The stratigraphy and history of Mars' northern lowlands through mineralogy of impact craters: A comprehensive survey

The basin-filling materials of the northern lowlands, which cover approximately one third of Mars' surface, record the long-term evolution of Mars' geology and climate. The buried stratigraphy was inferred through analyses of impact crater mineralogy, detected using data acquired by the Compact Reconnaissance Imaging Spectrometer for Mars. Examining 1045 impact craters across the northern lowlands, we find widespread olivine and pyroxene and diverse hydrated/hydroxylated minerals, including Fe/Mg smectite, chlorite, prehnite, and hydrated silica. The distribution of mafic minerals is consistent with infilling volcanic materials across the entire lowlands (~1–4 × 10^7 km^3), indicating a significant volume of volatile release by volcanic outgassing. Hydrated/hydroxylated minerals are detected more frequently in large craters, consistent with the scenario that the hydrated minerals are being excavated from deep basement rocks, beneath 1–2 km thick mafic lava flows or volcaniclastic materials. The prevalences of different types of hydrated minerals are similar to statistics from the southern highlands. No evidence of concentrated salt deposits has been found, which would indicate a long-lived global ocean. We also find significant geographical variations of local mineralogy and stratigraphy in different basins (geological provinces), independent of dust cover. For example, many hydrated and mafic minerals are newly discovered within the polar Scandia region (>60°N), and Chryse Planitia has more mafic mineral detections than other basins, possibly due to a previously unrecognized volcanic source

The stratigraphy and history of Mars' northern lowlands through mineralogy of impact craters: A comprehensive survey

The basin-filling materials of the northern lowlands, which cover approximately one third of Mars' surface, record the long-term evolution of Mars' geology and climate. The buried stratigraphy was inferred through analyses of impact crater mineralogy, detected using data acquired by the Compact Reconnaissance Imaging Spectrometer for Mars. Examining 1045 impact craters across the northern lowlands, we find widespread olivine and pyroxene and diverse hydrated/hydroxylated minerals, including Fe/Mg smectite, chlorite, prehnite, and hydrated silica. The distribution of mafic minerals is consistent with infilling volcanic materials across the entire lowlands (~1–4 × 10^7 km^3), indicating a significant volume of volatile release by volcanic outgassing. Hydrated/hydroxylated minerals are detected more frequently in large craters, consistent with the scenario that the hydrated minerals are being excavated from deep basement rocks, beneath 1–2 km thick mafic lava flows or volcaniclastic materials. The prevalences of different types of hydrated minerals are similar to statistics from the southern highlands. No evidence of concentrated salt deposits has been found, which would indicate a long-lived global ocean. We also find significant geographical variations of local mineralogy and stratigraphy in different basins (geological provinces), independent of dust cover. For example, many hydrated and mafic minerals are newly discovered within the polar Scandia region (>60°N), and Chryse Planitia has more mafic mineral detections than other basins, possibly due to a previously unrecognized volcanic source

GeneMatch: A novel recruitment registry using at‐home APOE genotyping to enhance referrals to Alzheimer’s prevention studies

IntroductionRecruitment for Alzheimer’s disease (AD) prevention research studies is challenging because of lack of awareness among cognitively healthy adults coupled with the high screen fail rate due to participants not having a genetic risk factor or biomarker evidence of the disease. Participant recruitment registries offer one solution for efficiently and effectively identifying, characterizing, and connecting potential eligible volunteers to studies.MethodsIndividuals aged 55‐75 years who live in the United States and self‐report not having a diagnosis of cognitive impairment such as MCI or dementia are eligible to join GeneMatch. Participants enroll online and are provided a cheek swab kit for DNA extraction and apolipoprotein E (APOE) genotyping. Participants are not told their APOE results, although the results may be used in part to help match participants to AD prevention studies.ResultsAs of August 2018, 75,351 participants had joined GeneMatch. Nearly 30% of participants have one APOE4 allele, and approximately 3% have two APOE4 alleles. The percentages of APOE4 heterozygotes and homozygotes are inversely associated with age (P < .001).DiscussionGeneMatch, the first trial‐independent research enrollment program designed to recruit and refer cognitively healthy adults to AD prevention studies based in part on APOE test results, provides a novel mechanism to accelerate prescreening and enrollment for AD prevention trials.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/152681/1/alzjjalz201812007.pd

Discovery of an orally active benzoxaborole prodrug effective in the treatment of Chagas disease in non-human primates

Trypanosoma cruzi, the agent of Chagas disease, probably infects tens of millions of people, primarily in Latin America, causing morbidity and mortality. The options for treatment and prevention of Chagas disease are limited and underutilized. Here we describe the discovery of a series of benzoxaborole compounds with nanomolar activity against extra- and intracellular stages of T. cruzi. Leveraging both ongoing drug discovery efforts in related kinetoplastids, and the exceptional models for rapid drug screening and optimization in T. cruzi, we have identified the prodrug AN15368 that is activated by parasite carboxypeptidases to yield a compound that targets the messenger RNA processing pathway in T. cruzi. AN15368 was found to be active in vitro and in vivo against a range of genetically distinct T. cruzi lineages and was uniformly curative in non-human primates (NHPs) with long-term naturally acquired infections. Treatment in NHPs also revealed no detectable acute toxicity or long-term health or reproductive impact. Thus, AN15368 is an extensively validated and apparently safe, clinically ready candidate with promising potential for prevention and treatment of Chagas disease

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

A Kinome RNAi Screen Identified AMPK as Promoting Poxvirus Entry through the Control of Actin Dynamics

Poxviruses include medically important human pathogens, yet little is known about the specific cellular factors essential for their replication. To identify genes essential for poxvirus infection, we used high-throughput RNA interference to screen the Drosophila kinome for factors required for vaccinia infection. We identified seven genes including the three subunits of AMPK as promoting vaccinia infection. AMPK not only facilitated infection in insect cells, but also in mammalian cells. Moreover, we found that AMPK is required for macropinocytosis, a major endocytic entry pathway for vaccinia. Furthermore, we show that AMPK contributes to other virus-independent actin-dependent processes including lamellipodia formation and wound healing, independent of the known AMPK activators LKB1 and CaMKK. Therefore, AMPK plays a highly conserved role in poxvirus infection and actin dynamics independent of its role as an energy regulator