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Recent documents in eScholarship@UMMS
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Insights into social insects from the genome of the honeybee Apis mellifera

Mon, 12/22/2014 - 7:30pm

Here we report the genome sequence of the honeybee Apis mellifera, a key model for social behaviour and essential to global ecology through pollination. Compared with other sequenced insect genomes, the A. mellifera genome has high A+T and CpG contents, lacks major transposon families, evolves more slowly, and is more similar to vertebrates for circadian rhythm, RNA interference and DNA methylation genes, among others. Furthermore, A. mellifera has fewer genes for innate immunity, detoxification enzymes, cuticle-forming proteins and gustatory receptors, more genes for odorant receptors, and novel genes for nectar and pollen utilization, consistent with its ecology and social organization. Compared to Drosophila, genes in early developmental pathways differ in Apis, whereas similarities exist for functions that differ markedly, such as sex determination, brain function and behaviour. Population genetics suggests a novel African origin for the species A. mellifera and insights into whether Africanized bees spread throughout the New World via hybridization or displacement.

Functional CpG methylation system in a social insect

Mon, 12/22/2014 - 7:30pm

DNA methylation systems are well characterized in vertebrates, but methylation in Drosophila melanogaster and other invertebrates remains controversial. Using the recently sequenced honey bee genome, we present a bioinformatic, molecular, and biochemical characterization of a functional DNA methylation system in an insect. We report on catalytically active orthologs of the vertebrate DNA methyltransferases Dnmt1 and Dnmt3a and b, two isoforms that contain a methyl-DNA binding domain, genomic 5-methyl-deoxycytosine, and CpG-methylated genes. The honey bee provides an opportunity to study the roles of methylation in social contexts.

Brahma links the SWI/SNF chromatin-remodeling complex with MeCP2-dependent transcriptional silencing

Mon, 12/22/2014 - 7:30pm

Transcriptional repression of methylated genes can be mediated by the methyl-CpG binding protein MeCP2. Here we show that human Brahma (Brm), a catalytic component of the SWI/SNF-related chromatin-remodeling complex, associates with MeCP2 in vivo and is functionally linked with repression. We used a number of different molecular approaches and chromatin immunoprecipitation strategies to show a unique cooperation between Brm, BAF57 and MeCP2. We show that Brm and MeCP2 assembly on chromatin occurs on methylated genes in cancer and the gene FMR1 in fragile X syndrome. These experimental findings identify a new role for SWI/SNF in gene repression by MeCP2.

DNA repair in a chromatin environment

Mon, 12/22/2014 - 7:30pm

DNA mutations and aberrations are a problem for all forms of life. Eukaryotes specifically have developed ways of identifying and repairing various DNA mutations in a complex and refractory chromatin environment. The chromatin structure is much more than a packaging unit for DNA; it is dynamic. Cells utilize and manipulate chromatin for gene regulation, genome organization and maintenance of genome integrity. Once a DNA aberration has occurred, the various DNA repair machineries interact with chromatin proteins, such as the histone variant H2A.X, and chromatin remodeling machines of the SWI/SNF family to gain access and repair the lesion in a timely manner. Recent studies have thus begun to address the roles of chromatin proteins in DNA repair as well as to dissect the functions of DNA repair machinery in vitro on more physiological, nucleosomal templates.

N-CoR-HDAC corepressor complexes: roles in transcriptional regulation by nuclear hormone receptors

Mon, 12/22/2014 - 7:30pm

Many nuclear hormone receptors (NHRs) actively repress the expression of their primary response genes through the recruitment of transcriptional corepressor complexes to regulated promoters. N-CoR and the highly related SMRT were originally isolated and characterized by their ability to interact exclusivelywith the unliganded forms of NHRs and confer transcriptional repression. Recently, both the N-CoR and SMRT corepressors have been found to exist in vivo in multiple, distinct macromolecular complexes. While these corepressor complexes differ in overall composition, a general theme is that they contain histone deacetylase enzymatic activity. Several of these complexes contain additional transcriptional corepressor proteins with functional ties to chromatin structure. Together, these data suggest that modulation of chromatin structure plays a central role in N-CoR mediated transcriptional repression from unliganded NHRs.

Differing patterns of selection and geospatial genetic diversity within two leading Plasmodium vivax candidate vaccine antigens

Mon, 12/22/2014 - 12:25pm

Although Plasmodium vivax is a leading cause of malaria around the world, only a handful of vivax antigens are being studied for vaccine development. Here, we investigated genetic signatures of selection and geospatial genetic diversity of two leading vivax vaccine antigens--Plasmodium vivax merozoite surface protein 1 (pvmsp-1) and Plasmodium vivax circumsporozoite protein (pvcsp). Using scalable next-generation sequencing, we deep-sequenced amplicons of the 42 kDa region of pvmsp-1 (n = 44) and the complete gene of pvcsp (n = 47) from Cambodian isolates. These sequences were then compared with global parasite populations obtained from GenBank. Using a combination of statistical and phylogenetic methods to assess for selection and population structure, we found strong evidence of balancing selection in the 42 kDa region of pvmsp-1, which varied significantly over the length of the gene, consistent with immune-mediated selection. In pvcsp, the highly variable central repeat region also showed patterns consistent with immune selection, which were lacking outside the repeat. The patterns of selection seen in both genes differed from their P. falciparum orthologs. In addition, we found that, similar to merozoite antigens from P. falciparum malaria, genetic diversity of pvmsp-1 sequences showed no geographic clustering, while the non-merozoite antigen, pvcsp, showed strong geographic clustering. These findings suggest that while immune selection may act on both vivax vaccine candidate antigens, the geographic distribution of genetic variability differs greatly between these two genes. The selective forces driving this diversification could lead to antigen escape and vaccine failure. Better understanding the geographic distribution of genetic variability in vaccine candidate antigens will be key to designing and implementing efficacious vaccines.

A qualitative analysis of acute care surgery in the United States: it's more than just "a competent surgeon with a sharp knife and a willing attitude"

Mon, 12/22/2014 - 12:25pm

BACKGROUND: Since acute care surgery (ACS) was conceptualized a decade ago, the specialty has been adopted widely; however, little is known about the structure and function of ACS teams.

METHODS: We conducted 18 open-ended interviews with ACS leaders (representing geographic [New England, Northeast, Mid-Atlantic, South, West, Midwest] and practice [Public/Charity, Community, University] diversity). Two independent reviewers analyzed transcribed interviews using an inductive approach (NVivo qualitative analysis software).

RESULTS: All respondents described ACS as a specialty treating "time-sensitive surgical disease" including trauma, emergency general surgery (EGS), and surgical critical care (SCC); 11 of 18 combined trauma and EGS into a single clinical team; 9 of 18 included elective general surgery. Emergency orthopedics, emergency neurosurgery, and surgical subspecialty triage were rare (1/18 each). Eight of 18 ACS teams had scheduled EGS operating room time. All had a core group of trauma and SCC surgeons; 13 of 18 shared EGS due to volume, human resources, or competition for revenue. Only 12 of 18 had formal signout rounds; only 2 of 18 had prospective EGS data registries. Streamlined access to EGS, evidence-based protocols, and improved education were considered strengths of ACS. ACS was described as the "last great surgical service" reinvigorated to provide "timely," cost-effective EGS by experts in "resuscitation and critical care" and to attract "young, talented, eager surgeons" to trauma/SCC; however, there was concern that ACS might become the "wastebasket for everything that happens at inconvenient times."

CONCLUSION: Despite rapid adoption of ACS, its implementation varies widely. Standardization of scope of practice, continuity of care, and registry development may improve EGS outcomes and allow the specialty to thrive.

The National Cancer Institute's Health Information National Trends Survey [HINTS]: a national cross-sectional analysis of talking to your doctor and other healthcare providers for health information

Mon, 12/22/2014 - 12:18pm

BACKGROUND: The need to understand preferred sources of health information remains important to providing patient-centered care. The Internet remains a popular resource for health information, but more traditional sources may still be valid for patients during a recent health need. This study sought to understand the characteristics of patients that turn to their doctor or healthcare provider first for a recent health or medical information need.

METHODS: Using the national cross-sectional survey, Health Information National Trend Study [HINTS], characteristics of those who sought a doctor or healthcare provider for a recent health information need were compared to other sources. Weighted survey responses from Cycle 1 and Cycle 2 of the HINTS survey were used for multivariable logistic regression.

RESULTS: A total 5,307 patient responses were analyzed. Overall, those who seek a doctor or healthcare provider first for a health need are female, 46-64 years, White non-Hispanic, educated, in good health and users of the Internet. Yet, adjusted logistic regressions showed that those who sought a doctor or healthcare provider first during a recent health information need compared to other sources were most likely to be 65+ years, in poor health, less educated and have health insurance.

CONCLUSIONS: Patients who seek their doctor or healthcare provider first for health information rather than other sources of information represent a unique population. Doctors or healthcare providers remain an important resource for these patients during recent needs, despite the wide use of the Internet as a source of health information.

Mating type specific chromosome conformation in Saccharomyces cerevisiae

Mon, 12/22/2014 - 12:18pm

Budding yeast switch their mating type by a gene conversion event at the MAT locus which uses either of two silent loci (HML or HMR) on opposite ends of chromosome three as a template. InMATa cells the left arm of Chr. Ill is “activated” which allows for the preferential recombination ofHML with the MAT locus. The left arm is otherwise “repressed” for recombination in MATα cells which then prefer to use HMR, on the right arm, as a template for gene conversion. We set out to analyze the potential role of chromosome conformation in this “activation”/”repression” phenomenon observed on the left arm of Chr. III. We used Chromosome Conformation Capture Carbon Copy (5C) to comprehensively analyze the conformation of chromosomes III, V, and XII in the two mating types. Our data reveals that the yeast genome is organized in a unique way compared to other species. We have found that global nuclearorganization such ascentromereclustering, telomere tethering to the periphery, and sequestration of the rDNA array into the nucleolus affect both the specific conformations of each chromosome but also the interactions between these chromosomes. Our analysis indicates that the overall architecture for these 3 chromosomes is very similar between the two mating types. Interestingly, a mating type specific difference in conformation of the left arm of Chr. Ill was identified. Furthermore, the 5C data was used, in conjunction with the Integrative Modeling Platform (IMP), to generate three dimensional models of Chr. III in both mating types. This method provides a more intuitive way of viewing 5C data and reveals that, in general, Chr. Ill has a more crumpled conformation in MATacells than in MATα. However, this crumpling is most evident on the left arm of the chromosome. Thus the phenomenon of “activation”/”repression” of the left arm of Chr. III which is associated with mating type-specific switching preference is, in fact, associated with a difference in the innate conformation of Chr. Ill between the two mating types. This difference in structure between mating types will be used as a phenotype to analyze the effect of cis and trans acting factors that play a role in switching preference through alteration of chromosome conformation.

Expression of the repeat genome and aberrant epigenetic factors in cancer

Mon, 12/22/2014 - 12:18pm

Nearly half of the human genome consists of noncoding repetitive DNA elements, including tandem satellite repeats in large blocks at the pericentric regions of chromosomes and intergenic repetitive elements. While both repeat types were long thought to remain mostly silent, recent evidence indicates that repeats can be expressed, but the extent and regulation of their expression or their potential function(s) remain to be elucidated. Due to their critical location within regions vital for cell division, it is expected that tight regulation of pericentric satellite sequences is essential for both epigenetic and genetic stability. Our data suggests aberrant expression of pericentric satellite RNA is tightly linked to epigenetic misregulation in cancer. It is well known that epigenetic changes can be important in cancer initiation and progression, but studies have focused primarily on the inappropriate silencing and methylation of tumor suppressor genes. While pathologists have long noted the loss of heterochromatic organization in cancer nuclei, and hypomethylation of satellite DNA has been observed, the misregulation of repeat RNAs has only recently been described. Our results provide a link between overexpression of repeat RNAs and aberrant distribution of epigenetic factors in cancer. Our data suggests regulation of the repeat genome has potentially important roles in both normal and neoplastic cells in their ability to affect distribution and recruitment of epigenetic factors.

The role of intraflagellar transport proteins in ciliary assembly and function

Mon, 12/22/2014 - 12:18pm

The sensory and motility functions of cilia play critical roles in the development of vertebrates and defects in these organelles lead to a wide range of structural birth defects. The intraflagellar transport (IFT) system is required for building all types of mammalian cilia. IFT particles are composed of about 20 proteins and these proteins are highly conserved across ciliated species. IFT25 and IFT27, however, are absent from certain ciliated organisms like Caenorhabditis andDrosophila suggesting that they may have a unique role distinct from ciliogenesis. We generatedIft25 and Ift27 null mice and show that these proteins are not required for ciliary assembly but are required for proper Hedgehog signaling, which in mammals occurs within cilia. Mutant mice die at birth with multiple phenotypes indicative of Hedgehog signaling dysfunction. Cilia lacking IFT25/27 have defects in the signal-dependent transport of multiple Hedgehog components including Patched-1, Smoothened, and Gli2 and fail to activate the pathway upon stimulation. These are the first examples of null IFT mutations that perturb Hedgehog signaling independent of ciliary architecture. Thus, IFT function is not restricted to assembling cilia where signaling occurs but also plays a direct role in signal transduction events.

Lv4, an activity that restricts nuclear entry of SIVMAC/SIVSM in human blood cells

Mon, 12/22/2014 - 12:18pm

SIVSM is a lentivirus endemic to the West African sooty mangabey (Cercocebus atys). HIV-2 and SIVMAC are zoonoses that resulted from SIVSM transmission to humans and Asian rhesus macaques (Macaca mulatto), respectively. Human leukemia cell lines, human peripheral blood mononuclear cells and CD4+ T cells, were 4 to 50-fold less permissive for SIVMAC and SIVSM than for HIV-1. In contrast, SIVMAC transduction of human adherent cell lines was equivalent to that of HIV-1. Consistent with adaptation to human cells, HIV-2 was not restricted as potently as was SIVMAC. SIVMAC transduction of human blood cells was rescued up to the level of HIV-1 by As2O3, a compound that increases the infectivity of viruses in the context of TRIM5-mediated restriction. Nonetheless, efficient knockdown of TRIM5 or cyclophilin A, a cytoplasmic factor that sometimes regulates TRIM5 restriction activity, did not rescue SIVMAC tranduction of these cells. Substitution of HIV-1 CA with the CA from SIVMAC rendered HIV-1 poorly infectious for Jurkat T cells. The block occurred after completion of reverse transcription and the formation of 2-LTR circles, but before establishment of the provirus. Heterokaryons resulting from fusion of permissive with restrictive cells exhibited the restrictive phenotype, indicating that SIV transduction of human blood cells is inefficient due to a dominant-acting restriction factor. These results demonstrate that the nucleus of human blood cells possesses a TRIM5-like restriction factor specific for the SIVMAC/SIVSM capsid and that, by extension, cross-species transmission of SIVSM to human cells necessitated adaptation of HIV-2 to this restriction factor.

Rational modification of an HIV-1 gp120 results in enhanced neutralization breadth when used as a DNA prime

Mon, 12/22/2014 - 12:18pm


The identification of phenotypic features of the HIV-1 envelope glycoprotein that correlate with neutralization breadth is an important goal of HIV vaccine research. Recently we compared the immunogenic potential of two gp120s differing in their ability to utilize CD4; B33 (highly macrophage topic) and LN40 (non-macrophage tropic). Using a DNA prime protein boost regimen in New Zealand White Rabbits, LN40-primed sera displayed enhanced breadth compared to the B33-primed group, with differences in immunogenicity between groups modulated by specific residues within and flanking the V3 loop and the CD4bs. To better understand the role of these residues in eliciting breadth, we introduced reciprocal mutations between LN40 and B33 at these critical positions. Methods

Three groups of four rabbits were primed with one of three chimeric LN40/B33 gp120 DNAs, followed by a polyvalent protein boost. Time course and endpoint titers were determined via ELISA. Neutralization breadth was analyzed by Monogram against a panel of sixteen viruses using a Phenosense neutralization assay. Anti-gp120 serum specificities were determined using a set of overlapping peptides spanning the entire gp120 via ELISA. Results

We found that sera primed with a B33 chimera containing specific LN40 residues within the V3 loop and the CD4 binding loop displayed enhanced neutralization breadth against a cross-clade panel of Tier 1 and 2 viruses compared to the B33-primed group. Interestingly, a second B33 chimera containing two additional LN40 substitutions (Stu-Bsu R373/N386) within C3/V4 primed the broadest response, being broader than even the LN40-primed group. Additionally, peptide ELISAs showed differences in reactivity between priming groups which were most pronounced for the C3/V4 region, suggesting an important role for these regions in modulating serum antibody responses against gp120.

Identifying features of the lentiviral genome crucial for the establishment of latency

Mon, 12/22/2014 - 12:18pm


Latently infected cells represent a major obstacle to the cure of infection with human immunodeficiency virus type 1 (HIV-1). We have observed that the propensity to establish latency varies greatly among primate lentiviruses. The purpose of our study is to identify the features that determine such variation in order to elucidate the fine molecular mechanisms regulating latency. Materials and methods

Using GFP–encoding reporter viruses, the level of infection by SIV, HIV-1 and HIV-2 was quantitated by flow cytometry in cells stably expressing HIV-1 Tat, SIV Tat or vector alone. Results

We have observed that SIVmac 239 infects human lymphoid cells much less efficiently than HIV-1. However, ectopic expression of HIV-1 Tat rescued SIV infection.

As host cell type can influence viral gene expression, we tested different cell lines for their ability to support lentiviral latency. In both T (Jurkat TAg and C8166) and T-B hybrid cell lines (CEMX174) SIV exhibited a greater ability to remain transcriptionally silent within the human genome than HIV-1 or HIV-2. The different behaviour in terms of latency was particularly evident in CEMX174 cells, where HIV Tat activation caused more than 20-fold increase in the number of GFP-positive cells infected with SIV, while it had little effect on cells challenged with HIV-1 or HIV-2. The lower level of productive infection displayed by SIVmac239 was not due to a reduced ability of SIV Tat to trigger viral expression in human cells because SIV Tat overexpression reactivated latent SIV as well as HIV Tat did. Moreover, HIV-1 chimeric viruses harboring the U3 region of SIV behaved like the parental HIV-1 viruses, suggesting that viral determinants of SIV latency reside in a part of the lentiviral genome different from the promoter region. Conclusions

In human cell lines transduction with SIVmac239 largely establishes a latent infection which is reactivated by overexpressing HIV-1 or SIVmac239 Tat. The tendency of SIVmac239 to establish latent infection is attributable neither to a defective SIV Tat activity nor to a reduced promoter activity of the U3 region in human lymphoid cells. The CEMX174 cell line offers a good model to explore the specific viral determinants which allow SIV to enter latency.

Folding principles of genomes

Mon, 12/22/2014 - 12:18pm

My laboratory studies how chromosomes are organized in three dimensions. The three-dimensional organization of the genome is critical for regulating gene expression by bringing genes in close spatial proximity to distal regulatory elements such as enhancers. We have developed powerful molecular approaches, based on our Chromosome Conformation Capture technology, to determine the folding of genomes at unprecedented resolution (Kb) and scale (genome-wide).

We have applied these methods to determine the spatial folding of 1% of the human genome (the ENCODE pilot regions) across a panel of cell lines. We discovered that chromosomes fold into extensive long-range interaction networks in which genes are interacting with distal gene regulatory elements. These results start to place genes and regulatory elements, that are often separated by large genomic distances, in three-dimensional context to reveal their functional relationships.

Our analysis of chromosome folding also revealed that chromosomes are compartmentalized in a series of “Topological Association Domains” (TADs) that are hundreds of Kb in size. Loci located within a TAD mingle freely, but interact far less frequently with loci located outside their TAD. TADs appear involved in gene expression, as we found that genes located within the same TAD tend to be co-expressed, but the mechanism(s) by which these domains affect gene regulation is still unknown. TADs represent novel universal and genetically encoded building blocks of chromosomes.

Melissa L. Anderson: APA/APAGS Award for Distinguished Graduate Student in Professional Psychology

Fri, 12/19/2014 - 2:28pm

Presents a short biography of the winner of the American Psychological Association/American Psychological Association of Graduate Students Award for Distinguished Graduate Student in Professional Psychology. The 2012 winner is Melissa L. Anderson for her ongoing commitment to understanding, treating, and preventing domestic violence in Deaf women and underserved populations in general. Anderson is passionate in her efforts to study the factors underlying violence toward women and in applying psychological science to intervene in and prevent such abuse. She is dedicated to improving the quality of life and well-being of underserved women and ensuring that services and programs become accessible to them. Anderson's Award citation is also presented. PsycINFO Database Record (c) 2012 APA, all rights reserved.

Does seeking safety reduce PTSD symptoms in women receiving physical disability compensation

Fri, 12/19/2014 - 2:28pm

OBJECTIVE: This secondary analysis investigated the impact of 12 sessions of Seeking Safety (SS) on reducing posttraumatic stress disorder (PTSD) symptoms in a sample of dually diagnosed women with physical disabilities versus nondisabled (ND) women. SS is an evidence-based and widely implemented manualized therapy for PTSD and/or substance use disorder. It is a present-focused model that promotes coping skills and psychoeducation.

DESIGN: As part of the National Institute on Drug Abuse Clinical Trials Network (NIDA CTN), 353 participants with current PTSD and substance use disorder (SUD) were randomly assigned to partial-dose SS or Women's Health Education (WHE) group therapy conducted in community-based substance abuse treatment programs. The women were categorized as participants with disabilities (PWD; n = 20) or ND (n = 333) based on the question, "Do you receive a pension for a physical disability?" PTSD was assessed on the Clinician-Administered PTSD Scale (CAPS) at baseline and follow-ups after treatment (1 week, 3 months, 6 months, and 12 months).

RESULTS: PWD experienced sustained reductions in PTSD symptoms when treated with SS but not WHE. Indeed, PTSD symptoms of PWD in WHE returned to baseline levels of severity by 12-month follow-up. This pattern of results was not observed among ND women, who sustained improvements on PTSD in both treatment conditions.

IMPLICATIONS: These results suggest strong potential for using SS to treat PTSD among women with physical disabilities, and speak to the genuine need to address trauma and PTSD more directly with PWD. Our results are also consistent with other findings from the NIDA CTN trial, in which virtually all significant results evidenced SS outperforming WHE.

Violence against Deaf women: effect of partner hearing status

Fri, 12/19/2014 - 2:28pm

Using a sample of Deaf female undergraduate students, the current study sought to investigate the prevalence, correlates, and characteristics of intimate partner violence victimization in hearing-Deaf and Deaf-Deaf relationships. Initial results suggest that similarities in hearing status and communication preference are associated with increased levels of negotiation within these relationships. However, compatibility in these areas did not co-occur with significant decreases in physical, psychological, or sexual partner violence. Recommendations for future research as well as implications for clinical and educational practice are outlined.

Is it abuse? Deaf female undergraduates' labeling of partner violence

Fri, 12/19/2014 - 2:28pm

The current study investigated the labeling of abuse experiences in a sample of 97 Deaf female undergraduate students, exploring the following questions: What is the prevalence of violent behaviors experienced by Deaf female undergraduates in their past-year relationships, what proportion of these relationships are identified as "abuse," and what scripts and strategies do Deaf female undergraduates utilize to label their experiences of partner violence? Results indicated that over half of the sample chose not to label past-year experiences of psychological aggression, physical assault, and sexual coercion as abuse, even when these experiences included severe violence. Implications for the Deaf education system will be discussed.

Intimate partner violence against deaf female college students

Fri, 12/19/2014 - 2:28pm

It has been estimated that roughly 25% of all Deaf women in the United States are victims of intimate partner violence (Abused Deaf Women's Advocacy Services [ADWAS]), a figure similar to annual prevalence rates of 16% to 30% for intimate partners in the general population. One goal of the present study was to ascertain the prevalence of intimate partner violence victimization in a sample of Deaf female college students. When comparing the prevalence of physical assault, psychological aggression, and sexual coercion victimization to hearing female undergraduates, the current sample was approximately two times as likely to have experienced victimization in the past year.