Molar mass and solution conformation of branched alpha(1 - 4), alpha(1 - 6) Glucans. Part I: Glycogens in water

Solution molar masses and conformations of glycogens from different sources (rabbit, oyster, mussel and bovine) were analysed using sedimentation velocity in the analytical ultracentrifuge, size-exclusion chromatography coupled to multi-angle laser light scattering (SEC-MALLS), size-exclusion chromatography coupled to a differential pressure viscometer and dynamic light scattering. Rabbit, oyster and mussel glycogens consisted of one population of high molar mass (weight averages ranging from 4.6 x 106 to 1.1 x 107 g/mol) as demonstrated by sedimentation velocity and SEC-MALLS, whereas bovine glycogen had a bimodal distribution of significantly lower molar mass (1.0 x 105 and 4.5 x 105 g/mol). The spherical structure of all glycogen molecules was demonstrated in the slopes of the Mark-Houwink-Kuhn-Sakurada-type power-law relations for sedimentation coefficient (s20,wo), intrinsic viscosity ([η]), radius of gyration (rg,z) and radius of hydration (rH,z), respectively, and was further supported by the � (=rg,z/rH,z) function, the fractal dimension and the Perrin function. The degree of branching was estimated to be ∼10% from the shrinking factors, g′ (=[η]branched/[η]linear) and also h (=(f/fo)branched/(f/fo)linear), respectively, where (f/fo) is the translational frictional ratio, consistent with expectation. © 2007 Elsevier Ltd. All rights reserved

Shape and Size Matter for Projectile Drag

Newtonian mechanics is a fundamental building block of physics education, allowing us to characterize the motion of various objects in every day life. Here, we set out to investigate the effect of air resistance on projectile motion. We use high-speed cameras to record the flight of three different projectiles and compare this motion to a trajectory generated based on our theoretical model. We find that we are able to fit our model to the actual trajectory reasonably well, and find evidence that drag depends on the size and shape of the projectile

Enhanced Methylation Analysis by Recovery of Unsequenceable Fragments.

Bisulfite sequencing is a valuable tool for mapping the position of 5-methylcytosine in the genome at single base resolution. However, the associated chemical treatment causes strand scission, which depletes the number of sequenceable DNA fragments in a library and thus necessitates PCR amplification. The AT-rich nature of the library generated from bisulfite treatment adversely affects this amplification, resulting in the introduction of major biases that can confound methylation analysis. Here, we report a method that enables more accurate methylation analysis, by rebuilding bisulfite-damaged components of a DNA library. This recovery after bisulfite treatment (ReBuilT) approach enables PCR-free bisulfite sequencing from low nanogram quantities of genomic DNA. We apply the ReBuilT method for the first whole methylome analysis of the highly AT-rich genome of Plasmodium berghei. Side-by-side comparison to a commercial protocol involving amplification demonstrates a substantial improvement in uniformity of coverage and reduction of sequence context bias. Our method will be widely applicable for quantitative methylation analysis, even for technically challenging genomes, and where limited sample DNA is available.GRM is supported by funding from Trinity College Cambridge and Herchel Smith. DB is supported by funding from the Wellcome Trust and Herchel Smith. EAR is a Herchel Smith Fellow. PVD is a Marie Curie Fellow of the European Union (FP7-PEOPLE-2013-IEF/624885). The Balasubramanian lab is supported by a Senior Investigator Award from the Wellcome Trust (099232/Z/12/Z to SB) and by core funding from Cancer Research UK.This is the final version of the article. It first appeared from PLOS via http://dx.doi.org/10.1371/journal.pone.015232

In vivo genome-wide profiling reveals a tissue-specific role for 5-formylcytosine.

BACKGROUND: Genome-wide methylation of cytosine can be modulated in the presence of TET and thymine DNA glycosylase (TDG) enzymes. TET is able to oxidise 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). TDG can excise the oxidative products 5fC and 5caC, initiating base excision repair. These modified bases are stable and detectable in the genome, suggesting that they could have epigenetic functions in their own right. However, functional investigation of the genome-wide distribution of 5fC has been restricted to cell culture-based systems, while its in vivo profile remains unknown. RESULTS: Here, we describe the first analysis of the in vivo genome-wide profile of 5fC across a range of tissues from both wild-type and Tdg-deficient E11.5 mouse embryos. Changes in the formylation profile of cytosine upon depletion of TDG suggest TET/TDG-mediated active demethylation occurs preferentially at intron-exon boundaries and reveals a major role for TDG in shaping 5fC distribution at CpG islands. Moreover, we find that active enhancer regions specifically exhibit high levels of 5fC, resulting in characteristic tissue-diagnostic patterns, which suggest a role in embryonic development. CONCLUSIONS: The tissue-specific distribution of 5fC can be regulated by the collective contribution of TET-mediated oxidation and excision by TDG. The in vivo profile of 5fC during embryonic development resembles that of embryonic stem cells, sharing key features including enrichment of 5fC in enhancer and intragenic regions. Additionally, by investigating mouse embryo 5fC profiles in a tissue-specific manner, we identify targeted enrichment at active enhancers involved in tissue development.MI is supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme FP7/2007-2013/under REA grant agreement no. 290123. GRM was supported by Trinity College and Herchel Smith studentships. MB was supported by the CRUK PhD Training Programme in Chemical Biology and Molecular Medicine. DB is supported by funding from the Wellcome Trust and Herchel Smith. The WR lab is supported by BBSRC, MRC, the Wellcome Trust, EU EpiGeneSys and BLUEPRINT. The SB lab is supported by core funding from Cancer Research UK and a Wellcome Trust Senior Investigator Award.This is the final version of the article. It first appeared from BioMed Central via http://dx.doi.org/10.1186/s13059-016-1001-5

Troubling identities: teacher education students` constructions of class and ethnicity

Working with diverse student populations productively depends on teachers and teacher educators recognizing and valuing difference. Too often, in teacher education programs, when markers of identity such as gender, ethnicity, \u27race\u27, or social class are examined, the focus is on developing student teachers\u27 understandings of how these discourses shape learner identities and rarely on how these also shape teachers\u27 identities. This article reports on a research project that explored how student teachers understand ethnicity and socio-economic status. In a preliminary stage of the research, we asked eight Year 3 teacher education students who had attended mainly Anglo-Australian, middle class schools as students and as student teachers, to explore their own ethnic and classed identities. The complexities of identity are foregrounded in both the assumptions we made in selecting particular students for the project and in the ways they constructed their own identities around ethnicity and social class. In this article we draw on these findings to interrogate how categories of identity are fluid, shifting and ongoing processes of negotiation, troubling and complex. We also consider the implications for teacher education.<br /

Two Novel Genetic Variants in the Mineralocorticoid Receptor Gene Associated with Spontaneous Preterm Birth

Background: Preterm birth is the leading cause of mortality and morbidity in newborn infants. Its etiology is multifactorial with genes and environmental factors, including chronic maternal stress, contributing to its risk. Our objective was to investigate whether single nucleotide polymorphisms (SNPs) in genes involved in the stress response are associated with spontaneous preterm birth using a candidate gene approach. Methods: A total of 210 cases (singleton spontaneous preterm birth at \u3c37 \u3eweeks) and 412 controls (singleton term birth at 38–42 weeks without a history of preterm birth) were studied. High quality maternal DNA was available from saliva samples of 190 cases and 369 controls and compared. Sociodemographic and medical data were collected. Sixteen SNPs, either tag SNPs located in key genes involved in the stress response identified in the Preterm Birth Genome Project database or SNPs found to be associated with adverse mental health outcomes in the published literature, were selected for genotyping and sequencing. SNPs were genotyped using Taqman® SNP genotyping assays. Univariate and multivariate logistic regression were performed. Results: Multivariate analysis showed that two SNPs located in the mineralocorticoid receptor gene were significantly associated with spontaneous preterm birth: rs17484063 (OR 0.50, p = 0.038) and rs2883929 (OR 0.49, p = 0.017), regardless of maternal age, smoking, alcohol use, educational status, and history of spontaneous miscarriage. Conclusion: This report demonstrates an association between mineralocorticoid receptor gene polymorphisms, rs17484063 and rs2883929, and preterm birth, supporting a role for genetics in the association between chronic maternal stress and preterm birth. Potentially, this information may be used to predicting the risk of having a preterm delivery

Respiratory viral pathogens among Singapore military servicemen 2009 - 2012: Epidemiology and clinical characteristics

10.1186/1471-2334-14-204BMC Infectious Diseases141-BIDM

One share - one vote: the theory

The theoretical literature on security-voting structure can be organized around three questions: What impact do nonvoting shares have on takeover outcomes? How does disproportional voting power affect the incentives of blockholders? What are the repercussions of mandating one share - one vote for firms' financing and ownership choices? Overall, the costs and benefits of separating cash flow and votes reflect the fundamental governance trade off between disempowering blockholders and empowering managers. It is therefore an open question whether mandating one share - one vote would improve the quality of corporate governance, notably in systems that so far relied on active owners

Chemical biology of genomic DNA: minimizing PCR bias.

The exquisite selectivity of chemical reactions enables the study of rare DNA bases. However, chemical modification of the genome can affect downstream analysis. We report a PCR bias caused by such modification, and exemplify a solution with the synthesis and characterization of a cleavable aldehyde-reactive biotinylation probe.GRM is supported by Trinity College and Herchel Smith studentships. EAR is a Herchel Smith Fellow. The SB lab is supported by core funding from Cancer Research UK. SB is a Wellcome Trust Senior Investigator.This is the final version of the article. It first appeared from the Royal Society of Chemistry via http://dx.doi.org/10.1039/C4CC05107

VAMP3/Syb and YKT6 are required for the fusion of constitutive secretory carriers with the plasma membrane

The cellular machinery required for the fusion of constitutive secretory vesicles with the plasma membrane in metazoans remains poorly defined. To address this problem we have developed a powerful, quantitative assay for measuring secretion and used it in combination with combinatorial gene depletion studies in Drosophila cells. This has allowed us to identify at least three SNARE complexes mediating Golgi to PM transport (STX1, SNAP24/29 and Syb; STX1, SNAP24/29 and YKT6; STX4, SNAP24 and Syb). RNAi mediated depletion of YKT6 and VAMP3 in mammalian cells also blocks constitutive secretion suggesting that YKT6 has an evolutionarily conserved role in this process. The unexpected role of YKT6 in plasma membrane fusion may in part explain why RNAi and gene disruption studies have failed to produce the expected phenotypes in higher eukaryotes