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Expression of the repeat genome and aberrant epigenetic factors in cancer

Mon, 12/22/2014 - 11:18am

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 - 11:18am

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 - 11:18am

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 - 11:18am

Background

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 - 11:18am

Background

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 - 11:18am

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 - 1:28pm

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 - 1:28pm

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 - 1:28pm

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 - 1:28pm

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 - 1:28pm

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.

Black deaf individuals' reading skills: influence of ASL, culture, family characteristics, reading experience, and education

Fri, 12/19/2014 - 1:28pm

Previous research on the reading abilities of Deaf individuals from various cultural groups suggests that Black Deaf and Hispanic Deaf individuals lag behind their White Deaf peers. The present study compared the reading skills of Black Deaf and White Deaf individuals, investigating the influence of American Sign Language (ASL), culture, family characteristics, reading experience, and education. (The descriptor Black is used throughout the present article, as Black Deaf individuals prefer this term to African American. For purposes of parallel construction, the term White is used instead of European American.) It was found that Black Deaf study participants scored lower on measures of both reading and ASL. These findings provide implications for possible interventions at the primary, secondary, and college levels of education.

Deaf students and their classroom communication: an evaluation of higher order categorical interactions among school and background characteristics

Fri, 12/19/2014 - 1:28pm

This article investigated to what extent age, use of a cochlear implant, parental hearing status, and use of sign in the home determine language of instruction for profoundly deaf children. Categorical data from 8,325 profoundly deaf students from the 2008 Annual Survey of Deaf and Hard-of-Hearing Children and Youth were analyzed using chi-square automated interaction detector, a stepwise analytic procedure that allows the assessment of higher order interactions among categorical variables. Results indicated that all characteristics were significantly related to classroom communication modality. Although younger and older students demonstrated a different distribution of communication modality, for both younger and older students, cochlear implantation had the greatest effect on differentiating students into communication modalities, yielding greater gains in the speech-only category for implanted students. For all subgroups defined by age and implantation status, the use of sign at home further segregated the sample into communication modality subgroups, reducing the likelihood of speech only and increasing the placement of students into signing classroom settings. Implications for future research in the field of deaf education are discussed.

Research Data MANTRA: A Labour of Love

Fri, 12/19/2014 - 9:15am

Research Data MANTRA (or Management Training) is a labour of love. It has been an integral part of the University of Edinburgh's Research Data Management (RDM) programme since 2012. The staff at EDINA and Data Library at the University of Edinburgh has been curating this resource, based on internal and external feedback and has just published its fourth release since 2011. MANTRA is an open, web-based training course intended for self-paced learning by PhD students and early career researchers or others who manage digital data as part of a research project. It informs about good practice in research data management with real life stories. MANTRA’s approach is to be fun, relevant, useful, interactive and timely (FRUIT!). Librarians’ training needs are catered for through a companion resource, the DIY RDM Training Kit for Librarians.

An Analysis of Data Management Plans in University of Illinois National Science Foundation Grant Proposals

Fri, 12/19/2014 - 9:05am

The University of Illinois at Urbana-Champaign (UIUC) Library conducted an analysis of 1,260 Data Management Plans (DMPs) submitted in National Science Foundation (NSF) proposals from July 2011 through November 2013. Each DMP was assigned controlled vocabulary and keyword terms which summarized the proposed data management mechanisms for storing and sharing data. A database composed of the proposal’s title, PI (Principal Investigator), PI’s department and college, NSF grant number, funded status, assigned DMP vocabulary, and keyword terms was constructed. As of May 2014, a total of 298 of these UIUC proposals had been funded by the NSF. Our analysis of this sample revealed no significant statistical differences in proposed data storage and reuse venues between funded and unfunded proposals. However, there was a statistically higher frequency of use of the campus institutional repository and disciplinary repositories in proposals submitted after October 2012.

Endometrial Cancer

Thu, 12/18/2014 - 9:30am

This chapter in Cancer Concepts: A Guidebook for the Non-Oncologist is about cancers of the endometrium and uterus, including the epidemiology, risk factors, diagnosis, genetic risk, histology, grading and type categorization, management, and prognosis.

Making It Work: Vocational Peer Mentors for Emerging Adults with Serious Mental Health Conditions

Wed, 12/17/2014 - 9:29am

The Transitions RTC and Thresholds Young Adult Program (YAP) developed a supported employment/ education model based on the Individual Placement and Support1 model (IPS) and added a vocational peer mentor for emerging adults with serious mental health conditions (SMHC). This model is still being developed, but preliminary research has identified several guidelines that could be helpful for others thinking about implementing peer mentors into their vocational services for emerging adults with SMHC.

The impact of sleep, stress, and depression on postpartum weight retention: A systematic review

Tue, 12/16/2014 - 9:09am

OBJECTIVE:

To review the impact of sleep, stress, and/or depression on postpartum weight retention. METHODS:

We searched three electronic databases, PubMed, ISI Web of Science, and PsycInfo. Studies were included if they were published between January 1990 and September 2013 in English, measured sleep, stress, and/or depression in the postpartum period, and assessed the association of these factors with postpartum weight retention. Two reviewers reviewed included articles and rated study quality using a modified version of the Downs and Black scale. RESULTS:

Thirteen studies met our pre-defined eligibility criteria, reporting on 9 study samples. Two were cross-sectional studies and eleven were longitudinal studies. The study sample size ranged from 74 to 37,127. All four studies examining short sleep duration and postpartum weight retention reported a positive association. The four studies examining postpartum stress and weight retention reported non-significant associations only. Of 7 studies examining postpartum depression and weight retention, 3 reported non-significant associations, and 4 reported positive associations. CONCLUSION:

Research investigating the impact of postpartum sleep, stress, depression on weight retention is limited. Future longitudinal studies are needed.

UMCCTS Newsletter, December 2014

Tue, 12/16/2014 - 8:51am

This is the December 2014 issue of the UMass Center for Clinical and Translational Science Newsletter containing news and events of interest.

Uba1 functions in Atg7- and Atg3-independent autophagy

Mon, 12/15/2014 - 3:42pm

Autophagy is a conserved process that delivers components of the cytoplasm to lysosomes for degradation. The E1 and E2 enzymes encoded by Atg7 and Atg3 are thought to be essential for autophagy involving the ubiquitin-like protein Atg8. Here, we describe an Atg7- and Atg3-independent autophagy pathway that facilitates programmed reduction of cell size during intestine cell death. Although multiple components of the core autophagy pathways, including Atg8, are required for autophagy and cells to shrink in the midgut of the intestine, loss of either Atg7 or Atg3 function does not influence these cellular processes. Rather, Uba1, the E1 enzyme used in ubiquitylation, is required for autophagy and reduction of cell size. Our data reveal that distinct autophagy programs are used by different cells within an animal, and disclose an unappreciated role for ubiquitin activation in autophagy.