Evolution and Phylogenetic Analysis of Full-Length VP3 Genes of Eastern Mediterranean Bluetongue Virus Isolates

Bluetongue virus (BTV) is the ‘type’ species of the genus Orbivirus within the family Reoviridae. The BTV genome is composed of ten linear segments of double-stranded RNA (dsRNA), each of which codes for one of ten distinct viral proteins. Previous phylogenetic comparisons have evaluated variations in genome segment 3 (Seg-3) nucleotide sequence as way to identify the geographical origin (different topotypes) of BTV isolates. The full-length nucleotide sequence of genome Seg-3 was determined for thirty BTV isolates recovered in the eastern Mediterranean region, the Balkans and other geographic areas (Spain, India, Malaysia and Africa). These data were compared, based on molecular variability, positive-selection-analysis and maximum-likelihood phylogenetic reconstructions (using appropriate substitution models) to 24 previously published sequences, revealing their evolutionary relationships. These analyses indicate that negative selection is a major force in the evolution of BTV, restricting nucleotide variability, reducing the evolutionary rate of Seg-3 and potentially of other regions of the BTV genome. Phylogenetic analysis of the BTV-4 strains isolated over a relatively long time interval (1979–2000), in a single geographic area (Greece), showed a low level of nucleotide diversity, indicating that the virus can circulate almost unchanged for many years. These analyses also show that the recent incursions into south-eastern Europe were caused by BTV strains belonging to two different major-lineages: representing an ‘eastern’ (BTV-9, -16 and -1) and a ‘western’ (BTV-4) group/topotype. Epidemiological and phylogenetic analyses indicate that these viruses originated from a geographic area to the east and southeast of Greece (including Cyprus and the Middle East), which appears to represent an important ecological niche for the virus that is likely to represent a continuing source of future BTV incursions into Europe

The adaptive evolution of the mammalian mitochondrial genome

<p>Abstract</p> <p>Background</p> <p>The mitochondria produce up to 95% of a eukaryotic cell's energy through oxidative phosphorylation. The proteins involved in this vital process are under high functional constraints. However, metabolic requirements vary across species, potentially modifying selective pressures. We evaluate the adaptive evolution of 12 protein-coding mitochondrial genes in 41 placental mammalian species by assessing amino acid sequence variation and exploring the functional implications of observed variation in secondary and tertiary protein structures.</p> <p>Results</p> <p>Wide variation in the properties of amino acids were observed at functionally important regions of cytochrome <it>b </it>in species with more-specialized metabolic requirements (such as adaptation to low energy diet <it>or </it>large body size, such as in elephant, dugong, sloth, and pangolin, and adaptation to unusual oxygen requirements, for example diving in cetaceans, flying in bats, and living at high altitudes in alpacas). Signatures of adaptive variation in the NADH dehydrogenase complex were restricted to the loop regions of the transmembrane units which likely function as protons pumps. Evidence of adaptive variation in the cytochrome <it>c </it>oxidase complex was observed mostly at the interface between the mitochondrial and nuclear-encoded subunits, perhaps evidence of co-evolution. The ATP8 subunit, which has an important role in the assembly of F₀, exhibited the highest signal of adaptive variation. ATP6, which has an essential role in rotor performance, showed a high adaptive variation in predicted loop areas.</p> <p>Conclusion</p> <p>Our study provides insight into the adaptive evolution of the mtDNA genome in mammals and its implications for the molecular mechanism of oxidative phosphorylation. We present a framework for future experimental characterization of the impact of specific mutations in the function, physiology, and interactions of the mtDNA encoded proteins involved in oxidative phosphorylation.</p

Upper Cretaceous radiolaria from the Atlantic Ocean and Cyprus

Micropalaeontological analyses, with special reference to radiolaria, have been carried out on 255 samples of Campanian - Maastrichtian sediments from 3 sections encountered at offshore DSDP/IPOD Sites in the Atlantic Ocean and 20 onshore sections in Cyprus in the Mediterranean sea. Radiolarian assemblages recorded here are integrated with calcareous nannofossils where possible, the studied sections having been carefully chosen in order to test existing biostratigraphical schemes using radiolaria and calcareous microfossils. Of the published zonation schemes for the Late Cretaceous, seven are discussed and their application to material recorded here considered. A number of interesting biostratigraphical observations confirmations and conclusions have been made in relation to the geological history of Cyprus, whilst the radiolarian biostratigraphical database from DSDP Sites 152 and 369A has been amended. A taxonomic atlas has been compiled, with extensive synonymy lists and the geographical and stratigraphical occurrence patterns both for published species and for new forms recorded exclusively in this study. The stratigraphical occurrences recorded here are correlated with co-occurring calcareous nannofossils. The taxonomic atlas includes 141 taxa and 47 genera which are described and/or figured. Of these morphotypes, 59 are left in open nomenclature, many of which represent new and undescribed species to be formally described when their occurrence patterns are fully researched. Eighty-two of the species recorded have published ranges which include the Campanian whilst the ranges of a further 11 species are here extended into the (stratigraphically higher) Campanian stage. Published radiolarian ranges are confirmed and extended. The organisation and storage of the lithological and micropalaeontological data from this study on a computer database allowed for rapid searches for correlative and inversely correlative sample characteristics. Equally, future rapid selection of samples for purposes such as refining zonation schemes or selection of particularly well-preserved specimens for photography or specific reappraisal is facilitated. Controls on production and preservation of siliceous microfossils are discussed and applied to the interpreted depositional conditions in the Late Cretaceous. The effects of these controls, as interpreted for the Late Cretaceous, are discussed in relation to biostratigraphical utilization of the group. A comprehensive assessment of sample processing and analytical techniques and a discussion on the technical problems encountered, together with their impact on recorded data, is included. Finally, future research areas have been defined in relation to the following : 1. developing/refining radiolarian biozonation; 2. standardization of preparation techniques, data production and storage; 3. advancement of stored computerised data to include pictorial representation of taxa; 4. more extensive work on Cyprus involving correlation with DSDP/ODP material

Genetics and Genomics of Forest Trees

Forest tree genetics and genomics are advancing at an accelerated rate, thanks to recent developments in high-throughput, next-generation sequencing capabilities, and novel biostatistical tools. Population and landscape genetics and genomics have seen the rise of new approaches implemented in large-scale studies that employ the use of genome-wide sampling. Such studies have started to discern the dynamics of neutral and adaptive variation in nature and the processes that underlie spatially explicit patterns of genetic and genomic variation in nature. The continuous development of genetic maps in forest trees and the expansion of QTL and association mapping approaches contribute to the unravelling of the genotype-phenotype relationship and lead to marker-assisted and genome-wide selection. However, major challenges lie ahead. Recent literature suggests that species demography and genetic diversity have been affected both by climatic oscillations and anthropogenically induced stresses in a way calls into question the possibility of future adaptation. Moreover, the pace of contemporary environmental change presents a great challenge to forest tree populations and their ability to adapt, taking into consideration their life history characteristics. Several questions emerge that include, but are not limited to, the interpretation of forest tree genome surveillance and their structural/functional properties, the adaptive and neutral processes that have shaped forest tree genomes, the analysis of phenotypic traits relevant to adaptation (especially adaptation under contemporary climate change), the link between epigenetics/epigenomics and phenotype/genotype, and the use of genetics/genomics as well as genetic monitoring to advance conservation priorities

Richard Nelson Perham. 27 April 1937—14 February 2015

Richard Nelson Perham, FRS, FMedSci, FRSA, was a British professor of structural biochemistry. He undertook his academic career at the University of Cambridge, holding positions as lecturer, reader, chair and head of the Department of Biochemistry, as well as becoming Master of St John's College. Perham published close to 300 scientific papers on protein structure and function, with a focus on mechanistic enzymology, particularly how large multienzyme complexes and flavin-containing enzymes work. He is most renowned for determining how reactive intermediates are transferred between enzyme active sites, for alterations of coenzyme and substrate specificity by his pioneering use of protein engineering and for developing protein display methodologies. Married to Nancy Lane-Perham, and with their two children, Perham enjoyed a full and active life in Cambridge and St John's College. He was a keen participator and supporter of sport and enjoyed art, literature, theatre and music. Perham was a vocal and active champion of equal opportunity in education. His legacy to science is a greater understanding of how enzymes work. His legacy to scientists is as a role model of how to attain the highest levels of achievement while maintaining a sense of personal modesty and a keen support for others

Richard Nelson Perham. 27 April 1937—14 February 2015

Richard Nelson Perham, FRS, FMedSci, FRSA, was a British professor of structural biochemistry. He undertook his academic career at the University of Cambridge, holding positions as lecturer, reader, chair and head of the Department of Biochemistry, as well as becoming Master of St John's College. Perham published close to 300 scientific papers on protein structure and function, with a focus on mechanistic enzymology, particularly how large multienzyme complexes and flavin-containing enzymes work. He is most renowned for determining how reactive intermediates are transferred between enzyme active sites, for alterations of coenzyme and substrate specificity by his pioneering use of protein engineering and for developing protein display methodologies. Married to Nancy Lane-Perham, and with their two children, Perham enjoyed a full and active life in Cambridge and St John's College. He was a keen participator and supporter of sport and enjoyed art, literature, theatre and music. Perham was a vocal and active champion of equal opportunity in education. His legacy to science is a greater understanding of how enzymes work. His legacy to scientists is as a role model of how to attain the highest levels of achievement while maintaining a sense of personal modesty and a keen support for others

The seagrass holobiont: What we know and what we still need to disclose for its possible use as an ecological indicator

Microbes and seagrass establish symbiotic relationships constituting a functional unit called the holobiont that reacts as a whole to environmental changes. Recent studies have shown that the seagrass microbial associated community varies according to host species, environmental conditions and the host’s health status, suggesting that the microbial communities respond rapidly to environmental disturbances and changes. These changes, dynamics of which are still far from being clear, could represent a sensitive monitoring tool and ecological indicator to detect early stages of seagrass stress. In this review, the state of art on seagrass holobiont is discussed in this perspective, with the aim of disentangling the influence of different factors in shaping it. As an example, we expand on the widely studied Halophila stipulacea’s associated microbial community, highlighting the changing and the constant components of the associated microbes, in different environmental conditions. These studies represent a pivotal contribution to understanding the holobiont’s dynamics and variability pattern, and to the potential development of ecological/ecotoxicological indices. The influences of the host’s physiological and environmental status in changing the seagrass holobiont, alongside the bioinformatic tools for data analysis, are key topics that need to be deepened, in order to use the seagrass-microbial interactions as a source of ecological information