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Find video protocols related to scientific articles indexed in Pubmed.
Time-variant clustering model for understanding cell fate decisions.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 10-22-2014
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Both spatial characteristics and temporal features are often the subjects of concern in physical, social, and biological studies. This work tackles the clustering problems for time course data in which the cluster number and clustering structure change with respect to time, dubbed time-variant clustering. We developed a hierarchical model that simultaneously clusters the objects at every time point and describes the relationships of the clusters between time points. The hidden layer of this model is a generalized form of branching processes. A reversible-jump Markov Chain Monte Carlo method was implemented for model inference, and a feature selection procedure was developed. We applied this method to explore an open question in preimplantation embryonic development. Our analyses using single-cell gene expression data suggested that the earliest cell fate decision could start at the 4-cell stage in mice, earlier than the commonly thought 8- to 16-cell stage. These results together with independent experimental data from single-cell RNA-seq provided support against a prevailing hypothesis in mammalian development.
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Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing.
Genome Res.
PUBLISHED: 08-05-2014
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It remains an open question when and how the first cell fate decision is made in mammals. Using deep single-cell RNA-seq of matched sister blastomeres, we report highly reproducible inter-blastomere differences among 10 2-cell and five 4-cell mouse embryos. Inter-blastomere gene expression differences dominated between-embryo differences and noise, and were sufficient to cluster sister blastomeres into distinct groups. Dozens of protein-coding genes exhibited reproducible bimodal expression in sister blastomeres, which cannot be explained by random fluctuations. The protein expression of one gene out of four of these bimodal genes tested, Gadd45a, exhibited clear inter-blastomeric contrasts. We traced some of the bimodal mRNA expressions to embryonic genome activation, and others to blastomere-specific RNA depletion. Inter-blastomere differences created coexpression gene networks that were much stronger and larger than those that can possibly be created by random noise. The highly correlated gene pairs at the 4-cell stage overlapped with those showing the same directions of differential expression between inner cell mass (ICM) and trophectoderm (TE). These data substantiate the hypothesis of inter-blastomere differences in 2- and 4-cell mouse embryos, and associate these differences with ICM/TE differences.
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Changes in WNT signaling-related gene expression associated with development and cloning in bovine extra-embryonic and endometrial tissues during the peri-implantation period.
Mol. Reprod. Dev.
PUBLISHED: 03-04-2013
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We determined if somatic cell nuclear transfer (SCNT) cloning is associated with WNT-related gene expression in cattle development, and if the expression of genes in the WNT pathway changes during the peri-implantation period. Extra-embryonic and endometrial tissues were collected at gestation days 18 and 34 (d18, d34). WNT5A, FZD4, FZD5, LRP5, CTNNB1, GNAI2, KDM1A, BCL2L1, and SFRP1 transcripts were localized in extra-embryonic tissue, whereas SFRP1 and DKK1 were localized in the endometrium. There were no differences in the localization of these transcripts in extra-embryonic tissue or endometrium from SCNT or artificial insemination (AI) pregnancies. Expression levels of WNT5A were 11-fold greater in the allantois of SCNT than AI samples. In the trophoblast, expression of WNT5A, FZD5, CTNNB1, and DKK1 increased significantly from d18 to d34, whereas expression of KDM1A and SFRP1 decreased, indicating that implantation is associated with major changes in WNT signaling. SCNT was associated with altered WNT5A expression in trophoblasts, with levels increasing 2.3-fold more in AI than SCNT conceptuses from d18 to d34. In the allantois, expression of WNT5A increased 6.3-fold more in SCNT than AI conceptuses from d18 to d34. Endometrial tissue expression levels of the genes tested did not differ between AI or SCNT pregnancies, although expression of individual genes showed variation across developmental stages. Our results demonstrate that SCNT is associated with altered expression of specific WNT-related genes in extra-embryonic tissue in a time- and tissue-specific manner. The pattern of gene expression in the WNT pathway suggests that noncanonical WNT signal transduction is important for implantation of cattle conceptuses. Mol. Reprod. Dev. 80: 977-987, 2013. © 2013 Wiley Periodicals, Inc.
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A retrospective model of oocyte competence: global mRNA and housekeeping transcripts are not associated with in vitro developmental outcome.
Zygote
PUBLISHED: 04-27-2009
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SummaryOocyte developmental competence depends on maternal stores that support development throughout a transcriptionally silent period during early embryogenesis. Previous attempts to investigate transcripts associated with oocyte competence have relied on prospective models, which are mostly based on morphological criteria. Using a retrospective model, we quantitatively compared mRNA among oocytes with different embryo development competence. A cytoplasm biopsy was removed from in vitro matured oocytes to perform comparative analysis of amounts of global polyadenylated (polyA) mRNA and housekeeping gene transcripts. After parthenogenetic activation of biopsied oocytes, presumptive zygotes were cultured individually in vitro and oocytes were classified according to embryo development: (i) blocked before the 8-cell stage; (ii) blocked between the 8-cell and morulae stages; or (iii) developed to the blastocyst stage. Sham-manipulated controls confirmed that biopsies did not alter development outcome. Total polyA mRNA amounts correlate with oocyte diameter but not with the ability to develop to the 8-cell and blastocyst stages. The last was also confirmed by relative quantification of GAPDH, H2A and Hprt1 transcripts. In conclusion, we describe a novel retrospective model to identify putative markers of development competence in single oocytes and demonstrate that global mRNA amounts at the metaphase II stage do not correlate with embryo development in vitro.
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The genome sequence of taurine cattle: a window to ruminant biology and evolution.
, Christine G Elsik, Ross L Tellam, Kim C Worley, Richard A Gibbs, Donna M Muzny, George M Weinstock, David L Adelson, Evan E Eichler, Laura Elnitski, Roderic Guigo, Debora L Hamernik, Steve M Kappes, Harris A Lewin, David J Lynn, Frank W Nicholas, Alexandre Reymond, Monique Rijnkels, Loren C Skow, Evgeny M Zdobnov, Lawrence Schook, James Womack, Tyler Alioto, Stylianos E Antonarakis, Alex Astashyn, Charles E Chapple, Hsiu-Chuan Chen, Jacqueline Chrast, Francisco Camara, Olga Ermolaeva, Charlotte N Henrichsen, Wratko Hlavina, Yuri Kapustin, Boris Kiryutin, Paul Kitts, Felix Kokocinski, Melissa Landrum, Donna Maglott, Kim Pruitt, Victor Sapojnikov, Stephen M Searle, Victor Solovyev, Alexandre Souvorov, Catherine Ucla, Carine Wyss, Juan M Anzola, Daniel Gerlach, Eran Elhaik, Dan Graur, Justin T Reese, Robert C Edgar, John C McEwan, Gemma M Payne, Joy M Raison, Thomas Junier, Evgenia V Kriventseva, Eduardo Eyras, Mireya Plass, Ravikiran Donthu, Denis M Larkin, James Reecy, Mary Q Yang, Lin Chen, Ze Cheng, Carol G Chitko-McKown, George E Liu, Lakshmi K Matukumalli, Jiuzhou Song, Bin Zhu, Daniel G Bradley, Fiona S L Brinkman, Lilian P L Lau, Matthew D Whiteside, Angela Walker, Thomas T Wheeler, Theresa Casey, J Bruce German, Danielle G Lemay, Nauman J Maqbool, Adrian J Molenaar, Seongwon Seo, Paul Stothard, Cynthia L Baldwin, Rebecca Baxter, Candice L Brinkmeyer-Langford, Wendy C Brown, Christopher P Childers, Timothy Connelley, Shirley A Ellis, Krista Fritz, Elizabeth J Glass, Carolyn T A Herzig, Antti Iivanainen, Kevin K Lahmers, Anna K Bennett, C Michael Dickens, James G R Gilbert, Darren E Hagen, Hanni Salih, Jan Aerts, Alexandre R Caetano, Brian Dalrymple, José Fernando García, Clare A Gill, Stefan G Hiendleder, Erdogan Memili, Diane Spurlock, John L Williams, Lee Alexander, Michael J Brownstein, Leluo Guan, Robert A Holt, Steven J M Jones, Marco A Marra, Richard Moore, Stephen S Moore, Andy Roberts, Masaaki Taniguchi, Richard C Waterman, Joseph Chacko, Mimi M Chandrabose, Andy Cree, Marvin Diep Dao, Huyen H Dinh, Ramatu Ayiesha Gabisi, Sandra Hines, Jennifer Hume, Shalini N Jhangiani, Vandita Joshi, Christie L Kovar, Lora R Lewis, Yih-Shin Liu, John López, Margaret B Morgan, Ngoc Bich Nguyen, Geoffrey O Okwuonu, San Juana Ruiz, Jireh Santibanez, Rita A Wright, Christian Buhay, Yan Ding, Shannon Dugan-Rocha, Judith Herdandez, Michael Holder, Aniko Sabo, Amy Egan, Jason Goodell, Katarzyna Wilczek-Boney, Gerald R Fowler, Matthew Edward Hitchens, Ryan J Lozado, Charles Moen, David Steffen, James T Warren, Jingkun Zhang, Readman Chiu, Jacqueline E Schein, K James Durbin, Paul Havlak, Huaiyang Jiang, Yue Liu, Xiang Qin, Yanru Ren, Yufeng Shen, Henry Song, Stephanie Nicole Bell, Clay Davis, Angela Jolivet Johnson, Sandra Lee, Lynne V Nazareth, Bella Mayurkumar Patel, Ling-Ling Pu, Selina Vattathil, Rex Lee Williams, Stacey Curry, Cerissa Hamilton, Erica Sodergren, David A Wheeler, Wes Barris, Gary L Bennett, André Eggen, Ronnie D Green, Gregory P Harhay, Matthew Hobbs, Oliver Jann, John W Keele, Matthew P Kent, Sigbjørn Lien, Stephanie D McKay, Sean McWilliam, Abhirami Ratnakumar, Robert D Schnabel, Timothy Smith, Warren M Snelling, Tad S Sonstegard, Roger T Stone, Yoshikazu Sugimoto, Akiko Takasuga, Jeremy F Taylor, Curtis P Van Tassell, Michael D MacNeil, Antonio R R Abatepaulo, Colette A Abbey, Virpi Ahola, Iassudara G Almeida, Ariel F Amadio, Elen Anatriello, Suria M Bahadue, Fernando H Biase, Clayton R Boldt, Jeffery A Carroll, Wanessa A Carvalho, Eliane P Cervelatti, Elsa Chacko, Jennifer E Chapin, Ye Cheng, Jungwoo Choi, Adam J Colley, Tatiana A de Campos, Marcos De Donato, Isabel K F de Miranda Santos, Carlo J F de Oliveira, Heather Deobald, Eve Devinoy, Kaitlin E Donohue, Peter Dovc, Annett Eberlein, Carolyn J Fitzsimmons, Alessandra M Franzin, Gustavo R Garcia, Sem Genini, Cody J Gladney, Jason R Grant, Marion L Greaser, Jonathan A Green, Darryl L Hadsell, Hatam A Hakimov, Rob Halgren, Jennifer L Harrow, Elizabeth A Hart, Nicola Hastings, Marta Hernàndez, Zhi-Liang Hu, Aaron Ingham, Terhi Iso-Touru, Catherine Jamis, Kirsty Jensen, Dimos Kapetis, Tovah Kerr, Sari S Khalil, Hasan Khatib, Davood Kolbehdari, Charu G Kumar, Dinesh Kumar, Richard Leach, Justin C-M Lee, Changxi Li, Krystin M Logan, Roberto Malinverni, Elisa Marques, William F Martin, Natalia F Martins, Sandra R Maruyama, Raffaele Mazza, Kim L McLean, Juan F Medrano, Barbara T Moreno, Daniela D Moré, Carl T Muntean, Hari P Nandakumar, Marcelo F G Nogueira, Ingrid Olsaker, Sameer D Pant, Francesca Panzitta, Rosemeire C P Pastor, Mario A Poli, Nathan Poslusny, Satyanarayana Rachagani, Shoba Ranganathan, Andrej Razpet, Penny K Riggs, Gonzalo Rincon, Nelida Rodriguez-Osorio, Sandra L Rodriguez-Zas, Natasha E Romero, Anne Rosenwald, Lillian Sando, Sheila M Schmutz, Libing Shen, Laura Sherman, Bruce R Southey, Ylva Strandberg Lutzow, Jonathan V Sweedler, Imke Tammen, Bhanu Prakash V L Telugu, Jennifer M Urbanski, Yuri T Utsunomiya, Chris P Verschoor, Ashley J Waardenberg, Zhiquan Wang, Robert Ward, Rosemarie Weikard, Thomas H Welsh, Stephen N White, Laurens G Wilming, Kris R Wunderlich, Jianqi Yang, Feng-Qi Zhao.
Science
PUBLISHED: 04-25-2009
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To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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Messenger RNA expression of Pabpnl1 and Mbd3l2 genes in oocytes and cleavage embryos.
Fertil. Steril.
PUBLISHED: 01-28-2009
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To identify genes specifically expressed in mammalian oocytes using an in silico subtraction, and to characterize the mRNA patterns of selected genes in oocytes, embryos, and adult tissues.
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Messenger RNAs in metaphase II oocytes correlate with successful embryo development to the blastocyst stage.
Zygote
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Summary The mRNAs accumulated in oocytes provide support for embryo development until embryo genomic activation. We hypothesized that the maternal mRNA stock present in bovine oocytes is associated with embryo development until the blastocyst stage. To test our hypothesis, we analyzed the transcriptome of the oocyte and correlated the results with the embryo development. Our goal was to identify genes expressed in the oocyte that correlate with its ability to develop to the blastocyst stage. A fraction of oocyte cytoplasm was biopsied using micro-aspiration and stored for further expression analysis. Oocytes were activated chemically, cultured individually and classified according to their capacity to develop in vitro to the blastocyst stage. Microarray analysis was performed on mRNA extracted from the oocyte cytoplasm fractions and correlated with its ability to develop to the blastocyst stage (good quality oocyte) or arrest at the 8-16-cell stage (bad quality oocyte). The expression of 4320 annotated genes was detected in the fractions of cytoplasm that had been collected from oocytes matured in vitro. Gene ontology classification revealed that enriched gene expression of genes was associated with certain biological processes: RNA processing, translation and mRNA metabolic process. Genes that are important to the molecular functions of RNA binding and translation factor activity, RNA binding were also enriched in oocytes. We identified 29 genes with differential expression between the two groups of oocytes compared (good versus bad quality). The content of mRNAs expressed in metaphase II oocytes influences the activation of the embryonic genome and enables further develop to the blastocyst stage.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.