Miracle-dz/UniFAR-FTUs huggingface dataset:
Cucumber mosaic virus (Cucumovirus) and associated satRNA in weed species under the natural epidemic conditions of tomato lethal necrosis in Croatia

To elucidate the potential role of weed species in an epidemic of tomato lethal necrosis, that has been going on for years in the southern coastal Croatia, 71 weed species were collected in a commercial tomato field with a high incidence of tomato lethal necrosis (about 80%), throughout 1995 and 1996. Bioassays, serological tests and dsRNA analyses were used to investigate the presence of CMV and the associated satRNA in all samples. CMV was found in eight weed species. In three species (Anagallis arvensis, Solanum nigrum and Sonchus sp.), CMV was associated with CrFG-satRNA, the same that was previously reported to codetermine tomato lethal necrosis. Since Solanum nigrum is bi-annual and Sonchus sp. a perennial plant species, they could easily enable overwintering of the virus and associated necrogenic satellite. The pathogen complex was also found in two cultivated species: squash (Lagenaria vulgaris) and pumpkin (Cucurbita pepo). Among 13 aphid species collected in the field, 7 are known CMV-vectors. Inoculation of the necrogenic CMV+satRNA complex on young tomato plants caused lethal necrosis in all of them.
Activation of peroxisome proliferator—activated receptor αin human endothelial cells increases plasminogen activator inhibitor type—1 expression

Objective To investigate the effect of peroxisome proliferator-activated receptors (PPARs) activators on plasminogen activator inhibitor 1 (PAI-1) expression in human umbilical vein endothelial cells and elucidate a possible mechanism.Methods Human umbilical vein endothelial cells (HUVECs) were obtained from normal fetus, and cultured conventionally. Then the HUVEC were exposed to fatty acids and prostaglandin J2 in varying concentrations with fresh media. RT-PCR and ELISA were used to determine the expression of PPAR and PAI-1 in HUVECs. Transient co-transfection of PAI-1 promoter and PPARα gene or PPARγ gene to ECV304 was performed.Results PPARα, PPARδ and PPARγ mRNA in HUVECs were detected by RT-PCR. Treatment of HUVECs with PPARα and PPARγ activators-linolenic acid, linoleic acid, oleic acid and prostaglandin J2, but not with stearic acid could augment PAI-I mRNA expression and protein secretion in a concentration-dependent manner. Proportional induction of PAI-1 promoter activity was observed through increasing amounts of PPARα DNA in HUVECs through a transient gene transfection assay, although the mRNA expression of the 3 subtypes of PPAR with their activators were not changed compared with controls.Conclusions HUVECs express PPARs. PPARs activators may increase PAI-1 expression in endothelial cells (EC). Although PPARs expression was not enhanced after being stimulated by their activators in EC, the functionally active PPARα is probably involved in regulating PAI-1 expression in EC.
Protein-Protein Interactions During Acyl Transfer In Polyketide Biosynthesis.

Polyketide metabolites are produced by diverse bacterial taxa, including soildwelling bacteria, cyanobacteria, and bacterial symbionts living within insects or marine invertebrates, and are generated by decarboxylative condensations of simple coenzyme A (CoA) building blocks. At present, polyketide natural products find clinical utility as antibiotics, antiparasitics, antifungals, anticancer drugs, and immunosuppressants. These comprehensive pharmacological activities provide continued motivation to unravel polyketide biosynthetic mechanisms to enable the discovery of novel compounds for the benefit of human health. This dissertational research explores the molecular basis for guiding ACP-mediated protein-protein interactions in three diverse pathways (pikromycin, bryostatin and germicidin). Accessing new members of the ketolide class of macrolide antibiotics remains an important goal given the increasing prevalence of drug-resistant pathogens. As a naturally occuring ketolide, the pikromycin could serve as a scaffold to build a diverse set of polyketides. The Sherman laboratory has spent over a decade investigating the catalytic mechanisms of pikromycin biosynthesis by the modular PKS-containing pathway found in Streptomyces venezuelae. Here, we explore the protein-protein interactions of the large, multifunctional polypeptides at the PikAIII/PikAIV interface. The combination of
Do Marine Mammals Experience Stress Related to Anthropogenic Noise

This paper could not have been written without the financial and organizational support from Dieter Paulmann and Jo Hastie respectively. Thanks are also due to two anonymous reviewers, whose comments on an earlier version of the manuscript greatly improved the paper. The views expressed in this paper are those of the authors alone and do not represent those of Stellwagen Bank National Marine Sanctuary, the U.S. National Marine Sanctuary Program, Southwest Fisheries Science Center, the U.S. National Marine Fisheries Service, NOAA and/or any other institution or agency. Correspondence concerning this article should be addressed to Andrew Wright, Leviathan Sciences, U.S.A. (marinebrit@gmail.com). Sound travels much further than light in the marine environment. As a result, marine mammals, especially cetaceans, rely heavily on sound for many important life functions, including breeding and foraging. This reliance on sound means it is quite likely that exposure to noise will have some detrimental effects on these life functions. However, there has been little application to marine mammals of the knowledge available in other species of stress responses to noise and other stressors. In this paper we begin to integrate what is known about marine mammals with the current knowledge gained in terrestrial mammals about stress physiology, specifically considering physiological and psychological context and thus also cumulative and synergistic impacts. We determined that it is reasonable to extrapolate information regarding stress responses in other species to marine mammals, because these responses are highly conserved among all species in which they have been examined to date. As a result, we determined that noise acts as a stressor to marine mammals. Furthermore, given that marine mammals will likely respond in a manner consistent with other species studied, repeated and prolonged exposures to stressors (including or induced by noise) will be problematic for marine mammals of all ages. A range of issues may arise from the extended stress response including, but not limited to, suppression of reproduction (physiologically and behaviorally), accelerated aging and sickness-like symptoms. We also determined that interpretation of a reduction in behavioral responses to noise as acclimation will be a mistake in many situations, as alternative reasons for the observed results are much more likely. We recommend that research be conducted on both stress responses and life-history consequences of noise exposure in marine mammals, while emphasizing that very careful study designs will be required. We also recommend that managers incorporate the findings presented here in decisions regarding activities that expose marine mammals to noise. In particular, the effects of cumulative and synergistic responses to stressors can be very important and should not be dismissed lightly.
Regulation of TLR9 dependent DNA Immune complex mediated cell activation by High Mobility Group Box Protein 1 (HMGB1) and Receptor for Advanced Glycation End products (RAGE) (128.35)

Stimulation of endosomal associated TLR9 by DNA plays an important role in activation of plasmacytoid dendritic cells (pDCs) and autoreactive B cells and may contribute to the pathogenesis of systemic lupus erythematosus (SLE). HMGB1 is a DNA binding protein that is liberated either from cells undergoing necrosis or following cytokine stimulation. Here we show that HMGB1 forms a high affinity complex with CpG-A oligodeoxynucleotides and augments the production of IFN-a from murine pDCs. We also show that HMGB1 is indeed a component of naturally formed DNA containing chromatin complexes. IFNa induced by either the exogenously formed HMGB1/CpG-A complex or naturally formed complex is TLR9 dependent and is inhibited by HMGB1 and RAGE antagonists. The complex without HMGB1 induces significantly less IFNa. HMGB1-RAGE interactions are required for activation of autoreactive B cells following stimulation with DNA immune complexes and are critical in the regulation of type I interferon gene induction by DNA complexes present in lupus plasma. Our data provide a novel mechanism by which HMGB1 confers potent stimulatory activity to DNA through a RAGE dependent mechanism and may contribute to the pathogenesis of lupus.
Induced resistance in plants and counter-adaptation by insect pests

Insect and plants have coevolved for millions of years. Plants respond to herbivory through various morphological, biochemical, and molecular mechanisms to counter/offset the effects of herbivore attack. These defense strategies against herbivores are wide-ranging, highly dynamic, and could be direct and/or indirect. Direct defense affects the herbivore’s growth and development due to antibiosis because of secondary metabolites produced constitutively and/or induced upon infestation by the insect pests. The indirect defense involves the recruitment of natural enemies of the insect pests. The natural enemies (parasitoids and predators) are attracted by the volatiles produced by the plants in response to insect herbivory. The direct and indirect defensive strategies either act separately or in conjunction with each other. However, insects have the ability to adapt to the plant defensive responses through physiological processes, metabolism and behavior to offset the adverse effects of the host plants’ defense systems. This process of defensive responses by the host plants and counter defense by the insect pests results in the breakdown of resistance, and evolution of new populations/biotypes of the insect pests. This co-evolution between the plants and insects poses a major threat for developing crop cultivars with stable resistance to the target pest for pest management.
Effect of Social Capital on Performance of Smallholder Farmer Organizations in Western Kenya

Development literature has recently promoted the use of producer organizations in linking farmers to better-paying commodity markets. However, empirical studies find mixed performance of such organizations. This study examines the producer organizations' internal factors that may explain the differences in the performance of producer organizations. The study specifically analyzes the role of social capital, within a producer organization, on the performance of such organization using quantitative techniques. The level of commercialization is used as proxy of organization's performance. The study finds that social capital positively affects the performance of producer organizations. These findings imply that development strategies that target the promotion commercialization of smallholder agriculture through producer organizations should pay attention to the internal factors within such organizations.
A Conceptual Model for Anostracan Biogeography

A conceptual model for anostracan biogeography based on the “Monopolisation Hypothesis” and the “Theory of Island Biogeography” is discussed and presented. In this model anostracan species evolve allopatrically (in geographically isolated, unoccupied insular habitats), cladogenically (in small, genetically isolated founder populations via strong priority effects), or anagenically through local adaptation to changing environmental conditions. The Monopolization Hypothesis drives speciation and reverses competitive dominance patterns, leading to selection mediated priority events. Conversely, the spatial distribution of anostracan habitats (basins) drive island biogeographical patterns depending upon the relative isolation and size of any one given pool. The conceptual model presented provides a simple framework for future research in anostracan biogeography.
Involvement of Complex Carbohydrate Chemistry in Alzheimer’s Disease

THE CARDINAL FEATURE OF Alzheimer disease is the ex- tracellular deposition of proteinaceous amyloid-β fibrils as senile plaques. Amyloid-β plays an essential role in disease diagnosis and is also thought by many to be a key mediator of disease pathogenesis. As such, there are tremen- dous efforts underway to understand mechanisms of amyloid deposition. In this context, it is notable that the actual term amyloid, represents a historical misnomer (being derived from amylose, i.e., starch) and since this realization, the contribution of carbohydrates in disease pathogenesis has largely been ig- nored. However, recently, two emerging lines of evidence indicate not only that the interaction of carbohydrates with amyloid is a key event in disease pathogenesis but also that therapeutic efforts targeted towards such pathways may prove therapeutically efficacious. First, just over a decade ago, we and others discovered that oxidative glycation, similar if not identical to that found in diabetes, was an early and chronic contributor to the disease. Second, we very recently found evidence for the presence of chitin-like polysaccharides in association with amyloid deposits in the diseased brain. Both carbohydrate- associated changes likely contribute to the physiochemical properties of amy- loid (and other disease-related proteins such as tau) and, as such, to the insolu- bility and protease-resistance of amyloid. In fact, taken together, the findings indicate an emerging and important role for carbohydrates in the pathogenesis of Alzheimer disease.
Étude de la diversité génétique chez la bactérie lactique Carnobacterium maltaromaticum et de son adaptation à l'environnement gastro-intestinal de mammifères

The bacterium Carnobacterium maltaromaticum is not used in industry due to limited knowledge about this organism and its virulence in fish. One objective of this thesis was to strengthen the body of knowledge by determining the complete genome sequence of the cheese strain and to evaluate the fate of this bacterium after ingestion by the consumer. Another objective was to improve the taxonomic knowledge within the species C. maltaromaticum through the development of a MLST scheme. The complete sequence of the strain C. maltaromaticum LMA 28 revealed a genome size of approximately 3.8 Mbp, which is unusually high in the genus Carnobacterium. The genome analysis of this strain indicates the presence of genes conferring the adaptation to the intestinal environment. The bacterium is able to survive during the gastro-intestinal transit in mice. Moreover, this strain is able to adhere to human intestinal epithelial cell lines and would have neutral or anti-inflammatory properties. These data suggest that C. maltaromaticum LMA 28 is adapted to the digestive tract of mammals. At the taxonomical level, it was shown that MLST is highly discriminatory for the species C. maltaromaticum. In addition, the MLST results suggest that milk and soft cheeses are poorly selective for strains of this species. In addition, two major clonal complexes suggest that a sub-population within this species is well adapted to the dairy environment or that a sub-population is submitted to a domestication process. A high proportion of singletons was obtained suggesting that the diversity was under-estimated and remains to be explored
Functional annotation of alternatively spliced isoforms of human G protein-coupled receptors (GPCRs)

The functional differences that exist between alternatively spliced isoforms of genes can be substantial; it could be variations of the function of the “primary” full-length protein, its antagonist function or not directly related to its function. Regardless of the functions of spliced isoforms there is a need for proper annotation. G protein-coupled receptors (GPCRs) are important trans-membrane proteins with important biological and pharmaceutical implications. Incorrect alternative splicing has been associated with a number of human diseases including diabetes and cancers. In this dissertation is presented a framework and results for annotating transcripts of GPCR genes that have originated from alternative splicing of their pre-mRNA. This was achieved by first assessing the genomic landscape of the GPCRs to determine the type of alternative splicing event that exist and the localization of such events. In addition, the influences of exon-intron structures of GPCRs on the alternative splicing of the genes are evaluated. Then, the molecular level functions are ascertained via motif identification. Furthermore, the cellular state in which each isoform could function was determined using tissues of expression from RNA-sequencing data. Lastly, isoform function is inferred from cis regulatory elements predicted to influence the transcription of the isoform in the specific cellular state. The results are presented here and made publicly available in a PHP/MySQL relational database. Results from the research analyses indicate that the genomic structures of GPCRs are complex; their exon-intron structures are not arbitrarily arranged; rather they are ordered in such a manner as to ease the alternative splicing of the gene for functional purposes. Also, that GPCR isoforms expression patterns differ across tissues. Additionally it was evident that GPCR isoforms have multiple cellular pathways in which they may be involved depending on the cellular conditions. Overall, 1044 human GPCR isoforms were annotated. These results are now publicly available via the Internet in the database called the G protein-coupled receptor transcriptional annotation of genes (gpcrTAG) database. The results from these analyses offer the promise of transcriptional drug control, as well as offer the framework to study functional diversity between isoforms of other genes families.
Omega-3 fatty acids : metabolism and biological effects

Chemistry and metabolism of omega-3 fatty acids antioxidants and omega-3 fatty acids eicosanoids and omega-3 fatty acids effects of fatty acids on receptor function and metabolism omega-3 fatty acids requirements and development biology omega-3 fatty acids, lipoproteins, atherosclerosis and thrombosis hypertension and omega-3 fatty acids inflammatory diseases and omega-3 fatty acids cancer and omega-3 fatty acids public health aspects of the fats derived from the ocean.
Studies on Tropical Pholcidae I Panjange, a new genus of Indo-Australian Leaf- and rock-dwelling Pholcid spiders (Araneae)

The study of tropical spiders was taken up in the last part of the nineteenth century by Thorell, Simon and others, but since then passed through a long dormant stage. Only during the last few decades there was some revival. In particular numerous spider species from leaf-litter, ground debris, etc. have been described after collecting by special methods such as sieving, Berlese funnels and pitfall trapping. Spiders from another common habitat in South East Asian rainforests, the underside of leaves, seem to have been inadequately treated in older publications. Certain spiders, e.g. pholcids and clubionids, do not readily drop when disturbed, but stick firmly to their leaf substrate or escape sideways through twigs and branches. At present there is no adequate collecting method for this category of leaf-inhabiting spiders but to turn thousands of leaves one by one and pick them off by hand. The particular way of collecting must be the only reason why most species, which we thus collected during several visits to South East Asia, appear to be new to science. These new species were collected in various types of dense, humid forest in Borneo (Sabah and Kalimantan), Java, Sulawesi, Sri Lanka, Malay Peninsula and Luzon, and by F. R. Wanless in Sarawak, V. E. Davies and collaborators in North East Queensland, and J. R. Thomson in Kalimantan. Collecting efforts in the areas mentioned have been very rewarding and this leads to the expectation that in the areas mentioned and also in Sumatra, New Guinea and the Philippine Islands many species of Pholcidae still await discovery. Special attention should be given yet to spiders living in the canopy. There may be a considerable amount of endemism in this spider group and it is to be feared that many species will have become extinct by the wholesale destruction of Asian rainforests even before their discovery.
Effect of explosive shallow hydrothermal vents on δ13C and growth performance in the seagrass Posidonia oceanica

1. Explosive volcanic submarine activity is expected to affect seagrass communities due to sudden and dramatic changes in the physical and chemical features of sea water and sediments, with possibly large ecosystem effects. However, seagrass response to the harsh environmental conditions that arise due to explosive volcanism is as yet unexplored as it is not easy to predict when and where an eruption will occur. Here, we investigate the uptake of hydrothermal carbon within the seagrass Posidonia oceanica by the analysis of δ13C and growth rates in tissue laid down before and after an exceptional and massive hydrothermal gas release in the Aeolian Islands (Italy, Mediterranean Sea).
Effect of Vitamin E Supplementation on Egg Yolk Quality and Oxidative Stability

This study was carried out to evaluate the effect of dietary vitamin E supplementation on oxidative stability in cooked egg yolk. A total of 240 ISA hens were used and divided into two uniform groups: water with a vitamin E supplementation (450 ppm) was used in the experimental group, while for the control group only pure water (100%) was used. Eggs were collected daily after 30 days of feeding and stored at 4°C. Lastly eggs were boiled in water at 100°C for 10 minutes and egg quality was immediately tested (0 days). The advance of the oxidative state was further assessed at 6 days of storage at 4°C after cooking. The obtained results show that the colour and α-tochopherol concentration of egg yolk were significantly different between the two groups, at 0 days. The malondialdehyde (MDA) value and hexanal % were higher at the two storage time after cooking in the control group than the experimental one, probably due to antioxidant activity of vitamin E. During storage, the oxidative stability decreases in both groups.
Enzymology And Medicinal Chemistry Of N5-Carboxyaminoimidazole Ribonucleotide Synthetase : A Novel Antibacterial Target

ENZYMOLOGY AND MEDICINAL CHEMISTRY OF NCARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE: A NOVEL ANTIBACTERIAL TARGET by HANUMANTHARAO PARITALA AUGUST 2010 Advisor: Dr. Steven M. Firestine Major: Pharmaceutical Sciences Degree: Doctor of Philosophy N-Carboxyaminoimidazole ribonucleotide synthetase (N-CAIR synthetase), a key enzyme in microbial de novo purine biosynthesis, catalyzes the conversion of aminoimidazole ribonucleotide (AIR) to N-CAIR. To date, this enzyme has been observed only in microorganisms, and thus, it represents an ideal target for antimicrobial drug development. Here, we report structural and functional studies on the Aspergillus clavatus N-CAIR synthetase and identification of inhibitors for the enzyme. In collaboration with Dr. Hazel Holden of the University of Wisconsin, the three-dimensional structure of Aspergillus clavatus N-CAIR synthetase was solved in the presence of either Mg2ATP or MgADP and AIR. These structures, determined to 2.1 and 2.0 Å resolution, respectively, revealed that AIR binds in a pocket analogous to that observed for other ATPgrasp enzymes involved in purine metabolism. On the basis of these models, a site-directed mutagenesis study was subsequently conducted that focused on five