Miracle-dz/UniFAR-FTUs huggingface dataset:
Presence of Wolbachia, A Potential Biocontrol Agent: Screening for Vertebrate Blood Meal Source and West Nile Virus in Mosquitoes in the North Texas Region

West Nile virus (WNV) is a geographically endemic mosquito-borne flavivirus that has spread across the United States infecting birds, mosquitos, humans, horses and other mammals. The wide spread nature of this virus is due to the ability of the mosquito vector to persist in broad, ecological diverse environments across the United States. In this study, mosquito populations in North Texas region were sampled for detection of Wolbachia, blood meal source, and WNV. The ultimate goal of this study was to examine the potential of a biocontrol agent, Wolbachia sp. that colonizes the hindgut of various insects, including mosquitos, as a natural means to interrupt virus transmission from mosquitos to other hosts, including humans. In Australia, Wolbachia sp. from fruit flies (Drosophila melanogaster) have been successfully used to block transmission of a similar pathogenic virus from mosquitos responsible for transmission of Dengue fever. Here, mosquitoes were collected using CDC style Gravid Traps in Denton, Texas, from October 2012 through September 2014. Collected mosquitoes were identified, sexed, and categorized as to the amount of host blood in their alimentary system using a Zeiss Axio Zoom microscope (Carl Zeiss Microscopy, LLC, Thornwood, NY). Culex quinquefaciatus was the dominant blood engorged species collected. Smaller populations of Culex tarsalis and Aedes albopictus, another known vector for WNV were also collected. Mosquito larva were also collected from the UNT water research field station and reared to adults. Cx. tarsalis was the dominant mosquito taken from this habitat. Samples of Cx. quinquefasciatus, Cx. tarsalis and A. albopictus were analyzed for Wolbachia sp. and to identify host blood in the mosquito alimentary system. Total DNA extraction from the pool of mosquito samples was by both commercially available DNA extraction kits (Qiagen, Valencia, CA) and salt extraction technique. Polymerase chain reaction (PCR) was used to amplify and identify Wolbachia sp. 16SrDNA and mitochondrial DNA from vertebrate blood. The maternally inherited endosymbiont, Wolbachia, were found to be uniformly distributed across the mosquitoes sampled in this study. Blood meal analysis by PCR showed that Cx. quinquefaciatus fed more on birds than on mammalian blood sources based on the previously developed primers used in this study.
Aspects of the ecology of fishes associated with salt marshes and adjacent habitats in a temperate South African estuary

There is a paucity of published infonnation on fish utilization of salt marshes outside North America. This dissertation represents the first intensive examination of the ichthyofauna associated with salt marshes in southern Africa and examines the species composition, diversity, size structure, distribution and estuarine dependence of fishes that utilize salt marshes in the Kariega Estuary. The research was concentrated on Taylor's salt marsh, with comparative studies being conducted on other salt marshes and habitats within the marine dominated Kariega Estuary. The possible importance of salt marshes as feeding and refuge areas for fishes was examined, as was the role of salt marshes in the food web of the estuary. The fishes frequenting salt marshes in the Kariega Estuary were predominantly the juveniles of marine species, with Mugilidae being the dominant family. The ichthyofauna was distributed primarily in the intertidal creeks with very few specimens captured on the vegetated Spartina maritima and Sarcocomia perennis flats. The different reaches of the intertidal creek were characterised by distinct fish assemblages. The fish assemblages associated with the intertidal salt marsh creeks were significantly different from those found in the eelgrass beds, the other dominant intertidal habitat in the Kariega Estuary. The eelgrass beds were dominated by estuarine fish species and had a higher density and standing stock of fishes when compared to the salt marsh creeks. The diversity of fishes in the two habitats was however similar.
Characterization of the S-adenosylmethionine-dependent regulation and physiological roles of genes in the S box system

ii Dedication . v Acknowledgments.vi Vita . vii List of Tables . xii List of Figures.xiii List of Abbreviations.xvi Chapters: 1. Regulation of gene expression in bacteria.1 1.1 Translating ribosomes.3 1.2 RNA-binding proteins.5 1.2.1 Positive-acting RNA-binding proteins. 6 1.2.1.1 E. coli BglG.6 1.2.1.2 B. subtilis GlpP.7 1.2.1.3 Pseudomonas aeruginosa AmiR.9 1.2.2 Negative-acting RNA-binding proteins.11 1.2.2.1 B. subtilis TRAP.11 1.2.2. 2 B. subtilis PyrR.14 1.3 Riboswitches.16 1.3.1 RNA thermosensors.17 1.3.2 T box system.20 1.3.3 Cellular metabolites.23 1.3.3.1 Thi box system.23 1.3.3.2 RFN element.25 1.3.3. 3 B12 element.25 1.3.3.4 pyrG.26 ix 1.3.3.5 G box system.28 1.3.3.6 GlcN6P ribozyme . 30 1.3.3.7 L box system.31 1.3.3.8 Glycine system.32 1.3.3.9 S box system.33 1.4 Goals of this study.37 2. Identification of S-adenosylmethionine as the molecular effector for transcription termination in the S box system.39 2.
Influence of the circadian clock on Arabidopsis defence against Botrytis cinerea

The circadian clock is an endogenous mechanism that provides a wide variety of organisms with the ability to anticipate daily environmental changes. It was shown that under cyclic and constant light growth conditions Arabidopsis exhibits rhythmicity in Botrytis cinerea resistance, with maximal resistance observed when leaves were inoculated at dawn. Crucially, this mechanism was confirmed to be under circadian clock regulation. To understand how the circadian clock was driving an effective defence response, genes that were more rapidly induced or repressed after inoculation at dawn compared to night were identified. This indicated a complex interaction between the circadian clock and the defence regulatory network. Phytohormone defence signalling, in particular, jasmonate (JA) and ethylene responses, was shown to contribute to the observed rhythmic variation in resistance. This was further confirmed by the identification of a JA signalling mutant (jaz6), which displayed no difference in resistance to B. cinerea following inoculation at dawn or night under cyclic or constant light conditions. Given the central role of JAZ6 in the circadian defence response against B. cinerea, it was likely transcription factors (TFs) bound by JAZ6 were potential links between the plant circadian clock and the defence response. Elucidating the TFs that interacted with JAZ6 revealed JAZ6 to be able to interact with a TF shown to be crucial to the B. cinerea defence response, EIN3. Moreover, JAZ6 was also able to interact with a central regulator of circadian clock, FHY3. Both TF interactors indicate JAZ6 is a linking protein between the circadian clock and the defence response against B. cinerea. To further understand how the circadian clock was mediating the plant defence response against B. cinerea genome-wide chromatin accessibility data was generated using ATAC-Seq. This aimed to enable the comparison of chromatin accessibility as well as TF binding in regions surrounding genes related to B. cinerea defences between the two time-points. This protocol was not optimized for plant tissue. Steps within in! laboratory-based ATAC-Seq protocol were therefore pinpointed for tissue specific optimization. Thus, a protocol specific to ATAC-Seq data analysis was proposed.
Antidiabetic activity of thin film containing astaxanthin-loaded nanoemulsion using carboxymethylcellulose sodium polymer on alloxan-induced diabetic rabbit

The present study was conducted to evaluate the potency of thin film containing astaxanthin-loaded nanoemulsion (FDT-As-NE) in lowering blood glucose levels on alloxan-induced diabetic rabbit (ADR). Astaxanthin nanoemulsion (As-NE) was prepared using self-nanoemulsifying method, followed by incorporated into the carboxymethylcellulose sodium matrix polymer using a solvent casting method to form a thin film. The evaluation of FDT-As-NE was performed by chemical, physical, and mechanical characterizations. The administration of thin film was done by an intraoral route. New Zealand albino rabbits were induced with alloxan to get experimental diabetic animals. The antidiabetic activity was carried out in three groups of treatment. Group I was ADR treated by FDT-As-NE, Group II was ADR treated by pure astaxanthin, while Group III was normal control. The measurement of fasting means blood glucose levels was carried out in 0 days (before treatment) and after 14 days of treatment. The histopathological analysis of the pancreas was also examined. Data were statistically evaluated using Kruskal–Wallis statistical test. P < 0.05 was considered statistically significant. FDT-As-NE had good physical and mechanical characteristics that suitable for intraoral administration. Group I reduced elevated blood glucose levels compared to Group II (P < 0.01). Histopathological examination of pancreatic tissue for a Group I showed the normal condition of pancreatic β-cell, suggesting the absence of any pathological lesions. These results suggest that thin film containing astaxanthin-loaded nanoemulsion administered by an intraoral route potentially useful for reducing glucose levels.
The complete mitochondrial genome characterization of Tridentiger obscurus (Gobiiformes: Gobiidae) and phylogenetic analyses of Gobionellinae

Abstract The dusky tripletooth goby, Tridentiger obscurus, is a good model organism for the small in size and reaching maturity within a single year. Previous studies mainly focused on the annual reproductive cycle, social behavior and life history, but little information is available of the mitochondrial genome and phylogenetic evolution of this gobioid fish. In this article, we described the complete mitogenome of T. obscurus and reconstructed the phylogenetic relationship of the relative species of Gobionellinae. The genome is 16,501 bp in length including 13 protein-coding, two ribosomal RNA, 22 transfer RNA genes, as well as a putative control region and an L-strand replication origin. The overall base composition is 28.1%, 27.0%, 28.0% and 16.9% for A, T, C and G, respectively. This result is expected for better understanding the systematic evolution of the genus Tridentiger and further phylogenetic study of Gobiiformes.
The role of the environment on the genetic divergence between two Boa imperator lineages

A fundamental problem in evolutionary biology has been understanding the role of environmental factors in the process of genetic diversification. Our main goal was to define the ecological niches of two Boa imperator lineages, in order to assess if environmental drivers could be associated with the divergence and genetic variation between them. We quantified the environmental niches at two evolutionary and geographical scales: regional‐historical (lineages) and local‐ecological (individuals within lineages).
Atmospheric Data for Ornithology: An Introduction

Abstract This paper introduces user-friendly atmospheric data, so-called objective analysis data, for ornithological studies. The data have been interpolated onto grid points distributed at a regular interval in space and time, and are suitable for analyzing using computer data analysis software. Data assimilation techniques, which are basically the application of optimization and control theories, are utilized for producing objective analysis data in order to reduce errors as much as possible and obtain the most reliable dataset. Some examples of objective analysis data are shown and their features are described. Some cautionary notes are also given in order to avoid misinterpretation of the data.
Warm and wet: robust lipase-producing bacteria from the indoor environment

Lipases are key biocatalysts with important biotechnological applications. With the aim of isolating robust lipolytic microbial strains, we have analyzed the bacterial communities inhabiting two domestic extreme environments: a thermophilic sauna and a dishwasher filter. Scanning electron microscopy revealed biofilm-forming and scattered microorganisms in the sauna and dishwasher sample, respectively. A culture-independent approach based on 16S rRNA analysis indicated a high abundance of Proteobacteria in the sauna sample; and, a large amount of Proteobacteria, Firmicutes, Cyanobacteria and Actinobacteria in the dishwasher filter. With a culture-dependent approach, we isolated 48 bacterial strains, screened their lipolytic activities on media with tributyrin as the main carbon source, and finally selected five isolates for further characterization. These strains, all of them identified as members of the genus Bacillus, displayed optimum lipolytic peaks at pH 6.5 and with 1-2% NaCl, and the activity proved very robust at a wide range of pH (up to 11.5) and added NaCl concentrations (up to 4%). The thermal, pH and salt robustness of the selected isolates is a valuable attribute for these strains, which are promising as highly tolerant biodetergents. To our knowledge, this is the first report regarding the isolation from an indoor environment of Bacillus strains with a high potential for industry.
Equilibrative-sensitive nucleoside transporter function and regulation in gemcitabine sensitivity and resistance, is there a potential therapeutic benefit for pancreatic cancer?

Salvage of preformed nucleosides requires transport across the plasma membrane by specific transport proteins and subsequent conversion to their riboand deoxyribonucleotide foms. In mammalian cells, plasma membrane transport occurs by sodiumdependent (concentrative) and sodium-independent (equilibrative) mechanisms. These transport systems are also the route of cellular uptake for many synthetic nucleoside analogue agents used in cancer treatment, including gemcitabine (a novel deoxycytidine analogue). This thesis examines the in vitro effects of gemcitabine on cytotoxicity and the modulation of these effects by the es-nucleoside transporter and two DNA synthesis inhibitors (5-fluorouracil and tomudex), with a specific focus on pancreatic cancer. Cytotoxicity was assessed by clonogenic assay in one human bladder (MGH-U1 ) and three human pancreatic cancer cell lines (PANC-1, HS-766T, PK8). Basal levels of es-NT were quantified in al1 four cell lines by flow cytometric analysis. Combination experiments were cawied out to determine if upregulating the es-NT modulates increases in sensitivity to gemcitabine. In two pancreatic cell lines (PANC-1, HS-766T), treatment with 5-FU followed by gemcitabine yielded increased cytotoxicity. This effect was also seen in the HS-7661 cell line when pre-treated with tomudex. For these concentrations of 5-FU and tomudex, es-NT content was found to be increased over basal levels.
First citizen-science population abundance and growth rate estimates for green sea turtles Chelonia mydas foraging in the northern Great Barrier Reef, Australia

Given that 12 years of data were analysed, the population was treated as open because losses and gains are expected, which was confirmed by formal tests of closure following Cooch and White (2017). A model with unconstrained apparent survival (ɸ) had lower AICc (secondorder bias corrected Akaike’s information criterion) than a model assuming 100% survival (ɸ =1). Similarly, a model with unconstrained recruitment (f) had lower AICc than the no recruitment model (f = 0). Data were therefore modelled with open Capture Mark Recapture (CMR models). Demographic estimates from CMR modelling can be strongly biased if the basic assumptions are violated (Williams et al 2002). For open population models, these assumptions are usually expressed as (after Pollock et al., 1990; Williams et al., 2002):
Determining Fiber and Protein Degradation Rates of Corn Milling (Co)Products and Their Effects on Rumen Bacterial Populations and Lactating Dairy Cow Performance

Determining Fiber and Protein Degradation Rates of Corn Milling (Co)Products and Their Effects on Rumen Bacterial Populations and Lactating Dairy Cow Performance. (May 2011) Whitney Lynn Williams, B.S., Texas A&M University Chair of Advisory Committee: Dr. Luis O. Tedeschi Corn milling (co)products (n=120) were evaluated for their neutral detergent fiber residue (NDR) and neutral detergent insoluble protein (NDIP) ruminal degradation rates using several in vitro methods. Two (co)products (BPX-DDGS and HP-DDG) were fed to lactating dairy cows (n=44) to evaluate effects on milk production. The Cornell-Penn-Miner Institute (CPM) Dairy model was used to formulate diets and predict milk production. In vitro determined NDR and NDIP rates and were compared to CPM-dairy feed library values, and model predictions were compared with observed milk production. Additionally, BPX-DDGS and HP-DDG were defatted and compared with their intact forms for fermentation characteristics using the in vitro gas production (IVGP) technique. Fermentations were analyzed for rumen bacterial population shifts using the 16S rDNA bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP) technique. Lastly, a novel ruminal in vitro method was described to measure the soluble protein fraction of feeds, with adjustments for microbial contamination.
Contribution à la faune helminthologique Sud-Africaine: Note préliminaire

Le matériel faisant l’objet de ce travail provient d’une grande collection de cestodes donnée à M. le professeur O. Fuhrmann par Sir Arnold Theiler, directeur du laboratoire de recherches vétéri­ naires de Prétoria. Dans cette note préliminaire nous ne nous occupperons que des espèces nouvelles pour la science et remettons à une publication ultérieure l’étude complète des cestodes de mammifè­ res de cette collection provenant des régions voisines de Pré toria. Tous les hôtes sont désignés d’après le catalogue des mammifè­ res de Trouessart. Les types de cette collection seront déposés dans la collection de M. le professeur O. Fuhrmann.
Peer Review) Sequence Variation and Phylogenetic analysis of Sansevieria trifasciata (Asparagaceae)

Sansevieria is an ornamental plant with fairly high economic value. It has many hybrids and varieties which make them difficult to identify. Among Sansevieria, the most commercialized species is S. trifasciata. There are at least 20 cultivars of this species which has been sold around the world. Morphological characters among those cultivars are somehow highly distinct, therefore they maybe considered as different species. This research aimed at analysing the sequence variation among S. trifasciata and their allied taxa in family Asparagaceae. Sequences of their matK gene are analyzed. The evolutionary history was inferred by using the Maximum Likelihood method. Estimation of evolutionary divergence between sequence was analysed using Kimura two-parameter. Evolutionary analysis were conducted in MEGA6. The evolutionary divergence shows that there is no distance within S. trifasciata. The phylogeny indicates that Pleomele is embedded within Dracaena. Overall evolutionary divergence of Asparagaceae shows very low interspecific divergence within Sansevieria and this genus is monophyletic.
Molecular studies of ATP-sensitive potassium channels : gating, pathology, and optogenetics

ATP-sensitive K+ (KATP) channels are ubiquitous channels designed to couple excitability to cellular energy. They perform this function by sensing the relative levels of the intracellular nucleotides ATP and ADP, with ATP blocking the channel and ADP activating it. Additionally, the phospholipid phosphatidylinositol 4,5-bisphosphate (PIP2) is known to be a strong regulator of KATP channels. These channels are present in many excitable tissues and involved in many physiological functions. The main aim of this thesis is to design a light-dependent KATP channel for use as a tool in physiological studies as well as in optogenetics. Light-dependent block was accomplished by attaching a photosensitive blocker to specific residues. This light-inhibited KATP channel, could be used to regulate action potentials with light to tune diverse aspects of cellular electrophysiology and potentially for photo-pharmacology treatment. We also performed a functional mapping of the Kir6.2 channel gate(s) under the control of membrane proteins interacting with the N-terminal domain. This was performed by using an artificial ligand-gated Kir6.2 channel formed by attaching a GPCR to its Nterminus. Crystallographic structures and functional characterizations of potassium channels suggested the presence of two gates in the transmembrane domains, the selectivity filter and the "A" gate at the cytoplasmic interface, and of a third gate, the G loop gate, in the cytoplasmic domain of Kir channels. Unexpectedly, our results demonstrated that several gates could be involved suggesting a concerted mechanism. Finally, we characterized two single-point mutations in the ABCC9 gene encoding SUR2 that are associated with Cantù syndrome (CS). These mutations are localized in transmembrane domain 0 (TMD0) of SUR2A, an essential domain which mediates the interaction between Kir6.2 and SUR within the K-ATP channel complex. Results suggest that the two mutations cause KATP channel hyperactivity through two divergent mechanisms: (1) a decreased sensitivity to ATP inhibition and (2) an increased sensitivity to activation by PIP2. These discoveries underline the essential role of TMD0 in the gating modulation of Kir6.2. They demonstrate in particular that it can control the response of the channel to intracellular effectors that bind to Kir6.2, implying tight interactions between Kir6.2 and the TMD0 region.
MSAP in Tiger Snakes: Island populations are epigenetically more divergent

Research on changes in phenotypic plasticity within wild animal populations is centuries old, however far fewer studies have investigated the role that epigenetics play in the development or persistence of natural variation in response to environmental change. Tiger snakes (Notechis scutatus) are an ideal study organism to investigate the link between epigenetics and phenotypic responses to environmental change, as they live on a range of offshore islands with different environments and prey types while exhibiting gigantism and dwarfism in body and head size. In this study, we have generated methylation sensitive amplified polymorphism (MSAP) data and found that, in general, Tiger Snakes are more epigenetically differentiated than genetically differentiated. Each island group has a distinctive epigenetic signal, suggesting the Tiger Snakes on each island group have adapted to their specific environment. This is also supported by the strong positive relationship between epigenetic differentiation and isolation age, as well as between epigenetic/genetic signal and both temperature and precipitation. The Tiger Snakes from Kangaroo Island, which has a complex landscape/environment like the mainland rather than the simple landscape/environment of each of the smaller islands, are both genetically and epigenetically more like the mainland. As the MSAP loci are randomly distributed across the genome, we believe a closer examination of the epigenetic modifications near genes involved in growth, development, and lipid metabolism will allow us to investigate the epigenetic basis for the natural variation in head size and body size on the islands.