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Identifying Nuclear Matrix-Attached DNA Across the Genome

Tue, 12/20/2016 - 6:11pm

Experimental approaches to define the relationship between gene expression and nuclear matrix attachment regions (MARs) have given contrasting and method-specific results. We have developed a next generation sequencing strategy to identify MARs across the human genome (MAR-Seq). The method is based on crosslinking chromatin to its nuclear matrix attachment sites to minimize changes during biochemical processing. We used this method to compare nuclear matrix organization in MCF-10A mammary epithelial-like cells and MDA-MB-231 breast cancer cells and evaluated the results in the context of global gene expression (array analysis) and positional enrichment of gene-regulatory histone modifications (ChIP-Seq). In the normal-like cells, nuclear matrix-attached DNA was enriched in expressed genes, while in the breast cancer cells, it was enriched in non-expressed genes. In both cell lines, the chromatin modifications that mark transcriptional activation or repression were appropriately associated with gene expression. Using this new MAR-Seq approach, we provide the first genome-wide characterization of nuclear matrix attachment in mammalian cells and reveal that the nuclear matrix-associated genome is highly cell-context dependent.

An alternative splicing program promotes adipose tissue thermogenesis

Tue, 12/20/2016 - 6:11pm

Alternative pre-mRNA splicing expands the complexity of the transcriptome and controls isoform-specific gene expression. Whether alternative splicing contributes to metabolic regulation is largely unknown. Here we investigated the contribution of alternative splicing to the development of diet-induced obesity. We found that obesity-induced changes in adipocyte gene expression include alternative pre-mRNA splicing. Bioinformatics analysis associated part of this alternative splicing program with sequence specific NOVA splicing factors. This conclusion was confirmed by studies of mice with NOVA deficiency in adipocytes. Phenotypic analysis of the NOVA-deficient mice demonstrated increased adipose tissue thermogenesis and improved glycemia. We show that NOVA proteins mediate a splicing program that suppresses adipose tissue thermogenesis. Together, these data provide quantitative analysis of gene expression at exon-level resolution in obesity and identify a novel mechanism that contributes to the regulation of adipose tissue function and the maintenance of normal glycemia.

Inhibition of spleen tyrosine kinase activation ameliorates inflammation, cell death, and steatosis in alcoholic liver disease

Tue, 12/20/2016 - 6:11pm

The spectrum of alcoholic liver disease (ALD) is a major cause of mortality with limited therapies available. Because alcohol targets numerous signaling pathways in hepatocytes and in immune cells, the identification of a master regulatory target that modulates multiple signaling processes is attractive. In this report, we assessed the role of spleen tyrosine kinase (SYK), a nonreceptor tyrosine kinase, which has a central modulatory role in multiple proinflammatory signaling pathways involved in the pathomechanism of ALD. Using mouse disease models that represent various phases in the progression of human ALD, we found that alcohol, in all of these models, induced SYK activation in the liver, both in hepatocytes and liver mononuclear cells. Furthermore, significant SYK activation also occurred in liver samples and peripheral blood mononuclear cells of patients with ALD/alcoholic hepatitis compared to controls. Functional inhibition of SYK activation in vivo abrogated alcohol-induced hepatic neutrophil infiltration, resident immune cell activation, as well as inflammasome and extracellular signal-regulated kinase 1 and 2-mediated nuclear factor kappa B activation in mice. Strikingly, inhibition of SYK activation diminished alcohol-induced hepatic steatosis and interferon regulatory factor 3-mediated apoptosis.

CONCLUSION: Our data demonstrate a novel, functional, and multicellular role for SYK phosphorylation in modulating immune cell-driven liver inflammation, hepatocyte cell death, and steatosis at different stages of ALD. These novel findings highlight SYK as a potential multifunctional target in the treatment of alcoholic steatohepatitis.

Cell Signaling and Stress Responses

Tue, 12/20/2016 - 6:10pm

Stress-signaling pathways are evolutionarily conserved and play an important role in the maintenance of homeostasis. These pathways are also critical for adaptation to new cellular environments. The endoplasmic reticulum (ER) unfolded protein response (UPR) is activated by biosynthetic stress and leads to a compensatory increase in ER function. The JNK and p38 MAPK signaling pathways control adaptive responses to intracellular and extracellular stresses, including environmental changes such as UV light, heat, and hyperosmotic conditions, and exposure to inflammatory cytokines. Metabolic stress caused by a high-fat diet represents an example of a stimulus that coordinately activates both the UPR and JNK/p38 signaling pathways. Chronic activation of these stress-response pathways ultimately causes metabolic changes associated with obesity and altered insulin sensitivity. Stress-signaling pathways, therefore, represent potential targets for therapeutic intervention in the metabolic stress response and other disease processes.

Multisite phosphorylation by MAPK

Tue, 12/20/2016 - 6:10pm

Summary: Reversible protein phosphorylation plays a fundamental role in signal transduction networks. Phosphorylation alters protein function by regulating enzymatic activity, stability, cellular localization, or binding partners. Over three-quarters of human proteins may be phosphorylated, with many targeted at multiple sites. Such multisite phosphorylation substantially increases the scope for modulating protein function—a protein with n phosphorylation sites has the potential to exist in 2n distinct phosphorylation states, each of which could, in theory, display modified functionality. Proteins can be substrates for several protein kinases, thereby integrating distinct signals to provide a coherent biological response. However, they can also be phosphorylated at multiple sites by a single protein kinase to promote a specific functional output that can be reversed by dephosphorylation by protein phosphatases. On page 233 of this issue, Mylona et al. (1) reveal an unexpected role for multisite phosphorylation, whereby a protein kinase progressively phosphorylates sites on a transcription factor to promote and then subsequently limit its activity independently of dephosphorylation.

ChREBP Regulates Fructose-induced Glucose Production Independently of Insulin Signaling

Tue, 12/20/2016 - 6:10pm

Obese, insulin-resistant states are characterized by a paradoxical pathogenic condition in which the liver appears to be selectively insulin resistant. Specifically, insulin fails to suppress glucose production, yet successfully stimulates de novo lipogenesis. The mechanisms underlying this dysregulation remain controversial. Here, we hypothesized that carbohydrate-responsive element-binding protein (ChREBP), a transcriptional activator of glycolytic and lipogenic genes, plays a central role in this paradox. Administration of fructose increased hepatic hexose-phosphate levels, activated ChREBP, and caused glucose intolerance, hyperinsulinemia, hypertriglyceridemia, and hepatic steatosis in mice. Activation of ChREBP was required for the increased expression of glycolytic and lipogenic genes as well as glucose-6-phosphatase (G6pc) that was associated with the effects of fructose administration. We found that fructose-induced G6PC activity is a major determinant of hepatic glucose production and reduces hepatic glucose-6-phosphate levels to complete a homeostatic loop. Moreover, fructose activated ChREBP and induced G6pc in the absence of Foxo1a, indicating that carbohydrate-induced activation of ChREBP and G6PC dominates over the suppressive effects of insulin to enhance glucose production. This ChREBP/G6PC signaling axis is conserved in humans. Together, these findings support a carbohydrate-mediated, ChREBP-driven mechanism that contributes to hepatic insulin resistance.

IL-10 prevents aging-associated inflammation and insulin resistance in skeletal muscle

Tue, 12/20/2016 - 6:10pm

Altered energy balance and insulin resistance are important characteristics of aging. Skeletal muscle is a major site of glucose disposal, and the role of aging-associated inflammation in skeletal muscle insulin resistance remains unclear. To investigate, we examined glucose metabolism in 18-mo-old transgenic mice with muscle-specific overexpression of IL-10 (MIL10) and in wild-type mice during hyperinsulinemic-euglycemic clamping. Despite similar fat mass and energy balance, MIL10 mice were protected from aging-associated insulin resistance with significant increases in glucose infusion rates, whole-body glucose turnover, and skeletal muscle glucose uptake ( approximately 60%; P < 0.05), as compared to age-matched WT mice. This protective effect was associated with decreased muscle inflammation, but no changes in adipose tissue inflammation in aging MIL10 mice. These results demonstrate the importance of skeletal muscle inflammation in aging-mediated insulin resistance, and our findings further implicate a potential therapeutic role of anti-inflammatory cytokine in the treatment of aging-mediated insulin resistance.

Altered Interleukin-10 Signaling in Skeletal Muscle Regulates Obesity-Mediated Inflammation and Insulin Resistance

Tue, 12/20/2016 - 6:10pm

Skeletal muscle insulin resistance is a major characteristic of obesity and type 2 diabetes. Although obesity-mediated inflammation is causally associated with insulin resistance, the underlying mechanism is unclear. Here, we examined the effects of chronic obesity in mice with muscle-specific overexpression of interleukin-10 (MIL10). After 16 weeks of a high-fat diet (HFD), MIL10 mice became markedly obese but showed improved insulin action compared to that of wild-type mice, which was largely due to increased glucose metabolism and reduced inflammation in skeletal muscle. Since leptin regulates inflammation, the beneficial effects of interleukin-10 (IL-10) were further examined in leptin-deficient ob/ob mice. Muscle-specific overexpression of IL-10 in ob/ob mice (MCK-IL10ob/ob) did not affect spontaneous obesity, but MCK-IL10ob/ob mice showed increased glucose turnover compared to that in ob/ob mice. Last, mice with muscle-specific ablation of IL-10 receptor (M-IL10R-/-) were generated to determine whether IL-10 signaling in skeletal muscle is involved in IL-10 effects on glucose metabolism. After an HFD, M-IL10R-/- mice developed insulin resistance with reduced glucose metabolism compared to that in wild-type mice. Overall, these results demonstrate IL-10 effects to attenuate obesity-mediated inflammation and improve insulin sensitivity in skeletal muscle, and our findings implicate a potential therapeutic role of anti-inflammatory cytokines in treating insulin resistance and type 2 diabetes.

The Origin of Human White, Brown, and Brite/Beige Adipocytes

Tue, 12/20/2016 - 12:03pm

During embryonic development, adipocytes emerge from microvasculature. Lineage-­‐tracing studies in mice have shown that adipocyte progenitors reside in the adipose tissue capillaries. However, the direct evidence of an association between adipocyte progenitors and vasculature in humans is lacking. A specific class of adipocytes (brown and beige/brite) expresses the uncoupling protein 1 (UCP1), which consumes glucose and fatty acids to generate heat. The abundance of UCP1- containing adipocytes correlates with a lean metabolically healthy phenotype in human. However, a causal relationship between the presence of these cells and metabolic benefits in human is not clear.

In this thesis, I report human adipocyte progenitors proliferate in response to pro-angiogenic factors in association with adipose capillary networks in-vitro. The capillary-derived adipocytes transform from being UCP1-negative to positive upon adenylate cyclase activation, a defining feature of the brite/beige phenotype. Activated cells have denser, round mitochondria with UCP1 protein, and display uncoupled respiration. When implanted into NOD-scid IL2rgnull (NSG) mice, the adipocytes can form a vascularized fat pad that induces vascularization and becomes integrated into mouse circulatory system. In normal or high fat diet-fed NSG mice, activated brite/beige adipocytes enhance systemic glucose tolerance and improved hepatic steatosis, thus providing evidence for their potential therapeutic use. The adipocytes also express neuroendocrine and secretory factors such as Interleukin-33, proprotein convertase PCSK1 and proenkephalin PENK, which are correlated with human obesity. Finally, analyses on single-cell clones of capillary-sprout cells reveal the existence of diverse adipogenic progenitor populations. Further characterization of the clones will define the identifying features of the diverse adipocyte progenitor types that exist in human adipose tissue.

HPV Vaccine Reminders at the Point of Service: Efficacy and Missed Opportunities. A Claims Based Study within One Health Plan

Mon, 12/19/2016 - 11:50am

Introduction: Our objective is to assess HPV vaccine series completion rates, whether on-screen Point of Service reminders (POS) make a difference, and missed opportunities for reminders to have an effect.

Methods: Retrospective, claims-based study of females aged 9-26 receiving an initial dose of HPV vaccine during 2 periods: before (period 1) and after (period 2) implementation of a POS reminder system in 1(“Change Group”) of 2 physician groups using EHRs for both periods. Completion rates, and missed opportunities during eligible periods were calculated for those with continuous enrollment in the health plan investigated.

Results: Completion rates within 1 year of the 1st dose were Period 1: 47% Change Group vs. 46% Control Group (p=0.847). Period 2: 50% Change group vs. 57% Control Group (p=0.158). No significant improvement occurred between the 2 periods in either group. Differences in 1 year completion rates by specialty of initiating provider or age group (<18 or ≥18) were not significant.

During period 2, among those with continuous insurance plan enrollment in the Change Group, 43 patients received 1 dose and 46 received 2 doses. Of those receiving 1 dose, 30 (70%) had a visit to the same group within an eligible time period (median # visits: 2, range 1-20); of those completing 2 doses, 4 (9%) had a visit to the same group within an eligible period (median # visits: 1, range: 1-3). Among those receiving 1 dose, 25 (58%) had a visit to the same group and same specialty as the initial dose (median # visits: 1, range 1-8); for those having received 2 doses, 3 (6%) had a subsequent visit to same group and specialty (median # visits: 1, range 1-3).

Conclusion: POS reminder systems was not associated with improved completion rates. POS reminders are limited by infrequent visits among non-completers in an eligible period.

Wireless Health

Mon, 12/19/2016 - 11:23am

Publisher's description: This book provides a candid assessment and practical knowledge about the current technological advancements of the wireless healthcare system. This book presents the competencies of modeling e-health framework, medical wireless body sensor networks, communication technologies for mobile health, nanotechnology innovations in medicine, security issues for medical records, personalized services in healthcare applications, and Big Data for wireless health.
This book covers multiple research perspectives in order to address the strong need for interdisciplinary research in the area of wireless health, such as the interactive research among biomedical sensor technology, intelligent textiles and advanced wireless network technology. The interactions involve experts from multidisciplinary fields including medical, information technology and computing fields. Designed as a study tool for graduate students, researchers, and medical professionals, this book is also valuable for business managers, entrepreneurs, and investors within the medical and healthcare industries. It is useful for anyone who cares about the future opportunities in healthcare systems.

Endoplasmic reticulum stress-induced hepatocellular death pathways mediate liver injury and fibrosis via Stimulator of Interferon Genes.

Mon, 12/19/2016 - 11:00am

Fibrosis, driven by inflammation, marks the transition from benign to progressive stages of chronic liver diseases. Although inflammation promotes fibrogenesis, it is not known whether other events, such as hepatocyte death, are required for the development of fibrosis. Interferon Regulatory Factor 3 (IRF3) regulates hepatocyte apoptosis and production of Type-I interferons (IFNs). In the liver, IRF3 is activated via Toll-like receptor 4 (TLR4) signaling or the ER adapter, Stimulator of Interferon Genes (STING). We hypothesized that IRF3-mediated hepatocyte death is an independent determinant of chemically-induced liver fibrogenesis. To test this, we performed acute or chronic carbontetrachloride (CCl4) administration to WT, IRF3-, TRAM-, TRIF-, and STING-deficient mice. We report that acute CCl4 administration to WT mice resulted in early ER stress, activation of IRF3 and Type-I IFNs, followed by hepatocyte apoptosis and liver injury, accompanied by liver fibrosis upon repeated administration of CCl4. Deficiency of IRF3 or STING prevented hepatocyte death and fibrosis both in acute or chronic CCl4. In contrast, mice deficient in Type-I IFN receptors or in TLR4-signaling adaptors, TRAM or TRIF, upstream of IRF3, were not protected from hepatocyte death and/or fibrosis suggesting that the pro-apoptotic role of IRF3 is independent of TLR signaling in fibrosis. Hepatocyte death is required for liver fibrosis with causal involvement of STING and IRF3. Thus, our results identify that IRF3, by its association with STING in the presence of ER stress, couples hepatocyte apoptosis with liver fibrosis, and indicate that innate immune signaling modulates outcomes of liver fibrosis via modulation of hepatocyte death in the liver.

Charting a New Path: The Evolution of the Journal of eScience Librarianship

Fri, 12/16/2016 - 1:21pm

The Journal of eScience Librarianship (JeSLIB) has been successful in providing quality and timely scholarship in the area of data science and library services. However, it is a wise strategy to gather feedback and suggestions from readership when planning future changes and initiatives.

Librarian as Researcher

Wed, 12/14/2016 - 12:00pm

In this webinar, four Institute for Research Design in Librarianship (IRDL) scholars shared how their research projects have developed over time, the IRDL application process, and how participants can also embrace the Librarian as Researcher role. This session reviewed the IRDL 2017 call for applications, and discussed how librarians with a passion for research and a desire to improve their research skills may utilize IRDL.

Macrophages Are Regulators of Whole Body Metabolism: A Dissertation

Mon, 12/12/2016 - 10:54am

Obesity is the top risk factor for the development of type 2 diabetes mellitus in humans. Obese adipose tissue, particularly visceral depots, exhibits an increase in macrophage accumulation and is described as being in a state of chronic low-grade inflammation. It is characterized by the increased expression and secretion of inflammatory cytokines produced by both macrophages and adipocytes, and is associated with the development of insulin resistance. Based on these observations, we investigated the potential role of macrophage infiltration on whole body metabolism, using genetic and diet-induced mouse models of obesity.

Using flow cytometry and immunofluorescence imaging we found that a significant percentage of macrophages proliferate locally in adipose tissue of obese mice. Importantly, we identified monocyte chemoattractant protein 1 (MCP-1) as the stimulating factor. We also found that ATMs can be targeted for specific gene silencing using glucan encapsulated siRNA particles (GeRPs). Knockdown of the cytokine osteopontin improved regulation of systemic glucose levels as well as insulin signaling in adipocytes. Conversely, targeting lipoprotein lipase (LPL) abrogated the buffering of lipid spillover from adipose tissue, resulting in increased hepatic glucose output. Finally, silencing of the master regulator of inflammation NF-κB in resident liver macrophages called Kupffer cells significantly improved hepatic insulin signaling. Thus this work demonstrates that macrophages can regulate whole body metabolism.

Identification of Essential Metabolic and Genetic Adaptations to the Quiescent State in Mycobacterium Tuberculosis: A Dissertation

Mon, 12/12/2016 - 10:54am

Mycobacterium tuberculosis stably adapts to respiratory limited environments by entering into a nongrowing but metabolically active state termed quiescence. This state is inherently tolerant to antibiotics due to a reduction in growth and activity of associated biosynthetic pathways. Understanding the physiology of the quiescent state, therefore, may be useful in developing new strategies to improve drug efficiency. Here, we used an established in vitro model of respiratory stress, hypoxia, to induce quiescence. We utilized metabolomic and genetic approaches to identify essential and active pathways associated with nongrowth. Our metabolomic profile of hypoxic M. tuberculosis revealed an increase in several free fatty acids, metabolite intermediates in the oxidative pathway of the tricarboxylic acid (TCA) cycle, as well as, the important chemical messenger, cAMP. In tandem, a high-throughput transposon mutant library screen (TnSeq) revealed that a cAMP-regulated protein acetyltransferase, MtPat, was conditionally essential for survival in the hypoxic state. Via 13C-carbon flux tracing we show an MtPat mutant is deficient in re-routing hypoxic metabolism away from the oxidative TCA cycle and that MtPat is involved in inhibiting fatty-acid catabolism in hypoxia. Additionally, we show that reductive TCA metabolism is required for survival of hypoxia by depletion of an essential TCA enzyme, malate dehydrogenase (Mdh) both in in vitro hypoxia and in vivo mouse infection. Inhibition of Mdh with a novel compound resulted in a significantly greater killing efficiency than the first-line anti-M. tuberculosis drug isoniazid (INH). In conclusion, we show that understanding the physiology of the quiescent state can lead to new drug targets for M. tuberculosis.

Imaging in the Lion City: Singapore Radiology Country Report

Fri, 12/09/2016 - 2:50pm

Singapore is a small tropical island city-state with limited natural resources that has achieved remarkable healthcare outcomes through effective long-term planning and judicious investment in human resources and technology. A full-range of medical imaging services is available in the country, with integrated care delivered to patients through a network of both government and private hospitals. Training in diagnostic radiology, interventional radiology, nuclear medicine and diagnostic radiography continue to evolve in Singapore, with an aim to further increase the range of subspecialty medical imaging services available and address projected challenges for the healthcare system in the future, such as an aging population. Continued government investment in technology and biomedical imaging is expected to further expand the scope and depth of medical imaging services in the future.

Creating a campus-wide research data services committee: The good, The bad, and The…... Part 2: Launching your collaboration

Thu, 12/08/2016 - 3:58pm

A panel of presenters in this two-part webinar series shared their experiences about how academic libraries are taking the lead in developing cross-campus collaborations in establishing research data committees to spearhead institutional efforts related to data stewardship and digital projects. This interactive session lead participants through the various steps needed in order to initiate a similar effort within their institutional context.

Part 2: Launching your collaboration

Learning Objectives:

  • Identify best practices and lessons learned for working with established committees who are working on broad-scale projects and programs
  • Evaluate different institutional models to compare and customize for different academic environments
  • Analyze best practices strategies for successful project management, collaboration, and program development for established committees

Creating a campus-wide research data services committee: The good, The bad, and The...... Part 1: Building bridges and planting seeds

Thu, 12/08/2016 - 3:58pm

A panel of presenters in this two-part webinar series shared their experiences about how academic libraries are taking the lead in developing cross-campus collaborations in establishing research data committees to spearhead institutional efforts related to data stewardship and digital projects. This interactive session lead participants through the various steps needed in order to initiate a similar effort within their institutional context.

Part 1: Building bridges and planting seeds

Learning Objectives:

  • Focus on early-stage efforts to build partnerships and bring key stakeholders to the table
  • Acquire practical tips for addressing the institutional challenges involved in developing a campus-wide data committee
  • Identify key individuals who could be instrumental in establishing a campus-wide data committee

Central IRBs: Enhanced Protections for Research Participants

Thu, 12/08/2016 - 10:14am

Institutional Review Boards (IRBs) play a critical role in research, and assure safety and fairness to participants enrolled in research studies. Multisite studies are often reviewed by multiple IRBs (an IRB review at each site participating in the study), which can slow down study approval, result in duplication of effort, and occasionally produce contradictory decisions by different IRBs. To address these problems, the federal government has promoted the use of single IRBs (referred to as Central IRBs or CIRBs), where a single IRB is responsible for the review of all sites where the research study is conducted. The National Institutes of Health (NIH) has recently announced that beginning in 2017 all research conducted at multiple sites must be reviewed by a CIRB. This CIRB process is new and requires careful study to understand its pitfalls and benefits. As such, UMass Medical School and Columbia University received a (NIH) grant to study how different institutions conduct reviews of research involving multiple sites.