Distribution of North Pacific right whales (Eubalaena japonica) as shown by 19th and 20th century whaling catch and sighting records

North Pacific right whales (Eubalaena japonica) were extensively exploited in the 19th century, and their recovery was further retarded (severely so in the eastern population) by illegal Soviet catches in the 20th century, primarily in the 1960s. Monthly plots of right whale sightings and catches from both the 19th and 20th centuries are provided, using data summarized by Scarff (1991, from the whale charts of Matthew Fontaine Maury) and Brownell et al. (2001), respectively. Right whales had an extensive offshore distribution in the 19th century, and were common in areas (such as the Gulf of Alaska and Sea of Japan) where few or no right whales occur today. Seasonal movements of right whales are apparent in the data, although to some extent these reflect survey and whaling effort. That said, these seasonal movements indicate a general northward migration in spring from lower latitudes, and major concentrations above 40°N in summer. Sightings diminished and occurred further south in autumn, and few animals were recorded anywhere in winter. These north-south migratory movements support the hypothesis of two largely discrete populations of right whales in the eastern and western North Pacific. Overall, these analyses confirm that the size and range of the right whale population is now considerably diminished in the North Pacific relative to the situation during the peak period of whaling for this species in the 19th century. For management purposes, new surveys are urgently required to establish the present distribution of this species; existing data suggest that the Bering Sea, the Gulf of Alaska, the Okhotsk Sea, the Kuril Islands and the coast of Kamchatka are the areas with the greatest likelihood of finding right whales today.

Use of chemical tracers in assessing the diet and foraging regions of eastern North Pacific killer whales

Top predators in the marine environment integrate chemical signals acquired from their prey that reflect both the species consumed and the regions from which the prey were taken. These chemical tracers—stable isotope ratios of carbon and nitrogen; persistent organic pollutant (POP) concentrations, patterns and ratios; and fatty acid profiles—were measured in blubber biopsy samples from North Pacific killer whales (Orcinus orca) (n = 84) and were used to provide further insight into their diet, particularly for the offshore group, about which little dietary information is available. The offshore killer whales were shown to consume prey species that were distinctly different from those of sympatric resident and transient killer whales. In addition, it was confirmed that the offshores forage as far south as California. Thus, these results provide evidence that the offshores belong to a third killer whale ecotype. Resident killer whale populations showed a gradient in stable isotope profiles from west (central Aleutians) to east (Gulf of Alaska) that, in part, can be attributed to a shift from off-shelf to continental shelf-based prey. Finally, stable isotope ratio results, supported by field observations, showed that the diet in spring and summer of eastern Aleutian Island transient killer whales is apparently not composed exclusively of Steller sea lions.

Use of chemical tracers in assessing the diet and foraging regions of eastern North Pacific killer whales

Top predators in the marine environment integrate chemical signals acquired from their prey that reflect both the species consumed and the regions from which the prey were taken. These chemical tracers—stable isotope ratios of carbon and nitrogen; persistent organic pollutant (POP) concentrations, patterns and ratios; and fatty acid profiles—were measured in blubber biopsy samples from North Pacific killer whales (Orcinus orca) (n = 84) and were used to provide further insight into their diet, particularly for the offshore group, about which little dietary information is available. The offshore killer whales were shown to consume prey species that were distinctly different from those of sympatric resident and transient killer whales. In addition, it was confirmed that the offshores forage as far south as California. Thus, these results provide evidence that the offshores belong to a third killer whale ecotype. Resident killer whale populations showed a gradient in stable isotope profiles from west (central Aleutians) to east (Gulf of Alaska) that, in part, can be attributed to a shift from off-shelf to continental shelf-based prey. Finally, stable isotope ratio results, supported by field observations, showed that the diet in spring and summer of eastern Aleutian Island transient killer whales is apparently not composed exclusively of Steller sea lions.

Taxonomy and Life Histories of Two North American Species of "Carneophallus" (=Microphallus) (Digenea: Microphallidae)

Discusses the taxonomy and life histories of two North American species of Carneophallus" (=Microphallus) (Digenea: Microphallidae).

Community structure and dynamics of Monogenea and Trematoda in three North American cyprinid species in the Salt Valley Watershed, Nebraska.

An investigation was made of the communities of gill monogene genus Dactylogyrus (Platyhelminthes, Monogenea) and the populations of blackspot parasite (Platyhelminthes, Trematoda) of Pimephales promelas, Notropis stramineus, and Semotilus atromaculatus in 3 distinct sites along the 3 converging tributaries in southeastern Nebraska from 2004 to 2006. This work constitutes the first multi-site, multi-year study of a complex community of Dactylogyrus spp. and their reproductive activities on native North American cyprinid species. The biological hypothesis that closely related species with direct lifecycles respond differently to shared environmental conditions was tested. It was revealed that in this system that, Cyprinid species do not share Dactylogyrus species, host size and sex are not predictive of infection, and Dactylogyrus community structure is stable, despite variation in seasonal occurrence and populations among sites. The biological hypothesis that closely related species have innate differences in reproductive activities that provide structure to their populations and influence their roles in the parasite community was tested. It was revealed that in this system, host size, sex, and collection site are not predictive of reproductive activities, that egg production is not always continuous and varies in duration among congeners, and that recruitment of larval Dactylogyrus is not continuous across parasites’ reproductive periods. Hatch timing and host availability, not reproductive timing, are the critical factors determining population dynamics of the gill monogenes in time and space. Lastly, the biological hypothesis that innate blackspot biology is responsible for parasite host-specificity, host recruitment strategies and parasite population structure was tested. Field collections revealed that for blackspot, host size, sex, and collection month and year are not predictive of infection, that parasite cysts survive winter, and that host movement is restricted among the 3 collection sites. Finally, experimental infections of hosts with cercaria isolated from 1st intermediate snail hosts reveal that cercarial biology, not environmental circumstances, are responsible for differences in infection among hosts.

Daily ration and feeding chronology of dominant diel vertical migrant fishes in the Subtropical Eastern North Atlantic Ocean

[EN] Diel Vertical Migrants (DVMs) are mainly zooplankton and micronekton which migrate upward from 400-500 m depth every night to feed on the productive epipelagic zone, coming back at dawn to the mesopelagic zone, where they defecate, excrete, and respire the ingested carbon. DVMs should contribute to the biological pump in the ocean and, accordingly, to the global CO2 balance. Although those migrants are mainly small fishes, cephalopods and crustaceans, the lanternfishes (myctophidae) usually contribute up to 80% of total DVMs biomass. Thus, myctophids may represent a pathway accounting for a substantial export of organic carbon to the deep ocean. However, the magnitude of this transport is still poorly known. In order to assess this active flux of carbon, we performed a preliminary study of mesopelagic organisms around the Canary Islands. Here we present the results of diet, daily rations and feeding chronology of Lobianchia dofleini, Hygophum hygomii and Ceratoscopelus maderensis, 3 dominant species of myctophids performing diel vertical migrations in the Subtropical Eastern North Atlantic Ocean. Samples were obtained on board the RV La Bocaina during June 2009. Myctophids were sorted and fixed in 4% buffered formalin and the stomach contents of target species were examined and weighted. Feeding chronology was approached by studying stomach fullness and state of digestion of prey items in individuals from hauls performed at different times and depths. Our results provide further information about lanternfishes feeding ecology in relation to their vertical migration patterns as well as their contribution to the biological carbon pump.

A candidate gene approach to identify DNA markers associated with meat quality and production traits: investigation of several cathepsin genes in Italian heavy pigs.

The cathepsin enzymes represent an important family of lysosomal proteinases with a broad spectrum of functions in many, if not in all, tissues and cell types. In addition to their primary role during the normal protein turnover, they possess highly specific proteolytic activities, including antigen processing in the immune response and a direct role in the development of obesity and tumours. In pigs, the involvement of cathepsin enzymes in proteolytic processes have important effects during the conversion of muscle to meat, due to their influence on meat texture and sensory characteristics, mainly in seasoned products. Their contribution is fundamental in flavour development of dry-curing hams. However, several authors have demonstrated that high cathepsin activity, in particular of cathepsin B, is correlated to defects of these products, such as an excessive meat softness together with abnormal free tyrosine content, astringent or metallic aftertastes and formation of a white film on the cut surface. Thus, investigation of their genetic variability could be useful to identify DNA markers associated with these dry cured hams parameters, but also with meat quality, production and carcass traits in Italian heavy pigs. Unfortunately, no association has been found between cathepsin markers and meat quality traits so far, in particular with cathepsin B activity, suggesting that other genes, besides these, affect meat quality parameters. Nevertheless, significant associations were observed with several carcass and production traits in pigs. A recent study has demonstrated that different single nucleotide polymorphisms (SNPs) localized in cathepsin D (CTSD), F (CTSF), H and Z genes were highly associated with growth, fat deposition and production traits in an Italian Large White pig population. The aim of this thesis was to confirm some of these results in other pig populations and identify new cathepsin markers in order to evaluate their effects on cathepsin activity and other production traits. Furthermore, starting from the data obtained in previous studies on CTSD gene, we also analyzed the known polymorphism located in the insulin-like growth factor 2 gene (IGF2 intron3-g.3072G>A). This marker is considered the causative mutation for the quantitative trait loci (QTL) affecting muscle mass and fat deposition in pigs. Since IGF2 maps very close to CTSD on porcine chromosome (SSC) 2, we wanted to clarify if the effects of the CTSD marker were due to linkage disequilibrium with the IGF2 intron3-g.3072G>A mutation or not. In the first chapter, we reported the results from these two SSC2 gene markers. First of all, we evaluated the effects of the IGF2 intron3-g.3072G>A polymorphism in the Italian Large White breed, for which no previous studies have analysed this marker. Highly significant associations were identified with all estimated breeding values for production and carcass traits (P<0.00001), while no effects were observed for meat quality traits. Instead, the IGF2 intron3-g.3072G>A mutation did not show any associations with the analyzed traits in the Italian Duroc pigs, probably due to the low level of variability at this polymorphic site for this breed. In the same Duroc pig population, significant associations were obtained for the CTSD marker for all production and carcass traits (P < 0.001), after excluding possible confounding effects of the IGF2 mutation. The effects of the CTSD g.70G>A polymorphism were also confirmed in a group of Italian Large White pigs homozygous for the IGF2 intron3-g.3072G allele G (IGF2 intron3-g.3072GG) and by haplotype analysis between the markers of the two considered genes. Taken together, all these data indicated that the IGF2 intron3-g.3072G>A mutation is not the only polymorphism affecting fatness and muscle deposition in pigs. In the second chapter, we reported the analysis of two new SNPs identified in cathepsin L (CTSL) and cathepsin S (CTSS) genes and the association results with meat quality parameters (including cathepsin B activity) and several production traits in an Italian Large White pig population. Allele frequencies of these two markers were evaluated in 7 different pig breeds. Furthermore, we mapped using a radiation hybrid panel the CTSS gene on SSC4. Association studies with several production traits, carried out in 268 Italian Large White pigs, indicated positive effects of the CTSL polymorphism on average daily gain, weight of lean cuts and backfat thickness (P<0.05). The results for these latter traits were also confirmed using a selective genotype approach in other Italian Large White pigs (P<0.01). In the 268 pig group, the CTSS polymorphism was associated with feed:gain ratio and average daily gain (P<0.05). Instead, no association was observed between the analysed markers and meat quality parameters. Finally, we wanted to verify if the positive results obtained for the cathepsin L and S markers and for other previous identified SNPs (cathepsin F, cathepsin Z and their inhibitor cystatin B) were confirmed in the Italian Duroc pig breed (third chapter). We analysed them in two groups of Duroc pigs: the first group was made of 218 performance-tested pigs not selected by any phenotypic criteria, the second group was made of 100 Italian Duroc pigs extreme and divergent for visible intermuscular fat trait. In the first group, the CTSL polymorphism was associated with weight of lean cuts (P<0.05), while suggestive associations were obtained for average daily gain and backfat thickness (P<0.10). Allele frequencies of the CTSL gene marker also differed positively among the visible intermuscular extreme tails. Instead, no positive effects were observed for the other DNA markers on the analysed traits. In conclusion, in agreement with the present data and for the biological role of these enzymes, the porcine CTSD and CTSL markers: a) may have a direct effect in the biological mechanisms involved in determining fat and lean meat content in pigs, or b) these markers could be very close to the putative functional mutation(s) present in other genes. These findings have important practical applications, in particular the CTSD and CTSL mutations could be applied in a marker assisted selection (MAS) both in the Italian Large White and Italian Duroc breeds. Marker assisted selection could also increase in efficiency by adding information from the cathepsin S genotype, but only in the Italian Large White breed.

Different approaches to identify markers for meat quality and production traits in pigs: analysis of the transcriptome in post mortem skeletal muscle and investigation of candidate genes

Due to the growing attention of consumers towards their food, improvement of quality of animal products has become one of the main focus of research. To this aim, the application of modern molecular genetics approaches has been proved extremely useful and effective. This innovative drive includes all livestock species productions, including pork. The Italian pig breeding industry is unique because needs heavy pigs slaughtered at about 160 kg for the production of high quality processed products. For this reason, it requires precise meat quality and carcass characteristics. Two aspects have been considered in this thesis: the application of the transcriptome analysis in post mortem pig muscles as a possible method to evaluate meat quality parameters related to the pre mortem status of the animals, including health, nutrition, welfare, and with potential applications for product traceability (chapters 3 and 4); the study of candidate genes for obesity related traits in order to identify markers associated with fatness in pigs that could be applied to improve carcass quality (chapters 5, 6, and 7). Chapter three addresses the first issue from a methodological point of view. When we considered this issue, it was not obvious that post mortem skeletal muscle could be useful for transcriptomic analysis. Therefore we demonstrated that the quality of RNA extracted from skeletal muscle of pigs sampled at different post mortem intervals (20 minutes, 2 hours, 6 hours, and 24 hours) is good for downstream applications. Degradation occurred starting from 48 h post mortem even if at this time it is still possible to use some RNA products. In the fourth chapter, in order to demonstrate the potential use of RNA obtained up to 24 hours post mortem, we present the results of RNA analysis with the Affymetrix microarray platform that made it possible to assess the level of expression of more of 24000 mRNAs. We did not identify any significant differences between the different post mortem times suggesting that this technique could be applied to retrieve information coming from the transcriptome of skeletal muscle samples not collected just after slaughtering. This study represents the first contribution of this kind applied to pork. In the fifth chapter, we investigated as candidate for fat deposition the TBC1D1 [TBC1 (tre-2/USP6, BUB2, cdc16) gene. This gene is involved in mechanisms regulating energy homeostasis in skeletal muscle and is associated with predisposition to obesity in humans. By resequencing a fragment of the TBC1D1 gene we identified three synonymous mutations localized in exon 2 (g.40A>G, g.151C>T, and g.172T>C) and 2 polymorphisms localized in intron 2 (g.219G>A and g.252G>A). One of these polymorphisms (g.219G>A) was genotyped by high resolution melting (HRM) analysis and PCR-RFLP. Moreover, this gene sequence was mapped by radiation hybrid analysis on porcine chromosome 8. The association study was conducted in 756 performance tested pigs of Italian Large White and Italian Duroc breeds. Significant results were obtained for lean meat content, back fat thickness, visible intermuscular fat and ham weight. In chapter six, a second candidate gene (tribbles homolog 3, TRIB3) is analyzed in a study of association with carcass and meat quality traits. The TRIB3 gene is involved in energy metabolism of skeletal muscle and plays a role as suppressor of adipocyte differentiation. We identified two polymorphisms in the first coding exon of the porcine TRIB3 gene, one is a synonymous SNP (c.132T> C), a second is a missense mutation (c.146C> T, p.P49L). The two polymorphisms appear to be in complete linkage disequilibrium between and within breeds. The in silico analysis of the p.P49L substitution suggests that it might have a functional effect. The association study in about 650 pigs indicates that this marker is associated with back fat thickness in Italian Large White and Italian Duroc breeds in two different experimental designs. This polymorphisms is also associated with lactate content of muscle semimembranosus in Italian Large White pigs. Expression analysis indicated that this gene is transcribed in skeletal muscle and adipose tissue as well as in other tissues. In the seventh chapter, we reported the genotyping results for of 677 SNPs in extreme divergent groups of pigs chosen according to the extreme estimated breeding values for back fat thickness. SNPs were identified by resequencing, literature mining and in silico database mining. analysis, data reported in the literature of 60 candidates genes for obesity. Genotyping was carried out using the GoldenGate (Illumina) platform. Of the analyzed SNPs more that 300 were polymorphic in the genotyped population and had minor allele frequency (MAF) >0.05. Of these SNPs, 65 were associated (P<0.10) with back fat thickness. One of the most significant gene marker was the same TBC1D1 SNPs reported in chapter 5, confirming the role of this gene in fat deposition in pig. These results could be important to better define the pig as a model for human obesity other than for marker assisted selection to improve carcass characteristics.

Thermochronologic and geodynamic evolution of the Pontides: Sakarya terrane (Karakaya Complex) and Istanbul terrane, Turkey.

An integrated array of analytical methods -including clay mineralogy, vitrinite reflectance, Raman spectroscopy on carbonaceous material, and apatite fission-track analysis- was employed to constrain the thermal and thermochronological evolution of selected portions of the Pontides of northern Turkey. (1) A multimethod investigation was applied for the first time to characterise the thermal history of the Karakaya Complex, a Permo-Triassic subduction-accretion complex cropping out throughout the Sakarya Zone. The results indicate two different thermal regimes: the Lower Karakaya Complex (Nilüfer Unit) -mostly made of metabasite and marble- suffered peak temperatures of 300-500°C (greenschist facies); the Upper Karakaya Complex (Hodul and the Orhanlar Units) –mostly made of greywacke and arkose- yielded heterogeneous peak temperatures (125-376°C), possibly the result of different degree of involvement of the units in the complex dynamic processes of the accretionary wedge. Contrary to common belief, the results of this study indicate that the entire Karakaya Complex suffered metamorphic conditions. Moreover, a good degree of correlation among the results of these methods demonstrate that Raman spectroscopy on carbonaceous material can be applied successfully to temperature ranges of 200-330°C, thus extending the application of this method from higher grade metamorphic contexts to lower grade metamorphic conditions. (2) Apatite fission-track analysis was applied to the Sakarya and the İstanbul Zones in order to constrain the exhumation history and timing of amalgamation of these two exotic terranes. AFT ages from the İstanbul and Sakarya terranes recorded three distinct episodes of exhumation related to the complex tectonic evolution of the Pontides. (i) Paleocene - early Eocene ages (62.3-50.3 Ma) reflect the closure of the İzmir-Ankara ocean and the ensuing collision between the Sakarya terrane and the Anatolide-Tauride Block. (ii) Late Eocene - earliest Oligocene (43.5-32.3 Ma) ages reflect renewed tectonic activity along the İzmir-Ankara. (iii) Late Oligocene- Early Miocene ages reflect the onset and development of the northern Aegean extension. The consistency of AFT ages, both north and south of the tectonic contact between the İstanbul and Sakarya terranes, suggest that such terranes were amalgamated in pre-Cenozoic times. (3) Fission-track analysis was also applied to rock samples from the Marmara region, in an attempt to constrain the inception and development of the North Anatolian Fault system in the region. The results agree with those from the central Pontides. The youngest AFT ages (Late Oligocene - early Miocene) were recorded in the western portion of the Marmara Sea region and reflect the onset and development of northern Aegean extension. Fission-track data from the eastern Marmara Sea region indicate rapid Early Eocene exhumation induced by the development of the İzmir-Ankara orogenic wedge. Thermochronological data along the trace of the Ganos Fault –a segment of the North Anatolian Fault system- indicate the presence of a tectonic discontinuity active by Late Oligocene time, i.e. well before the arrival of the North Anatolian Fault system in the area. The integration of thermochronologic data with preexisting structural data point to the existence of a system of major E-W-trending structural discontinuities active at least from the Late Oligocene. In the Early Pliocene, inception of the present-day North Anatolian Fault system in the Marmara region occurred by reactivation of these older tectonic structures. 


Characterization and exploiment of Microbial Strains to be used in Meat Processing and Fermentation

The principal aim of this research project has been the evaluation of the specific role of yeasts in ripening processes of dry-cured meat products, i.e. speck and in salami produced by adding Lactobacilli starter cultures, i.e. L. sakei, L. casei, L. fermentum, L. rhamnosus, L.sakei + S.xylosus. In particular the contribution of the predominant yeasts to the hydrolytic patterns of meat proteins has been studied both in model system and in real products. In fact, although several papers have been published on the microbial, enzymatic, aromatic and chemical characterization of dry-cured meat e.g. ham over ripening, the specific role of yeasts has been often underestimated. Therefore this research work has been focused on the following aspects: 1. Characterization of the yeasts and lactic acid bacteria in samples of speck produced by different farms and analyzed during the various production and ripening phases 2. Characterization of the superficial or internal yeasts population in salami produced with or without the use of lactobacilli as starter cultures 3. Molecular characterization of different strains of yeasts and detection of the dominant biotypes able to survive despite environmental stress factors (such as smoke, salt) 4. Study of the proteolytic profiles of speck and salami during the ripening process and comparison with the proteolytic profiles produced in meat model systems by a relevant number of yeasts isolated from speck and salami 5. Study of the proteolytic profiles of Lactobacilli starter cultures in meat model systems 6. Comparative statistical analysis of the proteolytic profiles to find possible relationships between specific bands and peptides and specific microorganisms 7. Evaluation of the aromatic characteristics of speck and salami to assess relationships among the metabolites released by the starter cultures or the dominant microflora

Analysis of the relationships between Spartina maritima and nutrient enrichment in North Adriatic salt marshes

Salt marshes are coastal ecosystem in the upper intertidal zone between internal water and sea and are widely spread throughout Italy, from Friuli Venezia Giulia, in the North, to Sicily, in the South. These delicate environments are threatened by eutrophication, habitat conversion (for land reclaiming or agriculture) and climate change impacts such as sea level rise. The objectives of my thesis were to: 1) analyse the distribution and biomass of the perennial native cordgrass Spartina maritima (one of the most relevant foundation species in the low intertidal saltmarsh vegetation in the study region) at 7 sites along the Northern Adriatic coast and relate it to critical environmental parameters and 2) to carry out a nutrient manipulation experiment to detect nutrient enrichment effects on S. maritima biomass and vegetation characteristics. The survey showed significant differences among sites in biological response variables - i.e., live belowground, live aboveground biomass, above:belowground (R:S) biomass ratio, % cover, average height and stem density – which were mainly related to differences in nitrate, nitrite and phosphate contents in surface water. Preliminary results from the experiment (which is still ongoing) showed so far no significant effects of nutrient enrichment on live aboveground and belowground biomass, R:S ratio, leaf %Carbon, average height, stem density and random shoot height; however, a significantly higher (P=0.018) increase in leaf %Nitrogen content in treated plots indicated that nutrient uptake had occurred.

Making research relevant to policy-makers, development actors, and local communities: NCCR North-South report on effectiveness of research for development

Bridging the gap between research and policy is of growing importance in international development. The National Centre of Competence in Research (NCCR) North-South has rich experience in collaborating beyond academic boundaries to make their research relevant to various societal actors. This publication is the first to provide an overview of the effectiveness of NCCR North-South researchers’ efforts to interact with policy, practice, and local communities with a view to effecting a change in practices. A systematic assessment of researchers’ interactions with non-academic partners is presented, based on principles of monitoring and evaluation. On this basis, tools for collective learning and widespread adaptation are proposed. The report shows with what types of societal actors NCCR North-South researchers collaborate and analyses examples of how researchers conduct dialogue beyond academic boundaries, leading to specific outcomes. It also explains the frame conditions considered decisive for successful and sustainable policy dialogue and concludes with recommendations about how the NCCR North-South can increase the effectiveness of its research for development. The publication is a valuable source of inspiration for those interested in better understanding how to generate the multiple benefits of making science relevant to society.