Suppressing Aneuploidy-Associated Phenotypes Improves the Fitness of Trisomy 21 Cells

An abnormal number of chromosomes, or aneuploidy, accounts for most spontaneous abortions, causes developmental defects, and is associated with aging and cancer. The molecular mechanisms by which aneuploidy disrupts cellular function remain largely unknown. Here, we show that aneuploidy disrupts the morphology of the nucleus. Mutations that increase the levels of long-chain bases suppress nuclear abnormalities of aneuploid yeast independent of karyotype identity. Quantitative lipidomics indicates that long-chain bases are integral components of the nuclear membrane in yeast. Cells isolated from patients with Down syndrome also show that abnormal nuclear morphologies and increases in long-chain bases not only suppress these abnormalities but also improve their fitness. We obtained similar results with cells isolated from patients with Patau or Edward syndrome, indicating that increases in long-chain bases improve the fitness of aneuploid cells in yeast and humans. Targeting lipid biosynthesis pathways represents an important strategy to suppress nuclear abnormalities in aneuploidy-associated diseases

Metabolic Effects of Cyclic Parenteral Nutrition Infusion in Adults and Children

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141574/1/ncp0277.pd

Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation.

GWAS have identified a breast cancer susceptibility locus on 2q35. Here we report the fine mapping of this locus using data from 101,943 subjects from 50 case-control studies. We genotype 276 SNPs using the 'iCOGS' genotyping array and impute genotypes for a further 1,284 using 1000 Genomes Project data. All but two, strongly correlated SNPs (rs4442975 G/T and rs6721996 G/A) are excluded as candidate causal variants at odds against >100:1. The best functional candidate, rs4442975, is associated with oestrogen receptor positive (ER+) disease with an odds ratio (OR) in Europeans of 0.85 (95% confidence interval=0.84-0.87; P=1.7 × 10(-43)) per t-allele. This SNP flanks a transcriptional enhancer that physically interacts with the promoter of IGFBP5 (encoding insulin-like growth factor-binding protein 5) and displays allele-specific gene expression, FOXA1 binding and chromatin looping. Evidence suggests that the g-allele confers increased breast cancer susceptibility through relative downregulation of IGFBP5, a gene with known roles in breast cell biology

Experiences of assessment in data and security courses using personal response systems

This paper details an experience report of two interventions which explored the use of a audience response system in summative assessment in two different ways within a conversion Masters degree programme. One course explored students understanding of topics and self-assessment of ability through small multiple-choice quizzes. The other course was based around cyber security and used the audience response system to ensure engagement with the pre-class reading material. Both interventions were designed in an attempt to encourage students to engage more effectively with the material. This paper aims to identify and contrast the ways in which the audience response system was used in assessment in higher education computing science with a view to suggesting key considerations for implementing such an intervention

What Does It Mean for a Case to be ‘Local’?: the Importance of Local Relevance and Resonance for Bioethics Education in the Asia-Pacific Region

Contemporary bioethics education has been developed predominately within Euro-American contexts, and now, other global regions are increasingly joining the field, leading to a richer global understanding. Nevertheless, many standard bioethics curriculum materials retain a narrow geographic focus. The purpose of this article is to use local cases from the Asia-Pacific region as examples for exploring questions such as ‘what makes a case or example truly local, and why?’, ‘what topics have we found to be best explained through local cases or examples?’, and ‘how does one identify a relevant local case?’ Furthermore, we consider the global application of local cases to help extend the possible scope of the discussion, opening new avenues for the development of practical bioethics educational materials. We begin with a background description and discussion of why local cases enhance bioethics education, move to an overview of what is currently available and what is not for the region, and then outline a discussion of what it means to be local using example cases drawn from Hong Kong, Australia, Pakistan, and Malaysia. We are not creating a casebook but rather constructing by example a toolbox for designing active and dynamic learning cases using regional diversity as contextualised cases with generalised principles

Variable levels of drift in tunicate cardiopharyngeal gene regulatory elements.

Background: Mutations in gene regulatory networks often lead to genetic divergence without impacting gene expression or developmental patterning. The rules governing this process of developmental systems drift, including the variable impact of selective constraints on different nodes in a gene regulatory network, remain poorly delineated. Results: Here we examine developmental systems drift within the cardiopharyngeal gene regulatory networks of two tunicate species, Corella inflata and Ciona robusta. Cross-species analysis of regulatory elements suggests that trans-regulatory architecture is largely conserved between these highly divergent species. In contrast, cis-regulatory elements within this network exhibit distinct levels of conservation. In particular, while most of the regulatory elements we analyzed showed extensive rearrangements of functional binding sites, the enhancer for the cardiopharyngeal transcription factor FoxF is remarkably well-conserved. Even minor alterations in spacing between binding sites lead to loss of FoxF enhancer function, suggesting that bound trans-factors form position-dependent complexes. Conclusions: Our findings reveal heterogeneous levels of divergence across cardiopharyngeal cis-regulatory elements. These distinct levels of divergence presumably reflect constraints that are not clearly associated with gene function or position within the regulatory network. Thus, levels of cis-regulatory divergence or drift appear to be governed by distinct structural constraints that will be difficult to predict based on network architectur

A validated ultra-performance liquid chromatography with diode array detection coupled to electrospray ionization and triple quadrupole mass spectrometry method to simultaneously quantify taurine, homotaurine, hypotaurine and amino acids in macro- and microalgae

A fast and reliable method for the simultaneous quantification of Taurine, Homotaurine, Hypotaurine and 19 amino acids in algae samples by Ultra-performance liquid chromatography coupled with diode array and tandem mass spectrometry (UHPLC–DAD-MS/MS) was optimized and validated. Target compounds were chromatographically resolved in less than 15 min. (ESI)-MS/MS electrospray ionization and pure analytical standards were used to confirm the identity of all analytes, while quantitation was carried out with diode array detection. Validation parameters of the method were satisfactory: Resolution of peak pairs was always higher than 1.55; all analytical curves showed R2 > 0.99, with working ranges between 0.04 mg/g to 33.1 mg/g and 9.13 mg/g to 107 mg/g and the Lack-of-fit test was not significant. The intra and inter-day precision of the method (expressed as relative standard deviation) were lower than 6% and recovery values ranged between 95% and 105%. The method was demonstrated to be robust to small deliberate variations of seven variables such sample weight, volume of hydrolysis reagent, hydrolysis time and temperature, derivatization time, column temperature and flow rate. The mean expanded uncertainty for all the target compounds were 0.7 mg/g with a coverage factor of 2. Method Limits of detection and quantification varied from 0.005 * 10−3 mg/g to 0.11 * 10−3 mg/g and 0.01* 10−3 mg/g to 0.22 * 10-3 mg/g respectively, allowing the routine determination of these bioactive compounds in algae extracts. Therefore, the method was successfully applied for the quantitative determination of the 22 target compounds in five seaweed commercial samples. Relevant compounds were quantified for the first time in the five algae species, namely: i) Taurine in Gracilaria longissima and Chlorella spp., ii) Gamma-aminobutyric acid in G. longissima and L. japonica, iii) Hydroxyproline in G. longissima, Ulva lactuca, Porphyra spp., and L. japonica and iv) Homotaurine and Hypotaurine in the five species studied.info:eu-repo/semantics/acceptedVersio

Variable Levels Of Drift In Tunicate Cardiopharyngeal Gene Regulatory Elements

Background: Mutations in gene regulatory networks often lead to genetic divergence without impacting gene expression or developmental patterning. The rules governing this process of developmental systems drift, including the variable impact of selective constraints on different nodes in a gene regulatory network, remain poorly delineated. Results: Here we examine developmental systems drift within the cardiopharyngeal gene regulatory networks of two tunicate species, Corella inflata and Ciona robusta. Cross-species analysis of regulatory elements suggests that trans-regulatory architecture is largely conserved between these highly divergent species. In contrast, cis-regulatory elements within this network exhibit distinct levels of conservation. In particular, while most of the regulatory elements we analyzed showed extensive rearrangements of functional binding sites, the enhancer for the cardiopharyngeal transcription factor FoxF is remarkably well-conserved. Even minor alterations in spacing between binding sites lead to loss of FoxF enhancer function, suggesting that bound trans-factors form position-dependent complexes. Conclusions: Our findings reveal heterogeneous levels of divergence across cardiopharyngeal cis-regulatory elements. These distinct levels of divergence presumably reflect constraints that are not clearly associated with gene function or position within the regulatory network. Thus, levels of cis-regulatory divergence or drift appear to be governed by distinct structural constraints that will be difficult to predict based on network architecture

Measurement challenge : protocol for international case–control comparison of mammographic measures that predict breast cancer risk

Introduction: For women of the same age and body mass index, increased mammographic density is one of the strongest predictors of breast cancer risk. There are multiple methods of measuring mammographic density and other features in a mammogram that could potentially be used in a screening setting to identify and target women at high risk of developing breast cancer. However, it is unclear which measurement method provides the strongest predictor of breast cancer risk. Methods and analysis: The measurement challenge has been established as an international resource to offer a common set of anonymised mammogram images for measurement and analysis. To date, full field digital mammogram images and core data from 1650 cases and 1929 controls from five countries have been collated. The measurement challenge is an ongoing collaboration and we are continuing to expand the resource to include additional image sets across different populations (from contributors) and to compare additional measurement methods (by challengers). The intended use of the measurement challenge resource is for refinement and validation of new and existing mammographic measurement methods. The measurement challenge resource provides a standardised dataset of mammographic images and core data that enables investigators to directly compare methods of measuring mammographic density or other mammographic features in case/control sets of both raw and processed images, for the purposes of the comparing their predictions of breast cancer risk. Ethics and dissemination: Challengers and contributors are required to enter a Research Collaboration Agreement with the University of Melbourne prior to participation in the measurement challenge. The Challenge database of collated data and images are stored in a secure data repository at the University of Melbourne. Ethics approval for the measurement challenge is held at University of Melbourne (HREC ID 0931343.3)