Although much is known about molecular and chromosomal characteristics that distinguish glioma histological subtypes, DNA methylation patterns of gliomas and their association with other tumor ...features such as mutation of isocitrate dehydrogenase (IDH) genes have only recently begun to be investigated.
DNA methylation of glioblastomas, astrocytomas, oligodendrogliomas, oligoastrocytomas, ependymomas, and pilocytic astrocytomas (n = 131) from the Brain Tumor Research Center at the University of California San Francisco, as well as nontumor brain tissues (n = 7), was assessed with the Illumina GoldenGate methylation array. Methylation data were subjected to recursively partitioned mixture modeling (RPMM) to derive methylation classes. Differential DNA methylation between tumor and nontumor was also assessed. The association between methylation class and IDH mutation (IDH1 and IDH2) was tested using univariate and multivariable analysis for tumors (n = 95) with available substrate for sequencing. Survival of glioma patients carrying mutant IDH (n = 57) was compared with patients carrying wild-type IDH (n = 38) using a multivariable Cox proportional hazards model and Kaplan-Meier analysis. All statistical tests were two-sided.
We observed a statistically significant association between RPMM methylation class and glioma histological subtype (P < 2.2 × 10(-16)). Compared with nontumor brain tissues, across glioma tumor histological subtypes, the differential methylation ratios of CpG loci were statistically significantly different (permutation P < .0001). Methylation class was strongly associated with IDH mutation in gliomas (P = 3.0 × 10(-16)). Compared with glioma patients whose tumors harbored wild-type IDH, patients whose tumors harbored mutant IDH showed statistically significantly improved survival (hazard ratio of death = 0.27, 95% confidence interval = 0.10 to 0.72).
The homogeneity of methylation classes for gliomas with IDH mutation, despite their histological diversity, suggests that IDH mutation is associated with a distinct DNA methylation phenotype and an altered metabolic profile in glioma.
Farmers, regulators, and researchers rely on pesticide use data to assess the effects of pesticides on crop yield, farm economics, off-target organisms, and human health. The publicly available ...pesticide use data in the United States do not currently account for pesticides applied as seed treatments. We find that seed treatment use has increased in major field crops over the last several decades but that there is a high degree of uncertainty about the extent of acreage planted with treated seeds, the amount of regional variability, and the use of certain active ingredients. One reason for this uncertainty is that farmers are less likely to know what pesticides are on their seed than they are about what pesticides are applied conventionally to their crops. This lack of information affects the quality and availability of seed treatment data and also farmers’ ability to tailor pesticide use to production and environmental goals.
Structural variants (SVs) and short tandem repeats (STRs) comprise a broad group of diverse DNA variants which vastly differ in their sizes and distributions across the genome. Here, we identify ...genomic features of SV classes and STRs that are associated with gene expression and complex traits, including their locations relative to eGenes, likelihood of being associated with multiple eGenes, associated eGene types (e.g., coding, noncoding, level of evolutionary constraint), effect sizes, linkage disequilibrium with tagging single nucleotide variants used in GWAS, and likelihood of being associated with GWAS traits. We identify a set of high-impact SVs/STRs associated with the expression of three or more eGenes via chromatin loops and show that they are highly enriched for being associated with GWAS traits. Our study provides insights into the genomic properties of structural variant classes and short tandem repeats that are associated with gene expression and human traits.
The relationship between pesticides and pollinators, while attracting no shortage of attention from scientists, regulators, and the public, has proven resistant to scientific synthesis and fractious ...in matters of policy and public opinion. This is in part because the issue has been approached in a compartmentalized and intradisciplinary way, such that evaluations of organismal pesticide effects remain largely disjoint from their upstream drivers and downstream consequences. Here, we present a socioecological framework designed to synthesize the pesticide-pollinator system and inform future scholarship and action. Our framework consists of three interlocking domains-pesticide use, pesticide exposure, and pesticide effects–each consisting of causally linked patterns, processes, and states. We elaborate each of these domains and their linkages, reviewing relevant literature and providing empirical case studies. We then propose guidelines for future pesticide-pollinator scholarship and action agenda aimed at strengthening knowledge in neglected domains and integrating knowledge across domains to provide decision support for stakeholders and policymakers. Specifically, we emphasize (1) stakeholder engagement, (2) mechanistic study of pesticide exposure, (3) understanding the propagation of pesticide effects across levels of organization, and (4) full-cost accounting of the externalities of pesticide use and regulation. Addressing these items will require transdisciplinary collaborations within and beyond the scientific community, including the expertise of farmers, agrochemical developers, and policymakers in an extended peer community.
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•The relationship between pesticides and pollinators is a complex socioecological system.•Pesticide-pollinator research has tended to be compartmentalized and intradisciplinary.•The pesticide-pollinator system spans from upstream drivers to higher-order effects on populations and ecosystems.•We present a framework consisting of three overlapping domains: pesticide use, pesticide exposure, and pesticide effects.•Future scholarship would benefit from integration across these domains and the filling of gaps within them.
Infection of animal cells by numerous viruses is detected and countered by a variety of means, including recognition of nonself nucleic acids. The zinc finger antiviral protein (ZAP) depletes ...cytoplasmic RNA that is recognized as foreign in mammalian cells by virtue of its elevated CG dinucleotide content compared with endogenous mRNAs. Here, we determined a crystal structure of a protein-RNA complex containing the N-terminal, 4-zinc finger human (h) ZAP RNA-binding domain (RBD) and a CG dinucleotide-containing RNA target. The structure reveals in molecular detail how hZAP is able to bind selectively to CG-rich RNA. Specifically, the 4 zinc fingers create a basic patch on the hZAP RBD surface. The highly basic second zinc finger contains a pocket that selectively accommodates CG dinucleotide bases. Structure guided mutagenesis, cross-linking immunoprecipitation sequencing assays, and RNA affinity assays show that the structurally defined CG-binding pocket is not required for RNA binding per se in human cells. However, the pocket is a crucial determinant of high-affinity, specific binding to CG dinucleotide-containing RNA. Moreover, variations in RNA-binding specificity among a panel of CG-binding pocket mutants quantitatively predict their selective antiviral activity against a CG-enriched HIV-1 strain. Overall, the hZAP RBD RNA structure provides an atomic-level explanation for how ZAP selectively targets foreign, CG-rich RNA.
Many tissue-specific stem cells maintain the ability to produce multiple cell types during long periods of non-division, or quiescence. FOXO transcription factors promote quiescence and stem cell ...maintenance, but the mechanisms by which FOXO proteins promote multipotency during quiescence are still emerging. The single FOXO ortholog in C. elegans, daf-16, promotes entry into a quiescent and stress-resistant larval stage called dauer in response to adverse environmental cues. During dauer, stem and progenitor cells maintain or re-establish multipotency to allow normal development to resume after dauer. We find that during dauer, daf-16/FOXO prevents epidermal stem cells (seam cells) from prematurely adopting differentiated, adult characteristics. In particular, dauer larvae that lack daf-16 misexpress collagens that are normally adult-enriched. Using col-19p::gfp as an adult cell fate marker, we find that all major daf-16 isoforms contribute to opposing col-19p::gfp expression during dauer. By contrast, daf-16(0) larvae that undergo non-dauer development do not misexpress col-19p::gfp. Adult cell fate and the timing of col-19p::gfp expression are regulated by the heterochronic gene network, including lin-41 and lin-29. lin-41 encodes an RNA-binding protein orthologous to LIN41/TRIM71 in mammals, and lin-29 encodes a conserved zinc finger transcription factor. In non-dauer development, lin-41 opposes adult cell fate by inhibiting the translation of lin-29, which directly activates col-19 transcription and promotes adult cell fate. We find that during dauer, lin-41 blocks col-19p::gfp expression, but surprisingly, lin-29 is not required in this context. Additionally, daf-16 promotes the expression of lin-41 in dauer larvae. The col-19p::gfp misexpression phenotype observed in dauer larvae with reduced daf-16 requires the downregulation of lin-41, but does not require lin-29. Taken together, this work demonstrates a novel role for daf-16/FOXO as a heterochronic gene that promotes expression of lin-41/TRIM71 to contribute to multipotent cell fate in a quiescent stem cell model.
The brain is one of the most common metastatic sites among breast cancer patients, especially in those who have Her2-positive or triple-negative tumors. The brain microenvironment has been considered ...immune privileged, and the exact mechanisms of how immune cells in the brain microenvironment contribute to brain metastasis remain elusive. In this study, we found that neutrophils are recruited and influenced by c-Met high brain metastatic cells in the metastatic sites, and depletion of neutrophils significantly suppressed brain metastasis in animal models. Overexpression of c-Met in tumor cells enhances the secretion of a group of cytokines, including CXCL1/2, G-CSF, and GM-CSF, which play critical roles in neutrophil attraction, granulopoiesis, and homeostasis. Meanwhile, our transcriptomic analysis demonstrated that conditioned media from c-Met high cells significantly induced the secretion of lipocalin 2 (LCN2) from neutrophils, which in turn promotes the self-renewal of cancer stem cells. Our study unveiled the molecular and pathogenic mechanisms of how crosstalk between innate immune cells and tumor cells facilitates tumor progression in the brain, which provides novel therapeutic targets for treating brain metastasis.
Chlamydia pneumoniae is an obligate intracellular bacterium that causes respiratory infection. There may exist an association between C. pneumoniae, asthma, and production of immunoglobulin (Ig) E ...responses in vitro. Interleukin (IL-4) is required for IgE production. We previously demonstrated that doxycycline suppresses C. pneumoniae-induced production of IgE and IL-4 responses in peripheral blood mononuclear cells (PBMC) from asthmatic subjects. Whereas macrolides have anti-chlamydial activity, their effect on in vitro anti-inflammatory (IgE) and IL-4 responses to C. pneumoniae have not been studied. PBMC from IgE- adult atopic subjects (N = 5) were infected +/- C. pneumoniae BAL69, +/- azithromycin (0.1, 1.0 ug/mL) for 10 days. IL-4 and IgE levels were determined in supernatants by ELISA. IL-4 and IgE were detected in supernatants of PBMC (day 10). When azithromycin (0.1, 1.0 ug/ml) was added, IL-4 levels decreased. At low dose, IgE levels increased and at high dose, IgE levels decreased. When PBMC were infected with C. pneumoniae, both IL-4 and IgE levels decreased. Addition of azithromycin (0.1, 1.0 ug/mL) decreased IL-4 levels and had no effect on IgE levels. These findings indicate that azithromycin decreases IL-4 responses but has a bimodal effect on IgE responses in PBMC from atopic patients in vitro.
Neonatal ocular prophylaxis with silver nitrate does not prevent neonatal conjunctivitis due to Chlamydia trachomatis. The efficacy of antibiotic containing preparations for prevention of neonatal ...chlamydial conjunctivitis (NCC) has not been established.
To examine published literature to determine whether antibiotic containing preparation are efficacious for prevention of NCC and C. trachomatis in the nasopharynx.
A literature search of MEDLINE and EMBASE. Articles were selected for review if their content included 4 key criteria: (1) Prospective/comparative study. (2) Prenatal screening of mothers for C. trachomatis with results reported. (3) Follow-up of infants born to chlamydia-positive women. (4) Infants prospectively followed at regular intervals and tested for C. trachomatis in the eye/ nasopharynx (NP).
The search yielded 159 studies; 11 were selected for full reviews, eight were excluded; three addressed the four criteria. Rates of C. trachomatis conjunctivitis in infants in included studies who received silver nitrate was 20-33%; positive NP, 1-28% and pneumonia, 3-8%. Rates of C. trachomatis conjunctivitis in neonates who received erythromycin or tetracycline prophylaxis did not differ from silver nitrate; 0-15 and 11%, respectively, who received erythromycin or tetracycline developed NCC. Similarly, 4-33 and 5% of infants who received erythromycin or tetracycline, respectively, had positive NP cultures; 0-4% developed chlamydial pneumonia.
Neonatal ocular prophylaxis with erythromycin or tetracycline ophthalmic ointments does not reduce incidence of neonatal chlamydial conjunctivitis or respiratory infection in infants born to mothers with C. trachomatis infection compared to silver nitrate.
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