Rhodopsin gene polymorphism associated with divergent light environments in atlantic cod

The spectral sensitivity of visual pigments in vertebrate eyes is optimized for specific light conditions. One of such pigments, rhodopsin (RH1), mediates dim-light vision. Amino acid replacements at tuning sites may alter spectral sensitivity, providing a mechanism to adapt to ambient light conditions and depth of habitat in fish. Here we present a first investigation of RH1 gene polymorphism among two ecotypes of Atlantic cod in Icelandic waters, which experience divergent light environments throughout the year due to alternative foraging behaviour. We identified one synonymous single nucleotide polymorphism (SNP) in the RH1 protein coding region and one in the 3' untranslated region (3'-UTR) that are strongly divergent between these two ecotypes. Moreover, these polymorphisms coincided with the well-known panthophysin (Pan I) polymorphism that differentiates coastal and frontal (migratory) populations of Atlantic cod. While the RH1 SNPs do not provide direct inference for a specific molecular mechanism, their association with this dim-sensitive pigment indicates the involvement of the visual system in local adaptation of Atlantic cod.

A genomic island linked to ecotype divergence in Atlantic cod

The genomic architecture underlying ecological divergence and ecological speciation with gene flow is still largely unknown for most organisms. One central question is whether divergence is genome-wide or localized in 'genomic mosaics' during early stages when gene flow is still pronounced. Empirical work has so far been limited, and the relative impacts of gene flow and natural selection on genomic patterns have not been fully explored. Here, we use ecotypes of Atlantic cod to investigate genomic patterns of diversity and population differentiation in a natural system characterized by high gene flow and large effective population sizes, properties which theoretically could restrict divergence in local genomic regions. We identify a genomic region of strong population differentiation, extending over approximately 20 cM, between pairs of migratory and stationary ecotypes examined at two different localities. Furthermore, the region is characterized by markedly reduced levels of genetic diversity in migratory ecotype samples. The results highlight the genomic region, or 'genomic island', as potentially associated with ecological divergence and suggest the involvement of a selective sweep. Finally, we also confirm earlier findings of localized genomic differentiation in three other linkage groups associated with divergence among eastern Atlantic populations. Thus, although the underlying mechanisms are still unknown, the results suggest that 'genomic mosaics' of differentiation may even be found under high levels of gene flow and that marine fishes may provide insightful model systems for studying and identifying initial targets of selection during ecological divergence.

Mineralogy, chemistry and biological contingents of an early-middle Miocene Antarctic paleosol and its relevance as a Martian analogue

Fossil mesofauna and bacteria recovered from a paleosol in a moraine situated adjacent to the inland ice, Antarctica, and dating to the earliest glacial event in the Antarctic Dry Valleys opens several questions. The most important relates to understanding of the mineralogy and chemistry of the weathered substrate habitat in which Coleoptera apparently thrived at some point in the Early/Middle Miocene and perhaps earlier. Here, Coleoptera remains are only located in one of six horizons in a paleosol formed in moraine deposited during the alpine glacial event (> 15 Ma). A tendency for quartz to decrease upward in the section may be a detrital effect or a product of dissolution in the early stage of profile morphogenesis when climate was presumably milder and the depositing glacier of temperate type. Discontinuous distributions of smectite, laumontite, and hexahydrite may have provided nutrients and water to mesofauna and bacteria during the early stage of biotic colonization of the profile. Because the mesofauna were members of burrowing Coleoptera species, future work should assess the degree to which the organisms occupied other sites in the Dry Valleys in the past. Whereas there is no reasonable expectations of finding Coleoptera/insect remains on Mars, the chemistry and mineralogy of the paleosol is within a life expectancy window for the presence of microorganisms, principally bacteria and fungi. Thus, parameters discussed here within this Antarctic paleosol could provide an analogue to identifying similar fossil or life-bearing weathered regolith on Mars.

The effect of stress on egg quality in farmed Atlantic Cod (Gadus morhua L.)

Dissertação de mestrado, Aquacultura, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2011

Validation of plant dynamic model by online and laboratory measurements – a tool to predict online COD loads out of production of mechanical printing papers

COD discharges out of processes have increased in line with elevating brightness demands for mechanical pulp and papers. The share of lignin-like substances in COD discharges is on average 75%. In this thesis, a plant dynamic model was created and validated as a means to predict COD loading and discharges out of a mill. The assays were carried out in one paper mill integrate producing mechanical printing papers. The objective in the modeling of plant dynamics was to predict day averages of COD load and discharges out of mills. This means that online data, like 1) the level of large storage towers of pulp and white water 2) pulp dosages, 3) production rates and 4) internal white water flows and discharges were used to create transients into the balances of solids and white water, referred to as “plant dynamics”. A conversion coefficient was verified between TOC and COD. The conversion coefficient was used for predicting the flows from TOC to COD to the waste water treatment plant. The COD load was modeled with similar uncertainty as in reference TOC sampling. The water balance of waste water treatment was validated by the reference concentration of COD. The difference of COD predictions against references was within the same deviation of TOC-predictions. The modeled yield losses and retention values of TOC in pulping and bleaching processes and the modeled fixing of colloidal TOC to solids between the pulping plant and the aeration basin in the waste water treatment plant were similar to references presented in literature. The valid water balances of the waste water treatment plant and the reduction model of lignin-like substances produced a valid prediction of COD discharges out of the mill. A 30% increase in the release of lignin-like substances in the form of production problems was observed in pulping and bleaching processes. The same increase was observed in COD discharges out of waste water treatment. In the prediction of annual COD discharge, it was noticed that the reduction of lignin has a wide deviation from year to year and from one mill to another. This made it difficult to compare the parameters of COD discharges validated in plant dynamic simulation with another mill producing mechanical printing papers. However, a trend of moving from unbleached towards high-brightness TMP in COD discharges was valid.

Micromorphology of Last Glacial Maximum Grounding line sediments around the Antarctic Peninsula

Sediments recovered from seven Last Glacial Maximum grounding lines sites, around the Antarctic Peninsula, were analyzed using micromorphology. This is the first evidence that grounding line sediments from around the Antarctic Peninsula have complex deformational histories and subglacial origins. It was determined that grounding zone wedge contain multiple units, or diamicton layers, with homogenized boundaries. The multiple diamicton units / layers are due to the accretionary formation of a grounding line wedge. All the sediments were deposited via deformation, and continual reincorporation, homogenization of lower diamicton layers by upper diamicton layers produced what macroscopically appeared to be a single massive diamicton unit. The morainal ridge that was sampled, alternatively, is composed of a single unit, or diamicton layer, that was subglacial in origin and believed to have been pushed out to form a ridge that was subsequently deformed via glacial push.

Caractérisation du système d’acquisition de fer codé par le locus iro chez Salmonella enterica sérovar Typhi

Le fer est un élément essentiel pour les bactéries. Puisqu’elles ne peuvent le synthétiser elles-mêmes, elles utilisent un ou plusieurs systèmes d’acquisition de fer afin de se le procurer dans l’environnement, ou chez l’hôte pour leurs propres métabolismes. Différentes stratégies coexistent chez les bactéries pathogènes dues à la faible concentration de cet élément, autant chez l’hôte que dans l’environnement. Salmonella enterica sérovar Typhi (S. Typhi) est une entérobactérie Gram négative causant une maladie systémique, soit la fièvre typhoïde, qui est spécifique à l’homme. Les mécanismes de pathogènese de ce sérovar sont peu connus jusqu’à ce jour, puisque son tropisme pour l’humain empêche l’utilisation d’un modèle animal adéquat. L’objectif de cette recherche est de caractériser le système d’acquisition de fer chez S. Typhi encodé par le locus iro. Les gènes du locus, iroBCDEN ont fait l’objet de plusieurs recherches chez différents pathogènes, notamment E. coli et Salmonella Typhimurium. Bien qu’un rôle dans la virulence ait été établi pour ce locus chez ces bactéries, très peu d’informations sont disponibles quant au rôle chez S. Typhi, qui emprunte plutôt la voie systémique d’infection. Nous avons évalué le rôle de la synthèse, de l’exportation et de l’importation du sidérophore salmochéline, codé par les gènes iroBCDEN. En inactivant le locus puis par la suite les gènes de façon indépendante par échange allélique, il a été possible d’observer leurs implications in vitro lors d’infections de cellules humaines. Le rôle dans l’adhésion et l’invasion des cellules épithéliales ainsi que le rôle dans la phagocytose et la survie dans les macrophages ont donc été déterminés. De plus, le mécanisme de sécrétion par lequel la salmochéline peut traverser la membrane externe est inconnu à ce jour. La pompe à efflux TolC est responsable de la sécrétion de plusieurs molécules, y compris l’entérobactine, un sidérophore analogue à la salmochéline. Par mutagénèse, nous avons effectué un mutant de délétion tolC afin de vérifier son implication dans l’interaction avec les cellules épithéliales et les macrophages. Afin de caractériser in vitro les mutants, nous avons effectué des courbes de croissance dans différents milieux. La sensibilité au peroxyde d’hydrogène a été vérifiée par la suite, puis dû aux résultats d’infections, la mobilité de la souche ΔtolC a été évaluée. Ces différents tests nous ont permis de mieux comprendre l’implication du locus iro, de ses composantes et de la pompe à efflux TolC lors de l’interaction avec les cellules cibles d’une infection systémique causée par Salmonella Typhi.

Taxonomy, Bionomics and Biofouling of Bryozoans from the Coasts of India and the Antarctic Waters

The study of bryozoans, an important group of coelomates in the marine environment is an integral part of faunistic investigations. Bryozones are an ancient, aberrant phylum of microscopic but fascinating and often beautiful animals that build intricate colonies sometimes resembling minicolonies. In this study taxonomy, bionomics and biofouling of bryozoans from the coasts of India and the Antarctic waters. The marine biofouling is found to be hazardous. Bryozoans are microscopic , sessile,colonical coelomates that are permanently fastened in exoskeletal cases or gelatinous material of their own secretion.It is hoped that this work would help the future researchers to devote attention on microbenthos of the continental shelf of India when samples are made available through collections conducted by any ocean going vessel. In the present work an extensive study on the bryozoan foulers that occur at five selected sites of the cochin estury had to be examined and since the hydrographic parameters such as salinity, temperature, pH and dissolved oxygen in the estury,vary greatly from that in the open ocean, a frequent monitoring of these parameters was essential.

INDIAN AND ANTARCTIC BRYOZOANS - TAXONOMY AND OBSERVATIONS ON TOXICOLOGY

This thesis embodies findings on a taxonomical investigation of a group of lower marine invertebrates belonging to the category coelomata. Bryozoans are well known both in fossil and recent taxonomical history. They comprise of about 5,000 living and 16000 fossil species. Bryozoans are well known for their taxonomic abundance and structural diversity,representing the various ecological niches ranging from the intertidal to the abyssal benthic. At a time when global marine biological diversity has become a concern of not only to the scientists but also to the policy makers,an understanding of species diversity and abundance are cardinal aspects of biological studies. Geological time scales which is known that by Pre-Cambrian, marine invertebrate diversity reach the maximum and this diversity has become more comprehensive as time advanced. Taxonomists a vanishing species of scientists have become more concerned in discerning patterns of species diversity. The basic tool for this is identification fo animals. with this idea in mind a detailed study of taxonomy of bryozoan was undertaken . The major part of this thesis is devoted to describe various species of bryozoans with detailed description and ecotypical variations.The pattern of distribution and abundance which are important aspects of animal groups have also been documented. Possible effects of heavy metal contamination on the tolerance and growth of bryozoans, a few species of which have been eliminated from the chronically polluted areas of Cochin backwaters have also been documented.

Geochemistry of core sediment from antarctic region

Southern Ocean (SO) is the fourth largest Ocean comprising the southern portions of the Atlantic Ocean, Indian Ocean and Pacific Ocean. Sediment core sample (660 34’S and 580 40’E)was collected onboard O.R.V Sagar Nidhi from January to March 2010 in the Fourth Southern Ocean expedition cruise launched by the National Centre for Antarctic and Ocean Research, Goa . Sedimentary records from this area reveal the sensitivity and climatic variability’s of the region over a large time scale. Organic matter (OM) and textural behaviour of the samples were analyzed and processed concurrently. Distribution of OM, Total Organic Carbon (TOC), Protein, Lipid and Carbohydrate along with the trace metal was highlighted. Textural variation was in the array of Sand >Clay >Silt. Sand content ranges from 30.29% to 80.11%. The order of relative distribution of OM was Lipid >Protein > TOC > Carbohydrate. The average concentrations of TOC, Protein, Lipid and Carbohydrate were 2.2 mg/g, 1.2 mg/g, 3.3 mg/g and 1.1mg/g respectively. Protein to carbohydrate ratio and lipid to carbohydrate ratio were also encountered to understand the respective freshness and nutritional quality of the sediments. Trace metal distribution showed the average concentration was maximum for Mn and minimum for Co.

Praxisrelevante Auswirkungen des Vorschlages für eine EU-Verordnung KOM/2000/7/final, 2000/0212(COD) des europäischen Parlaments und des Rates von der Kommission der Europäischen Gemeinschaften auf die Verkehrsplanung des öffentlichen Personennahverkehrs

Die Arbeit behandelt den Vorschlag für eine EU-Verordnung KOM/2000/7/final, 2000/0212(COD) des europäischen Parlaments und des Rates von der Kommission der Europäischen Gemeinschaften als Grundlage einer Marktöffnungsverordnung und welche Veränderungen sich dadurch in Deutschland einstellen werden. Ausschreibungen von Verkehrsleistungen werden zunehmen. Die Ausschreibungsarten werden sich in ländlichen Regionen von denen in Verkehrszentren unterscheiden. In der Region werden sich Bedarfslösungen stärker durchsetzen. Kürzungen von Verkehrsleistungen werden hier stärker ausfallen als in den Zentren und damit zu einem kleineren Leistungsvolumen führen. Aufgrund des geringen Leistungsumfangs gibt es weniger Interessenten. Bei Standardausschreibungen werden deshalb auch häufig die Varianten der beschränkten oder die freihändige Vergabe gewählt. Funktionale Ausschreibungen haben nur eine untergeordnete Bedeutung. In den Verkehrszentren sind die Lose größer und damit für viele Anbieter interessant. Die Verkehrszusatzleistungen sind zudem komplexer. Standardausschreibungen in öffentlicher Vergabeart werden sich hier vermutlich als Norm durchsetzen. Die VOL/A wird sicherlich ihre Bedeutung und ihren dafür notwendigen Regelungsumfang in Deutschland als deutsches oder als europäisches Recht behalten. Ob der empfehlende Charakter der DIN EN 13816 Norm „ÖPNV: Definition, Festlegung von Leistungszielen und Messung der Servicequalität“ erhalten werden kann und nicht als Steuerungselement zur Standardisierung im ÖPNV beitragen wird, ist dabei zu bezweifeln. Durch diese Wettbewerbspflicht wird der Aufgabenträger zum Besteller von Verkehrsleistungen. Damit geht die Verkehrsplanung in die Verantwortung des Aufgabenträgers über und gerät stärker in den Einflussbereich der Politik. Die strategisch abstrakte und die konkrete Verkehrsplanung wachsen für den Normfall der Standardausschreibung zusammen. Die Hoffnung auf eine bessere Netzintegration und eine Standardisierung des ÖPNV Angebots und der ÖPNV Qualität entsteht. Es entwickelt sich dadurch aber auch die Gefahr der Abhängigkeit des Nahverkehrsangebots von der derzeitigen Haushaltslage oder der Interessenlage der Politik. Kontinuität in Angebot und Qualität werden zu erklärten Planungszielen. Der Verkehrsplaner auf der Bestellerseite muss die Planung in Ausschreibungsunterlagen umsetzen. Dies erfordert erweiterte Kompetenzen in den Bereichen Betriebswirtschaft, Logistik, Jura, Informatik und Führungskompetenzen. Ausbildende Institutionen müssen darauf bereits im Vorfeld der Umsetzung reagieren. Durch die zeitliche Verzögerung der Umsetzung der Planung durch die Ausschreibungsschritte sind in der Verkehrsplanung längere Planungsvorlaufzeiten einzukalkulieren. Vorausschauender zu planen, wird dabei wichtiger. Auch eventuelle Fehler in der Planung sind nicht mehr so einfach zu korrigieren. Durch den gestiegenen Einsatz von Technologien in den Fahrzeugen besteht für den Verkehrsplaner dafür häufiger die Möglichkeit, Planungsänderungen auf ihre Wirksamkeit im Hinblick auf Attraktivität für den Fahrgast anhand von den ermittelten Fahrgastzahlen zu kontrollieren. Dasselbe gilt auch für Marketing- und Vertriebsmaßnahmen, wie für die Tarifpolitik. Die Zahlen stehen nicht nur für diese Rückkopplung zur Verfügung, sondern dienen auch als Planungsgrundlage für zukünftige Maßnahmen. Dem Planer stehen konkretere Zahlen für die Planung zur Verfügung. Ein Aspekt, der aufgrund der Sanktionsmaßnahmen bei Ausschreibungen an Bedeutung gewinnen wird, ist die Möglichkeit, Qualität von Verkehrsleistungen möglichst objektiv beurteilen zu können. Praxisrelevante Auswirkungen auf die Verkehrsplanung des öffentlichen Personennahverkehrs ergeben sich hauptsächlich durch die gestiegene Komplexität in der Planung selbst und den dadurch unverzichtbaren gewordenen Einsatz von Computerunterstützung. Die Umsetzung in Ausschreibungsunterlagen der Planung und die Kontrolle stellen neue Elemente im Aufgabenbereich des Verkehrsplaners dar und erfordern damit breiter ausgelegte Kernkompetenzen. Es werden mehr Verkehrsplaner mit breiterer Ausbildung benötigt werden. Diese Arbeit hat aufgezeigt, dass sich mit der Integration des Ausschreibungsgedankens in den Ablauf der Verkehrsplanung eine sprunghafte Entwicklung in der Planungstätigkeit ergeben wird. Aufgrund der in Zukunft steigenden Qualität und Quantität der Planungsgrundlagen und der ebenfalls gestiegenen Ansprüche an die Bewertungsparameter ergeben sich Veränderungen und neue Anforderungen auf diesem Gebiet, die in erster Linie für die Hochschulen und andere ausbildende Einrichtungen, aber auch für die Verkehrsplanung unterstützende Industrie.

Is Antarctic climate most sensitive to ozone depletion in the middle or lower stratosphere?

Antarctic stratospheric ozone depletion has been associated with an observed downward trend in tropospheric geopotential height and temperature. Stratospheric ozone depletion peaks in October–November, whereas tropospheric trends are largest in December–January, concurrent with maximum ozone changes close to the tropopause. Surface temperatures are most sensitive to ozone loss near the tropopause, therefore it has been suggested that the observed tropospheric response is forced mainly by ozone depletion in the lower stratosphere. In this study the climate response to ozone depletion exclusively below 164 hPa is simulated using HadSM3-L64, and compared with simulations in which ozone depletion is prescribed exclusively above 164 hPa. Results indicate that the tropospheric response is dominated by ozone changes above 164 hPa, with ozone changes in the lowermost stratosphere playing an insignificant role. A tropospheric response is also seen in fall/winter which agrees well with observations and has not been found in modeling studies previously.