Miracle-dz/UniFAR-FTUs huggingface dataset:
THE ANTIVIRAL ROLES OF ATG1 IN DROSOPHILA MELANOGASTER: IMMUNE RESPONSES AGAINST DROSOPHILA X VIRUS

Title of dissertation: The Antiviral Roles of Atg1 Against Drosophila X Virus in Drosophila melanogaster Qian Wang, Doctor of Philosophy, 2014 Dissertation directed by: Professor Louisa Wu Department of Cell Biology and Molecular Genetics In mammals, autophagy is important for the immune response against select viruses and is responsible for delivering virus to the lysosome for degradation. In Drosophila melanogaster, the roles of autophagy genes in an antiviral immune response are not fully understood. Here we identify a novel antiviral role for Atg1 in Drosophila melanogaster upon infection with Drosophila X virus (DXV). Flies with a decreased level of Atg1 expression in the fat body developed an increased susceptibility to DXV and have a higher viral load compared to wildtype. However, silencing of other autophagy components (Atg7, Atg8) does not have the same effect. Moreover, we could find no evidence that classical autophagy is directly associated with DXV upon viral infection. This suggests that the antiviral function of Atg1 may be independent of classical autophagy. To address this, we examined the effect of Atg1 knockdown on the fly transcriptome in both DXV infected and uninfected flies. Interestingly, lipid droplet lipolysis and β-oxidation, two major processes responsible for energy production, are induced upon DXV infection. Facilitating lipolysis by knocking down lsd2, a positive regulator of lipase bmm, results in an increased host susceptibility to DXV, together with an increased viral load. In contrast, blocking lipolysis in the negative regulator lsd1 null mutant renders the host more resistant to the virus. This indicates that the increased energy production favors the virus for active replication and does not favor the elimination of virus. Surprisingly, silencing of Atg1, even in the absence of infection, also increases the rates of lipolysis and β-oxidation, shown by an increased expression of genes that are involved in lipid metabolism and an decreased lipid droplet size in the Atg1-silenced flies. The differences in gene expression and lipid droplet size between Atg1 RNAi flies and WT flies become more apparent as the infection progresses. In summary, we identify a novel role for Atg1 in restricting energy production and limiting DXV replication. This finding may shed light on antiviral studies against other dsRNA viruses that manipulate host energy homeostasis. Finally, our data reveal an important and unexpected role for Atg1 in innate immune antiviral responses independent of autophagy. THE ANTIVIRAL ROLES OF ATG1 IN DROSOPHILA MELANOGASTER: IMMUNE RESPONSES AGAINST DROSOPHILA X VIRUS
T-Cell Signaling of Macrophage Activation: Cell Contact-Dependent and Cytokine Signals

This text addresses the question of how T cells activate macrophage effector function. Current research is rapidly forcing a revision of our hypothesis on T cell-mediated macrophage activation. This book begins at a basic level, describing the different functions of macrophages and how they are induced and regulated, and leading the reader through to current research on cytokine and cell-contact dependent mechanisms by which T cells signal macrophage function.
Palmitylation of vaccinia virus proteins : identification of modification sites and biological relevance

approved: Vaccinia virus encodes at least eight proteins that are modified post-translationally by the addition of a 16-carbon saturated fatty acid through thioester linkage to cysteine residues. This is referred to as palmitylation of proteins. The purpose of this work was to gain an understanding of palmitylation, focusing on what defined the substrate for the modification, and the biological relevance of protein palmitylation in the vaccinia virus life cycle. A systematic approach was taken to identify the genes in vaccinia virus that encode these proteins. We found that vaccinia virus palmitylproteins are of the "late" temporal class, associate with intracellular membranes, and are specific for a particular form of the infectious virion. These criteria were used to narrow the number of genes expressed by vaccinia virus that potentially encode palmitylproteins. The "candidate" palmitylprotein genes were cloned and transiently expressed in mammalian tissue culture cells and analyzed for incorporation of palmitic acid. In addition to three previously identified vaccinia virus palmitylproteins, three new palmitylproteins were identified. The six known palmitylprotein genes were mutated to determine the site of modification, leading to the identification of the modification site for four of the six proteins. One of the proteins, p37, was analyzed further for biological significance of the palmitate modification. A recombinant Redacted for Privacy vaccinia virus was constructed that did not express the wild-type palmitylated form of p37, but expressed a nonpalmitylated form of the protein instead. This virus was severely inhibited from proceeding past a particular morphogenetic stage, leading to an attenuated phenotype in tissue culture systems. Although the expression of the nonpalmitylated protein appeared normal compared to the wild-type protein, the lack of the palmityl moiety resulted in the loss of a targeting signal that directed the protein to its normal intracellular location. By this work, significant contributions have been made toward understanding the process of protein palmitylation. We have identified, at least for vaccinia virus, primary structural determinants specifying the modification, leading to the identification of a palmitylation motif. Considering the attenuated phenotype of the mutant virus, our conclusion is that palmitylation is necessary for biological function, at least for p37. ©Copyright by Douglas W. Grosenbach April 29, 1999 All Rights Reserved Palmitylation of Vaccinia Virus Proteins: Identification of Modification Sites and Biological Relevance
Phenazine 1-carboxylic acid resistance in phenazine 1-carboxylic acid producing Bacillus sp. B-6

Phenazine 1-carboxylic acid (PCA) is an antifungal antibiotic isolated from a culture filtrate of Bacillus sp. B-6 producing an acyl CoA synthetase inhibitor. This antibiotic is reported as an inhibitor of an acyl CoA synthetase from Pseudomonas sp. Bacillus sp. B-6 was resistant to PCA up to 350 . We investigated the mechanism of the resistance of Bacillus sp. B-6 to PCA. The rate of growth in a medium containing up to 100 was as rapid as the PCA-free medium. At a PCA concentration of 300 , the growth rate was more than half that of the control. In this work, we purified acyl CoA synthetase from Bacillus sp. B-6 and found that this acyl CoA synthetase was much less sensitive to PCA than the acyl CoA synthetase from other source. These findings suggested that the insensitivity of Bacillus sp. B-6 acyl CoA synthetase plays an important role in the PCA resistance of this bacterium.
Assessment of Population Structure in Hungarian Otter Populations

The Eurasian otter (Lutra lutra) is widely distributed in Europe and has been down-listed from Vulnerable to Near Threatened on the IUCN Red List in 2004 following successful conservation interventions. River otter recoveries were driven by active and passive protection of wetlands and a decrease in environmental pollutants. In Hungary, although otter populations have been stable in recent decades, there is little information available regarding genetic diversity, population genetic or phylogeographic structure, and potential barriers affecting gene flow. This study, therefore, aimed to determine genetic diversity and structure across the range of this species in Hungary. To achieve this, we analyzed 255 tissue samples collected since 2002, mainly from road-kill incidents, in various regions of Hungary. We found a relatively high level of genetic diversity in Hungarian otter populations (expected heterozygosity: 0.69–0.74; mean number of alleles per locus: 6.8–7.7). At a regional level, we identified 2 distinct genetic clusters corresponding to 2 river basins (Danube and Tisza). We also identified isolation by distance and patterns of genetic differentiation that appear to reflect population divergence of otters that are spatially restricted to one of these 2 river basins. Our results show the strong influence of river networks on population structure and genetic divergence in otters and provide a framework for the development of conservation management plans for otters in Hungary.
Susceptibility of conifer shoots to infection by Phytophthora ramorum

Phytophthora ramorum is the pathogen that causes sudden oak death, which was first detected on tanoak in Marin County, California in 1995. The identification of several conifers as hosts of P. ramorum and the increased spread of this pathogen via shipment of ornamental nursery stock has the potential to severely impact the Christmas tree, conifer nursery and forestry industries if this pathogen spreads into major production areas. Four conifers (Douglas-fir, grand fir, yew and coast redwood) are among the naturally infected hosts that have been reported for this pathogen. There are large numbers of different types of conifers grown as Christmas trees and in conifer nurseries in the Pacific Northwest. To better understand the potential impact that this pathogen might have on the Christmas tree, conifer nursery and specialty forest products industries, a series of inoculation studies was conducted to determine the susceptibility of foliage and shoots from 25 conifers to P. ramorum. Growth stage and inoculum concentration had a significant effect on the susceptibility Douglas-fir. Needles on emerging shoots from dormant seedlings were only susceptible to infection when inoculated just after bud break. However, needles on actively growing terminals and side shoots of container-grown nursery seedlings were susceptible throughout their growing season. No disease developed when Douglas-fir and noble fir seedlings were inoculated with A1 or A2 mating types at inoculum concentrations below 104 zoospores per ml. Twenty of the conifers tested, including many of the important species that are used as Christmas trees, were susceptible to A2 mating types of P. ramorum. Symptoms included needle blight, a shoot blight resulting from needle infections, and stem dieback resulting from the growth of the pathogen from infected shoots into the stem. Significant shoot blight occurred on some Abies species. Our research indicates that a number of conifers are potentially susceptible to P. ramorum. In addition, host phenology and inoculum concentration are important factors affecting infection of conifers by P. ramorum.
Impact of QTL polymorphism on superiority of QTL-assisted selection in nucleus herds.

INTRODUCTION Studies that estimate effects and map positions of quantitative trait loci (QTL) favor marker loci that are highly polymorphic, so that pairs of individuals or lines are likely to carry different alleles at each locus (Falconer and Mackay, 1996). Studies that use marked loci in selection may also favor highly polymorphic markers, so that individuals are likely to be more differentiable and their kinship are more accurately estimated.
Creating a Consistent Oceanic Multi-Decadal Intercalibrated Trmm-Gpm Constellation Data Record

The Tropical Rainfall Measuring Mission (TRMM), launched in late November 1997 into a low earth orbit, produced the longest microwave radiometric data time series of 17 years from the TRMM Microwave Imager (TMI). The Global Precipitation Measuring (GPM) mission is the followâ€"on to TRMM, designed to provide data continuity and advance precipitation measurement capabilities. The GPM Microwave Imager (GMI) performs as a brightness temperature (Tb) calibration standard for the intersatellite radiometric calibration (XCAL) for the other constellation members, and before GPM was launched, TMI was the XCAL standard. This doctoral dissertation aims at creating a consistent multiâ€"decadal Tb data record that ensures a consistent longâ€"term precipitation record that covers TRMM and GPM eras. As the TMI and GMI share only a 13â€"month common operational period, the Naval Research Labâ€TMs WindSat radiometer, launched in 2003 and continuing today provides the calibration bridge between the two radiometers. The TMI/WindSat XCAL for their >9 years period (2005â€"2014), and WindSat/GMI XCAL for one year (CY 2015) are performed using a robust XCAL Double Difference (DD) technique to estimate the Tb bias of one relative to the other. The 3â€"way XCAL of GMI/TMI/WindSat for their joint overlap period is performed using an extended XCAL DD technique. Thus, a multiâ€"decadal oceanic Tb dataset will be created. Moreover, an important feature of this dataset is a quantitative estimate of the Tb uncertainty derived from a generic uncertainty estimation model (UEM). In the UEM, the overall uncertainty is first partitioned into separate and independent sources. Next, uncertainties from various source is quantified using different methods. Finally, the estimated individual independent uncertainties are combined into a single overall uncertainty using the root sum squared method. This dissertation work is remarkably important because it provides the science community with a consistent oceanic multiâ€"decadal TMIâ€"GMI Tb data record, and also allows the science community to better understand the uncertainty in precipitation products based upon the Tb uncertainties provided.
The Babesia bovis BvP36 gene is expressed at least in the asexual stage of Babesia merozoite.

igarcpmi@obihiro.ac. jp ABSTRACT Recently, Babesia bovis genome project identified a novel gene, which is homologous to the gene encoding sporozoite P36 antigen in Plasmodium parasites. In the present study, we isolated the P36 homologous gene from the genomic DNA of B. bovis and designated it as the BvP36 gene. The sequence of the BvP36 gene was identical to that reported previously. This gene was expressed in an Escherichia coli system to produce a recombinant protein (rBvP36). The rBvP36 protein was produced as a highly soluble form in E. coli and was detected by western blot analyses of sera collected from cattle experimentally infected with B. bovis and B. bigemina merozoites. In indirect immunofluorescence tests, sera collected from mice immunized with rBvP36 showed strong reactions to both B. bovis and B. bigemina merozoites. Our results indicate that the BvP36 antigen is expressed at least in the asexual merozoite stage of B. bovis and suggest that B. bigemina merozoite carries an antigen similar to
ROLE OF MOLECULAR MARKERS IN SOME PERENNIAL CROPS- BRIEF REVIEW

Molecular markers have provided tools suitable for rapid and detailed genetic analysis of plant species. The discovery of Polymerize chain reaction was a landmark in this effort and proved to be a unique process that brought about a new class of DNA profiling markers. This facilitated the development of marker-based gene tags, map-based cloning of agronomically important genes, variability studies, phylogenetic analysis etc., thus giving new dimensions to concerted efforts of breeding and marker-aided selection that can reduce the time span of developing new and better varieties. In this article, DNA markers developed during the last two decades of molecular biology research and utilized for various applications in the area of fruit production are reviewed.
Effects of nutrients from fish farms on culture of blue mussel (Mytilus edulis)

Intensive salmonid cage culture releases nutrients and organic matter that lead eutrophication of coastal waters. Integrated multi-trophic aquaculture (IMTA) is receiving great attention as a means of reducing organic/inorganic nutrient loads to the environment and increasing productivity by rearing viable secondary organisms. In this study blue mussels (Mytilus edulis) were cultured close to a salmon (Salmo salar) cage farm at Tristen, Bjugn in Sor Trondelag, Central Norway from June 2010 to February 2011. 3 experimental stations at the fish farming area and 2 reference stations (1.8 and 3.6 km away from the fish farm, respectively) were positioned to test if the integrated mussel culture reduces the environmental impact from salmon cage culture. Highest water temperature recorded was 14.3 °C in July. Water temperature was above 10 °C until middle of October and the lowest was 3.1 °C in winter. Total particulate matter (TPM) and chlorophyll a contents varied 6.3  10.5 mg L-1 and 0.1 - 2.5 µg L-1, respectively. The mussel (n=450) length increased from 31.1±0.04 mm (standard length±SE) to 41.5±0.17 mm. The mussel growth was high in summer (June  September) and was close to zero in the winter (October  February). Multiple regression analysis showed that water temperature was the prime factor affecting condition index (CI) (meat dry weight/shell dry weight) and specific growth rate (SGR) of mussel. No differences were found in the environmental variables and food availabilities among the stations. Significantly higher CIs at the experimental stations (station 1, 2 and 3) than at the reference stations were caused by utilization of fish farm discharges by the mussels. Fatty acids 18:1 (n-9), 18:2 (n-6) and 20:5 (n-3) signatures and the ratio of n-3 to n-6 in the digestive gland tissue of mussels collected in February support the findings. SGR in shell length was highest at reference station 5 (0.29 % day-1 in summer and 0.02 % day-1 in winter). This result might be caused by slow current speed at the station. It is concluded that, mussels may play an important role reducing environmental impact from salmon farm and it gives a possibility to integrating mussels on the salmon cage culture.
Composition of Starch and Protein in the Endosperm of Newly Generated Double Recessive Waxy and Opaque 2 Maize (Zea mays L.) Genotypes

Waxy maize with its pure amylopectin starch is the staple food of many ethnic minorities in hilly regions of Southeast Asia (SEA). A combination of waxy and quality protein maize (QPM) traits would improve the quality of protein of waxy maize for human consumption. Double recessive waxy-QPM (wx-o2) genotypes had been generated from Southern Chinese material by haploid induction of crosses heterozygous for the two quality traits with an absolutely conserved waxy type and an improved amino acid profile. The vitreous kernel trait (due to the additional modifier genes present in QPM) was lost in the wx-o2 plant material; this may be due to the waxy mutation, this is anyhow desirable for acceptance as waxy maize is preferred due to its soft grains. The content of the quality limiting amino acid lysine was greatly increased in double recessive wx-o2 genotypes compared to standard waxy maize, but still with a high variation among genotypes for future improvement. Conclusively, it was indeed possible to combine two grain quality mutations successfully within one genotype and prototypes of double quality wx-o2 are available now to contribute to meet human requirements in essential amino acids and thus reduce malnutrition in various regions of Asia.
The Coupling Between Folding, Zinc Binding, and Disulfide Bond Status of Human Cu, Zn Superoxide Dismutase: A Dissertation

Cu, Zn superoxide dismutase (SOD1) is a dimeric, β-sandwich, metalloenzyme responsible for the dismutation of superoxide. Mutations covering nearly 50% of the amino acid sequence of SOD1 have been found to acquire a toxic gain-of-function leading to amyotrophic lateral sclerosis. A hallmark of this disease is the presence of insoluble aggregates containing SOD1 found in the brain and spinal cord. While it is unclear how these aggregates or smaller, precursor oligomeric species may be the source of the toxicity, mutations leading to increased populations of unstable, partially folded species along the folding pathway of SOD1 may be responsible for seeding and propagating aggregation. In an effort to determine the responsible species, we have systematically characterized the stability and folding kinetics of five well studied ALS variants: A4V, L38V, G93A, L106V and S134N. The effect of the amino acid substitutions was determined on a variety of different constructs characterizing the various post-translational maturation steps of SOD1: folding, disulfide bond formation and Zn binding. Zn was found to bind progressively tighter along the folding pathway of SOD1, minimizing populations of monomeric species. In contrast, ALS variants were found to have the greatest perturbation in the equilibrium populations of the folded and unfolded state for the most
Pseudohemiodon thorectes, a new species of Mailed Catfish from the Rio Mamoré system, Bolivia (Pisces, Siluriformes, Loricariidae)

Pseudohemiodon thorectes, a new species of Mailed Catfish of the subfamily Loricariinae, is described and figured after the holotype (the only known specimen), originating from Buena Vista, west of Rio Palacios, a tributary of Rio Mamore, Bolivia. The relationships of the new species with the others of the genus Pseudohemiodon are discussed, and a preliminary key to the nominal species and subspecies is given.
Causes and Consequences of Thyroid Dysfunction throughout Life: a population-based and genetic approach

markdownabstract__Abstract__ Adequate thyroid hormone (TH) levels are essential for normal growth and differentiation, for the regulation of energy metabolism, and for the physiological function of virtually all human tissues. This is illustrated by the well-known effects of hypo- and hyperthyroidism. In addition, more recent studies show that also minor variation in serum TH levels, even within the normal range, can have important effects on clinical endpoints, such as bone mineral density, atrial fibrillation, metabolic syndrome (3) and cardiovascular mortality.
Approaches for the Direct estimation of rate of increase in population size (λ) using capture-recapture data

Recent developments in the modeling of capture-recapture data permit the direct estimation and modeling of population growth rate Pradel (1996). Resulting estimates reflect changes in numbers of birds on study areas, and such changes result from movement as well as survival and reproductive recruitment. One measure of the “importance” of a demographic vital rate to population growth is based on temporal covariation (i.e., do changes in population growth follow changes in vital rates). If data are available to estimate vital rates or their components, then such data can be combined with capture-recapture data in order to estimate parameters of the relationship between population growth and the vital rate. These methods are illustrated using capture-recapture and nest observation data for Blackthroated Blue Warblers, Dendroica caerulescens, from a long-term study at Hubbard Brook Experimental Forest, New Hampshire, USA. Population growth rate was found to be positively associated with the proportion of birds that double-brood. We encourage use of these methods and believe they will prove to be very useful in research on, and management of, migratory bird populations.
Internet of Things for long distance parent-adult child relationships

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