Applications of gene sequence polymorphisms in evolutionary genetic studies of Atlantic salmon (Salmo salar) and other teleost fish species

Evolutionary genetics incorporates traditional population genetics and studies of the origins of genetic variation by mutation and recombination, and the molecular evolution of genomes. Among the primary forces that have potential to affect the genetic variation within and among populations, including those that may lead to adaptation and speciation, are genetic drift, gene flow, mutations and natural selection. The main challenges in knowing the genetic basis of evolutionary changes is to distinguish the adaptive selection forces that cause existent DNA sequence variants and also to identify the nucleotide differences responsible for the observed phenotypic variation. To understand the effects of various forces, interpretation of gene sequence variation has been the principal basis of many evolutionary genetic studies. The main aim of this thesis was to assess different forms of teleost gene sequence polymorphisms in evolutionary genetic studies of Atlantic salmon (Salmo salar) and other species. Firstly, the level of Darwinian adaptive evolution affected coding regions of the growth hormone (GH) gene during the teleost evolution was investigated based on the sequence data existing in public databases. Secondly, a target gene approach was used to identify within population variation in the growth hormone 1 (GH1) gene in salmon. Then, a new strategy for single nucleotide polymorphisms (SNPs) discovery in salmonid fishes was introduced, and, finally, the usefulness of a limited number of SNP markers as molecular tools in several applications of population genetics in Atlantic salmon was assessed. This thesis showed that the gene sequences in databases can be utilized to perform comparative studies of molecular evolution, and some putative evidence of the existence of Darwinian selection during the teleost GH evolution was presented. In addition, existent sequence data was exploited to investigate GH1 gene variation within Atlantic salmon populations throughout its range. Purifying selection is suggested to be the predominant evolutionary force controlling the genetic variation of this gene in salmon, and some support for gene flow between continents was also observed. The novel approach to SNP discovery in species with duplicated genome fragments introduced here proved to be an effective method, and this may have several applications in evolutionary genetics with different species - e.g. when developing gene-targeted markers to investigate quantitative genetic variation. The thesis also demonstrated that only a few SNPs performed highly similar signals in some of the population genetic analyses when compared with the microsatellite markers. This may have useful applications when estimating genetic diversity in genes having a potential role in ecological and conservation issues, or when using hard biological samples in genetic studies as SNPs can be applied with relatively highly degraded DNA.

Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks

Background: Thermophilic proteins sustain themselves and function at higher temperatures. Despite their structural and functional similarities with their mesophilic homologues, they show enhanced stability. Various comparative studies at genomic, protein sequence and structure levels, and experimental works highlight the different factors and dominant interacting forces contributing to this increased stability. Methods: In this comparative structure based study, we have used interaction energies between amino acids, to generate structure networks called as Protein Energy Networks (PENs). These PENs are used to compute network, sub-graph, and node specific parameters. These parameters are then compared between the thermophile-mesophile homologues. Results: The results show an increased number of clusters and low energy cliques in thermophiles as the main contributing factors for their enhanced stability. Further more, we see an increase in the number of hubs in thermophiles. We also observe no community of electrostatic cliques forming in PENs. Conclusion: In this study we were able to take an energy based network approach, to identify the factors responsible for enhanced stability of thermophiles, by comparative analysis. We were able to point out that the sub-graph parameters are the prominent contributing factors. The thermophiles have a better-packed hydrophobic core. We have also discussed how thermophiles, although increasing stability through higher connectivity retains conformational flexibility, from a cliques and communities perspective.

Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks

Background: Thermophilic proteins sustain themselves and function at higher temperatures. Despite their structural and functional similarities with their mesophilic homologues, they show enhanced stability. Various comparative studies at genomic, protein sequence and structure levels, and experimental works highlight the different factors and dominant interacting forces contributing to this increased stability. Methods: In this comparative structure based study, we have used interaction energies between amino acids, to generate structure networks called as Protein Energy Networks (PENs). These PENs are used to compute network, sub-graph, and node specific parameters. These parameters are then compared between the thermophile-mesophile homologues. Results: The results show an increased number of clusters and low energy cliques in thermophiles as the main contributing factors for their enhanced stability. Further more, we see an increase in the number of hubs in thermophiles. We also observe no community of electrostatic cliques forming in PENs. Conclusion: In this study we were able to take an energy based network approach, to identify the factors responsible for enhanced stability of thermophiles, by comparative analysis. We were able to point out that the sub-graph parameters are the prominent contributing factors. The thermophiles have a better-packed hydrophobic core. We have also discussed how thermophiles, although increasing stability through higher connectivity retains conformational flexibility, from a cliques and communities perspective.

Evaluation. of Transverse Piezoelectric Coefficient of ZnO Thin Films Deposited on Different Flexible Substrates: A Comparative Study on the Vibration Sensing Performance

We report on the systematic comparative study of highly c-axis oriented and crystalline piezoelectric ZnO thin films deposited on four different flexible substrates for vibration sensing application. The flexible substrates employed for present experimental study were namely a metal alloy (Phynox), metal (aluminum), polyimide (Kapton), and polyester (Mylar). ZnO thin films were deposited by an RF reactive magnetron sputtering technique. ZnO thin films of similar thicknesses of 700 +/- 30 nm were deposited on four different flexible substrates to have proper comparative studies. The crystallinity, surface morphology, chemical composition, and roughness of ZnO thin films were evaluated by respective material characterization techniques. The transverse piezoelectric coefficient (d(31)) value for assessing the piezoelectric property of ZnO thin films on different flexible substrates was measured by a four-point bending method. ZnO thin films deposited on Phynox alloy substrate showed relatively better material characterization results and a higher piezoelectric d(31) coefficient value as compared to ZnO films on metal and polymer substrates. In order to experimentally verify the above observations, vibration sensing studies were performed. As expected, the ZnO thin film deposited on Phynox alloy substrate showed better vibration sensing performance. It has generated the highest peak to peak output voltage amplitude of 256 mV as compared to that of aluminum (224 mV), Kapton (144 mV), and Mylar (46 mV). Therefore, metal alloy flexible substrate proves to be a more suitable, advantageous, and versatile choice for integrating ZnO thin films as compared to metal and polymer flexible substrates for vibration sensing applications. The present experimental study is extremely important and helpful for the selection of a suitable flexible substrate for various applications in the field of sensor and actuator technology.

A comparative study of Young's modulus of single-walled carbon nanotube by CPMD, MD, and first principle simulations

Carbon nanotubes (CNTs), due to their exceptional magnetic, electrical and mechanical properties, are promising candidates for several technical applications ranging from nanoelectronic devices to composites. Young's modulus holds the special status in material properties and micro/nano-electromechanical systems (MEMS/NEMS) design. The excellently regular structures of CNTs facilitate accurate simulation of CNTs' behavior by applying a variety of theoretical methods. Here, three representative numerical methods, i.e., Car-Parrinello molecular dynamics (CPMD), density functional theory (DFT) and molecular dynamics (MD), were applied to calculate Young's modulus of single-walled carbon nanotube (SWCNT) with chirality (3,3). The comparative studies showed that the most accurate result is offered by time consuming DFT simulation. MID simulation produced a less accurate result due to neglecting electronic motions. Compared to the two preceding methods the best performance, with a balance between efficiency and precision, was deduced by CPMD.

Intertidal transect studies of northern Monterey Bay

In accordance with a contract dated 10/22/71 between the Association of the Monterey Bay Area Governments (AMBAG) and the University of California, Santa Cruz, (UCSC), two permanent intertidal transects with 14 permanent meter-square quadrats were established on the north shore of Monterey Bay during November, 1971. One transect (6 quadrats) was placed on the shore near the Santa Cruz Sanitation outfall, while the second (8 quadrats) was placed near the Eastcliff Sanitation District outfall at Soquel Polnt (Pleasure Point). Animals and plants within the quadrats were listed, their abundance estimated, and representative specimens collected for a reference collection maintained at UCSC. Additional species of animals and plants in the areas of the transects were collected for the reference collection. These collections will serve as a base-line for comparative studies which can follow the magnitude and direction of future changes in these areas.

Evolution of suitable trawl nets for medium size trawlers - 1: Comparative fishing efficiency between 32 m bulged belly, long wing and four panel trawls

Comparative studies of the efficiency of 32 m bulged belly, long wing and four panel trawls have shown that the bulged belly trawl to be superior to the other nets in catching bottom fishes and column fishes. 40% of the bottom fishes and 48% of the column fishes were caught by the bulged belly trawl. However, for prawn catch, the long wing trawl appears to be better as it landed 52% of the total prawn catch of the three nets. Bulged belly trawl was found to be next only to long wing trawl in this respect.

Studies on the chemical and nutritional quality of protein powders isolated from shrimp waste

Protein powders were prepared from processing waste of prawns either by mechanically squeezing the shell and freeze drying the resultant aqueous extract or by treating the shell with 0.5% sodium hydroxide, filtering it and freeze drying the filtrate. Comparative studies on the proximate composition, amino acid profile, consumer acceptability and nutritional quality of the protein powders showed that the product prepared by freeze drying of the press liquor obtained by passing the waste through a hand operated expeller is better in all aspects studied than the product prepared by mild alkali extraction.

Carbon isotopic studies of individual lipids in organisms from the Nansha sea area, China

Carbon isotopes of individual lipids in typical organisms from the Nansha sea area were measured by the GC-IRMS analytical technique. delta(13)C values of saturated fatty acids in different organisms examined are from -25.6parts per thousand to -29.7parts per thousand with the average values ranging from -26.4parts per thousand to -28.2parts per thousand and the variance range of 11.8parts per thousand, between different organisms is also observed. Unsaturated fatty acids have heavy carbon isotopic compositions and the mean differences of 2.9%.9-6.8parts per thousand compared to the same carbon number saturated fatty acids. delta(13)C values of n-alkanes range from -27.5%o to -29.7parts per thousand and their mean values, ranging from -28.6parts per thousand, to -28.9parts per thousand, are very close in different organisms. The mean difference in delta(13)C between the saturated fatty acids and n-alkanes is only 1.5parts per thousand, indicating that they have similar biosynthetic pathways. The carbon isotopic variations between the different carbon-number lipids are mostly within +/-2.0parts per thousand, reflecting that they experienced a biosynthetic process of the carbon chain elongation. At the same time, the carbon isotopic genetic relationships between the biological and sedimentary lipids are established by comparative studies of carbon isotopic compositions of individual lipids in organisms and sediments from the Nansha sea area, which provides scientific basis for carbon isotopic applied research of individual lipids.

Aiding classification of gene expression data with feature selection: a comparative study

C. Shang and Q. Shen. Aiding classification of gene expression data with feature selection: a comparative study. Computational Intelligence Research, 1(1):68-76.

Helicobacter pylori: comparative genomics and structure-function analysis of the flagellum biogenesis protein HP0958

Helicobacter pylori is a gastric pathogen which infects ~50% of the global population and can lead to the development of gastritis, gastric and duodenal ulcers and carcinoma. Genome sequencing of H. pylori revealed high levels of genetic variability; this pathogen is known for its adaptability due to mechanisms including phase variation, recombination and horizontal gene transfer. Motility is essential for efficient colonisation by H. pylori. The flagellum is a complex nanomachine which has been studied in detail in E. coli and Salmonella. In H. pylori, key differences have been identified in the regulation of flagellum biogenesis, warranting further investigation. In this study, the genomes of two H. pylori strains (CCUG 17874 and P79) were sequenced and published as draft genome sequences. Comparative studies identified the potential role of restriction modification systems and the comB locus in transformation efficiency differences between these strains. Core genome analysis of 43 H. pylori strains including 17874 and P79 defined a more refined core genome for the species than previously published. Comparative analysis of the genome sequences of strains isolated from individuals suffering from H. pylori related diseases resulted in the identification of “disease-specific” genes. Structure-function analysis of the essential motility protein HP0958 was performed to elucidate its role during flagellum assembly in H. pylori. The previously reported HP0958-FliH interaction could not be substantiated in this study and appears to be a false positive. Site-directed mutagenesis confirmed that the coiled-coil domain of HP0958 is involved in the interaction with RpoN (74-284), while the Zn-finger domain is required for direct interaction with the full length flaA mRNA transcript. Complementation of a non-motile hp0958-null derivative strain of P79 with site-directed mutant alleles of hp0958 resulted in cells producing flagellar-type extrusions from non-polar positions. Thus, HP0958 may have a novel function in spatial localisation of flagella in H. pylori

Picturing Probation: Exploring the utility of visual methods in comparative research

A previous review of research on the practice of offender supervision identified the predominant use of interview-based methodologies and limited use of other research approaches (Robinson and Svensson, 2013). It also found that most research has tended to be locally focussed (i.e. limited to one jurisdiction) with very few comparative studies. This article reports on the application of a visual method in a small-scale comparative study. Practitioners in five European countries participated and took photographs of the places and spaces where offender supervision occurs. The aims of the study were two-fold: firstly to explore the utility of a visual approach in a comparative context; and secondly to provide an initial visual account of the environment in which offender supervision takes place. In this article we address the first of these aims. We describe the application of the method in some depth before addressing its strengths and weaknesses. We conclude that visual methods provide a useful tool for capturing data about the environments in which offender supervision takes place and potentially provide a basis for more normative explorations about the practices of offender supervision in comparative contexts.

Criminal justice system in pondicherry - a comparative critical study of the past and the presen

The Union Territory of Pondicherry prior to its merger with the Indian Union was a French Colony. The erstwhile territory of Pondicherry along with its hamlets, namely, KARAIKKAL, MAHE and YANAM was administered by the French Regime. Before it was established by French in 1 6 74 A.D. it was part of Vijayanagara Empire. Prior to this, Pondicherry was a part of the Kingdom of Chola and Pallava Kings. During French Regime, the laws which were in force in France in relation to administration of civil and criminal justice were extended to the erstwhile Territory of Pondicherry. Thus while Pondicherry stood influenced by the Inquisitorial system since the beginning of the 18th century, the neighboring states forming part of the Indian Union since Independence came under the Influence of the British system, viz. accusatorial system. The territory of Pondicherry, for administrative reasons, came to be merged with the Indian Union in the early 60's. Following the merger, the Indian administration sought to extent its own laws from time to time replacing erstwhile French Laws, however, subject to certain savings. Thus the transitional period witnessed consequential changes in the administration of the territory, including the sphere of judicial system. Since I 963, the Union Territory of Pondicherry was brought under the spell of the Indian Legal System The people in Pondicherry ' thus have had the benefit of experiencing both the svstems. Their experiences will be of much help to those who undertake comparative studies in law. The plus and minus points of the respective systems help one to develop a detachment that helps independent evaluation of the svstents. The result of these studies could be relevant in revitalising our criminal systems.The present system is evaluated in the light of the past system. New dimensions are added by way' of an empirical study also.

Comparative biology of mammalian telomeres: hypotheses on ancestral states and the roles of telomeres in longevity determination

Progressive telomere shortening from cell division (replicative aging) provides a barrier for human tumor progression. This program is not conserved in laboratory mice, which have longer telomeres and constitutive telomerase. Wild species that do ⁄ do not use replicative aging have been reported, but the evolution of different phenotypes and a conceptual framework for understanding their uses of telomeres is lacking. We examined telomeres ⁄ telomerase in cultured cells from > 60 mammalian species to place different uses of telomeres in a broad mammalian context. Phylogeny-based statistical analysis reconstructed ancestral states. Our analysis suggested that the ancestral mammalian phenotype included short telomeres (< 20 kb, as we now see in humans) and repressed telomerase. We argue that the repressed telomerase was a response to a higher mutation load brought on by the evolution of homeothermy. With telomerase repressed, we then see the evolution of replicative aging. Telomere length inversely correlated with lifespan, while telomerase expression co-evolved with body size. Multiple independent times smaller, shorter-lived species changed to having longer telomeres and expressing telomerase. Trade-offs involving reducing the energetic ⁄ cellular costs of specific oxidative protection mechanisms (needed to protect < 20 kb telomeres in the absence oftelomerase) could explain this abandonment of replicative aging. These observations provide a conceptual framework for understanding different uses of telomeres in mammals, support a role for human-like telomeres in allowing longer lifespans to evolve, demonstrate the need to include telomere length in the analysis of comparative studies of oxidative protection in the biology of aging, and identify which mammals can be used as appropriate model organisms for the study of the role of telomeres in human cancer and aging. Key words: evolution of telomeres; immortalization; telomerase; replicative aging; senescence.

A comparative study of satellite and ground-based phenology

Long time series of ground-based plant phenology, as well as more than two decades of satellite-derived phenological metrics, are currently available to assess the impacts of climate variability and trends on terrestrial vegetation. Traditional plant phenology provides very accurate information on individual plant species, but with limited spatial coverage. Satellite phenology allows monitoring of terrestrial vegetation on a global scale and provides an integrative view at the landscape level. Linking the strengths of both methodologies has high potential value for climate impact studies. We compared a multispecies index from ground-observed spring phases with two types (maximum slope and threshold approach) of satellite-derived start-of-season (SOS) metrics. We focus on Switzerland from 1982 to 2001 and show that temporal and spatial variability of the multispecies index correspond well with the satellite-derived metrics. All phenological metrics correlate with temperature anomalies as expected. The slope approach proved to deviate strongly from the temporal development of the ground observations as well as from the threshold-defined SOS satellite measure. The slope spring indicator is considered to indicate a different stage in vegetation development and is therefore less suited as a SOS parameter for comparative studies in relation to ground-observed phenology. Satellite-derived metrics are, however, very susceptible to snow cover, and it is suggested that this snow cover should be better accounted for by the use of newer satellite sensors.