314 research outputs found
A Phylogenomic Study of the Genus Alphavirus Employing Whole Genome Comparison
The phylogenetics of the genus Alphavirus have historically been characterized using
partial gene, single gene or partial proteomic data. We have mined cDNA and
amino acid sequences from GenBank for all fully sequenced and some partially
sequenced alphaviruses and generated phylogenomic analyses of the genus Alphavirus
genus, employing capsid encoding structural regions, non-structural coding regions
and complete viral genomes. Our studies support the presence of the previously
reported recombination event that produced the Western Equine Encephalitis clade,
and confirm many of the patterns of geographic radiation and divergence of the
multiple species. Our data suggest that the Salmon Pancreatic Disease Virus and
Sleeping Disease Virus are sufficiently divergent to form a separate clade from
the other alphaviruses. Also, unlike previously reported studies employing limited
sequence data for correlation of phylogeny, our results indicate that the Barmah
Forest Virus and Middelburg Virus appear to be members of the Semliki Forest
clade. Additionally, our analysis indicates that the Southern Elephant Seal Virus
is part of the Semliki Forest clade, although still phylogenetically distant from all
known members of the genus Alphavirus. Finally, we demonstrate that the whole
Rubella viral genome provides an ideal outgroup for phylogenomic studies of the
genus Alphavirus
Single Nucleotide Polymorphism Discovery in Cultivated Tomato via Sequencing by Synthesis
AMBER: Assessment of Metagenome BinnERs
Meyer F, Hofmann P, Belmann P, et al. AMBER: Assessment of Metagenome BinnERs. GigaScience. 2018;7(6): giy069
Identification of functional genetic variation in exome sequence analysis
Recent technological advances have allowed us to study individual genomes at a base-pair resolution and have demonstrated that the average exome harbors more than 15,000 genetic variants. However, our ability to understand the biological significance of the identified variants and to connect these observed variants with phenotypes is limited. The first step in this process is to identify genetic variation that is likely to result in changes to protein structure and function, because detailed studies, either population based or functional, for each of the identified variants are not practicable. Therefore algorithms that yield valid predictions of a variant’s functional significance are needed. Over the past decade, several programs have been developed to predict the probability that an observed sequence variant will have a deleterious effect on protein function. These algorithms range from empirical programs that classify using known biochemical properties to statistical algorithms trained using a variety of data sources, including sequence conservation data, biochemical properties, and functional data. Using data from the pilot3 study of the 1000 Genomes Project available through Genetic Analysis Workshop 17, we compared the results of four programs (SIFT, PolyPhen, MAPP, and VarioWatch) used to predict the functional relevance of variants in 101 genes. Analysis was conducted without knowledge of the simulation model. Agreement between programs was modest ranging from 59.4% to 71.4% and only 3.5% of variants were classified as deleterious and 10.9% as tolerated across all four programs
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Final Report for Grant No. DE-FG02-01ER63220 "The Dynamics of Cellular Stress Responses in Deinococcus radiodurans"
Bacteria belonging to the family Deinococcaceae are some of the most ionizing radiation (IR) resistant organisms yet discovered. Deinococcus radiodurans is obligate aerobic, capable of growth under chronic IR (60 Gy/hour) and relatively resistant to many DNA damaging conditions including exposure to desiccation, ultraviolet radiation and hydrogen peroxide. The genes and cellular pathways underlying the survival strategies of D. radiodurans have been under investigation for fifty years. In the last decade, D. radiodurans was subjected to whole-genome sequencing, annotation and comparative analysis, whole-transcriptome and whole-proteome analyses, and numerous DNA repair studies. Collectively, published reports support that the key to survival of D. radiodurans resides in its ability to repair DNA, but the mechanisms responsible remain poorly defined. Unexpectedly, many novel genes implicated in recovery from IR by transcriptome and proteome profiling have had little effect on survival when disrupted, and there is reason to ask if something is missing from classical models of radiation resistance. The prevailing dogma of radiation toxicity has been that the cytotoxic and mutagenic effects of radiation are principally the result of DNA damage that occurs during IR. However, in light of available whole genome sequences, one broad observation that is difficult to reconcile with this view is that many organisms that encode a compliment of DNA repair and protection functions are killed at radiation doses that cause little DNA damage. This indicates that there are cellular targets involved in recovery that are more vulnerable to IR damage than DNA. It has been reported that D. radiodurans and other resistant organisms accumulate very high intracellular concentrations of Mn(II), and restricting the amount of Mn(II) during recovery from IR substantially reduced survival of D. radiodurans. At high intracellular concentrations, Mn(II) is known to act as a true catalyst of the dismutase of superoxde (O2?-), with Mn cycling between the divalent and trivalent states. Superoxide is generated during water radiolysis, particularly in the presence of iron redox-cycling processes, and has been implicated in damaging [4Fe-4S] cluster-containing proteins, with the release of bound Fe(II). Thus, it is possible that Mn(II) accumulation acts as keystone among antioxidant defenses which limits protein damage during both irradiation and recovery, with the result that DNA repair and other enzymic systems involved in recovery function with greater efficiency in D. radiodurans than other organisms
The influence of tertiary butyl hydrazine as a co-reactant on the atomic layer deposition of silver
Ultra-thin conformal silver films are the focus of development for applications such as anti-microbial surfaces, optical components and electronic devices. In this study, metallic silver films have been deposited using direct liquid injection thermal atomic layer deposition (ALD) using (hfac)Ag(1,5-COD) ((hexafluoroacetylacetonato)silver(I)(1,5-cyclooctadiene)) as the metal source and tertiary butyl hydrazine (TBH) as a co-reactant. The process provides a 23 °C wide ‘self-limiting’ ALD temperature window between 105 and 128 °C, which is significantly wider than is achievable using alcohol as a co-reactant. A mass deposition rate of ∼20 ng/cm2/cycle (∼0.18 Å/cycle) is observed under self-limiting growth conditions. The resulting films are crystalline metallic silver with a near planar film-like morphology which are electrically conductive. By extending the temperature range of the ALD window by the use of TBH as a co-reactant, it is envisaged that the process will be exploitable in a range of new low temperature applications
Measuring Biodiversity and Extinction – Present and Past
How biodiversity is changing in our time represents a major concern for all organismal biologists. Anthropogenic changes to our planet are decreasing species diversity through the negative effects of pollution, habitat destruction, direct extirpation of species, and climate change. But major biotic changes – including those that have both increased and decreased species diversity – have happened before in Earth’s history. Biodiversity dynamics in past eras provide important context to understand ecological responses to current environmental change. The work of assessing biodiversity is woven into ecology, environmental science, conservation, paleontology, phylogenetics, evolutionary and developmental biology, and many other disciplines; yet, the absolute foundation of how we measure species diversity depends on taxonomy and systematics. The aspiration of this symposium, and complementary contributed talks, was to promote better understanding of our common goals and encourage future interdisciplinary discussion of biodiversity dynamics. The contributions in this collection of papers bring together a diverse group of speakers to confront several important themes. How can biologists best respond to the urgent need to identify and conserve diversity? How can we better communicate the nature of species across scientific disciplines? Where are the major gaps in knowledge about the diversity of living animal and plant groups, and what are the implications for understanding potential diversity loss? How can we effectively use the fossil record of past diversity and extinction to understand current biodiversity loss
Cannabidiol regulation of learned fear: implications for treating anxiety-related disorders
Anxiety and trauma-related disorders are psychiatric diseases with a lifetime prevalence of up to 25%. Phobias and post-traumatic stress disorder (PTSD) are characterized by abnormal and persistent memories of fear-related contexts and cues. The effects of psychological treatments such as exposure therapy are often only temporary and medications can be ineffective and have adverse side effects. Growing evidence from human and animal studies indicates that cannabidiol, the main non-psychotomimetic phytocannabinoid present in Cannabis sativa, alleviates anxiety in paradigms assessing innate fear. More recently, the effects of cannabidiol on learned fear have been investigated in preclinical studies with translational relevance for phobias and PTSD. Here we review the findings from these studies, with an emphasis on cannabidiol regulation of contextual fear. The evidence indicates that cannabidiol reduces learned fear in different ways: (1) cannabidiol decreases fear expression acutely, (2) cannabidiol disrupts memory reconsolidation, leading to sustained fear attenuation upon memory retrieval, and (3) cannabidiol enhances extinction, the psychological process by which exposure therapy inhibits learned fear. We also present novel data on cannabidiol regulation of learned fear related to explicit cues, which indicates that auditory fear expression is also reduced acutely by cannabidiol. We conclude by outlining future directions for research to elucidate the neural circuit, psychological, cellular, and molecular mechanisms underlying the regulation of fear memory processing by cannabidiol. This line of investigation may lead to the development of cannabidiol as a novel therapeutic approach for treating anxiety and trauma-related disorders such as phobias and PTSD in the future
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