Global patterns of DNA polymorphism in noncoding regions in human populations

DNA sequence variation is currently a major source of data for studying human origins, evolution, and demographic history, and for detecting linkage association of complex diseases. In this dissertation, I investigated DNA variation in worldwide populations from two ∼10 kb autosomal regions on 22q11.2 (noncoding) and 1q24 (introns). A total of 75 variant sites were found among 128 human sequences in the 22q11.2 region, yielding an estimate of 0.088% for nucleotide diversity (π), and a total of 52 variant sites were found among 122 human sequences in the 1q24 region with an estimated π value of 0.057%. The data from these two regions and a 10 kb noncoding region on Xq13.3 all show a strong excess of low-frequency variants in comparison to that expected from an equilibrium population, indicating a relatively recent population expansion. The effective population sizes estimated from the three regions were 11,000, 12,700, and 8,600, respectively, which are close to the commonly used value of 10,000. In each of the two autosomal regions, the age of the most recent common ancestor (MRCA) was estimated to be older than 1 million years among all the sequences and ∼600,000 years among non-African sequences, providing first evidence from autosomal noncoding or intronic regions for a genetic history of humans much more ancient than the emergence of modern humans. The ancient genetic history of humans indicates no severe bottleneck during the evolution of humans in the last half million years; otherwise, much of the ancient genetic history would have been lost during a severe bottleneck. This study strongly suggests that both the “out of Africa” and the multiregional models are too simple for explaining the evolution of modern humans. A compilation of genome-wide data revealed that nucleotide diversity is highest in autosomal regions, intermediate in X-linked regions, and lowest in Y-linked regions. The data suggest the existence of background selection or selective sweep on Y-linked loci. In general, the nucleotide diversity in humans is low compared to that in chimpanzee and Drosophila populations. ^

Theoretical and experimental studies of linkage disequilibrium in human populations

Linkage disequilibrium (LD) is defined as the nonrandom association of alleles at two or more loci in a population and may be a useful tool in a diverse array of applications including disease gene mapping, elucidating the demographic history of populations, and testing hypotheses of human evolution. However, the successful application of LD-based approaches to pertinent genetic questions is hampered by a lack of understanding about the forces that mediate the genome-wide distribution of LD within and between human populations. Delineating the genomic patterns of LD is a complex task that will require interdisciplinary research that transcends traditional scientific boundaries. The research presented in this dissertation is predicated upon the need for interdisciplinary studies and both theoretical and experimental projects were pursued. In the theoretical studies, I have investigated the effect of genotyping errors and SNP identification strategies on estimates of LD. The primary importance of these two chapters is that they provide important insights and guidance for the design of future empirical LD studies. Furthermore, I analyzed the allele frequency distribution of 26,530 single nucleotide polymorphisms (SNPs) in three populations and generated the first-generation natural selection map of the human genome, which will be an important resource for explaining and understanding genomic patterns of LD. Finally, in the experimental study, I describe a novel and simple, low-cost, and high-throughput SNP genotyping method. The theoretical analyses and experimental tools developed in this dissertation will facilitate a more complete understanding of patterns of LD in human populations. ^

Population amalgamation and genetic variation: observations on artificially agglomerated tribal populations of Central and South America.

The interpretation of data on genetic variation with regard to the relative roles of different evolutionary factors that produce and maintain genetic variation depends critically on our assumptions concerning effective population size and the level of migration between neighboring populations. In humans, recent population growth and movements of specific ethnic groups across wide geographic areas mean that any theory based on assumptions of constant population size and absence of substructure is generally untenable. We examine the effects of population subdivision on the pattern of protein genetic variation in a total sample drawn from an artificial agglomerate of 12 tribal populations of Central and South America, analyzing the pooled sample as though it were a single population. Several striking findings emerge. (1) Mean heterozygosity is not sensitive to agglomeration, but the number of different alleles (allele count) is inflated, relative to neutral mutation/drift/equilibrium expectation. (2) The inflation is most serious for rare alleles, especially those which originally occurred as tribally restricted "private" polymorphisms. (3) The degree of inflation is an increasing function of both the number of populations encompassed by the sample and of the genetic divergence among them. (4) Treating an agglomerated population as though it were a panmictic unit of long standing can lead to serious biases in estimates of mutation rates, selection pressures, and effective population sizes. Current DNA studies indicate the presence of numerous genetic variants in human populations. The findings and conclusions of this paper are all fully applicable to the study of genetic variation at the DNA level as well.

Population genetics of VNTR loci and their applications in evolutionary studies

Variable number of tandem repeats (VNTR) are genetic loci at which short sequence motifs are found repeated different numbers of times among chromosomes. To explore the potential utility of VNTR loci in evolutionary studies, I have conducted a series of studies to address the following questions: (1) What are the population genetic properties of these loci? (2) What are the mutational mechanisms of repeat number change at these loci? (3) Can DNA profiles be used to measure the relatedness between a pair of individuals? (4) Can DNA fingerprint be used to measure the relatedness between populations in evolutionary studies? (5) Can microsatellite and short tandem repeat (STR) loci which mutate stepwisely be used in evolutionary analyses?^ A large number of VNTR loci typed in many populations were studied by means of statistical methods developed recently. The results of this work indicate that there is no significant departure from Hardy-Weinberg expectation (HWE) at VNTR loci in most of the human populations examined, and the departure from HWE in some VNTR loci are not solely caused by the presence of population sub-structure.^ A statistical procedure is developed to investigate the mutational mechanisms of VNTR loci by studying the allele frequency distributions of these loci. Comparisons of frequency distribution data on several hundreds VNTR loci with the predictions of two mutation models demonstrated that there are differences among VNTR loci grouped by repeat unit sizes.^ By extending the ITO method, I derived the distribution of the number of shared bands between individuals with any kinship relationship. A maximum likelihood estimation procedure is proposed to estimate the relatedness between individuals from the observed number of shared bands between them.^ It was believed that classical measures of genetic distance are not applicable to analysis of DNA fingerprints which reveal many minisatellite loci simultaneously in the genome, because the information regarding underlying alleles and loci is not available. I proposed a new measure of genetic distance based on band sharing between individuals that is applicable to DNA fingerprint data.^ To address the concern that microsatellite and STR loci may not be useful for evolutionary studies because of the convergent nature of their mutation mechanisms, by a theoretical study as well as by computer simulation, I conclude that the possible bias caused by the convergent mutations can be corrected, and a novel measure of genetic distance that makes the correction is suggested. In summary, I conclude that hypervariable VNTR loci are useful in evolutionary studies of closely related populations or species, especially in the study of human evolution and the history of geographic dispersal of Homo sapiens. (Abstract shortened by UMI.) ^

West Nile virus in the Rio Grande Valley: A seroprevalence study of juvenile dogs

This study used canine sentinel surveillance and collected a sample of adult mosquitoes to investigate the potential impact of West Nile virus (WNV) in human populations in the Rio Grande Valley along the Texas-Mexico border. Samples for this study were collected from juvenile dogs two months to one year of age in animal shelters located in the Rio Grande Valley. The sample was comprised of stray dogs in order to include animals with maximum nighttime exposures to Culex mosquitoes. Serum samples were collected following the 2007 WNV transmission season and were tested for IgG antibodies against WNV. Evidence of antibodies to WNV was found in 35.1% of the sample population consisting of 74 dogs. During this same time period, mosquitoes in Brownsville were trapped and morphologically identified to develop greater understanding of the mosquito populations in the region and to further understand other potential mosquito vectors for disease transmission. The vast majority of mosquitoes living in this area were Aedes albopictus (47.6%), Culex quinquefasciatus (23.7%), and Aedes aegypti (20.1%). This study shows that WNV and the vector responsible for WNV transmission are active in the Rio Grande Valley and pose a threat to the human and animal populations. ^

Perspectives on the public health implications of global climate change and the epidemiology of vector-borne disease

Global climate change is becoming an increasing concern among the public health community. Some researchers believe the earth is rapidly undergoing changes in temperature, sea level, population movement, and extreme weather phenomenon. With these geographic, meteorological, and social changes come increased threats to human health. One of these threats is the spread of vector-borne infectious diseases. The changes mentioned above are believed to contribute to increased arthropod survival, transmission, and habitation. These changes, in turn, lead to increased incidence among neighboring human populations. It is also argued that human action may play more of a role than climate change. This systematic review served to determine whether or not climate change poses a significant risk to human exposure and increased incidence of vector-borne disease. ^

A systematic review of the evidence for use of herbal medicine for the treatment of acute diarrhea

Background. Acute diarrhea (AD) is an important cause of morbidity and mortality among both children and adults. An ideal antidiarrheal treatment should be safe, effective, compatible with Oral Rehydration Solution, and inexpensive. Herbal medicines, if effective, should fit these criteria as well or better than standard treatment. ^ Objective. The objective of the present study was to assess the effectiveness of plant preparations in patients with AD in reports of randomized and non-randomized controlled trials. ^ Aims. The aims of the present study were to identify effective antidiarrheal herbs and to identify potential antidiarrheal herbs for future studies of efficacy through well designed clinical trials in human populations. ^ Methods. Nineteen published studies of herbal management of AD were examined to identify effective plant preparations. Ten plant preparations including Berberine (Berberis aristata), tormentil root ( Potentialla tormentilla), baohauhau (from the baobaosan plant), carob (Ceratonia siliqua), pectin (Malus domestica), wood creosote (Creosote bush), guava (Psidium guajava L.), belladonna (Atropa belladonna), white bean (Phaseolis vulgaris), and wheat (Triticum aestivum) were identified. ^ Results. Qualitative data analysis of nineteen clinical trials indicated berberine’s potentially valuable antisecretory effects against diarrhea caused by Vibrio cholerae and enterotoxigenic Escherichia coli. Tormentil root showed significant efficacy against rotavirus-induced diarrhea; carob exhibited antidiarrheal properties not only by acting to detoxify and constipate but by providing a rich source of calories; guava and belladonna are antispasmodics and have been shown to relieve the symptoms of AD. Finally, white bean and wheat yielded favorable clinical and dietary outcomes in children with diarrhea. ^ Conclusion. The present study is the first to review the evidence for use of herbal compounds for treatment of AD. Future randomized controlled trials are needed to evaluate their efficacy and safety.^

RESPIRATORY COMPENSATION MECHANISMS IN THE UPPER AND LOWER RESPIRATORY TRACTS OF AN ANIMAL MODEL AFTER SUBCHRONIC INHALATION EXPOSURE TO FORMALDEHYDE: IMPLICATIONS FOR TOXICOLOGY RISK ASSESSMENT (DEPOSITION, DOSE RECEIVED, RESPONSE)

The potential for significant human populations to experience long-term inhalation of formaldehyde and reports of symptomatology due to this exposure has led to a considerable interest in the toxicologic assessment of risk from subchronic formaldehyde exposures using animal models. Since formaldehyde inhalation depresses certain respiratory parameters in addition to its other forms of toxicity, there is a potential for the alteration of the actual dose received by the exposed individual (and the resulting toxicity) due to this respiratory effect. The respiratory responses to formaldehyde inhalation and the subsequent pattern of deposition were therefore investigated in animals that had received subchronic exposure to the compound, and the potential for changes in the formaldehyde dose received due to long-term inhalation evaluated. Male Sprague-Dawley rats were exposed to either 0, 0.5, 3, or 15 ppm formaldehyde for 6 hours/day, 5 days/week for up to 6 months. The patterns of respiratory response, deposition and the compensation mechanisms involved were then determined in a series of formaldehyde test challenges to both the upper and to the lower respiratory tracts in separate groups of subchronically exposed animals and age-specific controls (four concentration groups, two time points). In both the control and pre-exposed animals, there was a characteristic recovery of respiratory parameters initially depressed by formaldehyde inhalation to at or approaching pre-exposure levels within 10 minutes of the initiation of exposure. Also, formaldehyde deposition was found to remain very high in the upper and lower tracts after long-term exposure. Therefore, there was probably little subsequent effect on the dose received by the exposed individual that was attributable to the repeated exposures. There was a diminished initial minute volume response in test challenges of both the upper and lower tracts of animals that had received at least 16 weeks of exposure to 15 ppm, with compensatory increases in tidal volume in the upper tract and respiratory rate in the lower tract. However, this dose-related effect was probably not relevant to human risk estimation because this formaldehyde dose is in excess of that experienced by human populations. ^

Drug metabolism in human brain: high levels of cytochrome P4503A43 in brain and metabolism of anti-anxiety drug alprazolam to its active metabolite.

Cytochrome P450 (P450) is a super-family of drug metabolizing enzymes. P450 enzymes have dual function; they can metabolize drugs to pharmacologically inactive metabolites facilitating their excretion or biotransform them to pharmacologically active metabolites which may have longer half-life than the parent drug. The variable pharmacological response to psychoactive drugs typically seen in population groups is often not accountable by considering dissimilarities in hepatic metabolism. Metabolism in brain specific nuclei may play a role in pharmacological modulation of drugs acting on the CNS and help explain some of the diverse response to these drugs seen in patient population. P450 enzymes are also present in brain where drug metabolism can take place and modify therapeutic action of drugs at the site of action. We have earlier demonstrated an intrinsic difference in the biotransformation of alprazolam (ALP) in brain and liver, relatively more alpha-hydroxy alprazolam (alpha-OHALP) is formed in brain as compared to liver. In the present study we show that recombinant CYP3A43 metabolizes ALP to both alpha-OHALP and 4-hydroxy alprazolam (4-OHALP) while CYP3A4 metabolizes ALP predominantly to its inactive metabolite, 4-OHALP. The expression of CYP3A43 mRNA in human brain samples correlates with formation of relatively higher levels of alpha-OH ALP indicating that individuals who express higher levels of CYP3A43 in the brain would generate larger amounts of alpha-OHALP. Further, the expression of CYP3A43 was relatively higher in brain as compared to liver across different ethnic populations. Since CYP3A enzymes play a prominent role in the metabolism of drugs, the higher expression of CYP3A43 would generate metabolite profile of drugs differentially in human brain and thus impact the pharmacodynamics of psychoactive drugs at the site of action.

Human Trafficking Victims and Their Children: Assessing Needs, Vulnerabilities, Strengths, and Survivorship

Given the increased awareness and attention to human trafficking, including the establishment of federal laws and policies, federally funded task forces that provide law enforcement responses, and specialized victim services, it is important to assess the impact of these procedures and services on survivors/victims of international human trafficking and their immigrant children. By federal definition, certified victims of international human trafficking are eligible for all services provided to refugees in this country, including reunification with their minor children. This research is based on a qualitative study conducted in Austin and Houston, Texas with human trafficking victims/survivors. The project’s goal was to gain an understanding of the needs of human trafficking survivors after their rescue, their overall integration into American life, and the subsequent needs of their immigrant children after reunification. The project objectives examined the factors that either promote or hinder self-sufficiency, the determination of social service needs, and policy and practice recommendations to strengthen survivors, their children and their families living both locally and abroad. For this project, nine (n = 9) in-depth interviews were conducted with adult foreign-born victims of human trafficking. Researchers gathered data using a semi-structured questionnaire that queried about factors that promote or hinder victims’ services and needs. Interviews were conducted in participants’ homes using bilingual research staff and/or trained interpreters, were digitally-recorded, and subsequently transcribed. Participation in this study was completely voluntary. Specific steps were taken to ensure that the participants’ identities were protected. Open coding of data was utilized and the data were subsequently organized or grouped into properties and later developed into contextual themes around the research questions. The findings are grounded with the use of direct quotes from participants. As a result of progressive U.S. policy, many victims of human trafficking are being reunited with their minor children. Immigrant children are one of the largest and fastest growing populations in the U.S. and for a variety of reasons are vulnerable to exploitation. Research also indicates that victims of trafficking are identified by traffickers because of their perceived “vulnerabilities” or lack of opportunities (Clark, 2003). Therefore, it is important that practices and policies are developed to address the unique needs of these families with an eye toward positive outcomes for parent and child safety and well-being. Social service providers are provided a toolkit that may be utilized before and during the reunification period.

Drug metabolism in human brain: high levels of cytochrome P4503A43 in brain and metabolism of anti-anxiety drug alprazolam to its active metabolite.

Cytochrome P450 (P450) is a super-family of drug metabolizing enzymes. P450 enzymes have dual function; they can metabolize drugs to pharmacologically inactive metabolites facilitating their excretion or biotransform them to pharmacologically active metabolites which may have longer half-life than the parent drug. The variable pharmacological response to psychoactive drugs typically seen in population groups is often not accountable by considering dissimilarities in hepatic metabolism. Metabolism in brain specific nuclei may play a role in pharmacological modulation of drugs acting on the CNS and help explain some of the diverse response to these drugs seen in patient population. P450 enzymes are also present in brain where drug metabolism can take place and modify therapeutic action of drugs at the site of action. We have earlier demonstrated an intrinsic difference in the biotransformation of alprazolam (ALP) in brain and liver, relatively more alpha-hydroxy alprazolam (alpha-OHALP) is formed in brain as compared to liver. In the present study we show that recombinant CYP3A43 metabolizes ALP to both alpha-OHALP and 4-hydroxy alprazolam (4-OHALP) while CYP3A4 metabolizes ALP predominantly to its inactive metabolite, 4-OHALP. The expression of CYP3A43 mRNA in human brain samples correlates with formation of relatively higher levels of alpha-OH ALP indicating that individuals who express higher levels of CYP3A43 in the brain would generate larger amounts of alpha-OHALP. Further, the expression of CYP3A43 was relatively higher in brain as compared to liver across different ethnic populations. Since CYP3A enzymes play a prominent role in the metabolism of drugs, the higher expression of CYP3A43 would generate metabolite profile of drugs differentially in human brain and thus impact the pharmacodynamics of psychoactive drugs at the site of action.

Distribution of genes encoding MSCRAMMs and Pili in clinical and natural populations of Enterococcus faecium.

Enterococcus faecium has recently emerged as an important cause of nosocomial infections. We previously identified 15 predicted surface proteins with characteristics of MSCRAMMs and/or pili and demonstrated that their genes were frequently present in 30 clinical E. faecium isolates studied; one of these, acm, has been studied in further detail. To determine the prevalence of the other 14 genes among various E. faecium populations, we have now assessed 433 E. faecium isolates, including 264 isolates from human clinical infections, 69 isolates from stools of hospitalized patients, 70 isolates from stools of community volunteers, and 30 isolates from animal-related sources. A variable distribution of the 14 genes was detected, with their presence ranging from 51% to 98% of isolates. While 81% of clinical isolates carried 13 or 14 of the 14 genes tested, none of the community group isolates and only 13% of animal isolates carried 13 or 14 genes. The presence of these genes was most frequent in endocarditis isolates, with 11 genes present in all isolates, followed by isolates from other clinical sources. The number of genes significantly associated with clinical versus fecal or animal origin (P = 0.04 to <0.0001) varied from 10 to 13, depending on whether comparisons were made against individual clinical subgroups (endocarditis, blood, and other clinical isolates) or against all clinical isolates combined as one group. The strong association of these genes with clinical isolates raises the possibility that their preservation/acquisition has favored the adaptation of E. faecium to nosocomial environments and/or patients.

Nuclear proteins interacting with an AP-1/CRE-like promoter sequence in the human TNF$\alpha$ gene

Monocyte developmental heterogeneity is reflected at the cellular level by differential activation competence, at the molecular level by differential regulation of gene expression. LPS activates monocytes to produce tumor necrosis factor-$\alpha$ (TNF). Events occurring at the molecular level necessary for TNF regulation have not been elucidated, but depend both on activation signals and the maturation state of the cell: Peripheral blood monocytes produce TNF upon LPS stimulation, but only within the first 72 hours of culture. Expression of c-fos is associated with monocytic differentiation and activation; the fos-associated protein, c-jun, is also expressed during monocyte activation. Increased cAMP levels are associated with down regulation of macrophage function, including LPS-induced TNF transcription. Due to these associations, we studied a region of the TNF promoter which resembles the binding sites for both AP-1(fos/jun) and CRE-binding protein (or ATF) in order to identify potential molecular markers defining activation competent populations of monocytic cells.^ Nuclear protein binding studies using extracts from THP-1 monocytic cells stimulated with LPS, which stimulates, or dexamethasone (Dex) or pentoxyfilline (PTX), which inhibit TNF production, respectively, suggest that a low mobility doublet complex may be involved in regulation through this promoter region. PTX or Dex increase binding of these complexes equivalently over untreated cells; approximately two hours after LPS induction, the upper complex is undetectable. The upper complex is composed of ATF2 (CRE-BP1); the lower is a heterodimer of jun/ATF2. LPS induces c-jun and thus may enhance formation of jun-ATF2 complexes. The simultaneous presence of both complexes may reduce the amount of TNF transcription through competitive binding, while a loss of the upper (ATF2) and/or gain of the lower (jun-ATF2) allow increased transcription. AP-1 elements generally transduce signals involving PKC; the CRE mediates a cAMP response, involving PKA. Thus, this element has the potential of receiving signals through divergent signalling pathways. Our findings also suggest that cAMP-induced inhibition of macrophage functions may occur via down regulation of activation-associated genes through competitive binding of particular cAMP-responsive nuclear protein complexes. ^

Population and molecular evolution studies on the Melanocortin 1 receptor locus implicate its role in human pigmentation variation

Human pigmentation is a complex trait with the observed variation caused by the varied production of eumelanin (brown/black melanins) and phaeomelanin (red/yellow melanins) by the melanocytes. The melanocortin 1 receptor (MC1R), a G protein-coupled receptor expressed in the melanocytes, is a regulator eu- and phaeomelanin synthesis, and MC1R mutations causing skin and coat color changes are known in many mammals. To understand the role of MC1R in human pigmentation variation, I have sequenced the MC1R gene in 121 individuals sampled from world populations. In addition, I have sequenced the MC1R gene in common and pygmy chimpanzees, gorilla, orangutan, and baboon to study the evolution of MC1R and to infer the ancestral human MC1R sequence. The ancestral MC1R sequence is observed in all 25 African individuals studied, but at lower frequencies in the other populations examined, especially in East and Southeast Asians. The Arg163Gln variant is absent in the Africans studied, almost absent in Europeans, and at a low frequency in Indians, but is at an exceptionally high frequency (70%) in East and Southeast Asians. To further evaluate the role of MC1R variants in human pigmentation variation, I have combined these molecular evolution and population studies with functional assays on MC1R variants and primate MC1Rs. ^

THE LONG-TERM GROWTH OF NORMAL HUMAN B CELLS

The feasibility of establishment of continuously proliferating growth factor-dependent human B lymphocytes was investigated. Normal B lymphocytes prepared from peripheral venous blood were stimulated with a variety of known polyclonal B cell activators, in the continuous presence of various cytokine preparations. Continuously proliferating growth factor-dependent B cell populations were obtained from cultures activated with either insoluble anti-IgM ((mu)-chain specific), soluble anti-IgM, heat-killed Staphylococcus aureus Cowen I (SAC), or dextran sulphate (DxS), in the continuous presence of exogenously added growth factor preparations containing either IL-1, IL-2 and BCGF, or BCGF alone. Although growth factor-dependent B cell lines were obtained via all three methods of activation, the correlation of mode of activation and growth factor preparation proved to be critical. B cell lines could not be established with anti-(mu) activation in the presence of only BCGF; however, B cell lines were successfully obtained with SAC or DxS activation from those cultures continuously replenished with only BCGF. These cultured B lymphocyte populations were routinely maintained in logarithmic-phase growth in the presence of exogenously added growth factor, and exhibited a population doubling time of approximately 36 hours. They were shown to specifically absorb BCGF, suggesting the presence of membrane receptors for it. Also, these cultured B cells have been utilized for the development of a microassay for the assessment of a M(,r) 12,000-14,000 B cell growth factor activity that is accurate, sensitive, and precise. The pronounced sensitivity of this bioassay beyond that of the conventional peripheral blood B cell assay has aided in the purification to homogeneity of natural product extracellular BCGF (EC-BCGF), and in the determination of the nucleotide sequence for a gene coding for a protein exhibiting BCGF activity. Additionally, these B cell lines specifically absorb, and proliferate in the presence of, an affinity-purified M(,r) 60,000 trypsin-sensitive intracellular protein derived from freshly isolated human T lymphocytes, providing evidence for a putative intracellular precursor of EC-BCGF, or a novel high molecular weight BCGF species. ^