Integrative Genomics Viewer

Author Manuscript 2012 May 07.To the Editor: Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.National Institute of General Medical Sciences (U.S.) (R01GM074024)National Cancer Institute (U.S.) (R21CA135827)National Human Genome Research Institute (U.S.) (U54HG003067

Small molecule activators of SIRT1 replicate signaling pathways triggered by calorie restriction in vivo

<p>Abstract</p> <p>Background</p> <p>Calorie restriction (CR) produces a number of health benefits and ameliorates diseases of aging such as type 2 diabetes. The components of the pathways downstream of CR may provide intervention points for developing therapeutics for treating diseases of aging. The NAD⁺-dependent protein deacetylase SIRT1 has been implicated as one of the key downstream regulators of CR in yeast, rodents, and humans. Small molecule activators of SIRT1 have been identified that exhibit efficacy in animal models of diseases typically associated with aging including type 2 diabetes. To identify molecular processes induced in the liver of mice treated with two structurally distinct SIRT1 activators, SIRT501 (formulated resveratrol) and SRT1720, for three days, we utilized a systems biology approach and applied Causal Network Modeling (CNM) on gene expression data to elucidate downstream effects of SIRT1 activation.</p> <p>Results</p> <p>Here we demonstrate that SIRT1 activators recapitulate many of the molecular events downstream of CR <it>in vivo</it>, such as enhancing mitochondrial biogenesis, improving metabolic signaling pathways, and blunting pro-inflammatory pathways in mice fed a high fat, high calorie diet.</p> <p>Conclusion</p> <p>CNM of gene expression data from mice treated with SRT501 or SRT1720 in combination with supporting <it>in vitro </it>and <it>in vivo </it>data demonstrates that SRT501 and SRT1720 produce a signaling profile that mirrors CR, improves glucose and insulin homeostasis, and acts via SIRT1 activation <it>in vivo</it>. Taken together these results are encouraging regarding the use of small molecule activators of SIRT1 for therapeutic intervention into type 2 diabetes, a strategy which is currently being investigated in multiple clinical trials.</p

Intermittent auscultation versus continuous fetal monitoring: Exploring factors that influence birthing unit nurses' fetal surveillance practice using theoretical domains framework

Background: Intermittent Auscultation (IA) is the recommended method of fetal surveillance for healthy women in labour. However, the majority of women receive continuous electronic monitoring. We used the Theoretical Domains Framework (TDF) to explore the views of Birthing Unit nurses about using IA as their primary method of fetal surveillance for healthy women in labour. Methods: Using a semi-structured interview guide, we interviewed a convenience sample of birthing unit nurses throughout Ontario, Canada to elicit their views about fetal surveillance. Interviews were recorded and transcribed verbatim. Transcripts were content analysed using the TDF and themes were framed as belief statements. Domains potentially key to changing fetal surveillance behaviour and informing intervention design were identified by noting the frequencies of beliefs, content, and their reported influence on the use of IA Results: We interviewed 12 birthing unit nurses. Seven of the 12 TDF domains were perceived to be key to changing birthing unit nurses' behaviour The nurses reported that competing tasks, time constraints and the necessity to multitask often limit their ability to perform IA (domains Beliefs about capabilities; Environmental context and resources). Some nurses noted the decision to use IA was something that they consciously thought about with every patient while others stated it their default decision as long as there were no risk factors (Memory, attention and decision processes, Nature of behaviour). They identified positive consequences (e.g. avoid unnecessary interventions, mother-centered care) and negative consequences of using IA (e.g. legal concerns) and reported that the negative consequences can often outweigh positive consequences (Beliefs about consequences). Some reported that hospital policies and varying support from care teams inhibited their use of IA (Social influences), and that support from the entire team and hospital management would likely increase their use (Social influences; Behavioural regulation). Conclusion: We identified potential influences on birthing unit nurses' use of IA as their primary method of fetal surveillance. These beliefs suggest potential targets for behaviour change interventions to promote IA use

Developing and pre-testing a decision board to facilitate informed choice about delivery approach in uncomplicated pregnancy

<p>Abstract</p> <p>Background</p> <p>The rate of caesarean sections is increasing worldwide, yet medical literature informing women with uncomplicated pregnancies about relative risks and benefits of elective caesarean section (CS) compared with vaginal delivery (VD) remains scarce. A decision board may address this gap, providing systematic evidence-based information so that patients can more fully understand their treatment options. The objective of our study was to design and pre-test a decision board to guide clinical discussions and enhance informed decision-making related to delivery approach (CS or VD) in uncomplicated pregnancy.</p> <p>Methods</p> <p>Development of the decision board involved two preliminary studies to determine women's preferred mode of risk presentation and a systematic literature review for the most comprehensive presentation of medical risks at the time (VD and CS). Forty women were recruited to pre-test the tool. Eligible subjects were of childbearing age (18-40 years) but were not pregnant in order to avoid raising the expectation among pregnant women that CS was a universally available birth option. Women selected their preferred delivery approach and completed the Decisional Conflict Scale to measure decisional uncertainty before and after reviewing the decision board. They also answered open-ended questions reflecting what they had learned, whether or not the information had helped them to choose between birth methods, and additional information that should be included. Descriptive statistics were used to analyse sample characteristics and women's choice of delivery approach pre/post decision board. Change in decisional conflict was measured using Wilcoxon's sign rank test for each of the three subscales.</p> <p>Results</p> <p>The majority of women reported that they had learned something new (n = 37, 92%) and that the tool had helped them make a hypothetical choice between delivery approaches (n = 34, 85%). Women wanted more information about neonatal risks and personal experiences. Decisional uncertainty decreased (p < 0.001) and perceived effectiveness of decisions increased (p < 0.001) post-intervention.</p> <p>Conclusion</p> <p>Non-pregnant women of childbearing age were positive about the decision board and stated their hypothetical delivery choices were informed by risk presentation, but wanted additional information about benefits and experiences. This study represents a preliminary but integral step towards ensuring women considering delivery approaches in uncomplicated pregnancies are fully informed.</p

Communication and cross-examination in court for children and adults with intellectual disabilities: A systematic review

Courts in England, Wales and Northern Ireland have identified children and adults with intellectual disabilities (ID) as vulnerable witnesses. The call from the English Court of Appeal is for advocates to adjust questioning during cross-examination according to individual needs. This review systematically examined previous empirical studies with the aim of delineating the particular communication needs of children and adults with ID during cross-examination. Studies utilising experimental methodology similar to examination/cross-examination processes, or which assessed the communication of actual cross-examinations in court were included. A range of communication challenges were highlighted including: suggestibility to leading questions and negative feedback; acquiescence; accuracy; and understanding of court language. In addition, a number of influencing factors were identified, including: age; IQ level; question styles used; recall memory; and delays. This review highlights the need for further research using cross-examination methodology and live practice, that take into consideration the impact on communication of the unique environment and situation of the cross-examination process

Role of the Candida albicans MNN1 gene family in cell wall structure and virulence

Background The Candida albicans cell wall is the first point of contact with the host, and its outer surface is heavily enriched in mannoproteins modified through the addition of N- and O-mannan. Previous work, using mutants with gross defects in glycosylation, has clearly identified the importance of mannan in the host-pathogen interaction, immune recognition and virulence. Here we report the first analysis of the MNN1 gene family, which contains six members predicted to act as α-1,3 mannosyltransferases in the terminal stages of glycosylation. Findings We generated single null mutants in all members of the C. albicans MNN1 gene family, and disruption of MNN14 led to both in vitro and in vivo defects. Null mutants in other members of the family demonstrated no phenotypic defects, suggesting that these members may display functional redundancy. The mnn14Δ null mutant displayed hypersensitivity to agents associated with cell wall and glycosylation defects, suggesting an altered cell wall structure. However, no gross changes in cell wall composition or N-glycosylation were identified in this mutant, although an extension of phosphomannan chain length was apparent. Although the cell wall defects associated with the mnn14Δ mutant were subtle, this mutant displayed a severe attenuation of virulence in a murine infection model. Conclusion Mnn14 plays a distinct role from other members of the MNN1 family, demonstrating that specific N-glycan outer chain epitopes are required in the host-pathogen interaction and virulence

Genome-wide meta-analysis identifies five new susceptibility loci for pancreatic cancer.

In 2020, 146,063 deaths due to pancreatic cancer are estimated to occur in Europe and the United States combined. To identify common susceptibility alleles, we performed the largest pancreatic cancer GWAS to date, including 9040 patients and 12,496 controls of European ancestry from the Pancreatic Cancer Cohort Consortium (PanScan) and the Pancreatic Cancer Case-Control Consortium (PanC4). Here, we find significant evidence of a novel association at rs78417682 (7p12/TNS3, P = 4.35 × 10-8). Replication of 10 promising signals in up to 2737 patients and 4752 controls from the PANcreatic Disease ReseArch (PANDoRA) consortium yields new genome-wide significant loci: rs13303010 at 1p36.33 (NOC2L, P = 8.36 × 10-14), rs2941471 at 8q21.11 (HNF4G, P = 6.60 × 10-10), rs4795218 at 17q12 (HNF1B, P = 1.32 × 10-8), and rs1517037 at 18q21.32 (GRP, P = 3.28 × 10-8). rs78417682 is not statistically significantly associated with pancreatic cancer in PANDoRA. Expression quantitative trait locus analysis in three independent pancreatic data sets provides molecular support of NOC2L as a pancreatic cancer susceptibility gene

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead