Sequence and Target Specificity of the C. elegans Cell Fate Specification Factor POS-1: A Dissertation

In most metazoans, early embryogenesis is controlled by the translational regulation of maternally supplied mRNA. Sequence-specific RNA-binding proteins play an important role in regulating early embryogenesis, yet their specificities and regulatory targets are largely unknown. To understand how these RNA-binding proteins select their targets, my research focused on the C. elegans CCCH-type tandem zinc finger protein POS-1. Embryos lacking maternally supplied POS-1 die prior to gastrulation, and exhibit defects in the specification of pharyngeal, intestinal, and germline precursor cells. To identify the regulatory targets that contribute to the POS-1 mutant phenotype, we set out to determine the sequence specificity of POS-1 in vitro, and then use this information to identify regulatory targets in vivo. Using a candidate-based search, we identified a twelve-nucleotide fragment of the mex-3 3\u27 untranslated region (3\u27 UTR) to which POS-1 binds with high affinity. Using quantitative fluorescent electrophoretic mobility shift assays, I determined the affinity of the RNA-binding domain of POS-1 for a panel of single nucleotide mutations of this sequence, and then defined a consensus binding element based on this dataset. POS-1 recognizes the degenerate element UAU 2-3 RDN 1-3 G, where R is any purine (adenosine or guanine), and D is any base except cytosine. A bioinformatics analysis revealed the presence of this element in approximately 40% of C. elegans 3\u27 UTRs, suggesting that POS-1 is capable of binding to and perhaps regulating many transcripts in vivo. POS-1 binding sites alone are not sufficient to pattern the expression of a reporter, suggesting that other factors may contribute to POS-1 specificity. To address the mechanism of POS-1-mediated translational regulation, I investigated the translational regulation of the C. elegans Notch homolog glp-1. Previous work demonstrated that glp-1 translation is repressed in the early embryo in a POS-1-dependent fashion, though it was not clear if this regulation was direct. The glp-1 3\u27 UTR contains two POS-1 binding sites within five nucleotides of each other, and these sites are within a thirty nucleotide region of the 3\u27 UTR required for proper spatiotemporal translation of glp-1. The POS-1 sites overlap with a negative regulatory element that is recognized by GLD-1, and a positive regulatory element recognized by an unknown factor. Both POS-1 and GLD-1 bind to an RNA containing these sites in vitro, and POS-1 competes with GLD-1 for binding. Both proteins are required for translational repression of a glp-1 3\u27 UTR reporter in embryos. Furthermore, only one of the two POS-1 binding sites is required for repression, and the required site is wholly contained within a previously characterized positive regulatory element. Based on this, we propose that POS-1 does not regulate its targets by recruiting regulatory machinery, but instead by competing with factors that do. Thus, sites of POS-1 regulation are highly context dependent, which may contribute to POS-1 specificity

POS-1 and GLD-1 repress glp-1 translation through a conserved binding-site cluster

RNA-binding proteins (RBPs) coordinate cell fate specification and differentiation in a variety of systems. RNA regulation is critical during oocyte development and early embryogenesis, in which RBPs control expression from maternal mRNAs encoding key cell fate determinants. The Caenorhabditis elegans Notch homologue glp-1 coordinates germline progenitor cell proliferation and anterior fate specification in embryos. A network of sequence-specific RBPs is required to pattern GLP-1 translation. Here, we map the cis-regulatory elements that guide glp-1 regulation by the CCCH-type tandem zinc finger protein POS-1 and the STAR-domain protein GLD-1. Our results demonstrate that both proteins recognize the glp-1 3\u27 untranslated region (UTR) through adjacent, overlapping binding sites and that POS-1 binding excludes GLD-1 binding. Both factors are required to repress glp-1 translation in the embryo, suggesting that they function in parallel regulatory pathways. It is intriguing that two equivalent POS-1-binding sites are present in the glp-1 3\u27 UTR, but only one, which overlaps with a translational derepression element, is functional in vivo. We propose that POS-1 regulates glp-1 mRNA translation by blocking access of other RBPs to a key regulatory sequence

Calmodulation meta-analysis: Predicting calmodulin binding via canonical motif clustering

The calcium-binding protein calmodulin (CaM) directly binds to membrane transport proteins to modulate their function in response to changes in intracellular calcium concentrations. Because CaM recognizes and binds to a wide variety of target sequences, identifying CaM-binding sites is difficult, requiring intensive sequence gazing and extensive biochemical analysis. Here, we describe a straightforward computational script that rapidly identifies canonical CaM-binding motifs within an amino acid sequence. Analysis of the target sequences from high resolution CaM-peptide structures using this script revealed that CaM often binds to sequences that have multiple overlapping canonical CaM-binding motifs. The addition of a positive charge discriminator to this meta-analysis resulted in a tool that identifies potential CaM-binding domains within a given sequence. To allow users to search for CaM-binding motifs within a protein of interest, perform the meta-analysis, and then compare the results to target peptide-CaM structures deposited in the Protein Data Bank, we created a website and online database. The availability of these tools and analyses will facilitate the design of CaM-related studies of ion channels and membrane transport proteins

Laser microraman study of reduced synthesized spinel powders

The Raman effect is the excitation or de-excitation of vibrational modes resulting from the inelastic scattering of light from a gas, liquid, or solid with a shift in energy from that of the usually incident radiation. Raman microscopy was performed on synthesized spinel powders of solid solution FexCr3-xO4 to determine the dependence of the vibrational modes upon the metal cations. The powders were synthesized in a combustion reaction using metal nitrates and urea. The oxide powders were reduced in a hydrogen/argon gas flow at high temperature

Promoting the achievement in schools of children and young people in care

As of March 2017, there were 72,670 children and young people in care in England. The number of looked after children has continued to increase steadily over the last eight years. Sixty per cent of these children are in care because of abuse or neglect and three-quarters are placed in foster care arrangements. Children and young people who are in or have experienced care remain one of the lowest performing groups in terms of educational outcomes. The average Attainment 8 score for children in care is 19.3 compared to 44.5 for non-looked after children and 19.3 for children in need. In 2017 there was an increase in the percentage of children in care achieving a pass in English and Mathematics from 17.4% to 17.5% and also in entering EBacc. Care leavers can experience poorer employment and health outcomes after leaving school compared to their peers. They are over-represented amongst the offender population and those who experience homelessness. However, research is emerging to show that children and young people in care can have very positive experiences of school if they are supported effectively to reach their full potential academically and socially. The purpose of this report is to share practice in local authorities (LA) from across England and Wales that is contributing to improved outcomes and school experiences for children and young people in care. The case studies were all undertaken as part of the Promoting the Achievement of Looked after Children (PALAC) programme between 2014 and 2017. This report presents an account of the programme, including the activities undertaken by the participants and the outcomes of the programme to date for pupils in care and staff in the participating virtual schools (VS) and local authorities

Trametinib versus standard of care in patients with recurrent low-grade serous ovarian cancer (GOG 281/LOGS): a randomised, open-label phase 2/3 trial

BACKGROUND: Low-grade serous carcinoma of the ovary or peritoneum is characterised by MAPK pathway aberrations and its reduced sensitivity to chemotherapy relative to high-grade serous carcinoma. We compared the MEK inhibitor trametinib to physician's choice standard of care in patients with recurrent low-grade serous carcinoma. METHODS: This international, randomised, open-label, multicentre, phase 2/3 trial was done at 84 hospitals in the USA and UK. Eligible patients were aged 18 years or older with recurrent low-grade serous carcinoma and measurable disease, as defined by Response Evaluation Criteria In Solid Tumors version 1.1, had received at least one platinum-based regimen, but not all five standard-of-care drugs, and had received an unlimited number of previous regimens. Patients with serous borderline tumours or tumours containing low-grade serous and high-grade serous carcinoma were excluded. Eligible patients were randomly assigned (1:1) to receive either oral trametinib 2 mg once daily (trametinib group) or one of five standard-of-care treatment options (standard-of-care group): intravenous paclitaxel 80 mg/m(2) by body surface area on days 1, 8, and 15 of every 28-day cycle; intravenous pegylated liposomal doxorubicin 40–50 mg/m(2) by body surface area once every 4 weeks; intravenous topotecan 4 mg/m(2) by body surface area on days 1, 8, and 15 of every 28-day cycle; oral letrozole 2·5 mg once daily; or oral tamoxifen 20 mg twice daily. Randomisation was stratified by geographical region (USA or UK), number of previous regimens (1, 2, or ≥3), performance status (0 or 1), and planned standard-of-care regimen. The primary endpoint was investigator-assessed progression-free survival while receiving randomised therapy, as assessed by imaging at baseline, once every 8 weeks for 15 months, and then once every 3 months thereafter, in the intention-to-treat population. Safety was assessed in patients who received at least one dose of study therapy. This trial is registered with ClinicalTrials.gov, NCT02101788, and is active but not recruiting. FINDINGS: Between Feb 27, 2014, and April 10, 2018, 260 patients were enrolled and randomly assigned to the trametinib group (n=130) or the standard-of-care group (n=130). At the primary analysis, there were 217 progression-free survival events (101 [78%] in the trametinib group and 116 [89%] in the standard-of-care group). Median progression-free survival in the trametinib group was 13·0 months (95% CI 9·9–15·0) compared with 7·2 months (5·6–9·9) in the standard-of-care group (hazard ratio 0·48 [95% CI 0·36–0·64]; p<0·0001). The most frequent grade 3 or 4 adverse events in the trametinib group were skin rash (17 [13%] of 128), anaemia (16 [13%]), hypertension (15 [12%]), diarrhoea (13 [10%]), nausea (12 [9%]), and fatigue (ten [8%]). The most frequent grade 3 or 4 adverse events in the standard-of-care group were abdominal pain (22 [17%]), nausea (14 [11%]), anaemia (12 [10%]), and vomiting (ten [8%]). There were no treatment-related deaths. INTERPRETATION: Trametinib represents a new standard-of-care option for patients with recurrent low-grade serous carcinoma. FUNDING: NRG Oncology, Cancer Research UK, Target Ovarian Cancer, and Novartis

Spatial and Sex-Specific Variation in Growth of Albacore Tuna (Thunnus alalunga) across the South Pacific Ocean

Spatial variation in growth is a common feature of demersal fish populations which often exist as discrete adult sub-populations linked by a pelagic larval stage. However, it remains unclear whether variation in growth occurs at similar spatial scales for populations of highly migratory pelagic species, such as tuna. We examined spatial variation in growth of albacore Thunnus alalunga across 90° of longitude in the South Pacific Ocean from the east coast of Australia to the Pitcairn Islands. Using length-at-age data from a validated ageing method we found evidence for significant variation in length-at-age and growth parameters (L∞ and k) between sexes and across longitudes. Growth trajectories were similar between sexes up until four years of age, after which the length-at-age for males was, on average, greater than that for females. Males reached an average maximum size more than 8 cm larger than females. Length-at-age and growth parameters were consistently greater at more easterly longitudes than at westerly longitudes for both females and males. Our results provide strong evidence that finer spatial structure exists within the South Pacific albacore stock and raises the question of whether the scale of their “highly migratory” nature should be re-assessed. Future stock assessment models for South Pacific albacore should consider sex-specific growth curves and spatial variation in growth within the stock

Adherence to antiretroviral therapy in young children in Cape Town, South Africa, measured by medication return and caregiver self-report: a prospective cohort study

<p>Abstract</p> <p>Background</p> <p>Antiretroviral therapy (ART) dramatically improves outcomes for children in Africa; however excellent adherence is required for treatment success. This study describes the utility of different measures of adherence in detecting lapses in infants and young children in Cape Town, South Africa.</p> <p>Methods</p> <p>In a prospective cohort of 122 HIV-infected children commenced on ART, adherence was measured monthly during the first year of treatment by medication return (MR) for both syrups and tablets/capsules. A questionnaire was administered to caregivers after 3 months of treatment to assess experience with giving medication and self-reported adherence. Viral and immune response to treatment were assessed at the end of one year and associations with measured adherence determined.</p> <p>Results</p> <p>Medication was returned for 115/122 (94%) children with median age (IQR) of 37 (16 – 61) months. Ninety-one (79%) children achieved annual average MR adherence ≥ 90%. This was an important covariate associated with viral suppression after adjustment for disease severity (OR = 5.5 [95%CI: 0.8–35.6], p = 0.075), however was not associated with immunological response to ART. By 3 months on ART, 13 (10%) children had deceased and 11 (10%) were lost to follow-up. Questionnaires were completed by 87/98 (90%) of caregivers of those who remained in care. Sensitivity of poor reported adherence (missing ≥ 1 dose in the previous 3 days) for MR adherence <90% was only 31.8% (95% CI: 10.7% – 53.0%). Caregivers of 33/87 (38.4%) children reported difficulties with giving medication, most commonly poor palatability (21.8%). Independent socio-demographic predictors of MR adherence ≥ 90% were secondary education of caregivers (OR = 4.49; 95%CI: 1.10 – 18.24) and access to water and electricity (OR = 2.65; 95%CI: 0.93 – 7.55). Taking ritonavir was negatively associated with MR adherence ≥ 90% (OR = 0.37; 95%CI: 0.13 – 1.02).</p> <p>Conclusion</p> <p>Excellent adherence to ART is possible in African infants and young children and the relatively simple low technology measure of adherence by MR strongly predicts viral response. Better socio-economic status and more palatable regimens are associated with better adherence.</p

MHC class I–specific antibody binding to nonhematopoietic cells drives complement activation to induce transfusion-related acute lung injury in mice

In a manner partially independent of activating Fcγ receptors, antibody-mediated production of complement component C5a and recruitment of macrophages elicit transfusion-related acute lung injury in mice

Quaking Regulates Hnrnpa1 Expression through Its 3′ UTR in Oligodendrocyte Precursor Cells

In mice, Quaking (Qk) is required for myelin formation; in humans, it has been associated with psychiatric disease. QK regulates the stability, subcellular localization, and alternative splicing of several myelin-related transcripts, yet little is known about how QK governs these activities. Here, we show that QK enhances Hnrnpa1 mRNA stability by binding a conserved 3′ UTR sequence with high affinity and specificity. A single nucleotide mutation in the binding site eliminates QK-dependent regulation, as does reduction of QK by RNAi. Analysis of exon expression across the transcriptome reveals that QK and hnRNP A1 regulate an overlapping subset of transcripts. Thus, a simple interpretation is that QK regulates a large set of oligodendrocyte precursor genes indirectly by increasing the intracellular concentration of hnRNP A1. Together, the data show that hnRNP A1 is an important QK target that contributes to its control of myelin gene expression