Functional analysis of structural variants in single cells using Strand-seq

Somatic structural variants (SVs) are widespread in cancer, but their impact on disease evolution is understudied due to a lack of methods to directly characterize their functional consequences. We present a computational method, scNOVA, which uses Strand-seq to perform haplotype-aware integration of SV discovery and molecular phenotyping in single cells by using nucleosome occupancy to infer gene expression as a readout. Application to leukemias and cell lines identifies local effects of copy-balanced rearrangements on gene deregulation, and consequences of SVs on aberrant signaling pathways in subclones. We discovered distinct SV subclones with dysregulated Wnt signaling in a chronic lymphocytic leukemia patient. We further uncovered the consequences of subclonal chromothripsis in T cell acute lymphoblastic leukemia, which revealed c-Myb activation, enrichment of a primitive cell state and informed successful targeting of the subclone in cell culture, using a Notch inhibitor. By directly linking SVs to their functional effects, scNOVA enables systematic single-cell multiomic studies of structural variation in heterogeneous cell populations

Narrowband imaging of Escaping Lyman-Continuum Emission in the SSA22 Field

We present the results of an ultradeep, narrowband imaging survey for Lyman-continuum (LyC) emission at z~3 in the SSA22a field. We employ a custom narrowband filter centered at 3640A (NB3640), which probes the LyC region for galaxies at z>3.06. We also analyze new and archival NB4980 imaging tuned to the wavelength of the Lya emission line at z=3.09, and archival broadband B, V, and R images of the non-ionizing UV continuum. Our NB3640 images contain 26 z>3.06 Lyman Break Galaxies (LBGs) as well as a set of 130 Lya emitters (LAEs), identified by their excess NB4980 flux relative to the BV continuum. Six LBGs and 28 LAEs are detected in the NB3640 image. LBGs appear to span a range of NB3640-R colors, while LAEs appear bimodal in their NB3640-R properties. We estimate average UV to LyC flux density ratios, corrected for foreground contamination and intergalactic medium absorption, finding ^{LBG} = 11.3^{+10.3}_{-5.4}, which implies a LBG LyC escape fraction f_{esc}^{LyC} ~ 0.1, and ^{LAE} = 2.2^{+0.9}_{-0.6}. The strikingly blue LAE flux density ratios defy interpretation in terms of standard stellar population models. Assuming ^{LBG} applies down to L=0.1L*, we estimate a galaxy contribution to the intergalactic hydrogen ionization rate that is consistent with independent estimates based on the Lya forest opacity at z~3. If we assume that ^{LAE} holds at the faintest luminosities, the galaxy contribution significantly exceeds that inferred from the Lya forest. Further follow-up study of these faint LAEs is crucial, given the potentially important contribution similar objects make to the process of reionization. (Abridged)Comment: 30 pages, 15 figures; Accepted for publication by Ap

Search for supersymmetry in events with b-quark jets and missing transverse energy in pp collisions at 7 TeV

Results are presented from a search for physics beyond the standard model based on events with large missing transverse energy, at least three jets, and at least one, two, or three b-quark jets. The study is performed using a sample of proton-proton collision data collected at sqrt(s) = 7 TeV with the CMS detector at the LHC in 2011. The integrated luminosity of the sample is 4.98 inverse femtobarns. The observed number of events is found to be consistent with the standard model expectation, which is evaluated using control samples in the data. The results are used to constrain cross sections for the production of supersymmetric particles decaying to b-quark-enriched final states in the context of simplified model spectra.Comment: Submitted to Physical Review

Integration of water, sanitation, and hygiene for the prevention and control of neglected tropical diseases: a rationale for inter-sectoral collaboration.

Improvements of water, sanitation, and hygiene (WASH) infrastructure and appropriate health-seeking behavior are necessary for achieving sustained control, elimination, or eradication of many neglected tropical diseases (NTDs). Indeed, the global strategies to fight NTDs include provision of WASH, but few programs have specific WASH targets and approaches. Collaboration between disease control programs and stakeholders in WASH is a critical next step. A group of stakeholders from the NTD control, child health, and WASH sectors convened in late 2012 to discuss opportunities for, and barriers to, collaboration. The group agreed on a common vision, namely "Disease-free communities that have adequate and equitable access to water and sanitation, and that practice good hygiene." Four key areas of collaboration were identified, including (i) advocacy, policy, and communication; (ii) capacity building and training; (iii) mapping, data collection, and monitoring; and (iv) research. We discuss strategic opportunities and ways forward for enhanced collaboration between the WASH and the NTD sectors

Woman-centered research on access to safe abortion services and implications for behavioral change communication interventions: a cross-sectional study of women in Bihar and Jharkhand, India

<p>Abstract</p> <p>Background</p> <p>Unsafe abortion in India leads to significant morbidity and mortality. Abortion has been legal in India since 1971, and the availability of safe abortion services has increased. However, service availability has not led to a significant reduction in unsafe abortion. This study aimed to understand the gap between safe abortion availability and use of services in Bihar and Jharkhand, India by examining accessibility from the perspective of rural, Indian women.</p> <p>Methods</p> <p>Two-stage stratified random sampling was used to identify and enroll 1411 married women of reproductive age in four rural districts in Bihar and Jharkhand, India. Data were collected on women's socio-demographic characteristics; exposure to mass media and other information sources; and abortion-related knowledge, perceptions and practices. Multiple linear regression models were used to explore the association between knowledge and perceptions about abortion.</p> <p>Results</p> <p>Most women were poor, had never attended school, and had limited exposure to mass media. Instead, they relied on community health workers, family and friends for health information. Women who had knowledge about abortion, such as knowing an abortion method, were more likely to perceive that services are available (β = 0.079; p < 0.05) and have positive attitudes toward abortion (β = 0.070; p < 0.05). In addition, women who reported exposure to abortion messages were more likely to have favorable attitudes toward abortion (β = 0.182; p < 0.05).</p> <p>Conclusions</p> <p>Behavior change communication (BCC) interventions, which address negative perceptions by improving community knowledge about abortion and support local availability of safe abortion services, are needed to increase enabling resources for women and improve potential access to services. Implementing BCC interventions is challenging in settings such as Bihar and Jharkhand where women may be difficult to reach directly, but interventions can target individuals in the community to transfer information to the women who need this information most. Interpersonal approaches that engage community leaders and influencers may also counteract negative social norms regarding abortion and associated stigma. Collaborative actions of government, NGOs and private partners should capitalize on this potential power of communities to reduce the impact of unsafe abortion on rural women.</p

Vaccinia Virus Proteins A52 and B14 Share a Bcl-2–Like Fold but Have Evolved to Inhibit NF-κB rather than Apoptosis

Vaccinia virus (VACV), the prototype poxvirus, encodes numerous proteins that modulate the host response to infection. Two such proteins, B14 and A52, act inside infected cells to inhibit activation of NF-κB, thereby blocking the production of pro-inflammatory cytokines. We have solved the crystal structures of A52 and B14 at 1.9 Å and 2.7 Å resolution, respectively. Strikingly, both these proteins adopt a Bcl-2–like fold despite sharing no significant sequence similarity with other viral or cellular Bcl-2–like proteins. Unlike cellular and viral Bcl-2–like proteins described previously, A52 and B14 lack a surface groove for binding BH3 peptides from pro-apoptotic Bcl-2–like proteins and they do not modulate apoptosis. Structure-based phylogenetic analysis of 32 cellular and viral Bcl-2–like protein structures reveals that A52 and B14 are more closely related to each other and to VACV N1 and myxoma virus M11 than they are to other viral or cellular Bcl-2–like proteins. This suggests that a progenitor poxvirus acquired a gene encoding a Bcl-2–like protein and, over the course of evolution, gene duplication events have allowed the virus to exploit this Bcl-2 scaffold for interfering with distinct host signalling pathways

Involvement of the Glycogen Synthase Kinase-3 Signaling Pathway in TBI Pathology and Neurocognitive Outcome

BACKGROUND: Traumatic brain injury (TBI) sets in motion cascades of biochemical changes that result in delayed cell death and altered neuronal architecture. Studies have demonstrated that inhibition of glycogen synthase kinase-3 (GSK-3) effectively reduces apoptosis following a number of stimuli. The Wnt family of proteins, and growth factors are two major factors that regulate GSK-3 activity. In the absence of stimuli, GSK-3 is constitutively active and is complexed with Axin, adenomatous polyposis coli (APC), and casein kinase Iα (CK1α) and phosphorylates ß-Catenin leading to its degradation. Binding of Wnt to Frizzled receptors causes the translocation of GSK-3 to the plasma membrane, where it phosphorylates and inactivates the Frizzled co-receptor lipoprotein-related protein 6 (LRP6). Furthermore, the translocation of GSK-3 reduces ß-Catenin phosphorylation and degradation, leading to ß-Catenin accumulation and gene expression. Growth factors activate Akt, which in turn inhibits GSK-3 activity by direct phosphorylation, leading to a reduction in apoptosis. METHODOLOGY/PRINCIPAL FINDINGS: Using a rodent model, we found that TBI caused a rapid, but transient, increase in LRP6 phosphorylation that is followed by a modest decrease in ß-Catenin phosphorylation. Phospho-GSK-3β immunoreactivity was found to increase three days post injury, a time point at which increased Akt activity following TBI has been observed. Lithium influences several neurochemical cascades, including inhibiting GSK-3. When the efficacy of daily lithium was assessed, reduced hippocampal neuronal cell loss and learning and memory improvements were observed. These influences were partially mimicked by administration of the GSK-3-selective inhibitor SB-216763, as this drug resulted in improved motor function, but only a modest improvement in memory retention and no overt neuroprotection. CONCLUSION/SIGNIFICANCE: Taken together, our findings suggest that selective inhibition of GSK-3 may offer partial cognitive improvement. As a broad spectrum inhibitor of GSK-3, lithium offers neuroprotection and robust cognitive improvement, supporting its clinical testing as a treatment for TBI