information on fish or cetaceans; a few scientists are listening for biological indicators of ecosystem health. Resource managers are interested in passive acoustics primarily for vessel detection in remote protected areas and secondarily to obtain biological and ecological information. The military has been monitoring with hydrophones for decades;however, data and signal processing software has not been readily available to the scientific community, and future collaboration is greatly needed. The challenges that impede future development of passive acoustics are surmountable with greater collaboration. Hardware exists and is accessible; the limits are in the software and in the interpretation of sounds and their correlation with ecological events. Collaboration with the military and the private companies it contracts will assist scientists and managers with obtaining and developing software and data analysis tools. Collaborative proposals among scientists to receive larger pools of money for exploratory acoustic science will further develop the ability to correlate noise with ecological activities. The existing technologies and data analysis are adequate to meet resource managers' needs for vessel detection. However, collaboration is needed among resource managers to prepare large-scale programs that include centralized processing in an effort to address the lack of local capacity within management agencies to analyze and interpret the data. Workshop participants suggested that ACT might facilitate such collaborations through its website and by providing recommendations to key agencies and programs, such as DOD, NOAA, and I00s. There is a need to standardize data formats and archive acoustic environmental data at the national and international levels. Specifically, there is a need for local training and primers for public education, as well as by pilot demonstration projects, perhaps in conjunction with National Marine Sanctuaries. Passive acoustic technologies should be implemented immediately to address vessel monitoring needs. Ecological and health monitoring applications should be developed as vessel monitoring programs provide additional data and opportunities for more exploratory research. Passive acoustic monitoring should also be correlated with water quality monitoring to ease integration into long-term monitoring programs, such as the ocean observing systems. [PDF contains 52 pages]

Donut-Shaped Fingerprint In Homologous Polypeptide Relationships-A Topological Feature Related To Pathogenic Structural Changes In Conformational Disease

Features of homologous relationship of proteins can provide us a general picture of protein universe, assist protein design and analysis, and further our comprehension of the evolution of organisms. Here we carried Out a Study of the evolution Of protein molecules by investigating homologous relationships among residue segments. The motive was to identify detailed topological features of homologous relationships for short residue segments in the whole protein universe. Based on the data of a large number of non-redundant Proteins, the universe of non-membrane polypeptide was analyzed by considering both residue mutations and structural conservation. By connecting homologous segments with edges, we obtained a homologous relationship network of the whole universe of short residue segments, which we named the graph of polypeptide relationships (GPR). Since the network is extremely complicated for topological transitions, to obtain an in-depth understanding, only subgraphs composed of vital nodes of the GPR were analyzed. Such analysis of vital subgraphs of the GPR revealed a donut-shaped fingerprint. Utilization of this topological feature revealed the switch sites (where the beginning of exposure Of previously hidden "hot spots" of fibril-forming happens, in consequence a further opportunity for protein aggregation is Provided; 188-202) of the conformational conversion of the normal alpha-helix-rich prion protein PrPC to the beta-sheet-rich PrPSc that is thought to be responsible for a group of fatal neurodegenerative diseases, transmissible spongiform encephalopathies. Efforts in analyzing other proteins related to various conformational diseases are also introduced. (C) 2009 Elsevier Ltd. All rights reserved.

A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features

As a basic tool of modern biology, sequence alignment can provide us useful information in fold, function, and active site of protein. For many cases, the increased quality of sequence alignment means a better performance. The motivation of present work is to increase ability of the existing scoring scheme/algorithm by considering residue–residue correlations better. Based on a coarse-grained approach, the hydrophobic force between each pair of residues is written out from protein sequence. It results in the construction of an intramolecular hydrophobic force network that describes the whole residue–residue interactions of each protein molecule, and characterizes protein's biological properties in the hydrophobic aspect. A former work has suggested that such network can characterize the top weighted feature regarding hydrophobicity. Moreover, for each homologous protein of a family, the corresponding network shares some common and representative family characters that eventually govern the conservation of biological properties during protein evolution. In present work, we score such family representative characters of a protein by the deviation of its intramolecular hydrophobic force network from that of background. Such score can assist the existing scoring schemes/algorithms, and boost up the ability of multiple sequences alignment, e.g. achieving a prominent increase (50%) in searching the structurally alike residue segments at a low identity level. As the theoretical basis is different, the present scheme can assist most existing algorithms, and improve their efficiency remarkably.

Studies on the biology of Gymnarchus niloticus in Lake Chad: Age determination and growth; meristic and morphometric characters

The meristic and morphometric characteristics of Gymnarchus niloticus are described and linear equations relating various parts of the body to the head length or total length are given. The age of G. niloticus in Lake Chad (Nigeria) was determined from growth marks on the opercular bones. The mean lengths for age, and mean weights for age obtained for the first five years of life are given. The assymptotic length and the von Betarlanffy growth parameters for the males and females combined are given

Preliminary observations on the feeding, habits and reproduction biology of Gymnarchus niloticus from Lake Chad

The preliminary results obtained from the study of stomach contents of specimens of Gymnarchus niloticus of a size ranging from 56 cm (66 grams) to 152 cm (12.0 kg.) from August to December, 1982 indicate for these sizes an exclusively piscivorous diet. The predominant prey species in Lake Chad are Tilapia/Sarotherodon , and Clarias . The prey is often cut in two parts before it is swallowed. Small prey may be swallowed whole. The implication of this prey capture method on prey-predator relationship and therefore the impact of the predator is discussed. The breeding season of Gymnarchus niloticus in Lake Chad has been deduced from observation of changes in gonad maturity stages and the results indicate that breeding takes place between August and November. Data are also presented on the fecundity, size of ripe eggs and probable size at maturity

Conservation needs of fisheries resources and reorientation for sustainable captive and culture practices

A discussion is presented on the importance of conservation of fishery resources, considering in particular the situation in Nigeria and providing also an outline of various legislations made by government. Suggestions are given regarding the following: education on the importance of conservation; fish farming or aquaculture; restocking or rejuvenation of depleted water bodies; stock assessment; monitoring and surveillance; provision of fishing inputs; and, extension research linkage

Reproductive biology of black skipjack, Euthynnus lineatus, an Eastern Pacific tuna

(PDF contains 94 pages.)

Whales and Sonar: Environmental Exemptions for the Navy's Mid-Frequency Active Sonar Training.

Mid-frequency active (MFA) sonar emits pulses of sound from an underwater transmitter to help determine the size, distance, and speed of objects. The sound waves bounce off objects and reflect back to underwater acoustic receivers as an echo. MFA sonar has been used since World War II, and the Navy indicates it is the only reliable way to track submarines, especially more recently designed submarines that operate more quietly, making them more difficult to detect. Scientists have asserted that sonar may harm certain marine mammals under certain conditions, especially beaked whales. Depending on the exposure, they believe that sonar may damage the ears of the mammals, causing hemorrhaging and/or disorientation. The Navy agrees that the sonar may harm some marine mammals, but says it has taken protective measures so that animals are not harmed. (PDF contains 20 pages)

Contributions to the biology of the engraulid Anchoa naso (Gilbert and Pierson, 1898) from Ecuadorian waters

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.)

Distribucion del genero Anodontites (Mollusca: Bivalvia: Mycetopodidae) en Uruguay

Distribution of the genus Anodontites (Mollusca: Bivalvia: Mycetopodidae) in Uruguay. Seven species of the freshwater mussel genus Anodontites were recorded from Uruguay. The populations of these bivalves suffer the negative effects of invasive bivalves, damming, industrial and urban discharges, and agrotoxic runoff. The distribution of these species is generally characterized at the level of basin or politic divisions, and precise geographic records are scarce. In order to detail the distribution of those species, the most representative collections of Uruguay were examined, the material of Anodontites was identified (612 records) and geographic coordenates were assigned at each locality (213 localities), using Geographic Information System (GIS) to obtain a distribution map for each species. Most of the localities with Anodontites were located in the left margin of Uruguay River and southwest of Uruguay, mainly in Soriano, Artigas, Salto and Colonia departments. The Salto Grande basin presented the highest species richness. The species with a highest number of records was A. patagonicus, which was also recorded in all basins. A. trapesialis and A. tenebricosus had a wide distribution and a high number of records. A. lucidus and A. ferrarisii, had a wide distribution (more than 6 basins) but comparatively lower number of records. Finally A. trapezeus and A. trigonus showed a limited distribution. There is a critical lack of samples in Merín Lagoon, Atlantic and Upper Negro River basins. It is necessary to carry out new sampling considering many variables in order to evaluate the current distribution and the ecologic preferences for each species.

Spawning seasons of Rasbora tawarensis (Pisces: Cyprinidae) in Lake Laut Tawar, Aceh Province, Indonesia

Rasbora tawarensis is an endemic freshwater fish in Lake Laut Tawar, Aceh Province, Indonesia. Unfortunately, its status is regarded a critical endangered with populations decreasing in recent years. To date no information on the spawning activities of the fish are available. Therefore, this study provides a contribution to the. knowledge on reproductive biology of R. tawarensis especially on spawning seasons as well as basic information for conservation of the species. Monthly sampling was conducted from April 2008 to March 2009 by using selective gillnets. The gonadosomatic index, size composition and sex ratio were assessed. The gonadal development was evaluated based on macroscopic and microscopic examinations of the gonads. The gonadosomatic index (GSI) varied between 6.65 to 18.16 in female and 4.94 to 8.56 for male. GSI of the female R. tawarensis was higher in March, September and December indicating the onset of reproductive seasons, the GSI and oocyte size being directly correlated with gonadal development stages. Although, a greater proportion of mature male than female was detected during the study, the sex ratio showed that the overall number of female was higher than male. The ovaries had multiple oocyte size classes at every stage of gonadal development, thus R. tawarensis can be classified as a group synchronous spawner or a fractional multiple spawner. The spawning seasons of R. tawarensis were three times a year and September being the peak of the reproductive season and the female was the predominant sex. This species is classified as a group synchronous spawner. (PDF contains 8 pages)

Aspects of the biology of the lagoon crab Callinectes amnicola (Derocheburne) in Badagry, Lagos and Lekki lagoons, Nigeria

A preliminary report of the size, composition, growth pattern and food habits of the blue crab, Callinectes amnicola, (De Rocheburne) in the Badagry, Lagos and Lekki Lagoons (Nigeria) is presented. The collection of crabs from the three lagoons covered the period from May 1999 to October 2000. The carapace length for Badagry Lagoon ranged from 2.2 cm to 16.4 cm with weight of 4.4 g to 252.6 g. The crabs showed a unimodal size distribution. For the Lagos Lagoon, crabs sizes ranged from 3.5 cm to 16.8 cm and weighed 3.28 to 277.1 g. The sizes of crabs in the Lekki Lagoon ranged from 3.5 cm to 16.1 cm and weighed 3.5 g to 262.7 g. Crabs from the three lagoons exhibited negative allometric growth. The food items were similar in the three lagoons and comprised mainly mollusc shells, fish parts, shrimps and crab appendages and occasionally higher plant materials

Aspects of the reproductive biology of Mugil cephalus (Linnaeus, 1857) in Bonny Estuary

Aspects of the reproductive biology of Mugil cephalus in the Bonny estuary (Nigeria) were studied between January and December 1996. Males were observed to be more slender than females while the females have deeper bodies. The male:female ratio (1:0:95) was not significantly different. The minimum size at maturity was 16.6cm (0.5 yr). Fish matured at 24.3cm TL(1.76 yr) with median maturity size of 19.5cm TL(0.71 yr). Median maturity for male and female fish were 16.4cm TL(0.41 yr) and 18.2cm TL(0.60 yr) respectively. Breeding occurred once a year between September and December, from late rainy season to early dry season. Mean absolute fecundity was 1,403, 808 eggs (range 107, 729-4,445, 423 eggs) for fish of 17.0.29.5cm TL (mean 22.5cm TL). Fecundity correlated positively with fish total weight, length, ovary weight and age

A review of the biology, ecology and management of Scirpus Olneyi. Volume 1: An annotated bibliography of selected references

This annotated bibliography of selected literature on Olney's three7square (Scirpus olneyi Gray )compiled basically for two reasons: 1) to assist a task force in its pursuit of an explanation for the substantial reduction in marsh acreage at the Blackwater National Wildlife Refuge in Dorchester County, Maryland, and 2) to serve as the author's foundation for the initiation of ecological research on this species as partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Botany Department of the University of Maryland. Both purposes are directly related in that the Author's research will be of use to the task force, along I with its other technical information and research results, in under-standing and possibly correcting the marshland loss problem at the Refuge. (PDF contains 100 pages)

Reproductive biology of Orechromis niloticus (L.) (Pisces: Cichlidae) in the Nyanza Gulf of Lake Victoria

Fish samples were collected using seine and trawl nets in Nyanza Gulf, Lake Victoria (Kenya) in order to study the reproductive and gonadal patterns of Oreochromis niloticus; samples were collected from June 1998 to February 1999. The variation in relative condition factor and monthly variation in gonad weight showed spawning took place between June and July. Most ripe fish were recovered between November and February, while a slight drop in GSI for males was noted between November and January. External factors triggering reproductive strategy are now being addressed