Histone H3K9 acetylation level modulates gene expression and may affect parasite growth in human malaria parasite Plasmodium falciparum

Three-dimensional positioning of the nuclear genome plays an important role in the epigenetic regulation of genes. Although nucleographic domain compartmentalization in the regulation of epigenetic state and gene expression is well established in higher organisms, it remains poorly understood in the pathogenic parasite Plasmodium falciparum. In the present study, we report that two histone tail modifications, H3K9Ac and H3K14Ac, are differentially distributed in the parasite nucleus. We find colocalization of active gene promoters such as Tu1 (tubulin-1 expressed in the asexual stages) with H3K9Ac marks at the nuclear periphery. By contrast, asexual stage inactive gene promoters such as Pfg27 (gametocyte marker) and Pfs28 (ookinete marker) occupy H3K9Ac devoid zones at the nuclear periphery. The histone H3K9 is predominantly acetylated by the PCAF/GCN5 class of lysine acetyltransferases, which is well characterized in the parasite. Interestingly, embelin, a specific inhibitor of PCAF/GCN5 family histone acetyltransferase, selectively decreases total H3K9Ac acetylation levels (but not H3K14Ac levels) around the var gene promoters, leading to the downregulation of var gene expression, suggesting interplay among histone acetylation status, as well as subnuclear compartmentalization of different genes and their activation in the parasites. Finally, we found that embelin inhibited parasitic growth at the low micromolar range, raising the possibility of using histone acetyltransferases as a target for antimalarial therapy.

Geomorphology reveals active decollement geometry in the central Himalayan seismic gap

The similar to 700-km-long ``central seismic gap'' is the most prominent segment of the Himalayan front not to have ruptured in a major earthquake during the last 200-500 yr. This prolonged seismic quiescence has led to the proposition that this region, with a population >10 million, is overdue for a great earthquake. Despite the region's recognized seismic risk, the geometry of faults likely to host large earthquakes remains poorly understood. Here, we place new constraints on the spatial distribution of rock uplift within the western similar to 400 km of the central seismic gap using topographic and river profile analyses together with basinwide erosion rate estimates from cosmogenic Be-10. The data sets show a distinctive physiographic transition at the base of the high Himalaya in the state of Uttarakhand, India, characterized by abrupt strike-normal increases in channel steepness and a tenfold increase in erosion rates. When combined with previously published geophysical imaging and seismicity data sets, we interpret the observed spatial distribution of erosion rates and channel steepness to reflect the landscape response to spatially variable rock uplift due to a structurally coherent ramp-flat system of the Main Himalayan Thrust. Although it remains unresolved whether the kinematics of the Main Himalayan Thrust ramp involve an emergent fault or duplex, the landscape and erosion rate patterns suggest that the decollement beneath the state of Uttarakhand provides a sufficiently large and coherent fault segment capable of hosting a great earthquake.

Genetic diversity and proviral DNA load in different neural compartments of HIV-1 subtype C infection

In India, the low prevalence of HIV-associated dementia (HAD) in the Human immunodeficiency virus type 1 (HIV-1) subtype C infection is quite paradoxical given the high-rate of macrophage infiltration into the brain. Whether the direct viral burden in individual brain compartments could be associated with the variability of the neurologic manifestations is controversial. To understand this paradox, we examined the proviral DNA load in nine different brain regions and three different peripheral tissues derived from ten human subjects at autopsy. Using a highly sensitive TaqMan probe-based real-time PCR, we determined the proviral load in multiple samples processed in parallel from each site. Unlike previously published reports, the present analysis identified uniform proviral distribution among the brain compartments examined without preferential accumulation of the DNA in any one of them. The overall viral DNA burden in the brain tissues was very low, approximately 1 viral integration per 1000 cells or less. In a subset of the tissue samples tested, the HIV DNA mostly existed in a free unintegrated form. The V3-V5 envelope sequences, demonstrated a brain-specific compartmentalization in four of the ten subjects and a phylogenetic overlap between the neural and non-neural compartments in three other subjects. The envelope sequences phylogenetically belonged to subtype C and the majority of them were R5 tropic. To the best of our knowledge, the present study represents the first analysis of the proviral burden in subtype C postmortem human brain tissues. Future studies should determine the presence of the viral antigens, the viral transcripts, and the proviral DNA, in parallel, in different brain compartments to shed more light on the significance of the viral burden on neurologic consequences of HIV infection.

Seismotectonics of the April-May 2015 Nepal earthquakes: An assessment based on the aftershock patterns, surface effects and deformational characteristics

Occurrence of the April 25, 2015 (Mw 7.8) earthquake near Gorkha, central Nepal, and another one that followed on May 12 (Mw 7.3), located similar to 140 km to its east, provides an exceptional opportunity to understand some new facets of Himalayan earthquakes. Here we attempt to assess the seismotectonics of these earthquakes based on the deformational field generated by these events, along with the spatial and temporal characteristics of their aftershocks. When integrated with some of the post-earthquake field observations, including the localization of damage and surface deformation, it became obvious that although the mainshock slip was mostly limited to the Main Himalayan Thrust (MHT), the rupture did not propagate to the Main Frontal Thrust (MFT). Field evidence, supported by the available InSAR imagery of the deformation field, suggests that a component of slip could have emerged through a previously identified out-of-sequence thrust/active thrust in the region that parallels the Main Central Thrust (MCT), known in the literature as a co-linear physiographic transitional zone called PT2. Termination of the first rupture, triggering of the second large earthquake, and distribution of aftershocks are also spatially constrained by the eastern extremity of PT2. Mechanism of the 2015 sequence demonstrates that the out-of-sequence thrusts may accommodate part of the slip, an aspect that needs to be considered in the current understanding of the mechanism of earthquakes originating on the MHT. (c) 2015 Elsevier Ltd. All rights reserved.

Characterization of the benthos, marine debris and bottom fish at Gray’s Reef National Marine Sanctuary

Executive Summary: Baseline characterization of resources is an essential part of marine protected area (MPA) management and is critical to inform adaptive management. Gray’s Reef National Marine Sanctuary (GRNMS) currently lacks adequate characterization of several key resources as identified in the 2006 Final Management Plan. The objectives of this characterization were to fulfill this need by characterizing the bottom fish, benthic features, marine debris, and the relationships among them for the different bottom types within the sanctuary: ledges, sparse live bottom, rippled sand, and flat sand. Particular attention was given to characterizing the different ledge types, their fish communities, and the marine debris associated with them given the importance of this bottom type to the sanctuary. The characterization has been divided into four sections. Section 1 provides a brief overview of the project, its relevance to sanctuary needs, methods of site selection, and general field procedures. Section 2 provides the survey methods, results, discussion, and recommendations for monitoring specific to the benthic characterization. Section 3 describes the characterization of marine debris. Section 4 is specific to the characterization of bottom fish. Field surveys were conducted during August 2004, May 2005, and August 2005. A total of 179 surveys were completed over ledge bottom (n=92), sparse live bottom (n=51), flat sand (n=20), and rippled sand (n=16). There were three components to each field survey: fish counting, benthic assessment, and quantification of marine debris. All components occurred within a 25 x 4 m belt transect. Two divers performed the transect at each survey site. One diver was responsible for identification of fish species, size, and abundance using a visual survey. The second diver was responsible for characterization of benthic features using five randomly placed 1 m2 quadrats, measuring ledge height and other benthic structures, and quantifying marine debris within the entire transect. GRNMS is composed of four main bottom types: flat sand, rippled sand, sparsely colonized live bottom, and densely colonized live bottom (ledges). Independent evaluation of the thematic accuracy of the GRNMS benthic map produced by Kendall et al. (2005) revealed high overall accuracy (93%). Most discrepancies between map and diver classification occurred during August 2004 and likely can be attributed to several factors, including actual map or diver errors, and changes in the bottom type due to physical forces. The four bottom types have distinct physical and biological characteristics. Flat and rippled sand bottom types were composed primarily of sand substrate and secondarily shell rubble. Flat sand and rippled sand bottom types were characterized by low percent cover (0-2%) of benthic organisms at all sites. Although the sand bottom types were largely devoid of epifauna, numerous burrows indicate the presence of infaunal organisms. Sparse live bottom and ledges were colonized by macroalgae and numerous invertebrates, including coral, gorgonians, sponges, and “other” benthic species (such as tunicates, anemones, and bryozoans). Ledges and sparse live bottom were similar in terms of diversity (H’) given the level of classification used here. However, percent cover of benthic species, with the exception of gorgonians, was significantly greater on ledge than on sparse live bottom. Percent biotic cover at sparse live bottom ranged from 0.7-26.3%, but was greater than 10% at only 7 out of 51 sites. Colonization on sparse live bottom is likely inhibited by shifting sands, as most sites were covered in a layer of sediment up to several centimeters thick. On ledge bottom type, percent cover ranged from 0.42-100%, with the highest percent cover at ledges in the central and south-central region of GRNMS. Biotic cover on ledges is influenced by local ledge characteristics. Cluster analysis of ledge dimensions (total height, undercut height, undercut width) resulted in three main categories of ledges, which were classified as short, medium, and tall. Median total percent cover was 97.6%, 75.1%, and 17.7% on tall, medium, and short ledges, respectively. Total percent cover and cover of macroalgae, sponges, and other organisms was significantly lower on short ledges compared to medium and tall ledges, but did not vary significantly between medium and tall ledges. Like sparse live bottom, short ledges may be susceptible to burial by sand, however the results indicate that ledge height may only be important to a certain threshold. There are likely other factors not considered here that also influence spatial distribution and community structure (e.g., small scale complexity, ocean currents, differential settlement patterns, and biological interactions). GRNMS is a popular site for recreational fishing and boating, and there has been increased concern about the accumulation of debris in the sanctuary and potential effects on sanctuary resources. Understanding the types, abundance, and distribution of debris is essential to improving debris removal and education efforts. Approximately two-thirds of all observed debris items found during the field surveys were fishing gear, and about half of the fishing related debris was monofilament fishing line. Other fishing related debris included leaders and spear gun parts, and non-gear debris included cans, bottles, and rope. The spatial distribution of debris was concentrated in the center of the sanctuary and was most frequently associated with ledges rather than at other bottom types. Several factors may contribute to this observation. Ledges are often targeted by fishermen due to the association of recreationally important fish species with this bottom type. In addition, ledges are structurally complex and are often densely colonized by biota, providing numerous places for debris to become stuck or entangled. Analysis of observed boat locations indicated that higher boat activity, which is an indication of fishing, occurs in the center of the sanctuary. On ledges, the presence and abundance of debris was significantly related to observed boat density and physiographic features including ledge height, ledge area, and percent cover. While it is likely that most fishing related debris originates from boats inside the sanctuary, preliminary investigation of ocean current data indicate that currents may influence the distribution and local retention of more mobile items. Fish communities at GRNMS are closely linked to benthic habitats. A list of species encountered, probability of occurrence, abundance, and biomass by habitat is provided. Species richness, diversity, composition, abundance, and biomass of fish all showed striking differences depending on bottom type with ledges showing the highest values of nearly all metrics. Species membership was distinctly separated by bottom type as well, although very short, sparsely colonized ledges often had a similar community composition to that of sparse live bottom. Analysis of fish communities at ledges alone indicated that species richness and total abundance of fish were positively related to total percent cover of sessile invertebrates and ledge height. Either ledge attribute was sufficient to result in high abundance or species richness of fish. Fish diversity (H`) was negatively correlated with undercut height due to schools of fish species that utilize ledge undercuts such as Pareques species. Concurrent analysis of ledge types and fish communities indicated that there are five distinct combinations of ledge type and species assemblage. These include, 1) short ledges with little or no undercut that lacked many of the undercut associated species except Urophycis earlii ; 2) tall, heavily colonized, deeply undercut ledges typically with Archosargus probatocephalus, Mycteroperca sp., and Pareques sp.; 3) tall, heavily colonized but less undercut with high occurrence of Lagodon rhomboides and Balistes capriscus; 4) short, heavily colonized ledges typically with Centropristis ocyurus, Halichoeres caudalis, and Stenotomus sp.; and 5) tall, heavily colonized, less undercut typically with Archosargus probatocephalus, Caranx crysos and Seriola sp.. Higher levels of boating activity and presumably fishing pressure did not appear to influence species composition or abundance at the community level although individual species appeared affected. These results indicate that merely knowing the basic characteristics of a ledge such as total height, undercut width, and percent cover of sessile invertebrates would allow good prediction of not only species richness and abundance of fish but also which particular fish species assemblages are likely to occur there. Comparisons with prior studies indicate some major changes in the fish community at GRNMS over the last two decades although the causes of the changes are unknown. Species of interest to recreational fishermen including Centropristis striata, Mycteroperca microlepis, and Mycteroperca phenax were examined in relation to bottom features, areas of assumed high versus low fishing pressure, and spatial dispersion. Both Mycteroperca species were found more frequently when undercut height of ledges was taller. They often were found together in small mixed species groups at ledges in the north central and southwest central regions of the sanctuary. Both had lower mode size and proportion of fish above the fishery size limit in heavily fished areas of the sanctuary (i.e. high boat density) despite the presence of better habitat in that region. Black sea bass, C. striata, occurred at 98% of the ledges surveyed and appeared to be evenly distributed throughout the sanctuary. Abundance was best explained by a positive relationship with percent cover of sessile biota but was also negatively related to presence of either Mycteroperca species. This may be due to predation by the Mycteroperca species or avoidance of sites where they are present by C. striata. Suggestions for monitoring bottom features, marine debris, and bottom fish at GRNMS are provided at the end of each chapter. The present assessment has established quantitative baseline characteristics of many of the key resources and use issues at GRNMS. The methods can be used as a model for future assessments to track the trajectory of GRNMS resources. Belt transects are ideally suited to providing efficient and quantitative assessment of bottom features, debris, and fish at GRNMS. The limited visibility, sensitivity of sessile biota, and linear nature of ledge habitats greatly diminish the utility of other sampling techniques. Ledges should receive the bulk of future characterization effort due to their importance to the sanctuary and high variability in physical structure, benthic composition, and fish assemblages. (PDF contains 107 pages.)

Vulnerabilidade socioambiental dos manguezais de Garapuá, Cairu/BA frente à inserção da indústria petroleira.

Manguezais são ecossistemas marinhos costeiros que ocorrem nas regiões tropicais e subtropicais do globo. A associação desses ambientes a formações recifais é restrita, particularmente no Brasil, onde se destaca a ilha de Tinharé, na costa sul do estado da Bahia, não só pela ocorrência desse sistema manguezal-recifes, mas também pelo desenvolvimento estrutural da floresta e pela atividade produtiva de mariscagem exercida pela população do povoado de Garapuá. Apesar da proximidade de Morro de São Paulo, atrator turístico internacional, este povoado experimentava certo isolamento socioeconômico até a chegada da indústria do petróleo que, em função de suas potencialidades e riscos, tensionou a vida da comunidade local. Este estudo tem por objetivo analisar a vulnerabilidade socioambiental dos manguezais adjacentes à Garapuá, Cairu-BA, frente a inserção da indústria petrolífera na região, a partir da caracterização estrutural das florestas de mangue e da caracterização social do povoado de Garapuá e, particularmente, das marisqueiras usuárias deste ecossistema. As abordagens metodológicas utilizadas podem ser classificadas como pesquisas quantitativas, empregadas no levantamento fitossociológico, e qualitativas, utilizadas a partir de observações de campo e entrevistas, além de levantamentos bibliográficos, para elaboração das análises sociais. Os resultados indicam florestas de mangue de porte variável, em bom estado de conservação, com altura média das dez árvores mais altas entre 2,40,2 metros (estação 7) e 22,71,1 metros (estação 29), geralmente dominadas por Rhizophora mangle (38 das 52 estações de amostragem). A partir da caracterização estrutural foi realizado teste estatístico de agrupamento que, aliado a aspectos da arquitetura das árvores, permitiu a classificação das florestas em 12 Tipos Estruturais. As análises relativas à vulnerabilidade ambiental fundamentaram-se nos aspectos de sensibilidade e na posição fisiográfica ocupada por cada Tipo de floresta e identificaram níveis distintos de vulnerabilidade a derramamentos de óleo. Com relação aos aspectos sociais, as informações sobre os sistemas socioeconômicos e culturais relacionados à saúde, à educação, às práticas produtivas e à geração de renda, ao transporte, à religião e à organização social, como um todo, evidenciaram vulnerabilidades frente à inserção da indústria do petróleo, apontando as marisqueiras como o segmento mais suscetível a vivenciar os riscos e os impactos desse empreendimento no local. A inserção da indústria do petróleo neste contexto socioambiental representa aumento de riscos e, consequentemente, de vulnerabilidade socioambiental, na medida em que o diálogo estabelecido entre empreendedor e população se apresenta de forma assimétrica, dificultando a participação da população local, sobretudo dos mais excluídos que, nesse caso, são representados pelos usuários dos manguezais.

Modelagem hidrológica da bacia hidrográfica do rio Bengalas, Nova Friburgo, RJ, utilizando o potencial de geotecnologias na definição de áreas de risco de inundação.

A presente pesquisa concentra-se no estudo hidrológico utilizando o potencial das geotecnologias na modelagem do escoamento na bacia do rio Bengalas, cujo rio principal de mesmo nome, corta o município de Nova Friburgo, RJ, no sentido Sul-Norte. Esse município, um dos mais importantes da região serrana, sofre frequentemente com inundações e deslizamentos, onde, dados históricos e acontecimentos recentes mostram que a ocupação inadequada de encostas e calhas dos rios são as áreas destacada e negativamente afetadas. A metodologia tem suporte no uso de um SIG, extraindo informações, que por sua vez, serão entrada de dados na fase de modelagem, e reforçando a apresentação dos resultados das simulações através de mapas. Ela está divida basicamente em três etapas: "SIG", "Modelagem" e "Suporte à Tomada de Decisão/Simulação". Esse primeiro estudo permitiu compor um banco de dados geográfico com as características fisiográficas da bacia; a seleção criteriosa de uma modelagem matemática e encadeamento de seus parâmetros com os componentes do ciclo hidrológico; realizar a calibração do modelo de transformação chuva-vazão, Soil Conservation Service (CN); e simular a passagem dos volumes gerados pela precipitação efetiva na calha do rio Bengalas, com o objetivo de identificar e analisar as áreas suscetíveis a inundações na porção central da cidade de Nova Friburgo. Modelagem dessa natureza vem sendo empregada, principalmente, no gerenciamento de recursos hídricos, onde a tomada de decisões embasada nos resultados de simulações computacionais, contribuem para evitar prejuízos materiais e financeiros, e ainda, perdas de vidas humanas em áreas de risco, neste caso, aquelas suscetíveis a inundações. Analisando os resultados encontrados temos que a área suscetível à inundação para uma chuva com tempo de recorrência de 50 anos, o mais crítico estudado, seja de aproximadamente 1,0 km, distribuídos nos seus 8,5km na região central de Nova Friburgo-RJ, sendo está, ora delimitada, prioritariamente edificada.

Influência do Complexo Vulcânico de Abrolhos na evolução tectono-sedimentar da porção centro-sul da bacia do Espírito Santo

A busca por novas acumulações de hidrocarbonetos necessita de esforços exploratórios contínuos, gerando novas possibilidades e modelos geológicos e diminuindo os riscos associados à atividade exploratória. O interesse no entendimento da formação de armadilhas, migração e reservatórios de hidrocarbonetos, associado à halocinese motivou a realização deste trabalho. Apresenta-se como principal objetivo deste trabalho a caracterização e a descrição da evolução halocinética na porção centro-sul da bacia do Espírito Santo. Dados de poços, sísmicos e gravimetria foram utilizados com o intuito de gerar uma interpretação geológica integrada, possibilitando entender à influência do Complexo Vulcânico de Abrolhos (CVA) na evolução tectonossedimentar da área, por meio da técnica de restauração de seção geológica. Na área estudada, ocorreu uma intensa atividade halocinética, já a partir do Albiano, em resposta a distensão causada pela subsidência da bacia e a abertura do Atlântico Sul. Durante o Neocretáceo, cunhas clásticas do Rio Doce adentraram na bacia provocando um novo pulso halocinético, resultando num aumento da taxa de sedimentação nas mini-bacias. Em outras regiões esta progradação causou a migração da camada-mãe de sal para porções distais da bacia, acarretando uma deficiência no suprimento de sal. Isto ocasionou o colapso de alguns diápiros associados a uma quiescência tectônica na área. A principal fase tectônica na área ocorreu no Eoterciário, época em que ocorre a implantação do CVA, formando estilos estruturais característicos de terrenos compressivos, com falhas de empurrão, popups, dobras e gotas de sal. Esta nova configuração tectônica na área mudou os eixos dos principais depocentros, que passaram a ser controlados pelos altos estruturais gerados pela tectônica compressiva, e pelos seus baixos relativos, que passaram a receber os sedimentos sin-tectônicos. (As associações destas características de remobilização tectonossedimentar formou uma nova compartimentação, a saber: a) Zona de translação; b) Zona dobrada e c) Zona de Cavalgamento com falhas de empurrão . Esta nova configuração tectônica tem sua formação diretamente relacionada à implantação do CVA.

Teorias da Conduta: uma análise crítica

Neste trabalho foram analisadas e comparadas as principais teorias da conduta. Com isso buscou-se não apenas aprofundar um debate frequentemente mediado pelos manuais, mas também, por meio do recurso aos aportes críticos da bibliografia latino-americana, verificar se a concepção ontológica de conduta é de fato a mais limitadora ao poder punitivo. Parte do eixo analítico deste trabalho passa pelo estudo da articulação entre o respeito à estrutura lógico-objetiva da conduta humana como base de sucessivas valorações e a função limitadora da conduta. Com isso, pretende-se debater se a minimização dessa estrutura lógico-objetiva, acarretando a um acréscimo potencial de uma normativização do direito penal, representaria uma maior exposição do sujeito ao poder punitivo. A partir do conceito de praxis, como desenvolvido por Lukács, busca-se paralelamente uma base filosófica que não se esgote na compartimentalização jurídica. Trata-se de uma corrente que reivindica criticamente a herança teórica das principais contribuições filosóficas ocidentais, desde proposições aristotélicas, passando pelos conceitos hegelianos, chegando ao debate sobre objetificação hegeliano-marxista.

Modelagem do uso de hábitat de cetáceos na região de Cabo Frio, estado do Rio de Janeiro, Brasil

Em estudos ecológicos é importante entender os processos que determinam a distribuição dos organismos. O estudo da distribuição de animais com alta capacidade de locomoção é um desafio para pesquisadores em todo o mundo. Modelos de uso de habitat são ferramentas poderosas para entender as relações entre animais e o ambiente. Com o desenvolvimento dos Sistemas de Informação Geográfica (SIG ou GIS, em inglês), modelos de uso de habitat são utilizados nas análises de dados ecológicos. Entretanto, modelos de uso de habitat frequentemente sofrem com especificações inapropriadas. Especificamente, o pressuposto de independência, que é importante para modelos estatísticos, pode ser violado quando as observações são coletadas no espaço. A Autocorrelação Espacial (SAC) é um problema em estudos ecológicos e deve ser considerada e corrigida. Nesta tese, modelos generalizados lineares com autovetores espaciais foram usados para investigar o uso de habitat dos cetáceos em relação a variáveis fisiográficas, oceanográficas e antrópicas em Cabo Frio, RJ, Brasil, especificamente: baleia-de-Bryde, Balaenoptera edeni (Capítulo 1); golfinho nariz-de-garrafa, Tursiops truncatus (Capítulo 2); Misticetos e odontocetos em geral (Capítulo 3). A baleia-de-Bryde foi influenciada pela Temperatura Superficial do Mar Minima e Máxima, no qual a faixa de temperatura mais usada pela baleia condiz com a faixa de ocorrência de sardinha-verdadeira, Sardinella brasiliensis, durante a desova (22 a 28C). Para o golfinho nariz-de-garrafa o melhor modelo indicou que estes eram encontrados em Temperatura Superficial do Mar baixas, com alta variabilidade e altas concentrações de clorofila. Tanto misticetos quanto os odontocetos usam em proporções similares as áreas contidas em Unidades de Conservação (UCs) quanto as áreas não são parte de UCs. Os misticetos ocorreram com maior frequência mais afastados da costa, em baixas temperaturas superficiais do mar e com altos valores de variabilidade para a temperatura. Os odontocetos usaram duas áreas preferencialmente: as áreas com as menores profundidades dentro da área de estudo e nas maiores profundidade. Eles usaram também habitats com águas frias e com alta concentração de clorofila. Tanto os misticetos quanto os odontocetos foram encontrados com mais frequência em distâncias de até 5km das embarcações de turismo e mergulho. Identificar habitats críticos para os cetáceos é um primeiro passo crucial em direção a sua conservação

A Biogeographic assessment off North/Central California: In support of the National Marine Sanctuaries of Cordell Bank, Gulf of the Farallones and Monterey Bay. Phase II - Environmental setting and update to marine birds and animals

NOAA’s National Centers for Coastal Ocean Science (NCCOS) conducts and supports research, monitoring, assessments, and technical assistance to meet NOAA’s coastal stewardship and management responsibilities. In 2001 the Biogeography Branch of NCCOS partnered with NOAA’s National Marine Sanctuary Program (NMSP) to conduct biogeographic assessments to support the management plan updates for the sanctuaries. The first biogeographic assessment conducted in this partnership focused on three sanctuaries off north/ central California: Cordell Bank, Gulf of the Farallones and Monterey Bay. Phase I of this assessment was conducted from 2001 to 2004, with the primary goal to identify and gather the best available data and information to characterize and identify important biological areas and time periods within the study area. The study area encompasses the three sanctuaries and extends along the coastal ocean off California from Pt. Arena to Pt. Sal (35°-39°N). This partnership project was lead by the NCCOS Biogeography Branch, but included over 90 contributors and 25 collaborating institutions. Phase I results include: 1) a report on the overall assessment that includes hundreds of maps, tables and analyses; 2) an ecological linkage report on the marine and estuarine ecosystems along the coast of north/central California, and 3) related geographic information system (GIS) data and other summary data files, which are available for viewing and download in several formats at the following website: http://ccma.nos.noaa.gov/products/biogeography/canms_cd/welcome.html Phase II (this report) was initiated in the Fall of 2004 to complete the analyses of marine mammals and update the marine bird colony information. Phase II resulted in significant updates to the bird and mammal chapters, as well as adding an environmental settings chapter, which contains new and existing data and maps on the study area. Specifically, the following Phase II topics and items were either revised or developed new for Phase II: •environmental, ecological settings – new maps on marine physiographic features, sea surface temperature and fronts, chlorophyll and productivity •all bird colony or roost maps, including a summary of marine bird colonies •updated at-sea data CDAS data set (1980-2003) •all mammal maps and descriptions •new overall density maps for eight mammal species •new summary pinniped rookery/haulout map •new maps on at-sea richness for cetaceans and pinnipeds •most text in the mammal chapter •new summary tables for mammals on population status and spatial and temporal patterns

Assessment and monitoring of marine debris in Gray's Reef National Marine Sanctuary

Gray’s Reef National Marine Sanctuary (GRNMS) is located 32.4 km offshore of Sapelo Island, Georgia. The ecological importance of this area is related to the transition between tropical and temperate waters, and the existence of a topographically complex system of ledges. Due to its central location, GRNMS can be used as a focal site to study the accumulation and impacts of marine debris on the Atlantic continental shelf offshore of the Southeast United States. Previously, researchers characterized marine debris in GRNMS and reported that incidence of the debris at the limited densely colonized ledge sites was significantly greater than at sand or sparsely colonized live bottom, and is further influenced by the level of boating activity and physiographic characteristics (e.g., ledge height). Information gleaned from the initial marine debris characterization was used to devise a strategy for prioritizing cleanup and monitoring efforts. However, a significant gap in knowledge was the rate of debris accumulation. The primary objective of this study was to select, mark, and perform initial marine debris surveys at permanent monitoring sites within GRNMS to quantify long-term trends in types, abundance, impacts, and accumulation rates of debris. Ledge sites were selected to compare types, abundance, and accumulation rates of marine debris between a) areas of high and low use and b) short and tall ledges. Nine permanent monitoring sites were marked and initially surveyed in 2007/2008. Surveys were conducted within a 50 x 4 m transect for a total survey area of 200 square meters. All debris was removed and detailed information was taken on the types of debris, quantity, and associations with benthic fauna. Information on associations with benthic fauna included degree of entanglement, type of organism with which it is entangled or resting on, degree of fouling, and visible impacts such as tissue abrasions. Sites were re-surveyed approximately one year later to quantify new accumulation. During the initial survey, a total of ten debris items, totaling 16.3 kg in weight, were removed from two monitoring stations, both “tall” sites within the area of high boat use. Year-one accumulation totaled five items and approximately 7 kg in weight. Similar to the initial survey, all debris was found at sites in the area of high boat use. However, in contrast to the initial survey, two of these items were found on medium-height ledges. Removed items included fishing line, leaders, rope, plastic, and fabric. Although items were often encrusted in benthic biota or entangled on the ledge, impacts such as abrasions or other injuries were not observed. During the 2009 monitoring efforts, volunteer divers were trained to conduct the survey. Monitoring protocols were documented for GRNMS staff and included as an appendix of this report to enable long-term monitoring of sites. Additionally, national reconnaissance data (e.g. satellite, radar, aerial surveys) and other information on known fishing locations were examined for patterns of resource use and correlations with debris occurrence patterns. A previous model predicting the density of marine debris based on ledge features and boat use was refined and the results were used to generate a map of predicted debris density for all ledges.

甘蓝(Brassica oleracea L. var. capitata L.)富集铊的环境地球化学研究

通过对甘蓝进行品种差异、亚细胞分析、根际分泌物提取污染土壤中的铊、营养元素添加以及野外甘蓝样品采集分析，结合地球化学理论。分析了甘蓝对铊吸收富集的机理，并得出以下几点结论： (1) 甘蓝叶、根及茎对铊的吸收存在着明显差异，表明在面临土壤铊胁迫时，叶是铊的主要储存部位，而根和茎主要起到了转运作用。甘蓝中铊含量的升高导致了对钙和镁吸收能力的提高。不同品种甘蓝之间的吸收能力差别不大，通过选择种植对铊吸收能力小的甘蓝来控制铊的食物链危害是不可行的。此外，还应该避免在高铊土壤地区种植甘蓝。 (2) 高达92%的铊存在于甘蓝叶细胞液组分中，表明细胞液组分是铊在甘蓝叶细胞中的一个重要储存部位。但是在不同品种甘蓝叶中，铊的亚细胞分布形态没有显著差异，在甘蓝面对铊胁迫时，其叶细胞器组分中铊含量始终维持很低的含量。甘蓝对铊的解毒机制很可能就是通过在细胞内的区隔化作用(compartmentalization)，把进入体内的铊结合到细胞液组分以及细胞壁上，从而减少了铊对重要细胞器官的损伤。铊在甘蓝叶各亚细胞组分中的分配与常量元素存在一定的关系。在甘蓝叶细胞内，Tl+往细胞液组分中的传输很有可能是通过Na+/K+/2Cl–联合传输机制、Ca2+活化的钾离子通道以及一些需Mg2+或Mn2+的K+活化酶完成的。需要Mn2+参与的K+活化酶可能对于铊往细胞器中的转移起到了主导作用。在细胞壁中，很可能Ca2+活化的K+通道或者是某些特定的需要Mn2+的K+活化酶对铊的迁移或固定起了影响作用。 (3) 随着氮、磷、钾营养元素的加入，甘蓝地上部的生物量有一定程度的上升。影响主次因素依次均为氮>磷>钾。随着氮、磷、钾营养元素的加入，甘蓝地上部和地下部的铊含量并没有上升，而是有一定程度的下降。甘蓝地上部中铊含量的影响主次因素依次为磷>氮>钾，甘蓝地下部中铊含量的影响主次因素依次为氮>磷>钾。氮、磷、钾营养元素的加入都提高了甘蓝对铊的吸收量。甘蓝对铊吸收量的影响主次因素依次均为氮>磷>钾。因此我们认为，氮，磷，钾的加入显著提高了甘蓝生物量和铊的吸收量，但是随之而来的生物稀释效应，导致了甘蓝地上部和地下部含量的降低。运用铊累积量来判断营养元素对甘蓝吸收铊的影响更为客观和可靠。 (4) 通过对比蒸馏水和根际分泌物提取液对污染土壤中铊的提取能力，发现甘蓝根际分泌物提取液(root exudates)对污染土壤中的铊具有明显的活化作用。提取液的pH和土壤铊的提取率存在一定的正相关(R2=0.1659)，也就是说提取液的pH与其对污染土壤中铊的提取能力成正比。但是甘蓝体内各部分铊含量与其根际分泌物提取液对土壤铊的提取率没有任何关系，表明大量的植物非必需元素铊进入甘蓝后，并没有对其根际分泌物的产生任何影响。土壤pH越高，生长的甘蓝的根际分泌物提取液对土壤提取率就越高，甘蓝分泌物提取液对铊的提取率升高可以补偿由于土壤pH升高而造成的水溶态存在的铊减少。 (5) 铊在甘蓝叶片和叶柄中的分布状况为老叶叶片>新叶叶片>老叶叶柄>新叶叶柄，表明叶柄也是运输铊的一个重要器官。但是叶柄对铊的转运能力并没有茎那么强烈，而叶片才是甘蓝中最主要的铊储存部位。铊在根、茎、老叶和新叶中亚细胞的分布均为细胞液>>细胞壁>细胞器，这和前期室内温室培养甘蓝叶片中的分布结果是一致的。根据植物采矿经济理论的计算结果，很显然甘蓝可以成为土壤铊污染的植物修复和采矿的备选对象。

Diversity index of mucosal resident T lymphocyte repertoire predicts clinical prognosis in gastric cancer

© 2015 Taylor & Francis Group, LLC.A characteristic immunopathology of human cancers is the induction of tumor antigen-specific T lymphocyte responses within solid tumor tissues. Current strategies for immune monitoring focus on the quantification of the density and differentiation status of tumor-infiltrating T lymphocytes; however, properties of the TCR repertoire - including antigen specificity, clonality, as well as its prognostic significance β remain elusive. In this study, we enrolled 28 gastric cancer patients and collected tumor tissues, adjacent normal mucosal tissues, and peripheral blood samples to study the landscape and compartmentalization of these patients’ TCR β repertoire by deep sequencing analyses. Our results illustrated antigen-driven expansion within the tumor compartment and the contracted size of shared clonotypes in mucosa and peripheral blood. Most importantly, the diversity of mucosal T lymphocytes could independently predict prognosis, which strongly underscores critical roles of resident mucosal T-cells in executing post-surgery immunosurveillance against tumor relapse.

Toward understanding the essence of post-translational modifications for the Mycobacterium tuberculosis immunoproteome

CD4⁺ T cells are prominent effector cells in controlling Mycobacterium tuberculosis (Mtb) infection but may also contribute to immunopathology. Studies probing the CD4⁺ T cell response from individuals latently infected with Mtb or patients with active tuberculosis using either small or proteome-wide antigen screens so far revealed a multi-antigenic, yet mostly invariable repertoire of immunogenic Mtb proteins. Recent developments in mass spectrometry-based proteomics have highlighted the occurrence of numerous types of post-translational modifications (PTMs) in proteomes of prokaryotes, including Mtb. The well-known PTMs in Mtb are glycosylation, lipidation, or phosphorylation, known regulators of protein function or compartmentalization. Other PTMs include methylation, acetylation, and pupylation, involved in protein stability. While all PTMs add variability to the Mtb proteome, relatively little is understood about their role in the anti-Mtb immune responses. Here,we reviewMtb protein PTMs and methods to assess their role in protective immunity against Mtb. © 2014 van Els, Corbière, Smits, vanGaans-van den Brink, Poelen, Mascart, Meiring and Locht.