Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of the Cowpox and Mousepox homologs of the Smallpox virus B22 protein and their roles in mouse disease models

Title of Dissertation: CHARACTERIZATION OF THE COWPOX AND MOUSEPOX HOMOLOGS OF THE SMALLPOX VIRUS B22 PROTEIN AND THEIR ROLES IN MOUSE DISEASE MODELS Sara Elizabeth Reynolds, Doctor of Philosophy, 2016 Dissertation directed by: Dr. Bernard Moss, Adjunct Professor, National Institutes of Health and Dr. James Culver, Professor, Biological Sciences Program Poxviruses are an important family of viruses with members capable of infecting humans including variola virus, the causative agent of smallpox. Homologs of the variola virus B22 protein are found in almost all chordopoxviruses and have estimated masses of greater than 200 kDa, making them the largest known poxvirus proteins, and leading to our initial interest in the role of this protein family. Most homologs are found in the variable region of the poxviral genome where less conserved host-interaction proteins are found, however, B22 homologs are remarkably well conserved, missing only from the parapox subfamily and vaccinia virus, and sometimes even found in multiples (crocodilepox, canarypox) despite their large size. We showed that the cowpox homolog, CPXV219, was expressed early during infection and cleaved into fragments that remained associated. CPXV219 was observed in the secretory pathway and at the plasma membrane with the majority of the protein extracellular. However, mutants that did not express CPXV219 replicated normally in cell culture and retained virulence in a mouse respiratory infection model. Next, we investigated the importance of the ectromelia virus homolog C15 in the natural infection model, mousepox. In the absence of C15 following footpad infection of BALB/c mice, there was less mortality and at high doses all mice survived, whereas none survived infection with wildtype virus. Similar virus loads were present at the site of infection with mutant or control virus whereas there was less virus in popliteal and inguinal lymph nodes, spleen and liver, key organs in mousepox disease, indicating decreased virus spread and replication in the absence of C15. Decreased spread was not the result of an intrinsic viral function of C15 as the survival of infected mice was dependent on host CD4+ and CD8+ T cells during infection. These results highlight the importance of choosing an appropriate animal model. The influence of B22 homologs displays a species-specificity as observed in the natural virus-host model of ectromelia virus, which provides an excellent model for the study of such host-defense molecules during poxvirus infection. Future work should focus on determining the mechanism of action of these homologs. CHARACTERIZATION OF THE COWPOX AND MOUSEPOX HOMOLOGS OF THE SMALLPOX VIRUS B22 PROTEIN AND THEIR ROLES IN MOUSE DISEASE MODELS
Mechanisms and biomarkers of cadmium induced neurobehavioral impairment in the olfactory system of coho salmon (Oncorhynchus kisutch)

Mechanisms and biomarkers of cadmium induced neurobehavioral impairment in the olfactory system of coho salmon (Oncorhynchus kisutch) Chase Rockwell Williams Professor Dr. Evan P. Gallagher Environmental and Occupational Health Sciences Pacific salmon populations on the west coast of the U.S. are increasingly threatened by anthropogenic activities. One potential factor driving the population declines is disruption of olfactory function via waterborne pollutants. The salmon olfactory system is highly susceptible to disruption by waterborne pollutants such as metals. A majority of the current research has focused on the olfactory toxicity of waterborne copper, while other metals such as cadmium (Cd) have gone relatively understudied. This is a large concern as Cd is a common pollutant in many urban and agricultural waterways, some of which can be important salmon migratory routes. For my doctoral research, I focused on understanding the mechanisms underlying Cd mediated olfactory dysfunction using juvenile coho salmon parr (Oncorhynchus kisutch). The research goals for aim 1 of my project were to analyze olfactory-mediated alarm responses, epithelial injury and recovery, and a suite of olfactory molecular biomarkers encoding genes critical in
Effects of food and thermal regimes on body condition indices and skin colouration in corn snakes

Abstract One of the open problems in evolutionary ecology is signal reliability. While the view that signals need to be costly to be honest has attracted most attention, this type of signals may apply only to some contexts. Also, different views exist about the nature of costs involved in signal honesty, and the classification and examination of these costs remains controversial. Pigmentarybased colouration of animal integuments has received considerable attention among researchers seeking to explain what maintains the honesty of visual signals, but support for existing hypotheses is far from conclusive. Here we use a whole-animal approach and consider a distinct time scale, the period of juvenile growth, to test the effects of different feeding and thermal regimes on different physical parameters and skin colouration in corn snakes Pantherophis guttatus. Postnatal body length growth rate and body mass index (BMI) were sensitive to the thermal, but not to the food regime. The length of intervals between skin shedding was shorter and the short-wavelength reflectance of dorsal skin was higher for snakes receiving food more frequently and having an uninterrupted possibility to thermoregulate. This work suggests that if juvenile corn snakes are environmentally constrained, their preferred life history strategy is to grow at faster rates. The study adds to the growing body of evidence in that BMI may not accurately reflect individual condition in reptiles. Instead, this study demonstrates that the length of shedding intervals and the short-wavelength component of skin colouration may be used in this animal system as proxies of the individual’s condition or quality, possibly reflecting exposure to environmental stress or an ability to cope with it.
Investigation into the Cell Wall and Cellulose Biosynthesis in Model Species and in the C4 Model Plant Setaria viridis

OF DISSERTATION A uniform feature of all plant cells is the presence of a cell wall. The cell wall functions in facilitating directional expansion and is therefore important for cell shape and morphogenesis. All plant cell walls contain cellulose microfibrils embedded in a network of polysaccharides, lignin and protein. Cellulose is evolutionarily conserved and is made by all plants as well as other members of various taxonomic kingdoms. From a human perspective, the field of renewable energy has had an ever increasing interest in using the cell wall for production of renewable platform chemicals and fuels. However, the biosynthesis of these components is complex and the intricacies are still being solved. Herein, a molecular genetics approach was taken to advance our understanding of cell wall biosynthesis. Initial work proposes a C4 model grass Setaria viridis as well as for the crop plant Sorghum bicolor for genetic analysis. The machinery that is responsible for the biosynthesis the cell wall such as the cellulose synthase (CESA) enzymes were identified and the compositional analysis of the cell wall was conducted. In addition, the role of a cellulose synthase like D1 (CSLD1) gene was studied using reverse genetics. Finally, regulatory features called microRNAs that may intersect with lignin biosynthesis were explored through a series of molecular genetic analyses using Arabidopsis.
Simvastatin reduces VCAM-1 expression in human umbilical vein endothelial cells exposed to lipopolysaccharide

Objective Reducing the expression of endothelial cell adhesion molecules (ECAMs) is known to decrease inflammation-induced vascular complications. In this paper we looked at whether statins can reduce inflammationinduced ECAM expression after lipopolysaccharide (LPS) treatment in endothelial cells. Methods Human umbilical vein endothelial cells (HUVECs) were pretreated with different concentrations of simvastatin, atorvastatin, and rosuvastatin and subsequently exposed to 5 lg/ml LPS. Semi-quantitative RTPCR analysis was used to measure the mRNA expression of ECAMs, including VCAM-1, ICAM-1, and E-selectin. Results VCAM-1 mRNA appeared to be the only target that was affected by the statins, with its expression being partially and almost completely reduced by simvastatin at 50 and 125 lM concentrations, respectively, and only partially reduced by atorvastatin, but not reduced by rosuvastatin. VCAM-1 protein production was inhibited by simvastatin at concentrations from 5 to 125 lM. Leukocyte‐endothelial cell adhesion assay revealed that simvastatin could inhibit the adhesion of labelled U937 cells to the HUVEC monolayer. Conclusions This study showed that simvastatin reduces VCAM-1 expression in HUVECs exposed to LPS and decreases leukocyte‐endothelial cell adhesion.
Lack of a response of the sub-tropical rodent (Saccostomus campestris) to a secondary plant compound, 6-methoxybenzoxazolinone - consequences for reproductive strategy

A potential strategy for southern African small mammals to maximise reproductive success is to cue breeding activity to rainfall and subsequent vegetative growth via a secondary plant compound such as 6-methoxybenzoxazolinone (6MBOA). This study investigated whether the sub-tropical rodent Saccostomus campestris utilised this compound to enhance reproductive activity. 6MBOA or control vehicle were injected into adult females and into peri-pubertal females under long day (LD) and short day (SO) photoperiods (adults n = 6 to 8: peripubertals n = 5 to 10/treatment). There was no significant effect of 6MBOA or photoperiod on uterine or ovarian masses nor on ovarian development in sacrificed animals. nor on age at vaginal opening of peri-pubertals. It was concluded that 6MBOA is not a major stimulant of reproduction in this species. Rather, we propose that seasonal breeding occurs in response to multiple environmental cues. This reproductive strategy and omnivory permit an opportunistic reproductive response to the unpredictable environment of the southern African region.
Phytochemical Investigation and In Vitro Antibacterial Evaluation on Root Extracts of Rumex abyssinicus

The dried and powdered root of Rumex abyssinicus was extracted with increasing gradient of solvents (petroleum ether, chloroform, acetone and methanol) and screened for antibacterial activity on four pathogenic bacterial strains: Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa and Salmonella thyphimurium. The acetone extract showed promissing antibacterial activity. Chromatographic separation of the acetone extract led to isolation of three compounds of which two of them (Betulone and oleic acid) were isolated for the first time from the plant. The structures of these compounds were charachterized with the help of spectroscopic methods (IR, NMR). Two compounds, RA-1 and RA-2, were identified to be betulone and oleic acid respectively based on spectroscopy data and literature reports, whereas the third compound RA-3 was only partially characterized. Ciprofloxacin was used as a reference drug during antibacterial assay.
Social call divergence in bats: a comparative analysis

Lay Summary Many ecological and evolutionary factors may induce acoustic divergence between species. Using a wide data set on bats, we show that interspecific divergence in social calls are determined primarily by sociality, body size, and phylogenetic relationships. Just as sexual selection, sociality may serve as a powerful social pressure driving acoustic phenotype diversity.
Checklist of digenean parasites of birds from Argentina

Helminth parasites of birds have been studied in Argentina for almost one century. Survey work on this group of parasites is far from complete. Here we present a checklist that summarizes the diversity of digeneans of birds from Argentina, each account is based on a literature search and gives, for each digenean species, their hosts, site of infection, localities, life cycle if known, and collection number of types where they are housed. Moreover, it presents a list of bird hosts with their digenean parasites and a list of intermediate hosts. To date, 95 digenean species have been reported; of which 27 species (29%) were new to science. These reports include 2 species of Brachylaimoidea, 2 Clinostomoidea, 5 Cyclocoeloidea, 3 Dicrocoelioidea, 21 Diplostomoidea, 26 Echinostomatoidea, 1 Gymnophalloidea, 10 Microphalloidea, 12 Opisthorchioidea, 1 Paramphistomoidea, 8 Pronocephaloidea, 2 Schistosomatoidea and 1 Troglotrematoidea. A total of 60 wild and domestic species of birds have been reported as natural hosts of digeneans in Argentina and 5 species as experimental hosts.
Investigation of the transcriptional landscape and RNA biology of Salmonella Typhimurium plasmids

As one part of this project, a bioinformatics pipeline was developed for the efficient analysis of RNA-Seq data. Overall, 106 RNA-Seq libraries and ~1.75 billion cDNA reads were processed using the analysis pipeline. The data for visualisation were generated using custom-made Perl scripts, and relative transcript abundance was determined with the Transcripts Per Million approach. The RNA-Seq pipeline has been used extensively and successfully to analyse RNA-Seq data generated from different bacterial species.
The first attempt at IVF on mammalian eggs was performed by Viennese embryologist

In vitro fertilization [5] (IVF) is an assisted reproductive technology [6] (ART) initially introduced by Patrick Steptoe [7] and Robert Edwards [8] in the 1970s to treat female infertility [9] caused by damaged or blocked fallopian tubes [10]. This major breakthrough in embryo research has provided large numbers of women the possibility of becoming pregnant, and subsequent advances have dramatically increased their chances. IVF is a laboratory procedure in which sperm [11] and egg [12] are fertilized outside the body; the term “in vitro” is Latin for “in glass. ”
Generation of a FHV-1 Viral Vaccine Against Gonadotropin Releasing Hormone for Immunocontraception of Felines

ii DEDICATION. iii ACKNOWLEDGEMENTS . iv LIST OF TABLES. vii LIST OF FIGURES . viii LIST OF ABBREVIATIONS. ix CHAPTER 1: INTRODUCTION/LITERATURE REVIEW. 1 1.1 The Problem: Feline Overpopulation . 1 1.2 Rationale for Viral Vector . 3 1.2.1 Rationale for Viral Vector: Feline Herpes Virus and Species Specificity. 3 1.2.2 Rationale for Viral Vector: Role of gD, gI, gE (Rationale for Deletion of gI) . 6 1.3 Rationale for Target Protein: GnRH . 10 1.4 Rationale for Immunogen: Flagellin . 15 1.5 Rationale for Visualization: EGFP. 17 CHAPTER 2: MATERIALS AND METHODS . 19 2.1 Generation of Clones. 19 2.1.1 pCRScript/EGFP/GnRH . 19 2.1.2 pRSetA/fliC/EGFP/GnRH (pRSetA/FEG) . 20 2.1.3 pRSetA/EGFP/GnRH (pRSetA/EG). 22 2.1.4 pFHV/fliC/EGFP/GnRH (pFHV/FEG) . 22 2.1.5 pFHV/EGFP/GnRH (pFHV/EG) . 24 2.1. 6 Sequencing to Confirm Constructs: pRSetA/FEG and pFHV/FEG . 24 2.1. 7 BL-21 Stocks: pRSetA/FEG, pRSetA/EG, pFHV/FEG, and pFHV/EG . 25 2.2 Verification of Protein Expression . 26 2.2.1 Western Blot: GnRH, FliC, and GFP Expression from pRSetA/FEG #31 . 26 2.3 Generation of Recombinant Virus. 27 2.3.1 Propagation of CRFK Cells . 27 2.3.2 Propagation of FHV-1, FHV/FEG, and FHV/EG . 28 2.3.3 Titering of Virus . 29 2.3. 4 Transient Transfection and Co-Transfection . 30 CHAPTER 3: RESULTS . 32 3.1 Generation of Clones. 32 3.1.1 pCRScript/EGFP/GnRH . 32 3.1.2 pRSetA/fliC/EGFP/GnRH (pRSetA/FEG) . 34 3.1.3 pRSetA/EGFP/GnRH (pRSetA/EG). 39 3.1.4 pFHV/fliC/EGFP/GnRH (pFHV/FEG) . 41 3.1.5 pFHV/EGFP/GnRH (pFHV/EG) . 46 3.1. 6 Sequencing to Confirm Constructs: pRSetA/FEG and pFHV/FEG . 47 3.1. 7 E. coli BL-21 Stocks: pRSetA/FEG, pRSetA/EG, pFHV/FEG, and pFHV/EG . 48 3.2 Verification of Protein Expression from pRSetA/FEG #31 and pRSetA/EG #2 . 48 3.2.1 Western Blot: GnRH, FliC, GFP. 48 3.3 Generation of Virus . 52 3.3.1 Propagation of CRFK Cells . 52 3.3.2 Propagation of FHV-1, FHV/FEG, and FHV/EG . 53 3.3.3 Titering of Virus: FHV-1, FHV/FEG, and FHV/EG . 53 3.3. 4 Transient Transfection and Co-Transfection . 53 CHAPTER 4: DISCUSSION. 55 CHAPTER 5: FUTURE WORK . 58 REFERENCES . 60 APPENDIX A. 66 CURRICULUM VITAE . 81
Effect of chicken breed and storage conditions of eggs on their quality

The aim of the study was to assess the quality of eggs stored in different conditions for 28 days after oviposition. The eggs were produced by two breeds of hens covered by the gene-pool protection programme, and by commercial hybrids. The experiment used eggs from Greenleg Partridge (line Z-11) and Rhode Island White hens (line A-33) and Hy-Line commercial hybrids. Sixty class M eggs were collected from each breed and divided into three groups. Group I contained fresh eggs which were weighed and evaluated for quality on the first day after oviposition. In group II, eggs were stored in a cool room for 28 days at an average temperature of 14°C and humidity of 39–46%. Group III were eggs refrigerated for 28 days at an average temperature of 5.5°C and humidity of 29–36%. Regardless of bird’s genotype, egg weight was found to decrease and egg yolk percentage to increase as a result of storing the eggs for 28 days. Storage of eggs contributed to decreasing the height of thick albumen and Haugh units (HU). Egg storage caused no significant changes in shell breaking strength. The effect of storage on reducing egg quality characteristics was much lower for Hy-Line hens compared to hens from the protected populations: Greenleg Partridge (Z-11) and Rhode Island White (A-33).
Molecular microbial ecology of ammonia oxidation in coastal sediments

VII 1) Chapter 1: General Introduction . 1 1.1 Nitrogen cycle . 1 1.1.1 Importance of the nitrogen cycle in coastal ecosystems . 3 1.1.2 Human impact . 4 1.2 Nitrification . 6 1.3 Nitrifiers . 8 1.3. 1 Ammonia Oxidising Bacteria (AOB) . 11 1.3. 2 Ammonia Oxidising Archaea (AOA) . 12 1.4 The influence environmental factors have on ammonia oxidisers . 14 1.4. 1 Ammonia substrates . 15 1.4. 2 pH. 18 1.4. 3 Temperature . 20 1.4. 4 Oxygen availability . 22 1.4. 5 Salinity . 23 1.5 Scope of thesis . 27 1.5. 1 Aims and objectives . 28 1.5. 2 Hypothesis . 29 2) Chapter 2: Co-occurrence of transcriptionally active ammonia oxidising bacteria and archaea in intertidal sediments. 31 2.
First Record of Setaria Tundra in Danish Roe Deer (Capreolus Capreolus)

(21/03/2019) First Record of Setaria Tundra in Danish Roe Deer (Capreolus Capreolus) No previous finds of the mosquito-borne filarioid nematode Setaria tundra have been reported from Denmark, although it was described decades ago in Swedish and Norwegian reindeer as well as in roe deer from Germany, Bulgaria and more recently also from Italy and Finland. Setaria spp. are usually considered harmless inhabitants of the abdominal cavity of ungulates causing only focal areas of mild chronic peritonitis. However, in recent years S. tundra has been associated with an emerging epidemic disease resulting in severe morbidity and mortality for both reindeer and moose in Finland. The Danish find of S. tundra was from a fawn shot in October 2010 near Randers, in the eastern part of Jutland. At slaughter several (>20) approximately 5 cm long, slender, white worms were observed in the peritoneal cavity. Morphology of the worms, revealed by light microscopy, correlated to that of S. tundra described by Rejewsky (1929) and Nikander et al. (2007). Sequences of the mitochondrial 12S rRNA and cox1 genes, 454 and 595 base pairs respectively, were 99.599. 7% identical to previously published S. tundra isolates from France and Italy. Roe deer are thought to be asymptomatic carriers of S. tundra, and may be connected to the spreading of this parasite. In reindeer heavy worm burdens of S. tundra have been found to cause severe peritonitis and negatively affect body condition score. Thus in the light of the possible climatic changes which could result in warmer, more humid weather in Scandinavia and thereby larger numbers of mosquitoes, it is important to monitor this vector-borne parasite. This will not only increase the understanding of factors promoting its expansion but also help to predict disease outbreaks.
Effects of Cd on Uptake of P in Potato Grown in Sierozems

ABSTRACT The effects of Cd on the bioaccumulation of P in soil-plant system have aroused wide interest and been widely explored. Sierozem has been contaminated by Cd in many areas in Northwest China. To investigate the effects of Cd on the uptake and translocation of P in plants in sierozem, pot experiments were carried out by cultivating potato (Solanum tuberosum L.) under Cd treatment. The fractions of Cd in the soil were examined by soil extraction; available P in the soil was determined; Cd and P accumulation in the plants was also determined. The result of the soil extraction shows that the acid-soluble Cd fraction gradually became the main fraction with the increasing Cd concentrations in the soil. This suggests that the change in the main fraction of Cd may promote the uptake of Cd in plants because acid-soluble Cd fraction may be utilized easily by plants. Given increasing Cd concentrations in the soil, Cd concentrations increased in each part of potato plants, whereas the soil available P and plant P contents were decreased. These results indicate that increasing Cd concentrations in sierozems exerts negative effects on the uptake and translocation of P in plants.
Timing and Location of Spawning Based on Larval Capture and Ultrasonic Telemetry of Atlantic Sturgeon in the Saint John River, New Brunswick

AbstractThe timing and location of spawning of Atlantic Sturgeon Acipenser oxyrinchus oxyrinchus were investigated using larval sampling and ultrasonic telemetry in 2010–2014 in the lower Saint John River, New Brunswick, Canada. Larval sampling was conducted to identify potential spawning areas using anchored D-frame drift nets and towed bongo nets. Forty-four adult Atlantic Sturgeon (138–213 cm) were ultrasonically tagged and passively tracked using hydrophone receivers located throughout the river. Spawning was confirmed with the first capture of Atlantic Sturgeon larvae in the river. Four Atlantic Sturgeon yolk sac larvae (13.44–14.43 mm) were captured on July 23, 2011, and one exogenous feeding larva (22.6 mm) on July 25, 2011, at river kilometer (rkm) 106 near Burton, New Brunswick. Spawning time was estimated using larval growth models and is likely to have occurred July 6–13, 2011, above rkm 106. Eleven tagged fish returned to the river in May and June after a minimum of 2 years at large: nine male.
Interactions between molecular chaperone P20 and Cyt2Ba7 toxin in Bacillus thuringiensis

P20 or 20-kilodalton protein is a molecular chaperone protein in Bacillus thuringiensis (Bt) which can increase yields and facilitates crystal formation of various insecticidal crystal proteins (ICPs). In previous studies, a B. thuringiensis insecticidal protein gene, cyt2Ba7, was cloned, expressed but its expression level is very low in B. thuringiensis. In this study, various expression vectors were constructed by incorporating p20 in forward or reverse direction in the upstream of cyt2Ba7 and transformed into a B. thuringiensis acrystalliferous strain 4Q7. The result showed that in the presence of P20, the expression of Cyt2Ba7 was significantly increased. Especially when p20 gene was reversely inserted in the upstream of cyt2Ba7 gene, the expression of Cyt2Ba7 was increased ∼3.2 times meanwhile more and bigger crystals were observed under electron microscopy. By using purified Cyt2Ba7, P20 protein and P20-specific antiserum, immunoblotting and ligand blot analysis demonstrated a strong binding affinity between P20 and Cyt2Ba7. These results reveal that P20 can promote the crystal formation and enhance the expression of Cyt2Ba7 as a molecular chaperone, which can be a powerful tool to boost the ICPs production in B. thuringiensis and help develop more effective insect control strategies.