Demonstration of a compact InGaAsP active crosspoint switch operating at 1.5 μm using novel reflective y-coupler components

An extremely compact active optoelectronic crosspoint switch, having overall dimensions of 400 μm×200 μm, is reported. The device provides unity facet-to-facet gain for both bar and cross state operation for TE or TM input signals.

Staging ovaries of Haddock (Melanogrammus aeglefinus): implications for maturity indices and field sampling practices

We build on recent efforts to standardize maturation staging methods through the development of a field-proof macroscopic ovarian maturity index for Haddock (Melanogrammus aeglefinus) for studies on diel spawning periodicity. A comparison of field and histological observations helped us to improve the field index and methods, and provided useful insight into the reproductive biology of Haddock and other boreal determinate fecundity species. We found reasonable agreement between field and histological methods, except for the regressing and regenerating stages (however, differentiation of these 2 stages is the least important distinction for determination of maturity or reproductive dynamics). The staging of developing ovaries was problematic for both methods partly because of asynchronous oocyte hydration during the early stage of oocyte maturation. Although staging on the basis of histology in a laboratory is generally more accurate than macroscopic staging methods in the field, we found that field observations can uncover errors in laboratory staging that result from bias in sampling unrepresentative portions of ovaries. For 2 specimens, immature ovaries observed during histological examination were incorrectly assigned as regenerating during macroscopic staging. This type of error can lead to miscalculation of length at maturity and of spawning stock biomass, metrics that are used to characterize the state of a fish population. The revised field index includes 3 new macroscopic stages that represent final oocyte maturation in a batch of oocytes and were found to be reliable for staging spawning readiness in the field. The index was found to be suitable for studies of diel spawning periodicity and conforms to recent standardization guidelines.

Preliminary report on bottlenose dolphin (Tursiops truncatus) uterine samples for parity analysis

There have been numerous studies on various mammalian species regarding vascular changes in uterine arteries elucidating the effects of parity. In equids, vascular changes of uterine arteries have been demonstrated to occur in uniparous and multiparous mares. The severity of these arteriole changes suggests a link to previous pregnancies. Differences in the number or range of pregnancies can be ascertained through microscopic evaluation of elastin deposition in the arterioles, perivascular fibrosis, and stromal cellularity. There has been little, if any, work performed on parity in the bottlenose dolphin (Tursiops truncatus). The objective of this preliminary study was to determine the feasibility of detecting similar vascular changes in the endometrium of known-aged female bottlenose dolphins to assess parity. Archived formalin fixed samples of uterus were obtained from nine bottlenose dolphins with known age and parity. Four slides were made from each sample and individually stained with four different techniques. From our small sample pool, it appears that uteri from nulliparous animals do not develop perivascular fibrosis. Parous uteri developed perivascular fibrosis and arteriolar elastosis. These changes agree with our expectations that some degeneration (elastosis) and compensation (fibrosis) occurs as a result of uterine expansion of pregnancy. The assessment of this technique for use in bottlenose dolphins would provide an important tool in the determination of the reproductive success of dolphin populations, identify individuals who are sexually mature but nulliparous, which could indicate reproductive dysfunction or increased calving intervals, and increase our knowledge on the role contaminants play in reproductive dysfunction.

Report of 2009 Bottlenose Dolphin (Tursiops truncatus) Life History Workshop: expanding network capabilities

The Virginia Aquarium & Marine Science Center Foundation’s Stranding Response Program (VAQS) was awarded a grant in 2008 to conduct life history analysis on over 10 years of Tursiops truncatus teeth and gonad samples from stranded animals in Virginia. A major part of this collaborative grant included a workshop involving life historians from Hubbs-Sea World Research Institute (HSWRI), NOS, Texas A & M University (TAMU), and University of North Carolina Wilmington (UNCW). The workshop was held at the NOAA Center for Coastal Environmental Health & Biomolecular Research in Charleston, SC on 7-9 July 2009. The workshop convened to 1) address current practices among the groups conducting life history analysis, 2) decide on protocols to follow for the collaborative Prescott grant between VAQS and HSWRI, 3) demonstrate tissue preparation techniques and discuss shortcuts and pitfalls, 4) demonstrate data collection from prepared testes, ovaries, and teeth, and 5) discuss data analysis and prepare an outline and timeline for a future manuscript. The workshop concluded with discussions concerning the current collaborative Tursiops Life History Prescott grant award and the beginnings of a collaborative Prescott proposal with members of the Alliance of Marine Mammal Parks and Aquariums to further clarify reproductive analyses. This technical memorandum serves as a record of this workshop.

Saline-saturated DMSO-EDTA as a storage medium for microbial DNA analysis from coral mucus swab samples

The mucus surface layer of corals plays a number of integral roles in their overall health and fitness. This mucopolysaccharide coating serves as vehicle to capture food, a protective barrier against physical invasions and trauma, and serves as a medium to host a community of microorganisms distinct from the surrounding seawater. In healthy corals the associated microbial communities are known to provide antibiotics that contribute to the coral’s innate immunity and function metabolic activities such as biogeochemical cycling. Culture-dependent (Ducklow and Mitchell, 1979; Ritchie, 2006) and culture-independent methods (Rohwer, et al., 2001; Rohwer et al., 2002; Sekar et al., 2006; Hansson et al., 2009; Kellogg et al., 2009) have shown that coral mucus-associated microbial communities can change with changes in the environment and health condition of the coral. These changes may suggest that changes in the microbial associates not only reflect health status but also may assist corals in acclimating to changing environmental conditions. With the increasing availability of molecular biology tools, culture-independent methods are being used more frequently for evaluating the health of the animal host. Although culture-independent methods are able to provide more in-depth insights into the constituents of the coral surface mucus layer’s microbial community, their reliability and reproducibility rely on the initial sample collection maintaining sample integrity. In general, a sample of mucus is collected from a coral colony, either by sterile syringe or swab method (Woodley, et al., 2008), and immediately placed in a cryovial. In the case of a syringe sample, the mucus is decanted into the cryovial and the sealed tube is immediately flash-frozen in a liquid nitrogen vapor shipper (a.k.a., dry shipper). Swabs with mucus are placed in a cryovial, and the end of the swab is broken off before sealing and placing the vial in the dry shipper. The samples are then sent to a laboratory for analysis. After the initial collection and preservation of the sample, the duration of the sample voyage to a recipient laboratory is often another critical part of the sampling process, as unanticipated delays may exceed the length of time a dry shipper can remain cold, or mishandling of the shipper can cause it to exhaust prematurely. In remote areas, service by international shipping companies may be non-existent, which requires the use of an alternative preservation medium. Other methods for preserving environmental samples for microbial DNA analysis include drying on various matrices (DNA cards, swabs), or placing samples in liquid preservatives (e.g., chloroform/phenol/isoamyl alcohol, TRIzol reagent, ethanol). These methodologies eliminate the need for cold storage, however, they add expense and permitting requirements for hazardous liquid components, and the retrieval of intact microbial DNA often can be inconsistent (Dawson, et al., 1998; Rissanen et al., 2010). A method to preserve coral mucus samples without cold storage or use of hazardous solvents, while maintaining microbial DNA integrity, would be an invaluable tool for coral biologists, especially those in remote areas. Saline-saturated dimethylsulfoxide-ethylenediaminetetraacetic acid (20% DMSO-0.25M EDTA, pH 8.0), or SSDE, is a solution that has been reported to be a means of storing tissue of marine invertebrates at ambient temperatures without significant loss of nucleic acid integrity (Dawson et al., 1998, Concepcion et al., 2007). While this methodology would be a facile and inexpensive way to transport coral tissue samples, it is unclear whether the coral microbiota DNA would be adversely affected by this storage medium either by degradation of the DNA, or a bias in the DNA recovered during the extraction process created by variations in extraction efficiencies among the various community members. Tests to determine the efficacy of SSDE as an ambient temperature storage medium for coral mucus samples are presented here.

An ecological characterization of the marine resources of Vieques, Puerto Rico Part II: Field studies of habitats, nutrients, contaminants, fish, and benthic communities

Since the 1940s, portions of the Island of Vieques, Puerto Rico have been used by the United States Navy (USN) as an ammunition support detachment and bombing and maneuver training range. In April 2001, the USN began phasing out military activities on the island and transferring military property to the U.S. Department of the Interior, the Municipality of Vieques, and the Puerto Rico Conservation Trust. A small number of studies have been commissioned by the USN in the past few decades to assess selected components of the coral reef ecosystem surrounding the island; however, these studies were generally of limited geographic scope and short duration. The National Oceanic and Atmospheric Administration’s (NOAA) National Centers for Coastal Ocean Science (NCCOS), in consultation with NOAA’s Office of Response and Restoration (OR&R) and other local and regional experts, conducted a more comprehensive characterization of coral reef ecosystems, contaminants, and nutrient distribution patterns around Vieques. This work was conducted using many of the same protocols as ongoing monitoring work underway elsewhere in the U.S. Caribbean and has enabled comparisons among coral reef ecosystems in Vieques and other locations in the region. This characterization of Vieques’ marine ecosystems consists of a two part series. First, available information on reefs, fish, birds, seagrasses, turtles, mangroves, climate, geology, currents, and human uses from previous studies was gathered and integrated into a single document comprising Part I of this two part series (Bauer et al. 2008). For Part II of the series, presented in this document, new field studies were conducted to fill data gaps identified in previous studies, to provide an island-wide characterization, and to establish baseline values for the distribution of habitats, nutrients, contaminants, fish, and benthic communities. An important objective underlying this suite of studies was to quantify any differences in the marine areas adjacent to the former and current land-use zoning around Vieques. Specifically of interest was the possibility that either Naval (e.g., practice bombing, munitions storage) or civilian activities (e.g., sewage pollutants, overfishing) could have a negative impact on adjacent marine resources. Measuring conditions at this time and so recently after the land transfer was essential because present conditions are likely to be reflective of past land-use practices. In addition, the assessment will establish benchmark conditions that can be influenced by the potentially dramatic future changes in land-use practices as Vieques considers its development. This report is organized into seven chapters that represent a suite of interrelated studies. Chapter 1 provides a short introduction to the island setting, the former and current land-use zoning, and how the land zoning was used to spatially stratify much of the sampling. Chapter 2 is focused on benthic mapping and provides the methods, accuracy assessment, and results of newly created benthic maps for Vieques. Chapter 3 presents the results of new surveys of fish, marine debris, and reef communities on hardbottom habitats around the island. Chapter 4 presents results of flora and fauna surveys in selected bays and lagoons. Chapter 5 examines the distribution of nutrients in lagoons, inshore, and offshore waters around the island. Chapter 6 is focused on the distribution of chemical contaminants in sediments and corals. Chapter 7 is a brief summary discussion that highlights key findings of the entire suite of studies.

Microbial community analysis of Acropora palamata mucus swabs, water and sediment samples from Hawksnest Bay, St. John, U.S. Virgin Islands

Colonies of the scleractinian coral Acropora palmata, listed as threatened under the US Endangered Species Act in 2006, have been monitored in Hawksnest Bay, within Virgin Islands National Park, St. John, from 2004 through 2010 by scientists with the US Geological Survey, National Park Service, and the University of the Virgin Islands. The focus has been on documenting the prevalence of disease, including white band, white pox (also called patchy necrosis and white patches), and unidentified diseases (Rogers et al., 2008; Muller et al., 2008). In an effort to learn more about the pathologies that might be involved with the diseases that were observed, samples were collected from apparently healthy and diseased colonies in July 2009 for analysis. Two different microbial assays were performed on Epicentre Biotechnologies DNA swabs containing A. palmata coral mucus, and on water and sediment samples collected in Hawksnest Bay. Both assays are based on polymerase chain reaction (PCR) amplification of portions of the small rRNA gene (16S). The objectives were to determine 1) if known coral bacterial pathogens Serratia marcescens (Acroporid Serratiosis), Vibrio coralliilyticus (temperature-dependent bleaching, White Syndrome), Vibrio shiloi (bleaching, necrosis), and Aurantimonas coralicida (White Plague Type II) were present in any samples, and 2) if there were any differences in microbial community profiles of each healthy, unaffected or diseased coral mucus swab. In addition to coral mucus, water and sediment samples were included to show ambient microbial populations. In the first test, PCR was used to separately amplify the unique and diagnostic region of the 16S rRNA gene for each of the coral pathogens being screened. Each pathogen test was designed so that an amplified DNA fragment could be seen only if the specific pathogen was present in a sample. A positive result was indicated by bands of DNA of the appropriate size on an agarose gel, which separates DNA fragments based on the size of the molecule. DNA from pure cultures of each of the pathogens was used as a positive control for each assay.

Assessing the precision of frequency distributions estimated from trawl-survey samples

In trawl surveys a cluster of fish are caught at each station, and fish caught together tend to have more similar characteristics, such as length, age, stomach contents etc., than those in the entire population. When this is the case, the effective sample size for estimates of the frequency distribution of a population characteristic can, therefore, be much smaller than the number of fish sampled during a survey. As examples, it is shown that the effective sample size for estimates of length-frequency distributions generated by trawl surveys conducted in the Barents Sea, off Namibia, and off South Africa is on average approximately one fish per tow. Thus many more fish than necessary are measured at each station (location). One way to increase the effective sample size for these surveys and, hence, increase the precision of the length-frequency estimates, is to reduce tow duration and use the time saved to collect samples at more stations.

Improving pinniped diet analyses through identification of multiple skeletal structures in fecal samples

Marine mammal diet is typically characterized by identifying fish otoliths and cephalopod beaks retrieved from stomachs and fecal material (scats). The use and applicability of these techniques has been the matter of some debate given inherent biases associated with the method. Recent attempts to identify prey using skeletal remains in addition to beaks and otoliths are an improvement; however, difficulties incorporating these data into quantitative analyses have limited results for descriptive analyses such as frequency of occurrence. We attempted to characterize harbor seal (Phoca vitulina) diet in an area where seals co-occur with several salmon species, some endangered and all managed by state or federal agencies, or both. Although diet was extremely variable within sampling date, season, year, and between years, the frequency and number of individual prey were at least two times greater for most taxa when prey structures in addition to otoliths were identified. Estimating prey mass in addition to frequency and number resulted in an extremely different relative importance of prey in harbor seal diet. These data analyses are a necessary step in generating estimates of the size, total number, and annual biomass of a prey species eaten by pinnipeds for inclusion in fisheries management plans.