Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of Sensory Neurogenesis in the Trigeminal Placode: Notch Pathway Genes, Pax3 Isoforms, and Wnt Ligands

Regulation of Sensory Neurogenesis in the Trigeminal Placode: Notch Pathway Genes, Pax3 Isoforms, and Wnt Ligands Jason S. Adams Department of Physiology and Developmental Biology, BYU Doctor of Philosophy This dissertation is divided into three chapters, each discussing the study of different regulatory molecules involved in sensory neurogenesis occurring in the trigeminal placode. Chapter one is a spatiotemporal description of Notch pathway genes in chick opV placode by stage-specific expression analysis, showing expression of many Notch pathway genes and effectors in the opV placode. Notch pathway gene expression is primarily confined to the ectoderm with highest expression of these genes at the beginning stages of peak neuronal differentiation. This information preceded studies of the functional roles that Notch signaling has in the opV placode and how it may affect the transcription factor, Pax3. Chapter two is a study of the transcription factor Pax3 and its role in opV placode development and sensory neuron differentiation. Pax3 is known to activate or repress gene transcription, and its activity may be dependent on the splice variant or isoform present. We show through RT-PCR that alternative splice forms of Pax3 are present at stages of chick development corresponding to cellular competence, cellular differentiation and ingression, and cellular aggregation. We have named these splice forms, Pax3V1 and Pax3V2. Using quantitative RT-PCR we show that Pax3V2 is consistently expressed at lower levels compared to Pax3 during cellular competence and differentiation. In order to determine the function of the three splice forms, we misexpressed them in the opV placode and analyzed the effect on neurogenesis. We looked at markers for neuronal differentiation of targeted cells after in ovo electroporation of Pax3, Pax3V1, and Pax3V2, which showed a significant difference between the control and each construct, but not between the groups of constructs. To enhance the process of neurogenesis we exposed the electroporated embryos to DAPT, a Notch signaling inhibitor that enhances sensory neurogenesis. Using this method we found that misexpression of Pax3 and Pax3V1 resulted in cells failing to differentiate, while Pax3V2 misexpression more closely resembles the neuronal differentiation seen in controls. These results show that the Pax3V2 isoform allows for neuronal differentiation of opV placodal cells after misexpression, while the Pax3 isoform and the Pax3V1 isoform block neuronal differentiation. Chapter three is a study of the necessity of Wnt signaling originating from the neural tube to induce Pax3 expression in the opV placode. A double knockout of Wnt1 and Wnt3a was produced to determine the necessity of these genes in opV placode development. Pax3 expression in the opV placode at E8.5 and E9.5 was markedly reduced in the double mutants when compared to wild type mice. This study shows that Wnt1 and Wnt3a genes are necessary for normal Pax3 expression, but that other signals may contribute to its induction.
Nutrient-Gene Interactions in Cancer

Nutrients and Gene Interactions in Cancer, E. Giovannucci Candidate Mechanisms for Interactions between Nutrients and Genes, J.C. Mathers Biomarkers for Nutrient-Gene Interactions, C.E. Robertson and P. Vineis Interaction between Folate and Methylene-tetrahydrofolate Reductase (MTHFR) Gene in Cancer, S. Friso and S. -W. Choi Genetic Variability in Folate-Mediated One-Carbon Metabolism and Cancer Risk, C.M. Ulrich S-Adenosylmethionine and Methionine Adenosyltransferase Genes, J.M. Mato, M.L. Martinez-Chantar, and S.C. Lu Effects of Carotenoid Supplementation on Signal Transduction Pathways: Significance in Lung Cancer Prevention, X. -D. Wang and S. King The Actions of the Vitamin D Receptor in Health and Malignancy Polymorphic Associations and Gene Regulatory Actions, M.J. Campbell and K. W. Colston The Role of Alcohol Dehydrogenase Polymorphism in Alcohol-Associated Carcinogenesis, H.K. Seitz and F. Stickel Genetic Polymorphism of N-Acetyltransferase Genes as Risk Modifiers of Colorectal Cancer from Consumption of Well-Done Meat, L.C. R. Kidd, R.C. G. Martin, J.H. Moore, and D.W. Hein Ferritin and Serine Hydroxymethyltransferase, P.J. Stover Brassica-Gene Interactions and Cancer Risk, J.H. Fowke Conclusions and Future Perspectives, S. Friso, R. Corrocher, and S. -W. Choi Index
Chlorpyrifos in Human Breast Milk

Date of Award 12-2005 Degree Type Dissertation Degree Name Doctor of Philosophy Major Nursing Major Professor Maureen Groer Committee Members Johnnie Mozingo, Mitzi Davis, Patricia Droppleman, Donald Creasia Abstract The widespread use of pesticides by farmers, pest control operators and even the general public can pose significant risks to children's health. One particular pesticide, chlorpyrifos, was the most widely used pesticide in the United States with total use estimated at approximately 30 million pounds per year. Young children and the developing fetus are far more susceptible to the effects of pesticide exposure as a result of unusual exposure patterns and developmental immaturities. Transplacental transfer and lactational exposure are the pathways exclusive to the developing fetus and infant. Chlorpyrifos exposure is of special concern in this population because of its potential for disruption of normal brain function and cognitive development.
Incorporating asymmetric connectivity into spatial decision making for conservation

Real patterns of ecological connectivity are seldom explicitly or systematically accounted for systematic conservation planning, in part because commonly used decision support systems can only capture simplistic notions of connectivity. Conventionally, the surrogates used to represent connectivity in conservation plans have assumed the connection between two sites to be symmetric in strength. In reality, ecological linkages between sites are rarely symmetric and often strongly asymmetric. Here, we develop a novel formulation that enabled us to incorporate asymmetric connectivity into the conservation decision support system Marxan. We illustrate this approach using hypothetical examples of a river catchment and a group of reefs, and then apply it to case studies in the Snowy River catchment and Great Barrier Reef, Australia. We show that incorporating asymmetric ecological connectivity in systematic reserve design leads to solutions that more effectively capture connectivity patterns, relative to either ignoring connectivity or assuming symmetric connectivity.
Virulence of the Populations of the Whitebacked Planthopper, Sogatella furcifera Reared on Different Resistant Rice Varieties

ARC and ND colony were obtained by rearing the whitebacked planthopper (WBPH), Sogatella furcifera(Horvath), exclusively on ARC10239 (ARC, carrying resistance gene Wbph2) and N'Diang Marie (ND, carrying resistance gene WbphS) till 15 generations. Taichung Native 1 (TN1) and Rathu Heenati (RHT) served as susceptible and resistant check, respectively. The results of electronic recording revealed that duration of salivation and X-waveform of the two colonies on their corresponding hosts was short while the duration of phloem ingestion was long. The amount of honeydew excreted by ARC and ND colony did not differ on their corresponding host varieties from TN1 and was much higher than that of RHT. The number of eggs laid on their host varieties and TN1 were significantly higher than that on RHT. No distinct change was observed for these two colonies in term of percentage of developed eggs. The nymph survival rate of ND colony on its selection host was 45.0%, significantly different from that on TN1(71.4%0) and RHT(21.0%), while that of ARCcolony was 68. 3%, not significantly different from that on TN1(77.5%), but much higher than that on RHT(22.6%). The nymphal development duration of these two colonies on the corresponding hosts was not different from that on TN1, but significantly shorter than that on RHT. In brief, these two colonies had almost adapted to their corresponding host varieties based on feeding and oviposition, but the nymphal survival rate of ND colony was still low.
EFFECTS OF MERIDIC DIETS ON THE Bacillus thuringiensis CRYSTALINOUS PROTEINS (Cry) TOXICITY UPON THREE COTTON PESTS (LEPIDOPTERA: NOCTUIDAE)

1 Ingeniero Agronomo. Programa jovenes investigadores e innovadores “virginia Gutierrez de Pineda” convenio Colciencias-U.D.C.A, Calle 222 No. 54-37, Bogota D.C. harevalo@udca.edu. co 2 I.A. Ph.D. Facultad de Ingenieria Agronomica, Universidad de Ciencias Aplicadas y Ambientales U.D.C.A izenner@udca.edu. co 3 Estudiante Facultad de Ingenieria Agronomica, Universidad de Ciencias Aplicadas y Ambientales U.D.C.A lauraromeror@hotmail.com
Immune mediated and direct killing of colorectal cancer by reovirus

Colorectal cancer remains the second most prevalent cancer in the world. Novel treatment strategies are necessary, especially for the treatment of metastatic disease. Reovirus is a naturally occurring oncolytic virus which acts by both direct and immune-mediated mechanisms. Having shown promise in early clinical trials, its therapeutic potential may be limited by inactivation following systemic delivery. This study addressed whether reovirus can be shielded from neutralising antibodies by cell carriage, and whether virus-loaded blood or hepatic innate immune effector cells are activated to kill colorectal cancer cells metastatic to the liver in human systems. Reovirus induced oncolysis of SW480, SW620, LoVo and LS174T tumour cells and the mode of cell death was apoptosis. Direct tumour cell killing by neat virus was significantly reduced in the presence of neutralising serum. Reovirus was protected from neutralisation when loaded onto peripheral blood mononuclear cells and could be handed off to tumour targets for direct oncolytic killing. Moreover, NK cells within reovirus-loaded patient blood mononuclear cells were stimulated to kill tumor targets but not normal hepatocytes; similarly, NK cells within liver mononuclear cells became selectively cytotoxic towards tumour cells when activated by reovirus. This blood cell carriage has the potential to instigate both direct and innate immune-mediated therapy against human colorectal cancer which has metastasised to the liver.
Estimadores de áreas pequeñas: cálculo de proporciones poblacionales para el caso ecuatoriano

This paper evaluates the possibility of improving the estimate of the proportion of indigenous and elderly people in Ecuador. Dealing with this problem is by using a set of estimators and exploiting the spatial similarity of the districts surveyed addressed. The scope of this work covers the provinces of Ecuador and the cantons of the province of Pichincha and Guayas in 2010. The survey of Employment and Underemployment is used for direct estimation, the Census of Population and Housing 2001 as auxiliary information and CPV 2010 for contrasting results.
VAM: Hypocycloid Mechanism for Efficient Bioinspired Robotic Gaits

We present variable amplitude module orthogonal slider (VAMOS), a novel two-motor hexapedal robot that is able to walk and turn with arbitrary curvature. The VAMOS walking mechanism is based around a variable amplitude module (VAM), a compact and modular gearbox that produces reciprocating sinusoidal output of continuously variable amplitude. The inputs to the VAM are a drive motor, rotating at a constant speed, and a single control input for changing the output amplitude. Unlike other methods for amplitude modulation, the VAM does not require modulation of the main drive input and we can, therefore, operate it at peak efficiency thoughout the gait cycle. As demonstrated by VAMOS, the VAM provides a versatile building block for biomimetic robotic gaits.
NETWORK-BASED MODEL FOR STUDYING CHRONIC OBSTRUCTIVE PULMONARY DISEASE

Recently, we developed SWIM, a wizard-like software that integrates gene expression data with network topological properties for identifying a small pool of genes (i.e., switch genes) critically associated with drastic changes in cell phenotype. SWIM was amenable to detect switch genes in different organisms and cell conditions, with the potential to uncover important players in biologically relevant scenarios, including but not limited to human diseases. In this work, we present an application of SWIM to the microarray gene expression profiling of a large sample of resected lung tissues from subjects with severe chronic obstructive pulmonary disease (COPD). COPD is a progressive and obstructive lung disease characterized by an airflow obstruction that leads to a chronic inflammation and for which no cure is known. We aimed to find switch genes in the comparison between 111 severe COPD cases and 40 control smokers, freely available from GEO dataset GSE76925. We found 397 differentially expressed genes (DEGs) at a 10% FDR; and four of them – DLG2, ELMO1, NNT, SPAG16 - were at significant GWAS loci. From DEGs, SWIM built the COPD correlation network, in which two nodes are connected if the absolute value of the Pearson correlation coefficient for their expression profiles is greater than 0.5. This network encompasses 355 DEGs. Partitioning the COPD correlation network in communities, we found 3 modules, ranging in size from 408 genes in module 1, 387 genes in module 2, and 126 genes in module 3. In particular, module 2 was found enriched for B cell pathways, and included SERPINE2, CD79A, BCL2, POU2AF1, BCL11A that were previously considered as putative interactors of genes at COPD GWAS loci [3]. Then, SWIM identified 33 switch genes in COPD correlation network; all switch genes except one (E2F6) resulted up-regulated in COPD case with respect to control smokers; 29 switch genes are protein coding, including 2 transcription factors, ZNF143 and E2F6. The top differentially expressed switch gene was ZNF143 which negatively interacts in the network (i.e. highly negatively correlated) with NNT, a known COPD GWAS gene (default p-value < 10 -5 ) from the NHGRI-EBI Catalog (www.ebi.ac.uk/gwas/), and positively interacts with BCL2 (i.e. highly positively correlated).
Infección por Blastocystis sp.: revisión de la literatura

A pesar de haber sido descrito hace mas de 100 anos y ser el parasito intestinal mayormente identificado en todo el planeta, Blastocystis sp. mantiene muchas incognitas en la comunidad cientifica en lo referente a su morfologia, estructura genetica, ciclo de vida, diagnostico y tratamiento. Otro elemento clave en los estudios relacionados con este parasito es el hecho de no existir consenso en relacion con su capacidad de producir enfermedad en el humano. Diferentes estudios sugieren que el parasito se transmite por via fecal oral y existe suficiente evidencia acerca de su capacidad de transmision directa de persona a persona.
Bdellovibrio - lone hunter "cousin" of the “pack hunting” Myxobacteria

This chapter describes about the isolation of Bdellovibrio and myxobacteria from similar soil environments, and the employment of an arsenal of hydrolytic enzymes to kill and digest other bacteria to provide for their own growth and division. It concentrates on the ecology and motility systems of Bdellovibrio, followed by an overview of the hydrolytic enzymes used in prey digestion. It is clear that the nonobligately symbiotic or parasitic, predatory bacteria like Bdellovibrio and Myxobacteria have large genomes akin to those of heterotrophs; thus, determining whether transfer of predatory gene islands is responsible for apparently quite diverse bacteria adapting to fit certain predatory niches is not trivial and can ultimately be answered only by full comparative analysis of multiple predatory genomes, although there is little evidence of recent horizontal gene transfer in the Bdellovibrio bacteriovorus HD100 genome. Gliding motility genes are implicated in myxococcal motility, but these systems seem to be not present in Bdellovibrio, or they were made redundant so long ago that the genes involved are no longer recognizable as such. Homology searches found no significant homologues of Myxococcus genes involved in gliding. Bdellovibrio preys upon only gram-negative bacteria, albeit a wide range of these, as it penetrates the outer layers and enters the periplasmic space of its prey. By far the largest group of hydrolases in both bacteria is proteases; this probably reflects the importance to predatory bacteria in breaking down prey proteins for uptake and consumption by the predator.
Epidemiology and molecular characterization of Pseudomonas species on blueberry plants

Severe bacterial blight occurs periodically in British Columbia’s blueberry fields for unknown reasons. Pseudomonas syringae pv. syringae (Pss) - the putative causal organism, P. viridiflava, P. fluorescens, P. tolaasii, and P.s. pathovars aceris, tagetis, apii, and antirrhini were isolated from historically blighted fields. Three Pss isolates screened on lilac plantlets were pathogenic. A two-year field study of Pss-inoculated blueberry plants showed that Pseudomonas strains are a predominant part of blueberry stem microflora. Internal populations overwintered at low levels (10^1-10^2 CFU/g), but when wounds were present during inoculation 10^6 CFU/g survived. Maximum epiphytic populations reached 10^5 CFU/g in March-April and internal populations reached 10^6-10^7 CFU/g in Feb-May. With wounding, maximum internal populations reached 10^7-10^8 CFU/g as early as Jan-Feb. A colony blot method was developed to identify Pss from diseased tissues. Combined factors including weather, inoculum load and host phenology may contribute to the sporadic nature of bacterial blight.
Nutritive quality of Chloris gayana leaf blades in vegetative stage. Effect of leaf size reduction and ageing

The indigestible fiber that accumulates with increasing leaf biomass affects dry matter digestibility (DMD) and voluntary intake of forages. This study sought to evaluate accumulation of neutral detergent fiber (NDF), indigestible NDF (iNDF), and apparent DMD in vitro of leaf blade of two sizes (long, L and short, S) of Chloris gayana K. cv. Finecut, with the aim of determining whether the accumulation of NDF or iNDF is dependent on leaf size. Two phases of a greenhouse experiment were conducted in 2008. In the first, three seeded microswards in 1 x 3.5 x 3 m, divided in two, were submitted to two different defoliation intensities for 33 d (24/01 to 26/02) to obtain plants of the two leaf blade sizes. In phase two, herbage grown for 40 d (27/02 to 7/04) at a mean ambient temperature of 24 ± 3oC was used to harvest about 200 shoots at different life stages at intervals following 58 ± 22 degree-days of growth (DDG). Base temperature for calculating leaf age (expressed as (DDG) was 12°C. Harvested material was frozen immediately (liquid N2) and stored for subsequent analysis. After thawing, blades were grouped by three successive leaf generations (G1, G2, and G3) and six age categories: two of early growth, one recently expanded with visible ligulae, and three at prescenesence adult maturity stages. Blade and sheath length were determined in all samples, whereas additional criteria, including NDF and 24-h in vitro incubation to estimate residual iNDF(iNDFr), were used with samples of the last four age categories. The iNDF valve was calculated as iNDFr/NDF and DMD as the difference between incubated DM and iNDFr, minus a metabolic factor of 119 mg/kg. The experimental design was split plots in completely randomized blocks (n = 3); principal plots were leaf size (n = 2) and subplots were leaf generation (n = 3). Relationships betweem NDF, iNDF, and DMD and age (DDG) specific leaf area (SLA) and leaf length were analyzed by linear regression. Defoliation decreased the maximum leaf length by 32% (885 ± 17 to 606 ± 15 mm) and SLA by 20% (102 ± 7 to 83 ± 8 cm2/g). Reduced leaf length was accompanied by reductions (P < 0.0001) of 3% in NDF content and 13% in iNDF and an increase of 10% in DMD. Variability in iNDF was more closely correlated with leaf length (R2 = 0.62) than with SLA (R2 = 0.53). Both variables explained a similar proportion of DMD variability (R2 = 0.45) and were not associated with NDF content. Ageing of leaf blades exerted different effects in each treatment. In S it was unrelated to NDF, iNDF, and DMD, but in L it was associated with 8% increased iNDF and 6% decreased DMB, absent an effect on NDF content. Conclusions were: (1) a reduction in leaf length increased the nutritive value of adult leaf blades of Chloris gayana; (2) the improved quality of shorter leaf blades was unaffected by ageing; (3) variability in quality was more clearly associated with leaf length than with ageing.
Screening Yeasts from Ruminal Fluid of Dairy Heifer Fed a Different Ratio Roughage to Concentrate Diets

The objective of these studies were to identify ruminal yeast in varying ratios of roughage to concentrate in TMR diets in order to explore yeast diversity by using molecular technique with similarity of rDNA sequence. The experiment was assigned to four 98.6% of cross bred Holstein Friesian heifers with 2 levels and two replicates of roughage to concentrate ratios as: 10:90 (T1) and 50:50 (T2). The experimental period was 14 days. Rumen fluid sample was collected by stomach tube for total DNA extraction by using silica gel method, and analysis of quantity and quality of DNA by Nanovue and agarose gel electrophoresis. The divergent D1/D2 domain of 26S rDNA was amplified by primers NL-1(5'-GCA TAT CAA TAA GCG GAG GAA AAG-3') and NL4 (5'-GGT CCG TGT TTCAAG ACG G-3') by polymerase chain reaction (PCR). The nucleotide sequences of D1/D2 domain of 26S rDNA were determined using PCR products. Generated sequences were aligned with related species by using the CLUSTAL W. The result showed that an average dry matter intake of T1 was 7.00 kg/d and T2 was 6.99 kg/d. DNA concentrate from T1R1, T1R2, T2R1 and T2R2 were 106, 131.5, 84 and 182.5 ng/μL, respectively. The purity of DNA was 1.57, 1.76, 1.78 and 1.86, respectively. The divergent D1/D2 domain of 26S rDNA of treatment could be amplified for T1R1 and T2R1 but could not for T1R2 and T2R2. The sequences of D1/D2 domain of 26S rDNA were compared with nucleotide database by BLAST programs (http://www.ncbi.nlm.nih.gov/BLAST), the T2R1 yeast-strain was closest to Yarrowia lipolytica. However, yeast strain in T1R1 could not be specifically identified because D1/D2 domain of 26S rDNA seem to represent variable region with number of nucleotide sequence showing 2-3 substitution from known species. The phylogenetic tree based on the sequences of the D1/D2 domain of 26S rDNA showed that T1R1 was related to Pichia and Candida (96%) and T2R1 was related to Yarrowia lypolytica (100%). This study indicated that ruminal yeast strains could be found varying in different ratio of roughage to concentrate.