microRNA156-targeted SPL/ SBP box transcription factors regulate tomato ovary and fruit development

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Computer intensive methods for controlling bias in a generalized species diversity index

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Reducing the Public Health Impact of Bovine Tuberculosis by Controlling Disease Transmission Between Cattle and White-Tailed Deer in Northwestern Minnesota

Bovine tuberculosis, caused by infection with Mycobacterium bovis, is a re-emerging zoonotic disease. It has staged a comeback by establishing infections in wildlife and cattle, creating the potential for human disease in locations where it was thought to be under control. In northwestern Minnesota, infected cattle and white-tailed deer were first discovered in 2005. A major bovine tuberculosis eradication campaign is underway in the state, with multiple efforts employed to control M. bovis infection in both cattle and deer populations. In order to effectively eradicate bovine tuberculosis in Minnesota, there is a need for better understanding of the factors that increase the risk of deer and cattle interacting in a way that facilitates tuberculosis transmission. By reducing the risk of disease transmission within the animal populations, we will also reduce the risk that bovine tuberculosis will again become a common disease in human populations. The purpose of this study is to characterize the risk of interactions between cattle and white-tailed deer in northern Minnesota in order to prevent M. bovis transmission. A survey originally developed to assess deer-cattle interactions in Michigan was modified for use in Minnesota, introducing a scoring method to evaluate the areas of highest priority at risk of potential deer-cattle interaction. The resulting semi-quantitative deer-cattle interaction risk assessment was used at 53 cattle herds located in the region adjacent to the bovine tuberculosis “Core Area”. Two evaluators each scored the farm separately, and then created a management plan for the farm that prioritized the areas of greatest risk for deer-cattle interactions. Herds located within the “Management Zone” were evaluated by Minnesota Board of Animal Health staff, and results from these surveys were used as a point of comparison.

Hepatocyte nuclear factors 1α/4α and forkhead box A2 regulate the solute carrier 2A2 (Slc2a2) gene expression in the liver and kidney of diabetic rats

AIMS: Solute carrier 2a2 (Slc2a2) gene codifies the glucose transporter GLUT2, a key protein for glucose flux in hepatocytes and renal epithelial cells of proximal tubule. In diabetes mellitus, hepatic and tubular glucose output has been related to Slc2a2/GLUT2 overexpression; and controlling the expression of this gene may be an important adjuvant way to improve glycemic homeostasis. Thus, the present study investigated transcriptional mechanisms involved in the diabetes-induced overexpression of the Slc2a2 gene. MAIN METHODS: Hepatocyte nuclear factors 1α and 4α (HNF-1α and HNF-4α), forkhead box A2 (FOXA2), sterol regulatory element binding protein-1c (SREBP-1c) and the CCAAT-enhancer-binding protein (C/EBPβ) mRNA expression (RT-PCR) and binding activity into the Slc2a2 promoter (electrophoretic mobility assay) were analyzed in the liver and kidney of diabetic and 6-day insulin-treated diabetic rats. KEY FINDINGS: Slc2a2/GLUT2 expression increased by more than 50% (P<0.001) in the liver and kidney of diabetic rats, and 6-day insulin treatment restores these values to those observed in non-diabetic animals. Similarly, the mRNA expression and the binding activity of HNF-1α, HNF-4α and FOXA2 increased by 50 to 100% (P<0.05 to P<0.001), also returning to values of non-diabetic rats after insulin treatment. Neither the Srebf1 and Cebpb mRNA expression, nor the SREBP-1c and C/EBP-β binding activity was altered in diabetic rats. SIGNIFICANCE: HNF-1α, HNF-4α and FOXA2 transcriptional factors are involved in diabetes-induced overexpression of Slc2a2 gene in the liver and kidney. These data point out that these transcriptional factors are important targets to control GLUT2 expression in these tissues, which can contribute to glycemic homeostasis in diabetes.

Modulation of hypoxia-inducible factors as a therapeutic target for multiple myeloma

Hypoxia-inducible factor-1 alpha (HIF-1α) plays a critical role in survival and is associated with poor prognosis in solid tumors. The role of HIF-1α in multiple myeloma is not completely known. In the present study, we explored the effect of EZN2968, an locked nucleic acid antisense oligonucleotide against HIF-1α, as a molecular target in MM. A panel of MM cell lines and primary samples from MM patients were cultured in vitro in the presence of EZN2968 . Under normoxia culture condition, HIF-1α mRNA and protein expression was detectable in all MM cell lines and in CD138+ cells from newly diagnosed MM patients samples. Significant up-regulation of HIF-1α protein expression was observed after incubation with IL6 or IGF-I, confirming that HIF-1α can be further induced by biological stimuli. EZN2968 efficiently induces a selective and stable down-modulation of HIF-1α and decreased the secretion of VEGF released by MM cell. Treatment with EZN2968 gave rise to a progressive accumulation of cells in the S and subG0 phase. The analysis of p21, a cyclin-dependent kinase inhibitors controlling cell cycle check point, shows upregulation of protein levels. These results suggest that HIF-1α inhibition is sufficient for cell cycle arrest in normoxia, and for inducing an apoptotic pathways.. In the presence of bone marrow microenvironment, HIF-1α inhibition blocks MAPK kinase pathway and secretion of pro-surviaval cytokines ( IL6,VEGF,IL8) In this study we provide evidence that HIF-1α, even in the absence of hypoxia signal, is expressed in MM plasma cells and further inducible by bone marrow milieu stimuli; moreover its inhibition is sufficient to induce a permanent cell cycle arrest. Our data support the hypothesis that HIF-1α inhibition may suppress tumor growth by preventing proliferation of plasma cells through p21 activation and blocking pro-survival stimuli from bone marrow microenvironment.

Factors influencing subjective quality of life in patients with schizophrenia and other mental disorders: a pooled analysis

Subjective quality of life (SQOL) is an important outcome in the treatment of patients with schizophrenia. However, there is only limited evidence on factors influencing SQOL, and little is known about whether the same factors influence SQOL in patients with schizophrenia and other mental disorders. This study aimed to identify the factors associated with SQOL and test whether these factors are equally important in schizophrenia and other disorders. For this we used a pooled data set obtained from 16 studies that had used either the Lancashire Quality of Life Profile or the Manchester Short Assessment of Quality of Life for assessing SQOL. The sample comprised 3936 patients with schizophrenia, mood disorders, and neurotic disorders. After controlling for confounding factors, within-subject clustering, and heterogeneity of findings across studies in linear mixed models, patients with schizophrenia had more favourable SQOL scores than those with mood and neurotic disorders. In all diagnostic groups, older patients, those in employment, and those with lower symptom scores had higher SQOL scores. Whilst the strength of the association between age and SQOL did not differ across diagnostic groups, symptom levels were more strongly associated with SQOL in neurotic than in mood disorders and schizophrenia. The association of employment and SQOL was stronger in mood and neurotic disorders than in schizophrenia. The findings may inform the use and interpretation of SQOL data for patients with schizophrenia.

IDENTIFICATION OF GENES CONTROLLING BIOLOGICAL PROCESSES AND PATHWAYS THROUGH STATISTICAL ANALYSIS AND NETWORK RECONSTRUCTION

The developmental processes and functions of an organism are controlled by the genes and the proteins that are derived from these genes. The identification of key genes and the reconstruction of gene networks can provide a model to help us understand the regulatory mechanisms for the initiation and progression of biological processes or functional abnormalities (e.g. diseases) in living organisms. In this dissertation, I have developed statistical methods to identify the genes and transcription factors (TFs) involved in biological processes, constructed their regulatory networks, and also evaluated some existing association methods to find robust methods for coexpression analyses. Two kinds of data sets were used for this work: genotype data and gene expression microarray data. On the basis of these data sets, this dissertation has two major parts, together forming six chapters. The first part deals with developing association methods for rare variants using genotype data (chapter 4 and 5). The second part deals with developing and/or evaluating statistical methods to identify genes and TFs involved in biological processes, and construction of their regulatory networks using gene expression data (chapter 2, 3, and 6). For the first part, I have developed two methods to find the groupwise association of rare variants with given diseases or traits. The first method is based on kernel machine learning and can be applied to both quantitative as well as qualitative traits. Simulation results showed that the proposed method has improved power over the existing weighted sum method (WS) in most settings. The second method uses multiple phenotypes to select a few top significant genes. It then finds the association of each gene with each phenotype while controlling the population stratification by adjusting the data for ancestry using principal components. This method was applied to GAW 17 data and was able to find several disease risk genes. For the second part, I have worked on three problems. First problem involved evaluation of eight gene association methods. A very comprehensive comparison of these methods with further analysis clearly demonstrates the distinct and common performance of these eight gene association methods. For the second problem, an algorithm named the bottom-up graphical Gaussian model was developed to identify the TFs that regulate pathway genes and reconstruct their hierarchical regulatory networks. This algorithm has produced very significant results and it is the first report to produce such hierarchical networks for these pathways. The third problem dealt with developing another algorithm called the top-down graphical Gaussian model that identifies the network governed by a specific TF. The network produced by the algorithm is proven to be of very high accuracy.

Upper ocean vertical supply: A neglected primary factor controlling the distribution of neodymium concentrations of open ocean surface waters?

Neodymium (Nd) isotopes are an important geochemical tool to trace the present and past water mass mixing as well as continental inputs. The distribution of Nd concentrations in open ocean surface waters (0�100 m) is generally assumed to be controlled by lateral mixing of Nd from coastal surface currents and by removal through reversible particle scavenging. However, using 228Ra activity as an indicator of coastal water mass influence, surface water Nd concentration data available on key oceanic transects as a whole do not support the above scenario. From a global compilation of available data, we find that more stratified regions are generally associated with low surface Nd concentrations. This implies that upper ocean vertical supply may be an as yet neglected primary factor in determining the basin-scale variations of surface water Nd concentrations. Similar to the mechanism of nutrients supply, it is likely that stratification inhibits vertical supply of Nd from the subsurface thermocline waters and thus the magnitude of Nd flux to the surface layer. Consistently, the estimated required input flux of Nd to the surface layer to maintain the observed concentrations could be nearly two orders of magnitudes larger than riverine/dust flux, and also larger than the model-based estimation on shelf-derived coastal flux. In addition, preliminary results from modeling experiments reveal that the input from shallow boundary sources, riverine input, and release from dust are actually not the primary factors controlling Nd concentrations most notably in the Pacific and Southern Ocean surface waters.

Genetic networks controlling retinal injury.

PURPOSE: The present study defines genomic loci underlying coordinate changes in gene expression following retinal injury. METHODS: A group of acute phase genes expressed in diverse nervous system tissues was defined by combining microarray results from injury studies from rat retina, brain, and spinal cord. Genomic loci regulating the brain expression of acute phase genes were identified using a panel of BXD recombinant inbred (RI) mouse strains. Candidate upstream regulators within a locus were defined using single nucleotide polymorphism databases and promoter motif databases. RESULTS: The acute phase response of rat retina, brain, and spinal cord was dominated by transcription factors. Three genomic loci control transcript expression of acute phase genes in brains of BXD RI mouse strains. One locus was identified on chromosome 12 and was highly correlated with the expression of classic acute phase genes. Within the locus we identified the inhibitor of DNA binding 2 (Id2) as a candidate upstream regulator. Id2 was upregulated as an acute phase transcript in injury models of rat retina, brain, and spinal cord. CONCLUSIONS: We defined a group of transcriptional changes associated with the retinal acute injury response. Using genetic linkage analysis of natural transcript variation, we identified regulatory loci and candidate regulators that control transcript levels of acute phase genes.

Genetic analysis of factors regulating mesenchymal cell fates

Formation of cartilage and bone involves sequential processes in which undifferentiated mesenchyme aggregates into primordial condensations which subsequently grow and differentiate, resulting in morphogenesis of the adult skeleton. While much has been learned about the structural molecules which comprise cartilage and bone, little is known about the nuclear factors which regulate chondrogenesis and osteogenesis. MHox is a homeobox-containing gene which is expressed in the mesenchyme of facial, limb, and vertebral skeletal precursors during mouse embryogenesis. MHox expression has been shown to require epithelial-derived signals, suggesting that MHox may regulate the epithelial-mesenchymal interactions required for skeletal organogenesis. To determine the functions of MHox, we generated a loss-of-function mutation in the MHox gene. Mice homozygous for a mutant MHox allele exhibit defects of skeletogenesis, involving the loss or malformation of craniofacial, limb and vertebral skeletal structures. The affected skeletal elements are derived from the cranial neural crest, as well as somitic and lateral mesoderm. Analysis of the mutant phenotype during ontogeny demonstrated a defect in the formation or growth of chondrogenic and osteogenic precursors. These findings provide evidence that MHox regulates the formation of preskeletal condensations from undifferentiated mesenchyme. In addition, generation of mice doubly mutant for the MHox and S8 homeobox genes reveal that these two genes interact to control formation of the limb and craniofacial skeleton. Mice carrying mutant alleles for S8 and MHox exhibit an exaggeration of the craniofacial and limb phenotypes observed in the MHox mutant mouse. Thus, MHox and S8 are components of a combinatorial genetic code controlling generation of the skeleton of the skull and limbs. ^

A study of the relationship between physical activity and cardiovascular fitness and coronary heart disease risk factors in female adolescents

The association of measures of physical activity with coronary heart disease (CHD) risk factors in children, especially those for atherosclerosis, is unknown. The purpose of this study was to determine the association of physical activity and cardiovascular fitness with blood lipids and lipoproteins in pre-adolescent and adolescent girls.^ The study population was comprised of 131 girls aged 9 to 16 years who participated in the Children's Nutrition Research Center's Adolescent Study. The dependent variables, blood lipids and lipoproteins, were measured by standard techniques. The independent variables were physical activity measured as the difference between total energy expenditure (TEE) and basal metabolic rate (BMR), and cardiovascular fitness, VO$\rm\sb{2max}$(ml/min/kg). TEE was measured by the doubly-labeled water (DLW) method, and BMR by whole-room calorimetry. Cardiovascular fitness, VO$\rm\sb{2max}$(ml/min/kg), was measured on a motorized treadmill. The potential confounding variables were sexual maturation (Tanner breast stage), ethnic group, body fat percent, and dietary variables. A systematic strategy for data analysis was used to isolate the effects of physical activity and cardiovascular fitness on blood lipids, beginning with assessment of confounding and interaction. Next, from regression models predicting each blood lipid and controlling for covariables, hypotheses were evaluated by the direction and value of the coefficients for physical activity and cardiovascular fitness.^ The main result was that cardiovascular fitness appeared to be more strongly associated with blood lipids than physical activity. An interaction between cardiovascular fitness and sexual maturation indicated that the effect of cardiovascular fitness on most blood lipids was dependent on the stage of sexual maturation.^ A difference of 760 kcal/d physical activity (which represents the difference between the 25th and 75th percentile of physical activity) was associated with negligible differences in blood lipids. In contrast, a difference in 10 ml/min/kg of VO$\rm\sb{2max}$ or cardiovascular fitness (which represents the difference between the 25th and 75th percentile in cardiovascular fitness) in the early stages of sexual maturation was associated with an average positive difference of 15 mg/100 ml ApoA-1 and 10 mg/100 ml HDL-C. ^

Progression of cardiovascular risk factors in black Africans: 3 year follow up of the SABPA cohort study

Recent work identified a high prevalence of modifiable risk factors for cardiovascular disease (CVD) among urban black South Africans. The aim was to track the progression of CVD risk factors in a multi-ethnic sample of South Africans. Participants were 173 black (aged 47.5 ± 7.8 yrs) and 186 white teachers (aged 49.6 ± 9.9 yrs) that were examined at baseline and 3 years follow-up. Blacks demonstrated a substantially higher prevalence of composite CVD burden (defined as history of physician diagnosed heart disease, use of anti-hypertensives, anti-diabetic, or statin medications at either time point) compared to whites (49.1 vs. 32.0%, p = 0.012) respectively. After controlling for baseline, the black participants demonstrated greater increases in 24 h systolic and diastolic blood pressure, total cholesterol, fasting glucose, fibrinogen, D-dimer, and waist circumference in comparison with whites. In summary, an adverse progression of CVD risk factors was observed in the whole sample, although to a larger degree in black participants. Aggressive treatment strategies for controlling risk factors in black Africans are needed to reduce the increasing burden of CVD in South Africa.

Case control study identifying the maternal risk factors for congenital syphilis in Texas: 1998--2001

Background. Congenital syphilis (CS) is the oldest recognized congenital infection in the world. CS infection can affect multiple organs and can even cause neonatal death. CS is largely preventable when maternal syphilis is treated in an adequate and timely manner. During the decade of the nineties, rates of CS in Texas have often exceeded the overall US rate. Few studies, with adequate sample sizes, have been conducted to determine the risk factors associated with CS while controlling for factors associated with adult (maternal) syphilis infection. Objective. To determine the current maternal risk factors for CS infection in Texas from 1998–2001. Methods. A total of 1083 women with positive serological tests for syphilis during pregnancy or at delivery were reported to, and assessed by, health department surveillance staff. Mothers delivering infants in Texas between January 1, 1998 and June 30, 2001 comprised the study population. Mothers of infants diagnosed with confirmed or presumptive CS (N = 291) were compared to mothers of infants diagnosed as non-cases (N = 792) to determine the risk factors for vertical transmission (while controlling for risk factors of horizontal transmission). Logistic regression analyses were conducted to determine the associated odds between selected maternal variables and the outcome of CS. Results. Among 291 case infants, 5 (1.7%), 12 (4.1%), 274 (94.2%) were classified as confirmed cases, syphilitic stillbirths, and presumptive cases, respectively. Lack of maternal syphilis treatment was the strongest predictor of CS: odds ratio (OR) = 199.57 (95% CI 83.45–477.25) compared to those receiving treatment before pregnancy, while women treated during their pregnancies were also at increased risk (OR = 6.67, 95% CI 4.01–11.08). Women receiving no prenatal care were more likely (OR = 2.77, 95% CI 1.60–4.79) to have CS infants than those receiving prenatal care. Single women had higher odds (OR = 1.90, 95% CI 1.10–3.26) than ever-married women. African-Americans (OR 0.91, 95% CI 0.37–2.23) and Hispanics (OR = 1.66, 95% CI 0.68–4.05) may be more likely to have a CS infant than non-Hispanic Whites. Conclusions. The burden of CS in Texas can be alleviated through the provision of quality health care services, particularly prenatal care and treatment for sexually transmitted diseases. ^

Factors associated with home health care costs

Characteristics of Medicare-certified home health agencies in Texas and the contributions of selected agency characteristics on home health care costs were examined. Cost models were developed and estimated for both nursing and total visit costs using multiple regression procedures. The models included home health agency size, profit status, control, hospital-based affiliation, contract-cost ratio, service provision, competition, urban-rural input-price differences, and selected measures of patient case-mix. The study population comprised 314 home health agencies in Texas that had been certified at least one year on July, 1, 1986. Data for the analysis were obtained from Medicare Cost Reports for fiscal year ending between July 1, 1985 to June 30, 1986.^ Home health agency size, as measured by the logs of nursing and total visits, has a statistically significant negative linear relationship with nursing visit and total visit costs. Nursing and total visit costs decrease at a declining rate as size increases. The size-cost relationship is not altered when controlling for any other agency characteristic. The number of visits per patient per year, a measure of patient case-mix, is also negatively related to costs, suggesting that costs decline with care of chronic patients. Hospital-based affiliation and urban location are positively associated with costs. Together, the four characteristics explain 19 percent of the variance in nursing visit costs and 24 percent of the variance in total visit costs.^ Profit status and control, although correlated with other agency characteristics, exhibit no observable effect on costs. Although no relationship was found between costs and competition, contract cost ratio, or the provision on non-reimburseable services, no conclusions can be made due to problems with measurement of these variables. ^

Blood pressure and dietary factors in Mexican-Americans of Starr County, Texas

This study examined the cross-sectional associations between blood pressure, hypertension and dietary factors among 580 Mexican-American adults residing in Starr County, Texas. The data were collected as part of Gallbladder Disease Study between April, 1985 and December, 1986.^ Dietary intake was assessed for the month previous to the interview by means of a 38 food item quantified frequency questionnaire representing foods and mixed dishes commonly consumed in the community. From the dietary information intake of calcium, cholesterol, total kilocalories, and percent of kilocalories contributed by total fat, saturated fat, monounsaturated fatty acids, polyunsaturated fatty acids, protein, carbohydrates were calculated. The effect of other factors associated with blood pressure, such as age, body mass index, body fat distribution, smoking, and drinking were controlled.^ Age was the most important predictor of both systolic and diastolic blood pressure and hypertension. For both males and females, systolic and diastolic blood pressure levels were consistently positively associated with body mass index but were not associated with waist hip ratio. However, a strong positive relationship between hypertension and waist hip ratio but not body mass index was observed.^ After controlling for age and body mass index it was noted that for males there were no significant associations between the dietary variables and systolic blood pressure. For diastolic blood pressure there were significant associations with percent fat, percent monounsaturated fatty acids, percent protein and percent carbohydrates.^ For females, there were significant associations between systolic blood pressure and percent protein, percent carbohydrates and cholesterol. There were no significant associations between dietary variables and diastolic blood pressure.^ After controlling for age and waist hip ratio significant associations between hypertension and percent fat, percent saturated fat, percent monounsaturated fatty acids, percent carbohydrate and percent protein were observed in males. Significant associations between hypertension and percent polyunsaturated fatty acids and percent protein were noted in females. ^