The effects of water quality on freshwater fish populations - final report

There is a need to determine quantitative relationships between fishery status and water quality in order to make informed judgements concerning fishery health and the setting of environmental quality standards for fishery protection. Such relationships would also assist in the formulation of a system for classifying fisheries. A national database of fisheries and water quality has been collated from the archives of pollution control authorities throughout the UK. A number of probable and potential water quality effects on fish populations have been identified from a thorough analysis of the database, notwithstanding large confounding effects such as habitat variation and fish mobility, and the generally sparse nature of water quality information. A number of different approaches to data analysis was utilised, and the value of each has been appraised. Recommendations concerning the integration of water quality assessment approaches have been made and further research on fishery status, and its measurement, in relation to water quality has been suggested.

Human Endogenous Retrovirus HERV-Fc1 Association with Multiple Sclerosis Susceptibility: A Meta-Analysis

Background: Human endogenous retroviruses (HERVs) are repetitive sequences derived from ancestral germ-line infections by exogenous retroviruses and different HERV families have been integrated in the genome. HERV-Fc1 in chromosome X has been previously associated with multiple sclerosis (MS) in Northern European populations. Additionally, HERV-Fc1 RNA levels of expression have been found increased in plasma of MS patients with active disease. Considering the North-South latitude gradient in MS prevalence, we aimed to evaluate the role of HERV-Fc1on MS risk in three independent Spanish cohorts. Methods: A single nucleotide polymorphism near HERV-Fc1, rs391745, was genotyped by Taqman chemistry in a total of 2473 MS patients and 3031 ethnically matched controls, consecutively recruited from: Northern (569 patients and 980 controls), Central (883 patients and 692 controls) and Southern (1021 patients and 1359 controls) Spain. Our results were pooled in a meta-analysis with previously published data. Results: Significant associations of the HERV-Fc1 polymorphism with MS were observed in two Spanish cohorts and the combined meta-analysis with previous data yielded a significant association [rs391745 C-allele carriers: p(M-H) = 0.0005; ORM-H (95% CI) = 1.27 (1.11-1.45)]. Concordantly to previous findings, when the analysis was restricted to relapsing remitting and secondary progressive MS samples, a slight enhancement in the strength of the association was observed [p(M-H) = 0.0003, ORM-H (95% CI) = 1.32 (1.14-1.53)]. Conclusion: Association of the HERV-Fc1 polymorphism rs391745 with bout-onset MS susceptibility was confirmed in Southern European cohorts.

Avaliação da presença de mutações de resistência no gene da NS5B e do prognóstico da infecção pelo HCV através da IL-28B em pacientes monoinfectados com HCV no RJ

Estima-se que a prevalência global da população mundial com hepatite C é de 3%. Pouco se sabe sobre a resposta ao tratamento com respeito à resistência viral. Algumas mutações no fragmento de 109 aminoácidos da NS5B são associadas com resistência ao interferon (IFN) e ribavirina (RBV). Estudos moleculares e clínicos identificaram fatores associados com o hospedeiro e vírus relacionados associada com a resposta ao tratamento, tal como o gene que codifica a IL-28B. Este estudo foi dividido em duas fases, cujos objetivos foram caracterizar a frequência de mutações que conferem resistência ao HCV e avaliar a relevância das mutações em pacientes Respondedores (R) ou Não Respondedores (NR) ao tratamento e caracterizar geneticamente as populações sobre polimorfismos genéticos nos SNPs da IL-28B em relação ao prognóstico da resposta ao tratamento. As amostras dos pacientes foram submetidas a testes de genotipagem e carga viral. As sequências geradas foram comparadas no BLAST e no banco de dados Los Alamos HCV. Realizamos o alinhamento das sequências homólogas e as mutações identificadas. Com base no genótipo e carga viral determinamos a classificação dos pacientes de acordo com a resposta à terapia. O DNA genômico foi isolado a partir de sangue periférico para a realização da tipagem de SNPs de IL-28B. A metodologia utilizada foi de PCR em tempo real utilizando sondas TaqMan SNP específico. A análise dos dados foi realizada utilizando GraphPad Prism com qui-quadrado, risco relativo (RR), Odds Ratio (OR) e intervalo de confiança de 95%, com um nível de significância de P <0,05. Foi encontrado na primeira fase deste estudo uma taxa significativa mutações associadas ao tratamento nas amostras estudadas. A prevalência de mutações associadas à resistência ao IFN e RBV bem como a novos medicamentos antivirais localizados no fragmento de 109 aminoácidos da NS5B foi examinado em 69 indivíduos infectados naïve no Rio de Janeiro, Brasil. Na segunda fase, as mutações foram clinicamente relevantes. Desde então, procuramos observar as diferenças entre melhor ou pior prognóstico de acordo com a imunogenética que mostrou diferenciação entre os grupos R e NR ao tratamento em relação ao prognóstico da resposta terapêutica. Quando as diferenças entre as sequências da NS5B e a resposta ao tratamento foram consideradas verificou-se que associada a mutação R254K, estava a C316N que poderia conduzir a uma não resposta à terapia no genótipo 1b. Os nossos dados também suportaram forte associação de IL-28B rs12979860, com elevada probabilidade de resposta à terapia de IFN + RBV. Nossos dados evidenciam a presença de pacientes virgens de tratamento que abrigam mutações de resistência previamente descritas na literatura. A análise dos fatores preditores de resposta virológica mostrou que a predição de boa resposta ou não ao tratamento e ainda da progressão da doença é dependente de uma importante interação entre a genética viral e a do hospedeiro. Fato este importante para que no momento de avaliação de diagnóstico e conduta terapêutica, o médico possa tomar medidas apropriadas para o tratamento de cada paciente individualmente independentemente do genótipo do HCV em questão.

Contrasting abundance and residency patterns of two sympatric populations of transient killer whales (Orcinus orca) in the northern Gulf of Alaska

Two sympatric populations of “transient” (mammal-eating) killer whales were photo-identified over 27 years (1984–2010) in Prince William Sound and Kenai Fjords, coastal waters of the northern Gulf of Alaska (GOA). A total of 88 individuals were identified during 203 encounters with “AT1” transients (22 individuals) and 91 encounters with “GOA” transients (66 individuals). The median number of individuals identified annually was similar for both populations (AT1=7; GOA=8), but mark-recapture estimates showed the AT1 whales to have much higher fidelity to the study area, whereas the GOA whales had a higher exchange of individuals. Apparent survival estimates were generally high for both populations, but there was a significant reduction in the survival of AT1 transients after the Exxon Valdez oil spill in 1989, with an abrupt decline in estimated abundance from a high of 22 in 1989 to a low of seven whales at the end of 2010. There was no detectable decline in GOA population abundance or survival over the same period, but abundance ranged from just 6 to 18 whales annually. Resighting data from adjacent coastal waters and movement tracks from satellite tags further indicated that the GOA whales are part of a larger population with a more extensive range, whereas AT1 whales are resident to the study area.

Genetic variation between outer-coastal and fjord populations of Pacific herring (Clupea pallasii) in the eastern Gulf of Alaska

Pacific herring (Clupea pallasii) from the Gulf of Alaska were screened for temporal and spatial genetic variation with 15 microsatellite loci. Thirteen collections were examined in this study: 11 from Southeast Alaska and 2 from Prince William Sound, Alaska. Although FST values were low, a neighbor-joining tree based on genetic distance, homogeneity, and FST values revealed that collectively, the Berners Bay and Lynn Canal (interior) collections were genetically distinct from Sitka Sound and Prince of Wales Island (outer-coastal) collections. Temporal genetic variation within regions (among three years of Berners Bay spawners and between the two Sitka Sound spawners) was zero, whereas 0.05% was attributable to genetic variation between Berners Bay and Sitka Sound. This divergence may be attributable to environmental differences between interior archipelago waters and outer-coast habitats, such as differences in temperature and salinity. Early spring collections of nonspawning Lynn Canal herring were nearly genetically identical to collections of spawning herring in Berners Bay two months later—an indication that Berners Bay spawners over-winter in Lynn Canal. Southeast Alaskan herring (collectively) were significantly different from those in Prince William Sound. This study illustrates that adequate sample size is needed to detect variation in pelagic fish species with a large effective population size, and microsatellite markers may be useful in detecting low-level genetic divergence in Pacific herring in the Gulf of Alaska.

Population connectivity among Dry Tortugas, Florida, and Caribbean populations of mutton snapper (Lutjanus analis), inferred from multiple microsatellite loci

Determining patterns of population connectivity is critical to the evaluation of marine reserves as recruitment sources for harvested populations. Mutton snapper (Lutjanus analis) is a good test case because the last known major spawning aggregation in U.S. waters was granted no-take status in the Tortugas South Ecological Reserve (TSER) in 2001. To evaluate the TSER population as a recruitment source, we genotyped mutton snapper from the Dry Tortugas, southeast Florida, and from three locations across the Caribbean at eight microsatellite loci. Both Fstatistics and individual-based Bayesian analyses indicated that genetic substructure was absent across the five populations. Genetic homogeneity of mutton snapper populations is consistent with its pelagic larval duration of 27 to 37 days and adult behavior of annual migrations to large spawning aggregations. Statistical power of future genetic assessments of mutton snapper population connectivity may benefit from more comprehensive geographic sampling, and perhaps from the development of less polymorphic DNA microsatellite loci. Research where alternative methods are used, such as the transgenerational marking of embryonic otoliths with barium stable isotopes, is also needed on this and other species with diverse life history characteristics to further evaluate the TSER as a recruitment source and to define corridors of population connectivity across the Caribbean and Florida.

Multiple stable reference points in oyster populations: biological relationships for the eastern oyster (Crassostrea virginica) in Delaware Bay

Abstract—In the first of two companion papers, a 54-yr time series for the oyster population in the New Jersey waters of Delaware Bay was analyzed to develop biological relationships necessary to evaluate maximum sustainable yield (MSY) reference points and to consider how multiple stable points affect reference point-based management. The time series encompassed two regime shifts, one circa 1970 that ushered in a 15-yr period of high abundance, and a second in 1985 that ushered in a 20-yr period of low abundance. The intervening and succeeding periods have the attributes of alternate stable states. The biological relationships between abundance, recruitment, and mortality were unusual in four ways. First, the broodstock–recruitment relationship at low abundance may have been driven more by the provision of settlement sites for larvae by the adults than by fecundity. Second, the natural mortality rate was temporally unstable and bore a nonlinear relationship to abundance. Third, combined high abundance and low mortality, though likely requiring favorable environmental conditions, seemed also to be a self-reinforcing phenomenon. As a consequence, the abundance –mortality relationship exhibited both compensatory and depensatory components. Fourth, the geographic distribution of the stock was intertwined with abundance and mortality, such that interrelationships were functions both of spatial organization and inherent populatio

Multiple stable reference points in oyster populations: implications for reference point-based management

In the second of two companion articles, a 54-year time series for the oyster population in the New Jersey waters of Delaware Bay is analyzed to examine how the presence of multiple stable states affects reference-point–based management. Multiple stable states are described by four types of reference points. Type I is the carrying capacity for the stable state: each has associated with it a type-II reference point wherein surplus production reaches a local maximum. Type-II reference points are separated by an intermediate surplus production low (type III). Two stable states establish a type-IV reference point, a point-of-no-return that impedes recovery to the higher stable state. The type-II to type-III differential in surplus production is a measure of the difficulty of rebuilding the population and the sensitivity of the population to collapse at high abundance. Surplus production projections show that the abundances defining the four types of reference points are relatively stable over a wide range of uncertainties in recruitment and mortality rates. The surplus production values associated with type-II and type-III reference points are much more uncertain. Thus, biomass goals are more easily established than fishing mortality rates for oyster population

Assessment of fish populations and habitat on Oculina Bank, a deep-sea coral marine protected area off eastern Florida

A portion of the Oculina Bank located off eastern Florida is a marine protected area (MPA) preserved for its dense populations of the ivory tree coral (Oculina varicosa), which provides important habitat for fish. Surveys of fish assemblages and benthic habitat were conducted inside and outside the MPA in 2003 and 2005 by using remotely operated vehicle video transects and digital still imagery. Fish species composition, biodiversity, and grouper densities were used to determine whether O. varicosa forms an essential habitat compared to other structure-forming habitats and to examine the effectiveness of the MPA. Multivariate analyses indicated no differences in fish assemblages or biodiversity among hardbottom habitat types and grouper densities were highest among the most complex habitats; however the higher densities were not exclusive to coral habitat. Therefore, we conclude that O. varicosa was functionally equivalent to other hardbottom habitats. Even though fish assemblages were not different among management areas, biodiversity and grouper densities were higher inside the MPA compared to outside. The percentage of intact coral was also higher inside the MPA. These results provide initial evidence demonstrating effectiveness of the MPA for restoring reef fish and their habitat. This is the first study to compare reef fish populations on O. varicosa with other structure-forming reef habitats and also the first to examine the effectiveness of the MPA for restoring fish populations and live reef cover.

Length-fecundity relationships of Nigerian fish populations

Parameters of the exponential body length (L)-fecundity (F) relationship of the form F=a.L super(b) are presented for 47 populations and 26 species of Nigerian fishes. Estimates of b varied between 1.563 (Ilisha africana) and 5.771 (Barbus callipterus) with a mean of 3.054 (s.d. = 1.024). The maximum sizes of fish populations examined did not significantly influence the relative magnitudes of b. The parameters Alpha and Beta of the linear length-fecundity relationships of the form F = Alpha + BetaL are also presented for five fish populations. Estimates of Beta ranged from 243.5 (Chrysichthys walkeri) to 1,334,895 (Tilapia mariae).

Weight-fecundity relationships of Nigerian fish populations

Parameters a and b of the power body weight (W) - fecundity (F=a W super(b)) are presented for 25 populations comprising 15 species of Nigerian fishes. Estimates of b varied between 0.511 (Parauchenoglanis akin) and 1.654 (Periophthalmus barbarus) with a mean of 1.087 (s.d.=0.520). The maximum weight of populations examined did not significantly influence the relative magnitude of b. The parameters proportional to and beta of the linear weight-fecundity relationship (F= proportional to + beta W) are also presented for 27 fish populations from 22 species. Estimates of beta ranged from 4.22 (Chromidotilapia guntheri) to 2,062.94 (Pellunula min), with a mean of 243.80 (s.d.=477.89). The magnitude of beta declined with increasing maximum weights of fishes examined.

Seroprevalence of Triatoma virus (Dicistroviridae: Cripaviridae) antibodies in Chagas disease patients

Background: Chagas disease is caused by Trypanosoma cruzi, and humans acquire the parasite by exposure to contaminated feces from hematophagous insect vectors known as triatomines. Triatoma virus (TrV) is the sole viral pathogen of triatomines, and is transmitted among insects through the fecal-oral route and, as it happens with T. cruzi, the infected insects release the virus when defecating during or after blood uptake. Methods: In this work, we analysed the occurrence of anti-TrV antibodies in human sera from Chagas disease endemic and non-endemic countries, and developed a mathematical model to estimate the transmission probability of TrV from insects to man, which ranged between 0.00053 and 0.0015. Results: Our results confirm that people with Chagas disease living in Bolivia, Argentina and Mexico have been exposed to TrV, and that TrV is unable to replicate in human hosts. Conclusions: We presented the first experimental evidence of antibodies against TrV structural proteins in human sera.