Nuclear Receptor HNF4α Binding Sequences are Widespread in Alu Repeats

<p>Abstract</p> <p>Background</p> <p>Alu repeats, which account for ~10% of the human genome, were originally considered to be junk DNA. Recent studies, however, suggest that they may contain transcription factor binding sites and hence possibly play a role in regulating gene expression.</p> <p>Results</p> <p>Here, we show that binding sites for a highly conserved member of the nuclear receptor superfamily of ligand-dependent transcription factors, hepatocyte nuclear factor 4alpha (HNF4α, NR2A1), are highly prevalent in Alu repeats. We employ high throughput protein binding microarrays (PBMs) to show that HNF4α binds > 66 unique sequences in Alu repeats that are present in ~1.2 million locations in the human genome. We use chromatin immunoprecipitation (ChIP) to demonstrate that HNF4α binds Alu elements in the promoters of target genes (<it>ABCC3, APOA4, APOM, ATPIF1, CANX, FEMT1A, GSTM4, IL32, IP6K2, PRLR, PRODH2, SOCS2, TTR</it>) and luciferase assays to show that at least some of those Alu elements can modulate HNF4α-mediated transactivation <it>in vivo </it>(<it>APOM, PRODH2, TTR, APOA4</it>). HNF4α-Alu elements are enriched in promoters of genes involved in RNA processing and a sizeable fraction are in regions of accessible chromatin. Comparative genomics analysis suggests that there may have been a gain in HNF4α binding sites in Alu elements during evolution and that non Alu repeats, such as Tiggers, also contain HNF4α sites.</p> <p>Conclusions</p> <p>Our findings suggest that HNF4α, in addition to regulating gene expression via high affinity binding sites, may also modulate transcription via low affinity sites in Alu repeats.</p

Improving Women&rsquo;s Opportunities to Succeed in the Workplace: Addressing Workplace Policies in Support of Menstrual Health and Hygiene in Two Kenyan Factories

Women globally experience challenges managing their periods, especially those living in environments that do not support adequate menstrual health and hygiene (MHH). For working women, these challenges may have critical implications for their health, well-being, and economic outcomes (e.g., earnings). As part of a larger initiative that sought to understand the relationship between MHH and women&rsquo;s economic empowerment, a policy analysis was conducted in two workplaces in Kenya to identify policy changes that would better support menstruating employees&rsquo; MHH needs. Policy analysis findings were synthesized with relevant baseline research findings from the same study to generate policy recommendations for participating companies. Key findings revealed limitations in hiring and induction processes, employee classification, representation and voice, toilet access, sick leave, and supervisor codes of conduct, all of which affected menstruating employees. Recommendations included updating supervisor codes of conduct, increasing women&rsquo;s representation in union committees, and strengthening employee induction processes. Priority areas for policy changes were shared with companies&rsquo; leadership, alongside technical assistance for implementation. Insight from two private-sector workplaces in Kenya offers guidance on how to identify relevant policy gaps and institutionalize policies and practices that promote adequate workplace MHH in pursuit of women&rsquo;s economic empowerment and improved business outcomes

Longitudinal Study of Nutrient and Food Intakes of White Preschool Children Aged 24 to 60 Months

Objective: To determine nutrient and food intakes of 72 white preschool children primarily from families of middle and upper socioeconomic status and to compare children\u27s nutrient intakes with current recommendations. Design: Six in-home interviews were conducted with mothers when children were 24 to 60 months old; at each time mothers provided 3 days of dietary information on the child. Children and mothers independently provided information on the child\u27s favorite and least favorite foods at 42 and 54 months. Subjects: Preschool children (24 to 60 months old) participating in a longitudinal study. Statistical analyses: Mean nutrient intakes were compared with the most recent Recommended Dietary Allowances/Adequate Intakes. Differences over time were tested with repeated-measures analysis of variance; gender differences were determined with t tests. Food frequencies (ie, percentage of children consuming specific foods) were determined from dietary recalls and food records. Dietary variety was assessed with the Variety Index for Toddlers or the Variety Index for Children. Results: Means were consistently less than the RDA/AI for energy, zinc, folate, and vitamins D and E. Energy, carbohydrate, and fat intakes were highest (P≤.01) at 60 months. Boys consumed more (P≤.05) protein (10 g), calcium (197 mg), magnesium (35 mg), and pantothenic acid (0.8 mg) at 60 months than did girls. Foods most commonly eaten were fruit drink, carbonated beverages, 2% milk, and french fries. The vegetable group consistently had the lowest variety scores; vegetables also dominated least favorite foods lists. Applications: Parents need to be encouraged to include more sources of zinc, folate, vitamin E, and vitamin D in children\u27s diets. Parents should also encourage their children to eat more vegetables, zinc- and folate-fortified cereals, lean red meats, seafood, vegetable oils, and low-fat milk

Longitudinal Study of Nutrient and Food Intakes of White Preschool Children Aged 24 to 60 Months

Objective: To determine nutrient and food intakes of 72 white preschool children primarily from families of middle and upper socioeconomic status and to compare children\u27s nutrient intakes with current recommendations. Design: Six in-home interviews were conducted with mothers when children were 24 to 60 months old; at each time mothers provided 3 days of dietary information on the child. Children and mothers independently provided information on the child\u27s favorite and least favorite foods at 42 and 54 months. Subjects: Preschool children (24 to 60 months old) participating in a longitudinal study. Statistical analyses: Mean nutrient intakes were compared with the most recent Recommended Dietary Allowances/Adequate Intakes. Differences over time were tested with repeated-measures analysis of variance; gender differences were determined with t tests. Food frequencies (ie, percentage of children consuming specific foods) were determined from dietary recalls and food records. Dietary variety was assessed with the Variety Index for Toddlers or the Variety Index for Children. Results: Means were consistently less than the RDA/AI for energy, zinc, folate, and vitamins D and E. Energy, carbohydrate, and fat intakes were highest (P≤.01) at 60 months. Boys consumed more (P≤.05) protein (10 g), calcium (197 mg), magnesium (35 mg), and pantothenic acid (0.8 mg) at 60 months than did girls. Foods most commonly eaten were fruit drink, carbonated beverages, 2% milk, and french fries. The vegetable group consistently had the lowest variety scores; vegetables also dominated least favorite foods lists. Applications: Parents need to be encouraged to include more sources of zinc, folate, vitamin E, and vitamin D in children\u27s diets. Parents should also encourage their children to eat more vegetables, zinc- and folate-fortified cereals, lean red meats, seafood, vegetable oils, and low-fat milk

A systematic review of the literature on counselling and psychotherapy for the prevention of suicide 1 : Quantitative outcome and process studies

Scope of review: The paper reports a meta-review of 15 previous systematic reviews and meta-analyses of the literature concerning the outcome of counselling and psychotherapy with people at risk of suicide; a meta-analysis of 67 outcome studies in this area; and a narrative review of 17 studies of the therapeutic process. Publication time span: The literature reviewed was published between 1981 and 2008. Publication origin: The majority of the literature reviewed was by authors from the USA or the UK, but there were also authors from other European countries, Australia, Canada, India, and Sri Lanka. Findings: There is evidence of the effectiveness of dialectical behaviour therapy, cognitive-behavioural therapy, and problem solving therapy, but also for other forms of therapy. Therapist and client variables, as well as the therapeutic relationship, appear to be related to treatment outcome. Conclusions: People at risk of suicide should have access to psychological interventions, including, but not necessarily limited to, those within the cognitive-behavioural spectrum. Therapies for which there have been promising findings, but which are under-researched, should be a research priority.Peer reviewe

Reference genome and demographic history of the most endangered marine mammal, the vaquita.

The vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline for more than 20&nbsp;years resulting from inadvertent deaths due to the increasing use of large-mesh gillnets. To understand the evolutionary and demographic history of the vaquita, we used combined long-read sequencing and long-range scaffolding methods with long- and short-read RNA sequencing to generate a near error-free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome-length autosome scaffolds and the X-chromosome scaffold, with a scaffold N50 of 115&nbsp;Mb. Genome-wide heterozygosity is the lowest (0.01%) of any mammalian species analysed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long-term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long-term population stability at less than 5,000 (Ne) for over 200,000&nbsp;years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health