TB research at UT-Houston--a review of cord factor: new approaches to drugs, vaccines and the pathogenesis of tuberculosis.

Tuberculosis remains a major threat as drug resistance continues to increase. Pulmonary tuberculosis in adults is responsible for 80% of clinical cases and nearly 100% of transmission of infection. Unfortunately, since we have no animal models of adult type pulmonary tuberculosis, the most important type of disease remains largely out of reach of modern science and many fundamental questions remain unanswered. This paper reviews research dating back to the 1950's providing compelling evidence that cord factor (trehalose 6,6 dimycolate [TDM]) is essential for understanding tuberculosis. However, the original papers by Bloch and Noll were too far ahead of their time to have immediate impact. We can now recognize that the physical and biologic properties of cord factor are unprecedented in science, especially its ability to switch between two sets of biologic activities with changes in conformation. While TDM remains on organisms, it protects them from killing within macrophages, reduces antibiotic effectiveness and inhibits the stimulation of protective immune responses. If it comes off organisms and associates with lipid, TDM becomes a driver of tissue damage and necrosis. Studies emanating from cord factor research have produced (1) a rationale for improving vaccines, (2) an approach to new drugs that overcome natural resistance to antibiotics, (3) models of caseating granulomas that reproduce multiple manifestations of human tuberculosis. (4) evidence that TDM is a key T cell antigen in destructive lesions of tuberculosis, and (5) a new understanding of the pathology and pathogenesis of postprimary tuberculosis that can guide more informative studies of long standing mysteries of tuberculosis.

Complete Genome Sequence of Treponema paraluiscuniculi, Strain Cuniculi A: The Loss of Infectivity to Humans Is Associated with Genome Decay.

Treponema paraluiscuniculi is the causative agent of rabbit venereal spirochetosis. It is not infectious to humans, although its genome structure is very closely related to other pathogenic Treponema species including Treponema pallidum subspecies pallidum, the etiological agent of syphilis. In this study, the genome sequence of Treponema paraluiscuniculi, strain Cuniculi A, was determined by a combination of several high-throughput sequencing strategies. Whereas the overall size (1,133,390 bp), arrangement, and gene content of the Cuniculi A genome closely resembled those of the T. pallidum genome, the T. paraluiscuniculi genome contained a markedly higher number of pseudogenes and gene fragments (51). In addition to pseudogenes, 33 divergent genes were also found in the T. paraluiscuniculi genome. A set of 32 (out of 84) affected genes encoded proteins of known or predicted function in the Nichols genome. These proteins included virulence factors, gene regulators and components of DNA repair and recombination. The majority (52 or 61.9%) of the Cuniculi A pseudogenes and divergent genes were of unknown function. Our results indicate that T. paraluiscuniculi has evolved from a T. pallidum-like ancestor and adapted to a specialized host-associated niche (rabbits) during loss of infectivity to humans. The genes that are inactivated or altered in T. paraluiscuniculi are candidates for virulence factors important in the infectivity and pathogenesis of T. pallidum subspecies.

Modern approaches to pediatric brain injury therapy.

Each year, pediatric traumatic brain injury (TBI) accounts for 435,000 emergency department visits, 37,000 hospital admissions, and approximately 2,500 deaths in the United States. TBI results in immediate injury from direct mechanical force and shear. Secondary injury results from the release of biochemical or inflammatory factors that alter the loco-regional milieu in the acute, subacute, and delayed intervals after a mechanical insult. Preliminary preclinical and clinical research is underway to evaluate the benefit from progenitor cell therapeutics, hypertonic saline infusion, and controlled hypothermia. However, all phase III clinical trials investigating pharmacologic monotherapy for TBI have shown no benefit. A recent National Institutes of Health consensus statement recommends research into multimodality treatments for TBI. This article will review the complex pathophysiology of TBI as well as the possible therapeutic mechanisms of progenitor cell transplantation, hypertonic saline infusion, and controlled hypothermia for possible utilization in multimodality clinical trials.

Molecular genetic approaches to defining lipid function.

Lipids fulfill multiple and diverse functions in cells. Establishing the molecular basis for these functions has been challenging due to the lack of catalytic activity of lipids and the pleiotropic effects of mutations that affect lipid composition. By combining molecular genetic manipulation of membrane lipid composition with biochemical characterization of the resulting phenotypes, the molecular details of novel lipid functions have been established. This review summarizes the results of such a combined approach to defining lipid function in bacteria.

Partnering with Parents: Promising Approaches to Improve Reunification Outcomes for Children in Foster Care

Family reunification is one of the central tenents of the child welfare system, yet research supporting effective practices to promote safe reunifications is limited. As a departure from previous initiatives, the Parent Partner (PP) program enlists as staff mothers and fathers who have experienced child removal, services, and reunification. This study examines outcomes for children served by the PP program. The experimental group includes 236 children whose parents were served by a Parent Partner and a matched comparison group of 55 children whose parents were served by the public child welfare agency in 2004, before the Parent Partner program was established. Cases were examined 12 months following case opening to determine reunification status. Results from the outcome study indicate that reunification may be more likely for children whose parents were served by Parent Partners. Although there are limitations to the data, findings from this study suggest that the Parent Partner model may hold promise as a child welfare intervention designed to support reunification.

Commentary on "Partnering with Parents: Promising Approaches to Improve Reunification Outcomes for Children in Foster Care"

In “Partnering with Parents: Promising Approaches to Improve Reunification Outcomes for Children in Foster Care,” authors J. D. Berrick, Edward Cohen and Elizabeth Anthony describe promising outcomes from a quasi-experimental study of reunification outcomes associated with the Parent Partner program in one western county

Estimation of male-to-female ratios of mutation rate in primates and rodents

Haldane (1935) developed a method for estimating the male-to-female ratio of mutation rate ($\alpha$) by using sex-linked recessive genetic disease, but in six different studies using hemophilia A data the estimates of $\alpha$ varied from 1.2 to 29.3. Direct genomic sequencing is a better approach, but it is laborious and not readily applicable to non-human organisms. To study the sex ratios of mutation rate in various mammals, I used an indirect method proposed by Miyata et al. (1987). This method takes advantage of the fact that different chromosomes segregate differently between males and females, and uses the ratios of mutation rate in sequences on different chromosomes to estimate the male-to-female ratio of mutation rate. I sequenced the last intron of ZFX and ZFY genes in 6 species of primates and 2 species of rodents; I also sequenced the partial genomic sequence of the Ube1x and Ube1y genes of mice and rats. The purposes of my study in addition to estimation of $\alpha$'s in different mammalian species, are to test the hypothesis that most mutations are replication dependent and to examine the generation-time effect on $\alpha$. The $\alpha$ value estimated from the ZFX and ZFY introns of the six primate specise is ${\sim}$6. This estimate is the same as an earlier estimate using only 4 species of primates, but the 95% confidence interval has been reduced from (2, 84) to (2, 33). The estimate of $\alpha$ in the rodents obtained from Zfx and Zfy introns is ${\sim}$1.9, and that deriving from Ube1x and Ube1y introns is ${\sim}$2. Both estimates have a 95% confidence interval from 1 to 3. These two estimates are very close to each other, but are only one-third of that of the primates, suggesting a generation-time effect on $\alpha$. An $\alpha$ of 6 in primates and 2 in rodents are close to the estimates of the male-to-female ratio of the number of germ-cell divisions per generation in humans and mice, which are 6 and 2, respectively, assuming the generation time in humans is 20 years and that in mice is 5 months. These findings suggest that errors during germ-cell DNA replication are the primary source of mutation and that $\alpha$ decreases with decreasing length of generation time. ^

Use of a hypomorphic allele of myogenin to analyze Myogenin-dependent processes in mouse development

Myogenin is a muscle-specific transcription factor essential for skeletal muscle differentiation. A severe reduction in the number of fused myotubes is seen in myogenin-null mice, and the expression of genes characteristic of differentiated skeletal muscle is reduced. Additionally, sternebrae defects are seen in myogenin-null mice, a secondary defect in the sternal cartilage precursors. Very little is known about the quantitative requirement for myogenin in muscle differentiation and thoracic skeletal development in vivo. In this thesis I describe experiments utilizing a mouse line harboring a hypomorphic allele of myogenin, generated by gene targeting techniques in embryonic stem cells. The nature of the hypomorphism was due to lowered levels of myogenin from this allele. In embryos homozygous for the hypomorphic allele, normal sternum formation and extensive muscle differentiation was observed. However, muscle hypoplasia and reduced muscle-specific gene expression were apparent in these embryos, and the mice were not viable after birth. These results suggest skeletal muscle differentiation is highly sensitive to the absolute amounts of myogenin, and reveal distinct threshold requirements for myogenin in skeletal muscle differentiation, sternum formation, and viability in vivo. The hypomorphic allele was utilized as a genetically sensitized background to identify other components of myogenin-mediated processes. Using a candidate gene approach I crossed null mutations in MEF2C and MRF4 into the hypomorphic background and examined whether these mutations affected muscle differentiation and skeleton formation in the myogenin hypomorph. Although MEF2C mutation did not affect any phenotypes seen in the hypomorphic background, MRF4 was observed to be an essential component of myogenin-mediated processes of thoracic skeletal development. Additionally, the hypomorphic allele was very sensitive to genetic effects, suggesting the existence of mappable genetic modifiers of the hypomorphic allele of myogenin. ^

Dielectrophoretic approaches to sample preparation and analysis

Dielectrophoresis (DEP) has been used to manipulate cells in low-conductivity suspending media using AC electrical fields generated on micro-fabricated electrode arrays. This has created the possibility of performing automatically on a micro-scale more sophisticated cell processing than that currently requiring substantial laboratory equipment, reagent volumes, time, and human intervention. In this research the manipulation of aqueous droplets in an immiscible, low-permittivity suspending medium is described to complement previous work on dielectrophoretic cell manipulation. Such droplets can be used as carriers not only for air- and water-borne samples, contaminants, chemical reagents, viral and gene products, and cells, but also the reagents to process and characterize these samples. A long-term goal of this area of research is to perform chemical and biological assays on automated, micro-scaled devices at or near the point-of-care, which will increase the availability of modern medicine to people who do not have ready access to large medical institutions and decrease the cost and delays associated with that lack of access. In this research I present proofs-of-concept for droplet manipulation and droplet-based biochemical analysis using dielectrophoresis as the motive force. Proofs-of-concept developed for the first time in this research include: (1) showing droplet movement on a two-dimensional array of electrodes, (2) achieving controlled dielectric droplet injection, (3) fusing and reacting droplets, and (4) demonstrating a protein fluorescence assay using micro-droplets. ^

Clinical relevance of polymorphic DNA copy number variation (CNV) in African American women with stage I-II breast cancer

Objectives. The chief goal of this study was to analyze copy number variation (CNV) in breast cancer tumors from 25 African American women with early stage breast cancer (BC) using molecular inversion probes (MIP) in order to: (1) compare the degree of CNV in tumors compared to normal lymph nodes, and (2) determine whether gains and/or losses of genes in specific chromosomes differ between pathologic subtypes of breast cancer defined by known prognostic markers, (3) determine whether gains/losses in CN are associated with known oncogenes or tumor suppressor genes, and (4) determine whether increased gains/losses in CN for specific chromosomes were associated with differences in breast cancer recurrence. ^ Methods. Twenty to 37 nanograms of DNA extracted from 25 formalin-fixed paraffin embedded (FFPE) tumor samples and matched normal lymph nodes were added to individual tubes. Oligonucleotide probes with recognition sequences at each terminus were hybridized with a genomic target sequence to form a circular structure. Probes are released from genomic DNA obtained from FFPE samples, and those which have been correctly "circularized" in the proper allele/nucleotide reaction combination are amplified using polymerase chain reaction (PCR) primers. Amplicons were fluorescently labeled and the tag sequences released from the genome homology regions by treatment with uracil-N-glycosylase to cleave the probe at the site where uracils are present, and detected using a complementary tag array developed by Affymetrix. ^ Results. Analysis of CN gains and losses from tumors and normal tissues showed marked differences in tumors with numerous chromosomes affected. Similar changes were not observed in normal lymph nodes. When tumors were stratified into four groups based on expression or lack of expression of the estrogen receptor and HER2/neu, distinct patterns of CNV for different chromosomes were observed. Gains or losses in CN for specific chromosomes correlated with amplifications/deletions of particular oncogenes or tumor suppressor genes (i.e. such as found on chromosome 17) known to be associated with aggressive tumor phenotype and poor prognosis. There was a trend for increases in CN observed for chromosome 17 to correlate inversely with time to recurrence of BC (p=0.14 for trend). CNV was also observed for chromosomes 5, 8, 10, 11, and 16, which are known sites for several breast cancer susceptibility alleles. ^ Conclusions. This study is the first to validate the MIP technique, to correlate differences in gene expression with known prognostic tumor markers, and to correlate significant increases/decreases in CN with known tumor markers associated with prognosis. The results of this study may have far reaching public health implications towards identifying new high-risk groups based on genomic differences in CNP, both with respect to prognosis and response to therapy, and to eventually identify new therapeutic targets for prevention and treatment of this disease. ^

Health beliefs and attitudes of HPV among Hispanic parents as predictors of intention to use the HPV vaccine

Human Papillomavirus (HPV) is the most common sexually transmitted disease in the United States. Although HPV prevalence is high in the United States, there are a limited number of research studies that focus on Hispanics, who have higher incidence rates of cervical cancer than their non-Hispanic counterparts. The HPV vaccine introduced in 2006 may offer a feasible solution to the issues surrounding high prevalence of HPV. Due to the high prevalence of HPV infection among adolescents and young adults it has been suggested that HPV vaccination begin prior to onset sexual activity and focus on non-sexually active adolescents and pre-adolescents. Consequently, it has become increasingly important to assess knowledge and awareness of HPV in order to develop effective intervention strategies. This pilot study evaluated the knowledge and health beliefs of Hispanic parents regarding HPV and the HPV vaccine using a newly developed questionnaire based on the constructs of the Health Belief Model. The sample was recruited from an ob-gyn office in El Paso, Texas. Descriptive data show that the majority of the sample was female (94.1%), Hispanic (76.5%), Catholic (64.7%), and had at least a high school education (55.9%). Chi-square analysis revealed that the following variables differed amongst parents who intended to vaccinate their child against HPV and those who did not: religion (p=0.038), perceived severity item "HPV infections are easily treated" (p=0.052), perceived benefits item "It is better to vaccinate a child against an STI before they become sexually active" (p=0.014) and perceived barriers item "The HPV vaccine may have serious side effects that could harm my child" (p=0.004). Univariate logistic regression indicated that religion (OR = 4.8, CI: 1.04, 21.8) and "The HPV vaccine may have serious side effects that could harm my child" (OR = 15.9, CI: 1.73, 145.8) were significant predictors of parental intention to vaccinate. Multivariate logistic regression, using backwards elimination, indicated that religion (OR = 7.7, CI: 1.25, 47.8) and "The HPV vaccine may have serious side effects that may harm my child" (OR = 7.6, CI: 1.15, 50.2) were the best predictive variables for parental intention to vaccinate. ^

A qualitative and quantitative assessment of cancer patients' perceptions of barriers to treatment

This study examined barriers that cancer patients experience in obtaining treatment. The principal aim of the study was to conduct a comprehensive quantitative and qualitative assessment of barriers to cancer treatment for Texas cancer patients. The three specific aims of the study were to: (1) conduct a review and critique of published and unpublished research on barriers to cancer treatment; (2) conduct focus groups for the qualitative assessment of cancer patients' perceived barriers to cancer treatment; and (3) survey a representative sample of cancer patients regarding perceived barriers to treatment. The study was guided by the Aday and Andersen access framework of predisposing, enabling, and need determinants of care-seeking.^ To address the first specific aim, a total of 732 abstracts were examined, from which 154 articles were selected for review. Of these 154 articles, 57 that related directly to research on barriers to cancer treatment were chosen for subsequent analysis. Criteria were applied to each article to evaluate the strength of the study design, sampling and measurement procedures. The major barriers that were consistently documented to influence whether or not cancer patients sought or continued required treatment included problems with communication between the patient and provider, lack of information on side effects, the cost of treatment and associated difficulties in obtaining and maintaining insurance coverage, and the absence of formal and informal networks of social support. Access barriers were generally greater for older, minority women, and patients of lower socioeconomic status.^ To address the second specific aim, a total of eight focus groups (n = 44) were conducted across the State of Texas with cancer patients identified by the Texas Community Oncology Network, American Cancer Society, and community health centers. One important finding was that cost is the greatest hurdle that patients face. Another finding was that with the health care/insurance crisis, an increasing number of physicians are working with their patients to develop individually-tailored payment plans. For people in rural areas, travel to treatment sites is a major barrier due to the travel costs as well as work time forfeited by patients and their family members. A third major finding was the patients' family and church play important roles in providing social and emotional support for cancer patients.^ To address the third aim, a total of 910 cancer patients were surveyed during October and November, 1993. Approximately 65% of the cancer patients responded to the survey. The findings showed that the major barriers to treatment included costs of medications and diagnostic tests, transportation, lack of social support, problems understanding the written information regarding their disease as well as losing coverage or having higher premiums or copayments once they were diagnosed (particularly among blacks).^ Significant differences in reported barriers were found between racial groups. The minority respondents (i.e., blacks and Hispanics) tended to experience more barriers to treatment compared to the white respondents. More specifically, Hispanics were more likely to report transportation as a barrier to treatment than both white and blacks. Future research is needed to better understand the problems that minority cancer patients experience in receiving treatment. (Abstract shortened by UMI.) ^

Systems Biology Approaches to Probe Gene Regulation in Bacteria

Mechanisms that allow pathogens to colonize the host are not the product of isolated genes, but instead emerge from the concerted operation of regulatory networks. Therefore, identifying components and the systemic behavior of networks is necessary to a better understanding of gene regulation and pathogenesis. To this end, I have developed systems biology approaches to study transcriptional and post-transcriptional gene regulation in bacteria, with an emphasis in the human pathogen Mycobacterium tuberculosis (Mtb). First, I developed a network response method to identify parts of the Mtb global transcriptional regulatory network utilized by the pathogen to counteract phagosomal stresses and survive within resting macrophages. As a result, the method unveiled transcriptional regulators and associated regulons utilized by Mtb to establish a successful infection of macrophages throughout the first 14 days of infection. Additionally, this network-based analysis identified the production of Fe-S proteins coupled to lipid metabolism through the alkane hydroxylase complex as a possible strategy employed by Mtb to survive in the host. Second, I developed a network inference method to infer the small non-coding RNA (sRNA) regulatory network in Mtb. The method identifies sRNA-mRNA interactions by integrating a priori knowledge of possible binding sites with structure-driven identification of binding sites. The reconstructed network was useful to predict functional roles for the multitude of sRNAs recently discovered in the pathogen, being that several sRNAs were postulated to be involved in virulence-related processes. Finally, I applied a combined experimental and computational approach to study post-transcriptional repression mediated by small non-coding RNAs in bacteria. Specifically, a probabilistic ranking methodology termed rank-conciliation was developed to infer sRNA-mRNA interactions based on multiple types of data. The method was shown to improve target prediction in Escherichia coli, and therefore is useful to prioritize candidate targets for experimental validation.

Evaluation of the impact of access to free influenza vaccine on immunization rates for children with cystic fibrosis

Children with cystic fibrosis are at increased risk of seasonal influenza associated complications, which makes them a judicious target of interventions designed to increase influenza vaccination rates. The Baylor College of Medicine/Texas Children's Hospital Pediatric Cystic Fibrosis (BCM/TCH CF) Care Center implemented an enhanced multi-component initiative designed to increase influenza vaccination rates in its patient population during the 2011-2012 influenza season. We evaluated the impact of specific components of this intervention on vaccination rates among the clinic's patient population via a historical medical chart review and examined the relationship between vaccination status and the number of pulmonary exacerbations requiring hospital admission during the influenza season. The multi-component intervention was comprised of providing influenza free of charge in the CF Care Center, reminders via phone call and letters, and drive through influenza vaccine clinics on nights and weekends. The intervention to increase influenza vaccination rates led to overall improved vaccination rates among the patients at the BCM/TCH CF Care Center, increasing from 90% adherence observed during the 2010-2011 season to 94% adherence during the 2011-2012 season. The availability of free influenza vaccine in the CF Care Center, combined with reminders about being vaccinated early in the season proved to be the most effective practices for improving the vaccination rate in the CF Care Center.^

A Path Forward: Evidence-Based Approaches to Educational Policy and Practice

In the complex landscape of public education, participants at all levels are searching for policy and practice levers that can raise overall performance and close achievement gaps. The collection of articles in this edition of the Journal of Applied Research on Children takes a big step toward providing the tools and tactics needed for an evidence-based approach to educational policy and practice.