17 results on '"Rathi, D."'
Search Results
2. Pathological angiogenesis in retinopathy engages cellular senescence and is amenable to therapeutic elimination via BCL-xL inhibition
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Ariel M. Wilson, Taner Dogan, Dan Marquess, Agnieszka Dejda, Pedro J. Beltran, Przemyslaw Sapieha, Rachel Juneau, Rathi D. Ryan, Frédérick A. Mallette, Gabrielle Girouard, Scott R. Armstrong, Vera Guber, Christian Beauséjour, Frédérique Pilon, Priyanka Patel, Frederik Fournier, Alexandre Dubrac, Sonali Dasgupta, Manuel Buscarlet, Sergio Crespo-Garcia, Surabhi R. Rao, Shawnta Y. Chaney, Christopher B. Yohn, Robert O’Brien, Gael Cagnone, Jean-Sebastien Joyal, and Pamela R. Tsuruda
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Male ,0301 basic medicine ,Senescence ,Flavonols ,Physiology ,Angiogenesis ,bcl-X Protein ,Apoptosis ,Mice, Transgenic ,Bcl-xL ,Tacrolimus ,Neovascularization ,Mice ,03 medical and health sciences ,0302 clinical medicine ,Retinal Diseases ,Animals ,Humans ,Medicine ,Senolytic ,Molecular Biology ,Cellular Senescence ,Cyclin-Dependent Kinase Inhibitor p16 ,Retina ,Neovascularization, Pathologic ,biology ,business.industry ,Endothelial Cells ,Cell Biology ,Diabetic retinopathy ,medicine.disease ,3. Good health ,Collagen Type I, alpha 1 Chain ,Mice, Inbred C57BL ,Disease Models, Animal ,030104 developmental biology ,medicine.anatomical_structure ,biology.protein ,Cancer research ,Female ,medicine.symptom ,business ,030217 neurology & neurosurgery ,Retinopathy - Abstract
Attenuating pathological angiogenesis in diseases characterized by neovascularization such as diabetic retinopathy has transformed standards of care. Yet little is known about the molecular signatures discriminating physiological blood vessels from their diseased counterparts, leading to off-target effects of therapy. We demonstrate that in contrast to healthy blood vessels, pathological vessels engage pathways of cellular senescence. Senescent (p16INK4A-expressing) cells accumulate in retinas of patients with diabetic retinopathy and during peak destructive neovascularization in a mouse model of retinopathy. Using either genetic approaches that clear p16INK4A-expressing cells or small molecule inhibitors of the anti-apoptotic protein BCL-xL, we show that senolysis suppresses pathological angiogenesis. Single-cell analysis revealed that subsets of endothelial cells with senescence signatures and expressing Col1a1 are no longer detected in BCL-xL-inhibitor-treated retinas, yielding a retina conducive to physiological vascular repair. These findings provide mechanistic evidence supporting the development of BCL-xL inhibitors as potential treatments for neovascular retinal disease.
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- 2021
3. Author Correction: Conversion of human fibroblasts to angioblast-like progenitor cells
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Cécile Volle-Challier, Sergio Ruiz, Louise C. Laurent, Caroline Pendaries, Ahmet M. Denli, Francesca S. Boscolo, Ignacio Sancho-Martinez, Rathi D Thiagarajan, Fred H. Gage, Jean-Marc Herbert, Ilir Dubova, Aitor Aguirre, Françoise Bono, Yun Xia, Leo Kurian, Nuria Montserrat, Mo Li, Concepcion Rodriguez, Krystal Moon, Jeanne F. Loring, Juan Carlos Izpisua Belmonte, Julian Pulecio, and Emmanuel Nivet
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Cell Biology ,Progenitor cell ,Biology ,Angioblast ,Molecular Biology ,Biochemistry ,Biotechnology ,Cell biology - Published
- 2020
4. Impact of Soil Health Card Scheme on Farmers’ Income – A Case Study of Kharif Crops in Madhya Pradesh
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Chouhan, R.S., Sharma, H.O., Rathi, D., and Niranjan, H.K.
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Agricultural and Food Policy - Published
- 2017
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- View/download PDF
5. Abnormalities in human pluripotent cells due to reprogramming mechanisms
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Brittany L. Daughtry, Eunju Kang, Paula Amato, Hong Ma, Riffat Ahmed, Robert Morey, Crystal Van Dyken, Masahito Tachibana, Alim Polat, Louise C. Laurent, Joseph R. Ecker, Karen Sabatini, Joseph R. Nery, Ryan C. O’Neil, Rebecca Tippner-Hedges, Shoukhrat Mitalipov, Matthew D. Schultz, Nuria Marti Gutierrez, Rosa Castanon, Atsushi Sugawara, Rathi D Thiagarajan, Don P. Wolf, Manoj Hariharan, Yupeng He, Michelle Sparman, and Sumita Gokhale
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Pluripotent Stem Cells ,Nuclear Transfer Techniques ,Cell type ,DNA Copy Number Variations ,General Science & Technology ,Somatic cell ,1.1 Normal biological development and functioning ,Stem Cell Research - Embryonic - Non-Human ,Biology ,Regenerative Medicine ,Chromosomes ,Cell Line ,Genomic Imprinting ,Stem Cell Research - Nonembryonic - Human ,MD Multidisciplinary ,Genetics ,Animals ,Humans ,Stem Cell Research - Induced Pluripotent Stem Cell - Non-Human ,Induced pluripotent stem cell ,Chromosome Aberrations ,Chromosomes, Human, X ,Multidisciplinary ,Stem Cell Research - Induced Pluripotent Stem Cell ,Stem Cell Research - Induced Pluripotent Stem Cell - Human ,5.2 Cellular and gene therapies ,Human Genome ,DNA Methylation ,Stem Cell Research ,Cellular Reprogramming ,Embryonic stem cell ,Cell biology ,Cell culture ,DNA methylation ,Somatic cell nuclear transfer ,Generic health relevance ,Transcriptome ,Reprogramming ,Human ,Genome-Wide Association Study - Abstract
Human pluripotent stem cells hold potential for regenerative medicine, but available cell types have significant limitations. Although embryonic stem cells (ES cells) from in vitro fertilized embryos (IVF ES cells) represent the 'gold standard', they are allogeneic to patients. Autologous induced pluripotent stem cells (iPS cells) are prone to epigenetic and transcriptional aberrations. To determine whether such abnormalities are intrinsic to somatic cell reprogramming or secondary to the reprogramming method, genetically matched sets of human IVF ES cells, iPS cells and nuclear transfer ES cells (NT ES cells) derived by somatic cell nuclear transfer (SCNT) were subjected to genome-wide analyses. Both NT ES cells and iPS cells derived from the same somatic cells contained comparable numbers of de novo copy number variations. In contrast, DNA methylation and transcriptome profiles of NT ES cells corresponded closely to those of IVF ES cells, whereas iPS cells differed and retained residual DNA methylation patterns typical of parental somatic cells. Thus, human somatic cells can be faithfully reprogrammed to pluripotency by SCNT and are therefore ideal for cell replacement therapies.
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- 2014
6. Conversion of human fibroblasts to angioblast-like progenitor cells
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Francesca S. Boscolo, Fred H. Gage, Ignacio Sancho-Martinez, Aitor Aguirre, Nuria Montserrat, Sergio Ruiz, Krystal Moon, Cécile Volle-Challier, Louise C. Laurent, Concepcion Rodriguez, Julian Pulecio, Rathi D Thiagarajan, Juan Carlos Izpisua Belmonte, Ahmet M. Denli, Ilir Dubova, Yun Xia, Caroline Pendaries, Jean-Marc Herbert, Emmanuel Nivet, Mo Li, Leo Kurian, Jeanne F. Loring, Françoise Bono, Neurobiologie des interactions cellulaires et neurophysiopathologie - NICN (NICN), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), SANOFI Recherche, Laboratoire de Chimie Physique D'Orsay (LCPO), Université Paris-Sud - Paris 11 (UP11)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)
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Technology ,Somatic cell ,Cellular differentiation ,Messenger ,Fluorescent Antibody Technique ,Angioblast ,Medical and Health Sciences ,Biochemistry ,Mice ,0302 clinical medicine ,Smooth Muscle ,Cell Movement ,[SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB] ,Cells, Cultured ,0303 health sciences ,Cultured ,Blotting ,Reverse Transcriptase Polymerase Chain Reaction ,Stem Cells ,Cell Differentiation ,Biological Sciences ,Flow Cytometry ,Cellular Reprogramming ,Cell biology ,Endothelial stem cell ,Stem cell ,Western ,Reprogramming ,Biotechnology ,Cells ,Blotting, Western ,Myocytes, Smooth Muscle ,Neovascularization, Physiologic ,Biology ,Real-Time Polymerase Chain Reaction ,Article ,03 medical and health sciences ,Vascular ,Animals ,Humans ,Cell Lineage ,RNA, Messenger ,Endothelium ,Progenitor cell ,Physiologic ,Molecular Biology ,Neovascularization ,Cell Proliferation ,030304 developmental biology ,Progenitor ,Myocytes ,Cell Biology ,Fibroblasts ,Molecular biology ,RNA ,Endothelium, Vascular ,Biomarkers ,030217 neurology & neurosurgery ,Developmental Biology - Abstract
Lineage conversion of one somatic cell type into another constitutes an attractive approach for research and clinical use. Lineage conversion can proceed in a direct manner, in the absence of proliferation and multipotent progenitor generation, or in an indirect manner, by the generation of expandable multipotent progenitor states. Here we report on the development of a combined reprogramming methodology that, transitioning through a plastic intermediate state, allows for the generation of human mesodermal progenitor cells while circumventing the traditional hallmarks of pluripotency. Converted mesodermal progenitor cells demonstrated bi-potent differentiation potential and were able to generate endothelial and smooth muscle lineages. Importantly, human fibroblasts can be converted into angioblast-like progenitor cells by non-integrative approaches. Differentiated angioblast-like cells exhibit neo-angiogenesis and anastomosis in vivo. The methodology for indirect lineage conversion to angioblast-like cells described here adds to the armamentarium of reprogramming approaches aimed at the clinical treatment of ischemic pathologies.
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- 2013
7. Using Local and Traditional Knowledge to Define a Digital Library for the Inuvialuit Settlement Region
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Stobbs, R., Campbell, Sandy, Farnel, S., Piltingsrud, A., Shiri, A., Rathi, D., Maloney, E., and Cockney, C.
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- 2016
- Full Text
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8. Analysis of early nephron patterning reveals a role for distal RV proliferation in fusion to the ureteric tip via a cap mesenchyme-derived connecting segment
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Dave Tang, Ernmanuelle Lesieur, M. Todd Valerius, S. Steven Potter, Han Sheng Chiu, Eric W. Brunskill, Kylie Georgas, Darrin Taylor, Rathi D Thiagarajan, Alexander N. Combes, Melissa H. Little, Bree Rumballe, Andrew P. McMahon, Bruce J. Aronow, and Sean M. Grimmond
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Calbindins ,Bone Morphogenetic Protein 2 ,Nephron ,urologic and male genital diseases ,Kidney ,Epithelium ,Renal connecting tubule formation ,Mesoderm ,Mice ,0302 clinical medicine ,Pregnancy ,Morphogenesis ,0303 health sciences ,Receptors, Notch ,Wnt signaling pathway ,Anatomy ,Cadherins ,Cell biology ,medicine.anatomical_structure ,Female ,Renal vesicle ,Collagen Type IV ,Mesenchyme ,LIM-Homeodomain Proteins ,In situ hybridization ,Biology ,03 medical and health sciences ,S100 Calcium Binding Protein G ,medicine ,Animals ,Humans ,Molecular Biology ,030304 developmental biology ,Cell Proliferation ,Basement membrane ,Homeodomain Proteins ,urogenital system ,Nephrons ,Cell Biology ,Wnt Proteins ,Nephron development ,Gene expression ,Nephron patterning ,Laminin ,Ureter ,030217 neurology & neurosurgery ,Transcription Factors ,Developmental Biology - Abstract
While nephron formation is known to be initiated by a mesenchyme-to-epithelial transition of the cap mesenchyme to form a renal vesicle (RV), the subsequent patterning of the nephron and fusion with the ureteric component of the kidney to form a patent contiguous uriniferous tubule has not been fully characterized. Using dual section in situ hybridization (SISH)/immunohistochemistry (IHC) we have revealed distinct distal/proximal patterning of Notch, BMP and Wnt pathway components within the RV stage nephron. Quantitation of mitoses and Cyclin D1 expression indicated that cell proliferation was higher in the distal RV, reflecting the differential developmental programs of the proximal and distal populations. A small number of RV genes were also expressed in the early connecting segment of the nephron. Dual ISH/IHC combined with serial section immunofluorescence and 3D reconstruction revealed that fusion occurs between the late RV and adjacent ureteric tip via a process that involves loss of the intervening ureteric epithelial basement membrane and insertion of cells expressing RV markers into the ureteric tip. Using Six2-eGFPCre×R26R-lacZ mice, we demonstrate that these cells are derived from the cap mesenchyme and not the ureteric epithelium. Hence, both nephron patterning and patency are evident at the late renal vesicle stage.
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- 2009
- Full Text
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9. Banking placental tissue: an optimized collection procedure for genome-wide analysis of nucleic acids
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Rathi D Thiagarajan, W. K. Kwan, Véronique Taché, Louise C. Laurent, Mana M. Parast, Francesca S. Boscolo, Lynlee Wolfe, Ronald Coleman, J. Kim, and Jeanne F. Loring
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Placenta ,Pregnancy Trimester, Third ,RNA integrity number ,Tissue Banks ,Biology ,Article ,Specimen Handling ,Andrology ,chemistry.chemical_compound ,Pregnancy ,Gene expression ,medicine ,Humans ,RNA, Messenger ,Gene Expression Profiling ,Obstetrics and Gynecology ,RNA ,Genomics ,DNA Methylation ,Molecular biology ,Gene expression profiling ,Pregnancy Trimester, First ,medicine.anatomical_structure ,Reproductive Medicine ,chemistry ,DNA methylation ,Nucleic acid ,Female ,DNA ,Developmental Biology ,Genome-Wide Association Study - Abstract
Introduction Banking of high-quality placental tissue specimens will enable biomarker discovery and molecular studies on diseases involving placental dysfunction. Systematic studies aimed at developing feasible standardized methodology for placental collection in a typical clinical setting are lacking. Methods To determine the acceptable timeframe for placental collection, we collected multiple samples from first and third trimester placentas at serial timepoints in a 2-h window after delivery, simultaneously comparing the traditional snap-freeze technique to commercial solutions designed to preserve RNA (RNA later ™), and DNA (DNAgard ® ). The performance of RNA later for preserving DNA was also tested. Nucleic acid quality was assessed by determining the RNA integrity number (RIN) and genome-wide microarray profiling for gene expression and DNA methylation. Results We found that samples collected in RNA later had higher and more consistent RINs compared to snap-frozen tissue. Similar RINs were obtained for tissue collected in RNA later as large (1 cm 3 ) and small (∼0.1 cm 3 ) pieces. RNA later appeared to better stabilize the time zero gene expression profile compared to snap-freezing for first trimester placenta. DNA methylation profiles remained quite stable over a 2 h time period after removal of the placenta from the uterus, with DNAgard being superior to other treatments. Discussion and conclusion The collection of placental samples in RNA later and DNAgard is simple, and eliminates the need for liquid nitrogen or a freezer on-site. Moreover, the quality of the nucleic acids and the resulting data from samples collected in these preservation solutions is higher than samples collected using the snap-freeze method and easier to implement in busy clinical environments.
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- 2014
10. The epigenome in pluripotency and differentiation
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Louise C. Laurent, Robert Morey, and Rathi D Thiagarajan
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Epigenomics ,Pluripotent Stem Cells ,Cancer Research ,Epigenetic regulation of neurogenesis ,Cellular differentiation ,epigenome ,Computational biology ,Biology ,Epigenesis, Genetic ,Histones ,Genomic Imprinting ,Genetic ,stem cells ,X Chromosome Inactivation ,Nuclear Reprogramming ,Genetics ,Epigenome editing ,Animals ,Humans ,Developmental ,histone modification ,Induced pluripotent stem cell ,Cell potency ,DNA methylation ,Genome ,Gene Expression Regulation, Developmental ,Cell Differentiation ,differentiation ,sequencing ,Epigenome ,DNA Methylation ,pluripotency ,Cellular Reprogramming ,X inactivation ,Gene Expression Regulation ,imprinting ,Reprogramming ,Epigenesis - Abstract
The ability to culture pluripotent stem cells and direct their differentiation into specific cell types in vitro provides a valuable experimental system for modeling pluripotency, development and cellular differentiation. High-throughput profiling of the transcriptomes and epigenomes of pluripotent stem cells and their differentiated derivatives has led to identification of patterns characteristic of each cell type, discovery of new regulatory features in the epigenome and early insights into the complexity of dynamic interactions among regulatory elements. This work has also revealed potential limitations of the use of pluripotent stem cells as in vitro models of developmental events, due to epigenetic variability among different pluripotent stem cell lines and epigenetic instability during derivation and culture, particularly at imprinted and X-inactivated loci. This review focuses on the two most well-studied epigenetic mechanisms, DNA methylation and histone modifications, within the context of pluripotency and differentiation.
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- 2014
11. Identification of molecular compartments and genetic circuitry in the developing mammalian kidney
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Joe E. Vaughan, David H. Rowitch, Karl Staser, Rathi D Thiagarajan, Alexander van Oudenaarden, Jing Yu, Qun Ren, Melissa H. Little, Charles D. Stiles, Philip Machanick, Qiufu Ma, A. Michaela Krautzberger, Kylie Georgas, Mary Duah, Bree Rumballe, Andrew P. McMahon, Jinjin Guo, Jan Philipp Junker, Jennifer K. Hansard, M. Todd Valerius, Jill A. McMahon, Paul A. Gray, Timothy L. Bailey, Sean M. Grimmond, and Diane Faria
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Cell type ,Cellular differentiation ,Cell ,Urogenital System ,Computational biology ,Biology ,Kidney ,03 medical and health sciences ,Mice ,0302 clinical medicine ,medicine ,Transcriptional regulation ,Animals ,Molecular Biology ,In Situ Hybridization ,Research Articles ,030304 developmental biology ,Regulation of gene expression ,Genetics ,0303 health sciences ,Gene Expression Profiling ,Kidney metabolism ,Gene Expression Regulation, Developmental ,3. Good health ,Gene expression profiling ,medicine.anatomical_structure ,Developmental biology ,030217 neurology & neurosurgery ,Developmental Biology - Abstract
Lengthy developmental programs generate cell diversity within an organotypic framework, enabling the later physiological actions of each organ system. Cell identity, cell diversity and cell function are determined by cell type-specific transcriptional programs; consequently, transcriptional regulatory factors are useful markers of emerging cellular complexity, and their expression patterns provide insights into the regulatory mechanisms at play. We performed a comprehensive genome-scale in situ expression screen of 921 transcriptional regulators in the developing mammalian urogenital system. Focusing on the kidney, analysis of regional-specific expression patterns identified novel markers and cell types associated with development and patterning of the urinary system. Furthermore, promoter analysis of synexpressed genes predicts transcriptional control mechanisms that regulate cell differentiation. The annotated informational resource (www.gudmap.org) will facilitate functional analysis of the mammalian kidney and provides useful information for the generation of novel genetic tools to manipulate emerging cell populations.
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- 2012
12. Identification of novel markers of mouse fetal ovary development
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Huijun Chen, Rathi D Thiagarajan, Dagmar Wilhelm, Melissa H. Little, Emmanuelle Lesieur, Cassy M. Spiller, Peter Koopman, Hansheng Sheng Chiu, James S. Palmer, Alexandra Schulz, Sean M. Grimmond, and Marcel E. Dinger
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Male ,Somatic cell ,Cellular differentiation ,Organogenesis ,lcsh:Medicine ,Gene Expression ,Cell Fate Determination ,Mice ,0302 clinical medicine ,Testis ,Molecular Cell Biology ,Morphogenesis ,lcsh:Science ,Oligonucleotide Array Sequence Analysis ,Regulation of gene expression ,Genetics ,0303 health sciences ,Sex Characteristics ,Multidisciplinary ,Sexual Differentiation ,Gene Expression Regulation, Developmental ,Embryo ,Cell Differentiation ,Cell biology ,Testis determining factor ,medicine.anatomical_structure ,Female ,Development of the gonads ,Cellular Types ,Germ cell ,Research Article ,Genetic Markers ,Ovary ,Biology ,03 medical and health sciences ,Fetus ,medicine ,Animals ,030304 developmental biology ,lcsh:R ,Sex Determination ,Embryo, Mammalian ,Germ Cells ,lcsh:Q ,Organism Development ,030217 neurology & neurosurgery ,Developmental Biology - Abstract
In contrast to the developing testis, molecular pathways driving fetal ovarian development have been difficult to characterise. To date no single master regulator of ovarian development has been identified that would be considered the female equivalent of Sry. Using a genomic approach we identified a number of novel protein-coding as well as non-coding genes that were detectable at higher levels in the ovary compared to testis during early mouse gonad development. We were able to cluster these ovarian genes into different temporal expression categories. Of note, Lrrc34 and AK015184 were detected in XX but not XY germ cells before the onset of sex-specific germ cell differentiation marked by entry into meiosis in an ovary and mitotic arrest in a testis. We also defined distinct spatial expression domains of somatic cell genes in the developing ovary. Our data expands the set of markers of early mouse ovary differentiation and identifies a classification of early ovarian genes, thus providing additional avenues with which to dissect this process.
- Published
- 2012
13. List of Contributors
- Author
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Lars Ährlund-Richter, Gulsah Altun, Isao Asaka, Marina Bibikova, Mathew Blurton-Jones, Francesca Boscolo, Stefan Braam, Oliver Brustle, Kevin S. Carbajal, Jessica Cedervall, Lu Chen, Jonathan Chesnut, Cleo Choong, Ronald Coleman, Hun Chy, Jeremy M. Crook, Cheryl Dambrot, Ivan Damjanov, Richard Davis, Mary Devereaux, Mahesh Dodla, Biljana Dumevska, Eyitayo S. Fakunle, Lisa A. Flanagan, Ibon Garitaonandia, Karin Gertow, Victoria Glenn, Johanna E. Goldmann, Joel M. Gottesfeld, Jason Gustin, Sangyoon Han, Nick Hannan, Yvonne Hoang, Natalie Hobson, Marlys Houck, Hans S. Keirstead, Philip Koch, Sherman Ku, Frank M. LaFerla, Uma Lakshmipathy, Jack Lambshead, Thomas E. Lane, Andrew L. Laslett, Louise C. Laurent, Michael Lenz, Trevor R. Leonardo, Tianjian Li, Pauline Lieu, Qiuyue Liu, Ying Liu, Jeanne F. Loring, Mai X. Luong, Kim Ly, Candace L. Lynch, Ian Lyons, Steven McArthur, Robert E. Morey, Franz-Josef Müller, Christine Mummery, Kristopher L. Nazor, Joy L. Nerhus, Elizabeth Ng, Kyle S. Nickey, Gabriel I. Nistor, Jamison L. Nourse, Carmel O’Brien, Theo Palmer, Mark L. Rohrbaugh, Oliver Z Pedersen, Suzanne E. Peterson, Mahendra Rao, Julia Schaft, John P. Schell, Ulrich Schmidt, Bernhard M. Schuldt, Philip H. Schwartz, Jason Sharp, James Shen, Ronald Simon, Ileana Slavin, Kelly P. Smith, Elisabetta Soragni, Glyn Stacey, Rathi D. Thiagarajan, Thomas Touboul, Bhaskar Thyagarajan, Ha T. Tran, Ludovic Vallier, Cathelijne Van Den Berg, Yu-Chieh Wang, Dorien Ward-van Oostwaard, Jason Weinger, Shinya Yamanaka, Xianmin Zeng, Qi Zhou, and Boback Ziaeian
- Published
- 2012
14. Analysis of Genome-Wide Gene Expression Data from Microarrays and Sequencing
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Louise C. Laurent, Rathi D Thiagarajan, and Kristopher L. Nazor
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Gene expression profiling ,Gene expression omnibus ,Microarray ,business.industry ,Gene expression ,Gene Expression Array ,Computational biology ,Biology ,DNA microarray ,business ,Genome ,Biotechnology - Abstract
Gene expression profiling using high throughput, genome-wide platforms has fundamentally transformed the way that we approach problems in the biomedical sciences by expanding the classic single-gene approach toward comprehensive analysis of gene expression networks. To date, gene expression array data from nearly 400,000 human samples have been made publicly accessible via the Gene Expression Omnibus (GEO) as a resource from the NIH funded National Center for Biotechnological Information (NCBI). Here we discuss the basics of a DNA microarray and RNA sequencing technologies and provide guidelines for designing experiments in a way that permits the discovery of biologically and statistically significant results.
- Published
- 2012
15. Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling
- Author
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Nicole Cloonan, Rathi D Thiagarajan, John S. Mattick, Jason A. Steen, Shivangi Wani, Dave Tang, Brooke Gardiner, Han Sheng Chiu, Melissa H. Little, Gabriel Kolle, Tim R. Mercer, Sean M. Grimmond, Keerthana Krishnan, Bree Rumballe, Kylie Georgas, and Ehsan Nourbakhsh
- Subjects
mesenchymal-epithelial transition ,Six2, Wt1 ,lcsh:QH426-470 ,Transcription, Genetic ,Microarray ,lcsh:Biotechnology ,Organogenesis ,miR-214, microRNA ,RNA-Seq ,Locus (genetics) ,Computational biology ,Biology ,Kidney ,Proteomics ,Transcriptome ,Mice ,03 medical and health sciences ,lcsh:TP248.13-248.65 ,Genetics ,Animals ,RNA, Antisense ,RNA, Messenger ,kidney development ,030304 developmental biology ,0303 health sciences ,Sequence Analysis, RNA ,030302 biochemistry & molecular biology ,High-Throughput Nucleotide Sequencing ,Kidney metabolism ,Exons ,Gene expression profiling ,lcsh:Genetics ,Alternative Splicing ,MicroRNAs ,DNA microarray ,sense-antisense transcripts ,microarray ,Research Article ,Biotechnology - Abstract
Background The developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Detailed spatial maps have been generated for gene expression profiling combined with systematic in situ screening. These studies, however, fall short of capturing the transcriptional complexity arising from each locus due to the limited scope of microarray-based technology, which is largely based on "gene-centric" models. Results To address this, the polyadenylated RNA and microRNA transcriptomes of the 15.5 dpc mouse kidney were profiled using strand-specific RNA-sequencing (RNA-Seq) to a depth sufficient to complement spatial maps from pre-existing microarray datasets. The transcriptional complexity of RNAs arising from mouse RefSeq loci was catalogued; including 3568 alternatively spliced transcripts and 532 uncharacterized alternate 3' UTRs. Antisense expressions for 60% of RefSeq genes was also detected including uncharacterized non-coding transcripts overlapping kidney progenitor markers, Six2 and Sall1, and were validated by section in situ hybridization. Analysis of genes known to be involved in kidney development, particularly during mesenchymal-to-epithelial transition, showed an enrichment of non-coding antisense transcripts extended along protein-coding RNAs. Conclusion The resulting resource further refines the transcriptomic cartography of kidney organogenesis by integrating deep RNA sequencing data with locus-based information from previously published expression atlases. The added resolution of RNA-Seq has provided the basis for a transition from classical gene-centric models of kidney development towards more accurate and detailed "transcript-centric" representations, which highlights the extent of transcriptional complexity of genes that direct complex development events.
- Published
- 2011
16. Identification of Anchor Genes during Kidney Development Defines Ontological Relationships, Molecular Subcompartments and Regulatory Pathways
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Emmanuelle Lesieur, Kylie Georgas, Darrin Taylor, Bree Rumballe, Rathi D Thiagarajan, Han Sheng Chiu, Melissa H. Little, Sean M. Grimmond, and Dave Tang
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Microarrays ,Organogenesis ,Gene Identification and Analysis ,Gene Expression ,lcsh:Medicine ,Kidney development ,Validation Studies as Topic ,Kidney ,Transcriptomes ,Mice ,0302 clinical medicine ,Morphogenesis ,Cluster Analysis ,Tissue Distribution ,lcsh:Science ,Oligonucleotide Array Sequence Analysis ,Laser capture microdissection ,Regulation of gene expression ,Genetics ,0303 health sciences ,Multidisciplinary ,Gene Expression Regulation, Developmental ,Genomics ,Cell biology ,DNA microarray ,Research Article ,Signal Transduction ,Biology ,Models, Biological ,Molecular Genetics ,03 medical and health sciences ,Genome Analysis Tools ,Animals ,Genes, Developmental ,Gene ,030304 developmental biology ,RBPJ ,Microarray analysis techniques ,Gene Expression Profiling ,lcsh:R ,Computational Biology ,Molecular Development ,Cell Compartmentation ,Gene expression profiling ,lcsh:Q ,Genome Expression Analysis ,Organism Development ,030217 neurology & neurosurgery ,Developmental Biology - Abstract
The development of the mammalian kidney is well conserved from mouse to man. Despite considerable temporal and spatial data on gene expression in mammalian kidney development, primarily in rodent species, there is a paucity of genes whose expression is absolutely specific to a given anatomical compartment and/or developmental stage, defined here as 'anchor' genes. We previously generated an atlas of gene expression in the developing mouse kidney using microarray analysis of anatomical compartments collected via laser capture microdissection. Here, this data is further analysed to identify anchor genes via stringent bioinformatic filtering followed by high resolution section in situ hybridisation performed on 200 transcripts selected as specific to one of 11 anatomical compartments within the midgestation mouse kidney. A total of 37 anchor genes were identified across 6 compartments with the early proximal tubule being the compartment richest in anchor genes. Analysis of minimal and evolutionarily conserved promoter regions of this set of 25 anchor genes identified enrichment of transcription factor binding sites for Hnf4a and Hnf1b, RbpJ (Notch signalling), PPARγ:RxRA and COUP-TF family transcription factors. This was reinforced by GO analyses which also identified these anchor genes as targets in processes including epithelial proliferation and proximal tubular function. As well as defining anchor genes, this large scale validation of gene expression identified a further 92 compartment-enriched genes able to subcompartmentalise key processes during murine renal organogenesis spatially or ontologically. This included a cohort of 13 ureteric epithelial genes revealing previously unappreciated compartmentalisation of the collecting duct system and a series of early tubule genes suggesting that segmentation into proximal tubule, loop of Henle and distal tubule does not occur until the onset of glomerular vascularisation. Overall, this study serves to illuminate previously ill-defined stages of patterning and will enable further refinement of the lineage relationships within mammalian kidney development.
- Published
- 2011
17. Biosynthesis of P(3HB-co-3HV-co-3HHp) terpolymer by Cupriavidus necator PHB-4 transformant harboring the highly active PHA synthase gene of Chromobacterium sp. USM2
- Author
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Rathi, D. -N, Jutemar, E. P., Maurer, F. H. J., and Kumar Sudesh
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P(3HB-co-3HV-co-3HHp) terpolymer ,Chromobacterium sp. USM2 ,sodium heptanoate ,lcsh:QR1-502 ,Cupriavidus necator ,lcsh:Microbiology - Abstract
Aims: This study evaluates potentials of Cupriavidus necator PHB4 transformant harboring the highly activepolyhydroxyalkanoate synthase gene (phaC) of a locally isolated Chromobacterium sp. USM2 for its ability toincorporate 3-hydroxyheptanoate (3HHp) monomer.Methodology and results: A mixture of fructose and sodium heptanoate fed to the culture gave rise to poly(3-hydroxybutyrate-co-3-hydroxyvalerate-co-3-hydroxyheptanoate), [P(3HB-co-3HV-co-3HHp)] terpolymer synthesis, withtraces of 3HHp monomers confirmed through gas chromatography (GC), proton (1H) and carbon (13C) NMR spectra.Conclusion, significance and impact of study: This study has revealed that the PHA synthase of Chromobacteriumsp. USM2 has a broad range of substrate specificity. The synthase is able to polymerize 3-hydroxyalkanoate monomershaving 4–7 carbon atoms.
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