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https://www.readbyqxmd.com/read/29457792/on-the-design-of-crispr-based-single-cell-molecular-screens
#1
Andrew J Hill, José L McFaline-Figueroa, Lea M Starita, Molly J Gasperini, Kenneth A Matreyek, Jonathan Packer, Dana Jackson, Jay Shendure, Cole Trapnell
Several groups recently coupled CRISPR perturbations and single-cell RNA-seq for pooled genetic screens. We demonstrate that vector designs of these studies are susceptible to ∼50% swapping of guide RNA-barcode associations because of lentiviral template switching. We optimized a published alternative, CROP-seq, in which the guide RNA also serves as the barcode, and here confirm that this strategy performs robustly and doubled the rate at which guides are assigned to cells to 94%.
February 19, 2018: Nature Methods
https://www.readbyqxmd.com/read/29457714/selective-recognition-of-rna-substrates-by-adar-deaminase-domains
#2
Yuru Wang, SeHee Park, Peter A Beal
Adenosine deamination is one of the most prevalent post-transcriptional modifications in mRNA and is catalyzed by ADAR1 and ADAR2 in humans. ADAR1 and ADAR2 have different substrate selectivity, which is believed to mainly originate from the proteins' deaminase domains (hADAR1d and hADAR2d, respectively). RNA-seq of the S. cerevisiae transcriptome subjected to ADAR-catalyzed RNA editing identified substrates with common secondary structure features preferentially edited by hADAR1d over hADAR2d. The relatively small size and efficient reaction of one of these substrates suggested it could be useful for further study of the hADAR1d reaction...
February 19, 2018: Biochemistry
https://www.readbyqxmd.com/read/29456764/integrative-analysis-of-the-epigenetic-basis-of-muscle-invasive-urothelial-carcinoma
#3
Thomas Sanford, Maxwell V Meng, Reema Railkar, Piyush K Agarwal, Sima P Porten
Background: Elucidation of epigenetic alterations in bladder cancer will lead to further understanding of the biology of the disease and hopefully improved therapies. Our aim was to perform an integrative epigenetic analysis of invasive urothelial carcinoma of the bladder to identify the epigenetic abnormalities involved in the development and progression of this cancer. Methods: Pre-processed methylation data and RNA-seq data were downloaded from The Cancer Genome Atlas (TCGA) and processed using the R package TCGA-Assembler...
2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/29456143/neocortical-association-cell-types-in-the-forebrain-of-birds-and-alligators
#4
Steven D Briscoe, Caroline B Albertin, Joanna J Rowell, Clifton W Ragsdale
The avian dorsal telencephalon has two vast territories, the nidopallium and the mesopallium, both of which have been shown to contribute substantially to higher cognitive functions. From their connections, these territories have been proposed as equivalent to mammalian neocortical layers 2 and 3, various neocortical association areas, or the amygdala, but whether these are analogies or homologies by descent is unknown. We investigated the molecular profiles of the mesopallium and the nidopallium with RNA-seq...
February 14, 2018: Current Biology: CB
https://www.readbyqxmd.com/read/29454997/regulatory-responses-of-hepatocytes-macrophages-and-vascular-endothelial-cells-to-magnesium-deficiency
#5
Mei Shigematsu, Shozo Tomonaga, Fumie Shimokawa, Masaru Murakami, Toru Imamura, Tohru Matsui, Masayuki Funaba
The liver is the organ that responds to nutritional disturbances including magnesium deficiency. The present study evaluated cellular responses to magnesium deficiency using model cells of the liver, namely, HepG2 cells as hepatocytes, RAW264.7 cells as Kupffer cells and human umbilical vein endothelial cells (HUVECs) as vascular endothelial cells; we examined effects of culture with magnesium deficient medium on cell responses in individual types of cells as well as interactive responses among cells. Metabolomic analyses indicated that magnesium deficiency differentially affected the cellular content of metabolites among HepG2 cells, RAW264...
February 2, 2018: Journal of Nutritional Biochemistry
https://www.readbyqxmd.com/read/29454387/the-transcriptome-response-of-the-ruminal-methanogen-methanobrevibacter-ruminantium-strain-m1-to-the-inhibitor-lauric-acid
#6
Xuan Zhou, Marc J A Stevens, Stefan Neuenschwander, Angela Schwarm, Michael Kreuzer, Anna Bratus-Neuenschwander, Johanna O Zeitz
OBJECTIVE: Lauric acid (C12 ) is a medium-chain fatty acid that inhibits growth and production of the greenhouse gas methane by rumen methanogens such as Methanobrevibacter ruminantium. To understand the inhibitory mechanism of C12 , a transcriptome analysis was performed in M. ruminantium strain M1 (DSM 1093) using RNA-Seq. RESULTS: Pure cell cultures in the exponential growth phase were treated with 0.4 mg/ml C12 , dissolved in dimethyl sulfoxide (DMSO), for 1 h and transcriptomic changes were compared to DMSO-only treated cells (final DMSO concentration 0...
February 17, 2018: BMC Research Notes
https://www.readbyqxmd.com/read/29453410/molecular-characterization-of-colorectal-adenomas-with-and-without-malignancy-reveals-distinguishing-genome-transcriptome-and-methylome-alterations
#7
Brooke R Druliner, Panwen Wang, Taejeong Bae, Saurabh Baheti, Seth Slettedahl, Douglas Mahoney, Nikolaos Vasmatzis, Hang Xu, Minsoo Kim, Matthew Bockol, Daniel O'Brien, Diane Grill, Nathaniel Warner, Miguel Munoz-Gomez, Kimberlee Kossick, Ruth Johnson, Mohamad Mouchli, Donna Felmlee-Devine, Jill Washechek-Aletto, Thomas Smyrk, Ann Oberg, Junwen Wang, Nicholas Chia, Alexej Abyzov, David Ahlquist, Lisa A Boardman
The majority of colorectal cancer (CRC) arises from precursor lesions known as polyps. The molecular determinants that distinguish benign from malignant polyps remain unclear. To molecularly characterize polyps, we utilized Cancer Adjacent Polyp (CAP) and Cancer Free Polyp (CFP) patients. CAPs had tissues from the residual polyp of origin and contiguous cancer; CFPs had polyp tissues matched to CAPs based on polyp size, histology and dysplasia. To determine whether molecular features distinguish CAPs and CFPs, we conducted Whole Genome Sequencing, RNA-seq, and RRBS on over 90 tissues from 31 patients...
February 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29453319/leptin-signaling-mediates-obesity-associated-csc-enrichment-and-emt-in-preclinical-tnbc-models
#8
Laura W Bowers, Emily L Rossi, Shannon B McDonell, Steven S Doerstling, Subreen A Khatib, Claire G Lineberger, Jody E Albright, Xiaohu Tang, Linda A deGraffenried, Stephen D Hursting
Obesity is associated with poor prognosis in triple-negative breast cancer (TNBC). Preclinical models of TNBC were used to test the hypothesis that increased leptin signaling drives obesity-associated TNBC development by promoting cancer stem cell (CSC) enrichment and/or epithelial-to-mesenchymal transition (EMT). MMTV-Wnt-1 transgenic mice, which develop spontaneous basal-like, triple-negative mammary tumors, received either a control diet (10% kcal from fat) or a diet-induced obesity regimen (DIO, 60% kcal from fat) for up to 42 weeks (n=15/group)...
February 16, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29453314/ar-expression-in-breast-cancer-ctcs-associates-with-bone-metastases
#9
Nicola Aceto, Aditya Bardia, Ben S Wittner, Maria C Donaldson, Ryan O'Keefe, Amanda Engstrom, Francesca Bersani, Yu Zheng, Valentine Comaills, Kira Niederhoffer, Huili Zhu, Olivia MacKenzie, Toshi Shioda, Dennis Sgroi, Ravi Kapur, David T Ting, Beverly Moy, Sridhar Ramaswamy, Mehmet Toner, Daniel A Haber, Shyamala Maheswaran
Molecular drivers underlying bone metastases in human cancer are not well understood, in part due to constraints in bone tissue sampling. Here, RNA sequencing (RNA-seq) was performed of circulating tumor cells (CTCs) isolated from blood samples of women with metastatic estrogen receptor (ER)+ breast cancer, comparing cases with progression in bone versus visceral organs. Among the activated cellular pathways in CTCs from bone-predominant breast cancer is androgen receptor (AR) signaling. AR gene expression is evident, as is its constitutively active splice variant AR-v7...
February 16, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29453232/a-randomized-multicenter-phase-ii-study-of-docosahexaenoic-acid-in-patients-with-a-history-of-breast-cancer-premalignant-lesions-or-benign-breast-disease
#10
Ayca Gucalp, Xi K Zhou, Elise D Cook, Judy E Garber, Katherine D Crew, Julie R Nangia, Priya Bhardwaj, Dilip D Giri, Olivier Elemento, Akanksha Verma, Hanhan Wang, J Jack Lee, Lana A Vornik, Carrie Mays, Diane Weber, Valerie Sepeda, Holly O'Kane, Margaret Krasne, Samantha Williams, Patrick G Morris, Brandy M Heckman-Stoddard, Barbara K Dunn, Clifford A Hudis, Powel H Brown, Andrew J Dannenberg
Obesity, a cause of subclinical inflammation, is a risk factor for the development of postmenopausal breast cancer (BC) and is associated with poorer cancer outcomes. Docosahexaenoic acid (DHA), an omega-3 fatty acid, possesses anti-inflammatory properties. We hypothesized that treatment with DHA would reduce the expression of proinflammatory genes and aromatase, the rate-limiting enzyme for estrogen biosynthesis, in benign breast tissue of overweight/obese women. A randomized, placebo-controlled, double-blind phase II study of DHA given for 12 weeks to overweight/obese women with a history of stage I-III BC, DCIS/LCIS, Paget's disease, or proliferative benign breast disease was carried out...
February 16, 2018: Cancer Prevention Research
https://www.readbyqxmd.com/read/29452083/tribolium-castaneum-gene-expression-changes-after-paranosema-whitei-infection
#11
Alberto Lopez-Ezquerra, Andreas Mitschke, Erich Bornberg-Bauer, Gerrit Joop
BACKGROUND: Microsporidia are obligate parasites that possess some of the smallest eukaryotic genomes. Several insect species are susceptible to infections by microsporidian parasites. Paranosema whitei frequently infects young larvae of Tribolium castaneum and obligately kills the host whereupon transmission to subsequent hosts is accomplished via spores. P. whitei infection results in developmental arrest of T. castaneum, preventing larvae from pupation. The mechanisms underlying P...
February 13, 2018: Journal of Invertebrate Pathology
https://www.readbyqxmd.com/read/29451494/single-cell-transcriptional-dynamics-of-flavivirus-infection
#12
Fabio Zanini, Szu-Yuan Pu, Elena Bekerman, Shirit Einav, Stephen R Quake
Dengue and Zika viral infections affect millions of people annually and can be complicated by hemorrhage or neurological manifestations, respectively. However, a thorough understanding of the host response to these viruses is lacking, partly because conventional approaches ignore heterogeneity in virus abundance across cells. We present viscRNA-Seq (virus-inclusive single cell RNA-Seq), an approach to probe the host transcriptome together with intracellular viral RNA at the single cell level. We applied viscRNA-Seq to monitor dengue and Zika virus infection in cultured cells and discovered extreme heterogeneity in virus abundance...
February 16, 2018: ELife
https://www.readbyqxmd.com/read/29451311/impaired-phloem-loading-in-zmsweet13a-b-c-sucrose-transporter-triple-knock-out-mutants-in-zea-mays
#13
Margaret Bezrutczyk, Thomas Hartwig, Marc Horshman, Si Nian Char, Jinliang Yang, Bing Yang, Wolf B Frommer, Davide Sosso
Crop yield depends on efficient allocation of sucrose from leaves to seeds. In Arabidopsis, phloem loading is mediated by a combination of SWEET sucrose effluxers and subsequent uptake by SUT1/SUC2 sucrose/H + symporters. ZmSUT1 is essential for carbon allocation in maize, but the relative contribution to apoplasmic phloem loading and retrieval of sucrose leaking from the translocation path is not known. Here we analysed the contribution of SWEETs to phloem loading in maize. We identified three leaf-expressed SWEET sucrose transporters as key components of apoplasmic phloem loading in Zea mays L...
February 16, 2018: New Phytologist
https://www.readbyqxmd.com/read/29450759/gene-expression-and-population-polymorphism-of-maize-iranian-mosaic-virus-in-zea-mays-and-intracellular-localization-and-interactions-of-viral-n-p-and-m-proteins-in-nicotiana-benthamiana
#14
Abozar Ghorbani, Keramatollah Izadpanah, Ralf G Dietzgen
Maize Iranian mosaic virus (MIMV; Mononegavirales, Rhabdoviridae, Nucleorhabdovirus) infects maize and several other poaceous plants. MIMV encodes six proteins, i.e., nucleocapsid protein (N), polymerase cofactor phosphoprotein (P), putative movement protein (P3), matrix protein (M), glycoprotein (G), and large RNA-dependent RNA polymerase (L). In the present study, MIMV gene expression and genetic polymorphism of an MIMV population in maize were determined. N, P, P3, and M protein genes were more highly expressed than the 5' terminal G and L genes...
February 15, 2018: Virus Genes
https://www.readbyqxmd.com/read/29449812/calycosin-orchestrates-osteogenesis-of-danggui-buxue-tang-in-cultured-osteoblasts-evaluating-the-mechanism-of-action-by-omics-and-chemical-knock-out-methodologies
#15
Amy G W Gong, Ran Duan, Huai Y Wang, Tina T X Dong, Karl W K Tsim
Danggui Buxue Tang (DBT), an ancient Chinese herbal decoction commonly used to mitigate menopausal osteoporosis, contains two herbs: Astragali Radix (AR) and Angelicae Sinensis Radix (ASR). The exact efficacy of individual chemical(s) within DBT, or in any herbal mixture, is hard to be revealed. Calycosin and ferulic acid have been reported to be the predominant chemicals found within DBT, and its roles in regulating osteoblastic differentiation have been proposed here. To probe the roles of calycosin and ferulic acid, these chemicals were specifically depleted from the DBT extracts...
2018: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/29449542/long-non-coding-rnas-in-ischemic-stroke
#16
REVIEW
Mei-Hua Bao, Vivian Szeto, Burton B Yang, Shu-Zhen Zhu, Hong-Shuo Sun, Zhong-Ping Feng
Stroke is one of the leading causes of mortality and disability worldwide. Uncovering the cellular and molecular pathophysiological processes in stroke have been a top priority. Long non-coding (lnc) RNAs play critical roles in different kinds of diseases. In recent years, a bulk of aberrantly expressed lncRNAs have been screened out in ischemic stroke patients or ischemia insulted animals using new technologies such as RNA-seq, deep sequencing, and microarrays. Nine specific lncRNAs, antisense non-coding RNA in the INK4 locus (ANRIL), metastasis-associate lung adenocarcinoma transcript 1 (MALAT1), N1LR, maternally expressed gene 3 (MEG3), H19, CaMK2D-associated transcript 1 (C2dat1), Fos downstream transcript (FosDT), small nucleolar RNA host gene 14 (SNHG14), and taurine-upregulated gene 1 (TUG1), were found increased in cerebral ischemic animals and/or oxygen-glucose deprived (OGD) cells...
February 15, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29449409/a-human-specific-switch-of-alternatively-spliced-afmid-isoforms-contributes-to-tp53-mutations-and-tumor-recurrence-in-hepatocellular-carcinoma
#17
Kuan-Ting Lin, Wai Kit Ma, Juergen Scharner, Yun-Ru Liu, Adrian R Krainer
Pre-mRNA splicing can contribute to the switch of cell identity that occurs in carcinogenesis. Here, we analyze a large collection of RNA-seq data sets and report that splicing changes in hepatocyte-specific enzymes, such as AFMID and KHK , are associated with HCC patients' survival and relapse. The switch of AFMID isoforms is an early event in HCC development and is associated with driver mutations in TP53 and ARID1A The switch of AFMID isoforms is human-specific and not detectable in other species, including primates...
February 15, 2018: Genome Research
https://www.readbyqxmd.com/read/29449307/rage-deletion-confers-renoprotection-by-reducing-responsiveness-to-transforming-growth-factor-%C3%AE-and-increasing-resistance-to-apoptosis
#18
Shinji Hagiwara, Karly Sourris, Mark Ziemann, Wu Tieqiao, Muthukumar Mohan, Aaron D McClelland, Eoin Brennan, Josephine Forbes, Melinda Coughlan, Brooke Harcourt, Sally Penfold, Bo Wang, Gavin Higgins, Raelene Pickering, Assam El-Osta, Merlin C Thomas, Mark E Cooper, Phillip Kantharidis
Signalling via the receptor of advanced glycation end-products (RAGE) although complex and not fully elucidated in the setting of diabetes, is considered a key injurious pathway in the development of diabetic nephropathy (DN). We report here that RAGE deletion resulted in increased expression of fibrotic (collagen I and IV, fibronectin) and the inflammatory marker, MCP-1 in primary mouse mesangial cells (MC) and in kidney cortex. RNA-seq analysis in MCs from RAGE -/- and wild type mice confirmed these observations...
February 15, 2018: Diabetes
https://www.readbyqxmd.com/read/29448940/comparative-analysis-of-alfalfa-medicago-sativa-l-leaf-transcriptomes-reveals-genotype-specific-salt-tolerance-mechanisms
#19
Yunting Lei, Yuxing Xu, Christian Hettenhausen, Chengkai Lu, Guojing Shen, Cuiping Zhang, Jing Li, Juan Song, Honghui Lin, Jianqiang Wu
BACKGROUND: Soil salinity is an important factor affecting growth, development, and productivity of almost all land plants, including the forage crop alfalfa (Medicago sativa). However, little is known about how alfalfa responds and adapts to salt stress, particularly among different salt-tolerant cultivars. RESULTS: Among seven alfalfa cultivars, we found that Zhongmu-1 (ZM) is relatively salt-tolerant and Xingjiang Daye (XJ) is salt-sensitive. Compared to XJ, ZM showed slower growth under low-salt conditions, but exhibited stronger tolerance to salt stress...
February 15, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29447837/analyses-of-the-molecular-mechanisms-associated-with-salinity-adaption-of-trachidermus-fasciatus-through-combined-itraq-based-proteomics-and-rna-sequencing-based-transcriptomics
#20
REVIEW
Qian Ma, Xinfu Liu, Wenrong Feng, Shufang Liu, Zhimeng Zhuang
Osmoregulation mechanism underlying acclimation and adaptation of migratory fish to different salinities has been studied for decades. Recently developed transcriptomic and proteomic techniques would make it possible to provide more reliable data to decipher the mechanism study at a molecular level. Here in this study, an integrative analysis of the kidney-specific transcriptome and proteome was performed to identify important regulators and pathways involved in salinity adaption of roughskin sculpin (Trachidermus fasciatus)...
February 12, 2018: Progress in Biophysics and Molecular Biology
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