Faculty & Staff Research
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This community includes faculty journal articles deposited per Rice's Open Access Policy (more information about the policy can be found in this library guide) and additional faculty work. Items found in this community can also be found in the authors' departmental faculty publication collections.
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Item Glossary of some divination related terms(Rice University, 1/13/2012) Smith, Richard J. (Richard Joseph), 1944-Item Glossary of some Yijing-related terms(Rice University, 1/13/2012) Smith, Richard J. (Richard Joseph), 1944-Item Wiretapping, Surveillance and the Internet(1/18/2008) Bronk, Christopher; James A. Baker III Institute for Public PolicyItem Morphological diversity of extracellular vesicles revealed by cryo-electron microscopy(ASEMV/AAEV, 10/1/2022) Kapoor, Kshipra S.; McAndrews, Kathleen M.; Biswal, Lisa S.; Kalluri, RaghuIntroduction: Exosomes are extracellular vesicles 80-150 nm in diameter, containing proteins, mRNAs, microRNAs, and lipids reflecting the parent cell. While there has been an extensive characterization of the cargo incorporated in exosomes, a detailed morphological analysis of exosomes purified by various isolation techniques has not been performed. Objective: We aimed to determine the heterogeneity of exosomes morphology and if such morphological features are conserved across sample types. Methods: Our study used Cryogenic Electron Microscopy (Cryo-EM) to examine exosome size and morphology. Results: Our results revealed significant diversity in extracellular vesicle morphology independent of the isolation method, suggesting that morphological subpopulations of these vesicles exist. Based on their shape, our analysis classified exosomes into seven categories. In addition, we developed a semi-automatic image analysis framework to accurately characterize exosome attributes and distribution to facilitate reliable quantification of specific bio-nanoparticle features in Cryo-EM micrographs. Conclusions: Morphological features of exosomes inform their biophysical properties, which influence both biodistribution and biological activity in vivo. Our data demonstrating the innate morphological diversity of exosomes may have implications for improving the specificity and precision of exosome-delivered therapeutics. Conflict of interest: R.K. and MD Anderson Cancer Center hold patents in exosome biology and are stock equity holders in Codiak Biosciences Inc. R.K. is a consultant and a scientific advisor of Codiak Biosciences Inc.Item The Permian Oilfield Water Wave: Challenges and Opportunities(James A. Baker III Institute for Public Policy, 10/11/2018) Collins, Gabriel; James A. Baker III Institute for Public PolicyItem Activating natural product synthesis using CRISPR interference and activation systems in Streptomyces(Rice University, 10/27/2021) Ameruoso, Andrea; Department of BiosciencesThe rise of antibiotic-resistant bacteria represents a major threat to global health, creating an urgent need to discover new antibiotics. Natural products derived from the genus Streptomyces represent a rich and diverse repertoire of chemical molecules from which new antibiotics are likely to be found. However, a major challenge is that the biosynthetic gene clusters (BGCs) responsible for natural product synthesis are often poorly expressed under laboratory culturing conditions, thus preventing isolation and screening of novel chemicals. To address this, we describe a novel approach to activate silent BGCs through rewiring endogenous regulation using synthetic gene regulators based upon CRISPR-Cas. First, we create CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) systems that allow for highly programmable and effective gene repression and activation in Streptomyces. We then harness these tools to activate a silent BGC through perturbing its endogenous regulatory network. Together, this work advances the synthetic regulatory toolbox for Streptomyces and facilitates the programmable activation of silent BGCs for novel chemical discovery.Item Natural Gas in the People's Republic of China(10/29/2013) Lewis, Steven W.; James A. Baker III Institute for Public PolicyPart of a study directed by the Center for Energy Studies at Rice Universityﾒs Baker Institute, Harvard University's Geopolitics of Energy Project at the Kennedy School and the University of California, Davis, Graduate School of Management.Item The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: summary and innovation in genomics(BioMed Central, 10/3/2017) Zhao, Zhongming; Liu, Zhandong; Chen, Ken; Guo, Yan; Allen, Genevera I; Zhang, Jiajie; Jim Zheng, W.; Ruan, JianhuaAbstract In this editorial, we first summarize the 2016 International Conference on Intelligent Biology and Medicine (ICIBM 2016) that was held on December 8–10, 2016 in Houston, Texas, USA, and then briefly introduce the ten research articles included in this supplement issue. ICIBM 2016 included four workshops or tutorials, four keynote lectures, four conference invited talks, eight concurrent scientific sessions and a poster session for 53 accepted abstracts, covering current topics in bioinformatics, systems biology, intelligent computing, and biomedical informatics. Through our call for papers, a total of 77 original manuscripts were submitted to ICIBM 2016. After peer review, 11 articles were selected in this special issue, covering topics such as single cell RNA-seq analysis method, genome sequence and variation analysis, bioinformatics method for vaccine development, and cancer genomics.Item RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification(BioMed Central, 10/30/2018) Nasko, Daniel J; Koren, Sergey; Phillippy, Adam M; Treangen, Todd JAbstract In order to determine the role of the database in taxonomic sequence classification, we examine the influence of the database over time on k-mer-based lowest common ancestor taxonomic classification. We present three major findings: the number of new species added to the NCBI RefSeq database greatly outpaces the number of new genera; as a result, more reads are classified with newer database versions, but fewer are classified at the species level; and Bayesian-based re-estimation mitigates this effect but struggles with novel genomes. These results suggest a need for new classification approaches specially adapted for large databases.Item Mechanical strength of water-saturated Solnhofen limestone at elevated temperatures(Rice University, 10/7/2021) French, Melodie; Zhu, Wenlu; Xiao, Xiaohui; Evans, Brian; Prior, David; National Science Foundation; U.S. Geological Survey; Earth, Environmental, and Planetary SciencesThe data is a record of the stress and strain during experimental deformation of Solnhofen limestone across its brittle (localized deformation) to ductile (distributed deformation) transition. We conducted conventional triaxial compression tests on both water-saturated and nominally dry cores of Solnhofen at temperatures up to 200 Celsius and effective confining pressures up to 350 MPa to evaluate the roles of pore water and temperature on the deformation mechanisms of low-porosity limestone at conditions of the upper crust.Item RRAD, IL4I1, CDKN1A, and SERPINE1 genes are potentially co-regulated by NF-κB and p53 transcription factors in cells exposed to high doses of ionizing radiation(BioMed Central, 11/12/2018) Szołtysek, Katarzyna; Janus, Patryk; Zając, Gracjana; Stokowy, Tomasz; Walaszczyk, Anna; Widłak, Wiesława; Wojtaś, Bartosz; Gielniewski, Bartłomiej; Cockell, Simon; Perkins, Neil D; Kimmel, Marek; Widlak, PiotrAbstract Background The cellular response to ionizing radiation involves activation of p53-dependent pathways and activation of the atypical NF-κB pathway. The crosstalk between these two transcriptional networks include (co)regulation of common gene targets. Here we looked for novel genes potentially (co)regulated by p53 and NF-κB using integrative genomics screening in human osteosarcoma U2-OS cells irradiated with a high dose (4 and 10 Gy). Radiation-induced expression in cells with silenced TP53 or RELA (coding the p65 NF-κB subunit) genes was analyzed by RNA-Seq while radiation-enhanced binding of p53 and RelA in putative regulatory regions was analyzed by ChIP-Seq, then selected candidates were validated by qPCR. Results We identified a subset of radiation-modulated genes whose expression was affected by silencing of both TP53 and RELA, and a subset of radiation-upregulated genes where radiation stimulated binding of both p53 and RelA. For three genes, namely IL4I1, SERPINE1, and CDKN1A, an antagonistic effect of the TP53 and RELA silencing was consistent with radiation-enhanced binding of both p53 and RelA. This suggested the possibility of a direct antagonistic (co)regulation by both factors: activation by NF-κB and inhibition by p53 of IL4I1, and activation by p53 and inhibition by NF-κB of CDKN1A and SERPINE1. On the other hand, radiation-enhanced binding of both p53 and RelA was observed in a putative regulatory region of the RRAD gene whose expression was downregulated both by TP53 and RELA silencing, which suggested a possibility of direct (co)activation by both factors. Conclusions Four new candidates for genes directly co-regulated by NF-κB and p53 were revealed.Item Life's Path: The Good, the Bad, and the Just Plain There(11/16/2012) Klein, Anne CarolynItem Gene characteristics predicting missense, nonsense and frameshift mutations in tumor samples(BioMed Central, 11/19/2018) Gorlov, Ivan P.; Pikielny, Claudio W.; Frost, Hildreth R.; Her, Stephanie C.; Cole, Michael D.; Strohbehn, Samuel D.; Wallace-Bradley, David; Kimmel, Marek; Gorlova, Olga Y.; Amos, Christopher I.Background: Because driver mutations provide selective advantage to the mutant clone, they tend to occur at a higher frequency in tumor samples compared to selectively neutral (passenger) mutations. However, mutation frequency alone is insufficient to identify cancer genes because mutability is influenced by many gene characteristics, such as size, nucleotide composition, etc. The goal of this study was to identify gene characteristics associated with the frequency of somatic mutations in the gene in tumor samples. Results: We used data on somatic mutations detected by genome wide screens from the Catalog of Somatic Mutations in Cancer (COSMIC). Gene size, nucleotide composition, expression level of the gene, relative replication time in the cell cycle, level of evolutionary conservation and other gene characteristics (totaling 11) were used as predictors of the number of somatic mutations. We applied stepwise multiple linear regression to predict the number of mutations per gene. Because missense, nonsense, and frameshift mutations are associated with different sets of gene characteristics, they were modeled separately. Gene characteristics explain 88% of the variation in the number of missense, 40% of nonsense, and 23% of frameshift mutations. Comparisons of the observed and expected numbers of mutations identified genes with a higher than expected number of mutations– positive outliers. Many of these are known driver genes. A number of novel candidate driver genes was also identified. Conclusions: By comparing the observed and predicted number of mutations in a gene, we have identified known cancer-associated genes as well as 111 novel cancer associated genes. We also showed that adding the number of silent mutations per gene reported by genome/exome wide screens across all cancer type (COSMIC data) as a predictor substantially exceeds predicting accuracy of the most popular cancer gene predicting tool - MutsigCV.Item Nuclear Nonproliferation: Policy Implications(11/2/2007) Lane, Neal F.; Abbey, George W.S.; James A. Baker III Institute for Public PolicyItem New Ways of Thinking About Oilfield Water in the Permian Basin(James A. Baker III Institute for Public Policy, 12/6/2018) Collins, Gabriel; James A. Baker III Institute for Public PolicyItem Hot Topic: Stem Cell Controversy: Are Human Skin Cells Really the Breakthrough?(James A. Baker III Institute for Public Policy, 12/7/2007) Lane, Neal F.; Matthews, Kirstin R.W.; James A. Baker III Institute for Public PolicyItem Increasing influence of medieval architecture upon the architecture of America(1928) Hooton, Claude EdgarItem Street Map, City of Houston, Texas, circa 1930(1930) Texas Map & Blueprint Co.Item Ornament in relation to modern architecture(1934) Talley, Robert WilliamItem The architectural development of the automobile filling station in America(1937) Barrick, Nolan Elmore