Resourcefulness matters: Student patterns for coping with structural and academic challenges

There is general agreement that there are many structural constraints beyond students’ control which influence the degree of success that students can attain as they learn to participate in academic practice. Less understood are the patterns of students’ experiences of the socio-economic environment of their schooling and university, their views of the enabling and constraining conditions of learning and their perceptions of their agency in overcoming these conditions. The data for our study were collected through a questionnaire survey of 591 Bachelor of Education students across three years of the degree at a South African University. Several patterns of resourcefulness and levels of articulation emerged which reveal complex sets of experiences and strategies as students reflect on adversities and challenges they encountered at school and at university. We argue for an in depth understanding of the nature of student agency which recognises its role in shaping their engagement with material, social, academic and affective challenges

Recent results on the properties of two-phase argon avalanche detectors

The characteristic properties of two-phase Ar avalanche detectors, including those obtained with CsI photocathode, are further studied. Such detectors are relevant in the field of coherent neutrino-nucleus scattering and dark matter search experiments. The detectors investigated comprised a 1 cm thick liquid Ar layer followed by a triple-GEM multiplier. In these detectors, typical gains reaching 10000 were obtained with good reproducibility and a stable operation for at least one day was demonstrated. Amplitude and pulse-shape characteristics are presented under irradiation with X-rays, gamma-rays and neutrons from different radioactive sources. The detection of both primary scintillation and ionization signals at higher gains, at a deposited energy of 60 keV, has been demonstrated.Comment: 6 pages, 11 figures. Presented at Xth Int. Conf. for Collid. Beam Phys., Feb 28 - March 6, 2008, Novosibirsk, to be published in Nucl. Instr. Meth.

The duration of sexual relationship and its effects on adverse pregnancy outcomes

This study aims to determine if a short duration of sexual relationship is more common among women who experience adverse pregnancy outcomes including gestational hypertension (GHT), preeclampsia, small for gestational age (SGA) pregnancies and spontaneous preterm birth (sPTB) with or without abnormal uterine artery Doppler compared to women who have uncomplicated pregnancies. 5591 nulliparous women from the Screening for Pregnancy Endpoints (SCOPE) study were included. The risk for pregnancy complications for women who had a duration of sexual relationship of ≤3 months, 4–6 months, 7–9 months, 10–12 months was compared with women who had a duration of sexual relationship of >12 months. Uterine artery Doppler was performed at 20 ± 1 weeks’ gestation. A short duration of sexual relationship (≤3 months) was more common among women with SGA in the presence of abnormal uterine artery Doppler [9.8% vs 3.0%, aOR (95% CI) 3.4 (1.6–7.08] compared to women who had uncomplicated pregnancies. A short duration of sexual relationship (≤3 months) was also more common among women who had abnormal uterine artery Doppler compared to those with normal uterine artery Doppler [6.1% vs 3.1%, aOR (95% CI) = 2.1 (1.4–3.2)]. A short duration of sexual relationship was not associated with preeclampsia after adjusting for confounders. A short duration of sexual relationship is more common among women who deliver SGA infants with features of placental insufficiency as indicated by abnormal uterine artery Doppler.Prabha Andraweera, Claire T. Roberts, Shalem Leemaqz, Lesley McCowan, Jenny Myers, Louise C. Kenny, James Walker, Lucilla Poston, Gus Dekker on behalf of the SCOP

Tumor innate immunity primed by specific interferon-stimulated endogenous retroviruses.

Mesenchymal tumor subpopulations secrete pro-tumorigenic cytokines and promote treatment resistance1-4. This phenomenon has been implicated in chemorefractory small cell lung cancer and resistance to targeted therapies5-8, but remains incompletely defined. Here, we identify a subclass of endogenous retroviruses (ERVs) that engages innate immune signaling in these cells. Stimulated 3 prime antisense retroviral coding sequences (SPARCS) are oriented inversely in 3' untranslated regions of specific genes enriched for regulation by STAT1 and EZH2. Derepression of these loci results in double-stranded RNA generation following IFN-γ exposure due to bi-directional transcription from the STAT1-activated gene promoter and the 5' long terminal repeat of the antisense ERV. Engagement of MAVS and STING activates downstream TBK1, IRF3, and STAT1 signaling, sustaining a positive feedback loop. SPARCS induction in human tumors is tightly associated with major histocompatibility complex class 1 expression, mesenchymal markers, and downregulation of chromatin modifying enzymes, including EZH2. Analysis of cell lines with high inducible SPARCS expression reveals strong association with an AXL/MET-positive mesenchymal cell state. While SPARCS-high tumors are immune infiltrated, they also exhibit multiple features of an immune-suppressed microenviroment. Together, these data unveil a subclass of ERVs whose derepression triggers pathologic innate immune signaling in cancer, with important implications for cancer immunotherapy

Transcriptome Kinetics Is Governed by a Genome-Wide Coupling of mRNA Production and Degradation: A Role for RNA Pol II

Transcriptome dynamics is governed by two opposing processes, mRNA production and degradation. Recent studies found that changes in these processes are frequently coordinated and that the relationship between them shapes transcriptome kinetics. Specifically, when transcription changes are counter-acted with changes in mRNA stability, transient fast-relaxing transcriptome kinetics is observed. A possible molecular mechanism underlying such coordinated regulation might lay in two RNA polymerase (Pol II) subunits, Rpb4 and Rpb7, which are recruited to mRNAs during transcription and later affect their degradation in the cytoplasm. Here we used a yeast strain carrying a mutant Pol II which poorly recruits these subunits. We show that this mutant strain is impaired in its ability to modulate mRNA stability in response to stress. The normal negative coordinated regulation is lost in the mutant, resulting in abnormal transcriptome profiles both with respect to magnitude and kinetics of responses. These results reveal an important role for Pol II, in regulation of both mRNA synthesis and degradation, and also in coordinating between them. We propose a simple model for production-degradation coupling that accounts for our observations. The model shows how a simple manipulation of the rates of co-transcriptional mRNA imprinting by Pol II may govern genome-wide transcriptome kinetics in response to environmental changes

CRISPR-Cas9 screens in human cells and primary neurons identify modifiers of C9ORF72 dipeptide-repeat-protein toxicity.

Hexanucleotide-repeat expansions in the C9ORF72 gene are the most common cause of amyotrophic lateral sclerosis and frontotemporal dementia (c9ALS/FTD). The nucleotide-repeat expansions are translated into dipeptide-repeat (DPR) proteins, which are aggregation prone and may contribute to neurodegeneration. We used the CRISPR-Cas9 system to perform genome-wide gene-knockout screens for suppressors and enhancers of C9ORF72 DPR toxicity in human cells. We validated hits by performing secondary CRISPR-Cas9 screens in primary mouse neurons. We uncovered potent modifiers of DPR toxicity whose gene products function in nucleocytoplasmic transport, the endoplasmic reticulum (ER), proteasome, RNA-processing pathways, and chromatin modification. One modifier, TMX2, modulated the ER-stress signature elicited by C9ORF72 DPRs in neurons and improved survival of human induced motor neurons from patients with C9ORF72 ALS. Together, our results demonstrate the promise of CRISPR-Cas9 screens in defining mechanisms of neurodegenerative diseases

Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening

Forward genetic screens are powerful tools for the unbiased discovery and functional characterization of specific genetic elements associated with a phenotype of interest. Recently, the RNA-guided endonuclease Cas9 from the microbial CRISPR (clustered regularly interspaced short palindromic repeats) immune system has been adapted for genome-scale screening by combining Cas9 with pooled guide RNA libraries. Here we describe a protocol for genome-scale knockout and transcriptional activation screening using the CRISPR-Cas9 system. Custom- or ready-made guide RNA libraries are constructed and packaged into lentiviral vectors for delivery into cells for screening. As each screen is unique, we provide guidelines for determining screening parameters and maintaining sufficient coverage. To validate candidate genes identified by the screen, we further describe strategies for confirming the screening phenotype, as well as genetic perturbation, through analysis of indel rate and transcriptional activation. Beginning with library design, a genome-scale screen can be completed in 9-15 weeks, followed by 4-5 weeks of validation.Paul & Daisy Soros Fellowships for New Americans (New York, N.Y.)McGovern Institute for Brain Research at MIT (Friends of McGovern Institute Fellowship)Massachusetts Institute of Technology. Poitras Center for Affective Disorders ResearchUnited States. Department of Energy (Computational Science Graduate Fellowship)National Institute of Mental Health (U.S.) (5DP1-MH100706)National Institute of Mental Health (U.S.) (1R01-MH110049)New York Stem Cell FoundationPoitras FoundationSimons FoundationPaul G. Allen Family FoundationVallee FoundationTom HarrimanB. Metcalf

CRISPR/Cas9 DNA cleavage at SNP-derived PAM enables both in vitro and in vivo KRT12 mutation-specific targeting

CRISPR/Cas9-based therapeutics hold the possibility for permanent treatment of genetic disease. The potency and specificity of this system has been used to target dominantly inherited conditions caused by heterozygous missense mutations through inclusion of the mutated base in the short-guide RNA (sgRNA) sequence. This research evaluates a novel approach for targeting heterozygous single-nucleotide polymorphisms (SNPs) using CRISPR/Cas9. We determined that a mutation within KRT12, which causes Meesmann's epithelial corneal dystrophy (MECD), leads to the occurrence of a novel protospacer adjacent motif (PAM). We designed an sgRNA complementary to the sequence adjacent to this SNP-derived PAM and evaluated its potency and allele specificity both in vitro and in vivo. This sgRNA was found to be highly effective at reducing the expression of mutant KRT12 mRNA and protein in vitro. To assess its activity in vivo we injected a combined Cas9/sgRNA expression construct into the corneal stroma of a humanized MECD mouse model. Sequence analysis of corneal genomic DNA revealed non-homologous end-joining repair resulting in frame-shifting deletions within the mutant KRT12 allele. This study is the first to demonstrate in vivo gene editing of a heterozygous disease-causing SNP that results in a novel PAM, further highlighting the potential for CRISPR/Cas9-based therapeutics