Soft-Shell Clam (Mya Arenaria) Distribution & Abundance at Selected Sites in the Great Bay Estuary

Previous surveys (1996 to 2002) provided distribution and abundance data for soft-shell clam (Mya arenaria) populations in ten areas of the Great Bay and Piscataqua River estuaries identified as potentially good clam habitat. The present study was designed to complete the overall survey by sampling six remaining areas: Weeks Point, Brackett\u27s Point, Squamscott River mouth, Moody Point, Herods Cove, and Upper Little Bay (western shore). The objectives of the present project were to: (1) visually inspect the six study areas for the general distribution of sediment types and soft-shell clams, (2) quantitatively sample the six areas to determine densities of soft-shell clams, (3) produce GIS maps based on the survey data, and (4) assess clam distributions considering data from the present study and previous research. At each of the six sampling areas, the approximate boundary of potential clam habitat (=intertidal soft sediments) was determined by visual inspection at low tide. Notes were made on changes in major sediment types, the presence of clam siphon holes, and empty clam shells. At each site, nine to fourteen 0.125 m2 quadrats were haphazardly tossed onto the sediment surface, excavated to at least 20 cm depth using clam rakes, and all excavated sediments washed through a 5 mm mesh sieve. All clams retained on the sieve were measured (shell length to nearest mm with calipers), counted, and returned to the general area. A sample of the upper 5 cm of sediment was collected from each quadrat and stored at Jackson Estuarine Laboratory. Quadrat locations were geo-referenced using DGPS.The general environmental conditions in all six areas appeared suitable as soft-shell clam habitat. However, very few live clams were collected and very few empty shells were observed. From a total of 65 excavated quadrats, only 8 live clams were collected with mean densities ranging from 0.0 to 3.1/m2 at the six sites. It was concluded that none of the six areas were productive clam flats at the time of sampling, and they probably had not been in the recent past. Previous research and the present study indicate that many of the expansive intertidal flats in the Great Bay/Piscataqua River system have not been productive clam habitat for decades, probably since at least the 1940s in some areas. However, moderate to high densities of clams have been reported in some areas, particularly in sandy sediments. Previous research also showed high densities of early post-set clams in some areas, suggesting that spat mortality (probably predation effects) may be an important cause of low densities of larger clams in these areas. Future research should focus on sandy sediments and mixed soft sediments with cobble to better characterize the distribution and abundance of clams in the Great Bay/Piscataqua River system. Future research also should assess the role of predation on newly set spat in controlling clam populations

Retinal pigmented epithelium does not transdifferentiate in adult goldfish

The neural retina of adult goldfish can regenerate from an intrinsic source of proliferative neuronal progenitor cells, but it is not known whether the retina can regenerate by transdifferentiation of the retinal pigmented epithelium (RPE), a phenomenon demonstrated in adult newts. In this study, we asked whether following surgical removal of the neural retina in adult goldfish the RPE was capable of autonomously transdifferentiating and generating new neural retina. The retina was prelabeled by injecting the fluorescent dye Fluoro-Gold (FG) into the eye prior to surgical removal; this procedure ensured that residual retina was labeled with FG and could therefore be distinguished from unlabeled, regenerated retina. To examine the time course of retinal regeneration, and to identify regenerated retinal neurons, the thymidine analogue bromodeoxyuridine was injected intraocularly, and retinas were examined up to 2 months later. We found that the RPE did not transdifferentiate; instead, retinas regenerated only when pieces of residual neural retina were left intact. Under these circumstances, newly regenerated cells derived from proliferating cells intrinsic to the residual neural retina. When retinas were completely removed, as was evident from a lack of FG labeling, there was no retinal regeneration. © 1995 John Wiley & Sons, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/50086/1/480270402_ftp.pd

Bottom habitat mapping using towed underwater videography: subtidal oyster reefs as an example application

Towed underwater video has become a widely used method for bottom habitat mapping in coastal waters, but very little has been published on this relatively new and effective approach. We use a case study on two oyster reefs to illustrate the pros and cons of towed video, visualization techniques, and future research topics. Towed video is deployed in similar fashion to single-beam sonars, yielding narrow swaths of video imagery that are recorded concurrently with global positioning system (GPS) data for georeferencing. The major advantages over acoustic (sonar) methods are that image processing and interpretation are relatively simple, and there is little or no need for subsequent ground-truthing. The system used in the present study consists of an underwater black and white camera mounted on a steel frame, differential GPS unit, and digital video camera for recording. It was assembled from off-the-shelf items, and total cost was approximately $3500 (2006 US$). The imagery from both study reefs was of sufficient quality to allow classification of the surveyed bottom into three categories: nonreef, low-density shell, and high-density shell. Some reef characteristics such as the amount of vertical relief were easily discernable and showed substantial differences between the two reefs. Reef bottom areal coverages determined from the video imagery compared well with recent previous studies on the two reefs using other methods. Water clarity limitations represent the major obstacle to widespread use of video for routine mapping of oyster reefs. Turbidity–image quality relations remain to be quantified

Effects of a Large Fishing Closure on Benthic Communitites in the Western Gulf of Maine: Recovery from the Effects of Gillnets and Otter Trawls

The recovery of benthic communities inside the western Gulf of Maine fishing closure area was evaluated by comparing invertebrate assemblages at sites inside and outside of the closure four to six years after the closure was established. The major restriction imposed by the closure was a year-round prohibition of bottom gillnets and otter trawls. A total of 163 seafloor sites (~half inside and half outside the closure) within a 515-km2 study area were sampled with some combination of Shipek grab, Wildco box corer, or underwater video. Bottom types ranged from mud (silt and clay) to boulders, and the effects of the closure on univariate measures (total density, biomass, taxonomic richness) of benthos varied widely among sediment types. For sites with predominantly mud sediments, there were mixed effects on inside and outside infauna and no effect on epifauna. For sites with mainly sand sediments, there were higher density, biomass, and taxonomic richness for infauna inside the closure, but no significant effects on epifauna. For sites dominated by gravel (which included boulders in some areas), there were no effects on infauna but strong effects on epifaunal density and taxonomic richness. For fishing gear, the data indicated that infauna recovered in sand from the impacts of otter trawls operated inside the closure but that they did not recover in mud, and that epifauna recovered on gravel bottoms from the impact of gillnets used inside the closure. The magnitudes of impact and recovery, however, cannot be inferred directly from our data because of a confounding factor of different fishing intensities outside the closure for a direct comparison of preclosure and postclosure data. The overall negative impact of trawls is likely underestimated by our data, whereas the negative impact of gillnets is likely overestimated

Biological, Social, and Urban Design Factors Affecting Young Street Tree Mortality in New York City

In dense metropolitan areas, there are many factors including traffic congestion, building development and social organizations that may impact the health of street trees. The focus of this study is to better understand how social, biological and urban design factors affect the mortality rates of newly planted street trees. Prior analyses of street trees planted by the New York City Department of Parks & Recreation between 1999 and 2003 (n=45,094) found 91.3% of those trees were alive after two years and 8.7% were either standing dead or missing completely. Using a site assessment tool, a randomly selected sample of 13,405 of these trees was surveyed throughout the City of New York during the summers of 2006 and 2007. Overall, 74.3% of the sample trees were alive when surveyed and the remainder were either standing dead or missing. Results of our initial analyses reveal that highest mortality rates occur within the first few years after planting, and that land use has a significant effect on street tree mortality. Trees planted in one- and two-family residential areas had the highest survival rates (82.7%), while young street trees planted in industrial areas, open space and vacant land had the lowest rates of street tree survival (60.3% -62.9%). Also significant in predicting street tree success and failure are species type, tree pit enhancements, direct tree care/stewardship, and local traffic conditions. These results are intended to inform urban forest managers in making decisions about the best conditions for planting new street trees

Crystal structures from the Plasmodium peroxiredoxins: new insights into oligomerization and product binding

<p>Abstract</p> <p>Background</p> <p><it>Plasmodium falciparum </it>is the protozoan parasite primarily responsible for more than one million malarial deaths, annually, and is developing resistance to current therapies. Throughout its lifespan, the parasite is subjected to oxidative attack, so <it>Plasmodium </it>antioxidant defences are essential for its survival and are targets for disease control.</p> <p>Results</p> <p>To further understand the molecular aspects of the <it>Plasmodium </it>redox system, we solved 4 structures of <it>Plasmodium </it>peroxiredoxins (Prx). Our study has confirmed <it>Pv</it>Trx-Px1 to be a hydrogen peroxide (H₂O₂)-sensitive peroxiredoxin. We have identified and characterized the novel toroid octameric oligomer of <it>Py</it>Trx-Px1, which may be attributed to the interplay of several factors including: (1) the orientation of the conserved surface/buried arginine of the NNLA(I/L)GRS-loop; and (2) the <it>C</it>-terminal tail positioning (also associated with the aforementioned conserved loop) which facilitates the intermolecular hydrogen bond between dimers (in an A-C fashion). In addition, a notable feature of the disulfide bonds in some of the Prx crystal structures is discussed. Finally, insight into the latter stages of the peroxiredoxin reaction coordinate is gained. Our structure of <it>Py</it>Prx6 is not only in the sulfinic acid (RSO₂H) form, but it is also with glycerol bound in a way (not previously observed) indicative of product binding.</p> <p>Conclusions</p> <p>The structural characterization of <it>Plasmodium </it>peroxiredoxins provided herein provides insight into their oligomerization and product binding which may facilitate the targeting of these antioxidant defences. Although the structural basis for the octameric oligomerization is further understood, the results yield more questions about the biological implications of the peroxiredoxin oligomerization, as multiple toroid configurations are now known. The crystal structure depicting the product bound active site gives insight into the overoxidation of the active site and allows further characterization of the leaving group chemistry.</p

The Prince and the Pauper: Evidence for the early high-redshift formation of the Galactic α\alpha-poor disc population

Context. The presence of [$\alpha$/Fe]-[Fe/H] bi-modality in the Milky Way disc has animated the Galactic archaeology community since more than two decades. Aims. Our goal is to investigate the chemical, temporal, and kinematical structure of the Galactic discs using abundances, kinematics, and ages derived self-consistently with the new Bayesian framework SAPP. Methods. We employ the public Gaia-ESO spectra, as well as Gaia EDR3 astrometry and photometry. Stellar parameters and chemical abundances are determined for 13 426 stars using NLTE models of synthetic spectra. Ages are derived for a sub-sample of 2 898 stars, including subgiants and main-sequence stars. The sample probes a large range of Galactocentric radii, $\sim$ 3 to 12 kpc, and extends out of the disc plane to $\pm$ 2 kpc. Results. Our new data confirm the known bi-modality in the [Fe/H] - [$\alpha$/Fe] space, which is often viewed as the manifestation of the chemical thin and thick discs. The over-densities significantly overlap in metallicity, age, and kinematics, and none of these is a sufficient criterion for distinguishing between the two disc populations. Different from previous studies, we find that the $\alpha$-poor disc population has a very extended [Fe/H] distribution and contains $\sim$ 20$\%$ old stars with ages of up to $\sim$ 11 Gyr. Conclusions. Our results suggest that the Galactic thin disc was in place early, at look-back times corresponding to redshifts z $\sim$ 2 or more. At ages $\sim$ 9 to 11 Gyr, the two disc structures shared a period of co-evolution. Our data can be understood within the clumpy disc formation scenario that does not require a pre-existing thick disc to initiate a formation of the thin disc. We anticipate that a similar evolution can be realised in cosmological simulations of galaxy formation.Comment: 14 pages, 10 figures, re-submitted to A&

Archeological Testing and Data Recovery at 41ZV202, Zavala County, Texas

At the request of the Texas Department of Transportation, Environmental Affairs Division (TxDOT-ENV), the Center for Archaeological Research (CAR) of The University of Texas at San Antonio (UTSA) conducted archeological significance testing at 41ZV202, a prehistoric site located in northwestern Zavala County, in March of 2003. The work, conducted under Texas Antiquities Permit No. 3071 issued to Dr. Steven A. Tomka, was done in anticipation of the potential widening by TxDOT of FM 481. While materials dating to the Archaic were also present, the testing demonstrated the presence of significant Late Prehistoric (Austin Interval) deposits with good integrity within a portion of the TxDOT right-of-way (ROW). As TxDOT construction could not avoid these deposits, and as both the Texas Historical Commission (THC) and TxDOT concurred with CAR’s recommendations that the deposits were eligible for listing on the National Register of Historic Places (NRHP) under criterion d of 36CFR 60.4, data recovery investigations were initiated. CAR began that work in July and August of 2003. The testing permit was amended to include the data recovery efforts. Dr. Russell Greaves served as project archeologist for both the testing and data recovery effort at 41ZV202. The testing and data recovery work consisted of the excavation of a 53-m-long Gradall trench, exposing and profiling a 75-m-long road cut, and the hand excavation of 52 1 x 1 meter units that removed approximately 34.6 m3 of soil. Testing identified two large, dark stained areas designated Features 4 and 5, an associated hearth (Feature 7), and a small cluster of FCR (Feature 6). Just over 1,000 chipped stone items were recovered, including several Scallorn points, one reworked dart point, several bifaces, and two flake tools. Eleven AMS radiocarbon dates were submitted from deposits, with eight clustering around 1000 BP. Data recovery efforts defined FCR features 8 through 13. In addition, 24 arrow points, several dart points, a variety of unifacial and bifacial tools, a small number of cores, roughly 6,000 pieces of debitage, and a variety of burned sandstone, were recovered. We also collected small quantities of bone and mussel shell along with about 14,350 gastropod shells, and a variety of soil samples. Finally, all calcium carbonate nodules were retained from the screens. Following the completion of data recovery efforts, the CAR was directed by TxDOT to develop a research design for the analysis of the material from 41ZV202. TxDOT and THC accepted that research design in November of 2004, at which time the CAR began analysis and report production. Unfortunately, by 2005 project archeologist Russell Greaves had left the CAR. At that point, CAR assistant director Dr. Raymond Mauldin took over the project. The analysis of the 41ZV202 Late Prehistoric data outlined in this report is conducted in the context of a large-scale, theoretically driven model of adaptation for hunters and gatherers loosely based on aspects of Optimal Foraging Theory. In addition to 41ZV202, the approach relies on comparative data sets from Late Archaic and other Late Prehistoric sites from South and South-Central Texas to investigate shifts in subsistence, technology, and mobility across this broad region. At this time, discard decisions have not been made. However, all artifacts and associated samples collected and retained during this project, along with all project-associated documentation, are to be permanently curated at the CAR according to Texas Historical Commission guidelines

Expression of rod and cone visual pigments in goldfish and zebrafish: A rhodopsin-like gene is expressed in cones

The primary purpose of the present study was to determine whether a rhodopsin-like gene, which has been postulated to represent the green cone pigment in several species, is in fact expressed in cone photoreceptors instead of rods. The expression patterns of rod opsin and blue and red cone opsins were also examined in both goldfish and zebrafish retinas using colorimetric in situ hybridization. The results demonstrate that the rhodopsin-like gene is expressed in green cones, as predicted. A subset of small cones that do not hybridize with these cRNA probes are tentatively identified as ultraviolet receptors. The results also demonstrate that opsin message in cones is restricted to the perinuclear region, whereas in rods, it is both perinuclear and adjacent to the ellipsoid.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/30780/1/0000433.pd