scholarly journals The people behind the papers – Brandon Carpenter and David Katz

Development ◽  
2021 ◽  
Vol 148 (3) ◽  
pp. dev199456
Keyword(s):  
Gene Expression ◽  
Caenorhabditis Elegans ◽  
Histone Methylation ◽  
Cell Biology ◽  
Large Scale ◽  
Associate Professor ◽  
School Of Medicine ◽  
The People ◽  
Emory University ◽  
Postdoctoral Researcher

ABSTRACTA dynamic pattern of histone methylation and demethylation controls gene expression during development, with some processes such as formation of the zygote involving large-scale reprogramming of methylation states. A new paper in Development investigates how inherited histone methylation regulates developmental timing and the germline/soma distinction in Caenorhabditis elegans. To hear more about the story we caught up with first author and postdoctoral researcher Brandon Carpenter, and his supervisor David Katz, Associate Professor in the Department of Cell Biology at Emory University School of Medicine in Atlanta, Georgia.

scholarly journals The people behind the papers – Kayt Scott and Bruce Appel

Development ◽  
2020 ◽  
Vol 147 (16) ◽  
pp. dev195735
Keyword(s):  
Motor Neurons ◽  
Cell Biology ◽  
Zebrafish Embryo ◽  
Cell Types ◽  
Colorado School ◽  
Molecular Control ◽  
University Of Colorado ◽  
School Of Medicine ◽  
The People ◽  
Developing Spinal Cord

ABSTRACTIn the developing spinal cord, progenitor cells sequentially give rise to motor neurons and precursors of one of the major glial cell types: oligodendrocytes. A new paper in Development unpicks the molecular control of the neuron-glia switch and the differentiation of oligodendrocyte precursors in the zebrafish embryo. To find out more about the work, we met first author and graduate student Kayt Scott and her supervisor Bruce Appel, who holds the Diane G. Wallach Chair of Pediatric Stem Cell Biology and is Professor and Head of the Section of Developmental Biology at the Department of Pediatrics, University of Colorado School of Medicine in Aurora.

scholarly journals Caenorhabditis elegans establishes germline versus soma by balancing inherited histone methylation

Development ◽  
2021 ◽  
Vol 148 (3) ◽  
pp. dev196600 ◽  
Author(s):  
Brandon S. Carpenter ◽  
Teresa W. Lee ◽  
Caroline F. Plott ◽  
Juan D. Rodriguez ◽  
Jovan S. Brockett ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Developmental Delay ◽  
Histone Modifications ◽  
Histone Methylation ◽  
Developmental Delays ◽  
Ectopic Expression ◽  
Epigenetic Reprogramming ◽  
The People ◽  
Germline Genes ◽  
Somatic Tissues

ABSTRACTFormation of a zygote is coupled with extensive epigenetic reprogramming to enable appropriate inheritance of histone methylation and prevent developmental delays. In Caenorhabditis elegans, this reprogramming is mediated by the H3K4me2 demethylase SPR-5 and the H3K9 methyltransferase, MET-2. In contrast, the H3K36 methyltransferase MES-4 maintains H3K36me2/3 at germline genes between generations to facilitate re-establishment of the germline. To determine whether the MES-4 germline inheritance pathway antagonizes spr-5; met-2 reprogramming, we examined the interaction between these two pathways. We found that the developmental delay of spr-5; met-2 mutant progeny is associated with ectopic H3K36me3 and the ectopic expression of MES-4-targeted germline genes in somatic tissues. Furthermore, the developmental delay is dependent upon MES-4 and the H3K4 methyltransferase, SET-2. We propose that MES-4 prevents crucial germline genes from being repressed by antagonizing maternal spr-5; met-2 reprogramming. Thus, the balance of inherited histone modifications is necessary to distinguish germline versus soma and prevent developmental delay.This article has an associated ‘The people behind the papers’ interview.

scholarly journals Cell scientist to watch – Prachee Avasthi

2021 ◽  
Vol 134 (18) ◽  
Keyword(s):  
San Francisco ◽  
Protein Trafficking ◽  
Cell Biology ◽  
Medical Center ◽  
Associate Professor ◽  
Integrative Physiology ◽  
University Of Utah ◽  
School Of Medicine ◽  
Set Up ◽  
The University

ABSTRACT Prachee Avasthi studied Molecular and Integrative Physiology at the University of Illinois at Urbana-Champaign. She received her PhD in neuroscience in 2009 from the lab of Wolfgang Baehr at the University of Utah for her work on the control of membrane protein trafficking in photoreceptors. Prachee then moved to Wallace Marshall's group at the University of California, San Francisco, for her postdoc, where she studied ciliary assembly and the regulation of ciliary length. She set up her lab at the University of Kansas Medical Center in 2015, and relocated to the Geisel School of Medicine at Dartmouth in 2020, where she is an Associate Professor of Biochemistry and Cell Biology. Her group investigates the biogenesis of cilia and the coordination of actin- and microtubule-based trafficking.

scholarly journals Western Faculty Profile: Dr. Susanne Schmid

2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Anthony Li
Keyword(s):  
Information Processing ◽  
Prepulse Inhibition ◽  
Cell Biology ◽  
Sensory Information ◽  
Associate Professor ◽  
Academic Affairs ◽  
School Of Medicine ◽  
Associate Dean ◽  
Sensory Information Processing ◽  
The University

Dr. Susanne Schmid is the Associate Dean Research, Graduate & Postdoctoral Studies at the Schulich School of Medicine & Dentistry and an Associate Professor in the Department of Anatomy & Cell Biology at Western University. Dr. Schmid has a background in biology and psychology and obtained a doctorate at the University Eye Hospital in Germany. Her research looks at early stages of sensory information processing and filtering, in particular habituation and prepulse inhibition. Anthony Li, a member of the Academic Affairs Committee for WURJHNS, had the pleasure of interviewing Dr. Schmid to learn more about her career path and her research.

scholarly journals Western Faculty Profile: Dr. Douglas Hamilton

2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Kevin X Zhou
Keyword(s):  
Tissue Engineering ◽  
Cell Biology ◽  
Scientific Research ◽  
Associate Professor ◽  
Cell Behavior ◽  
Surface Features ◽  
Implant Materials ◽  
School Of Medicine ◽  
The University

Dr. Douglas Hamilton is an Assistant Dean for Research and Associate Professor in Oral Biology and Anatomy & Cell Biology at the Schulich School of Medicine and Dentistry. Hamilton completed his Ph.D. at the University of St. Andrews in Scotland. His research is in the field of cell biology, biomaterials, and tissue engineering, with a focus on how the surface features of different implant materials affect cell behavior. Dr. Hamilton was interviewed for his professional and personal insights on how undergraduates can begin their journey into scientific research.

scholarly journals Titrating gene expression with series of systematically compromised CRISPR guide RNAs

2019 ◽  
Author(s):  
Marco Jost ◽  
Daniel A. Santos ◽  
Reuben A. Saunders ◽  
Max A. Horlbeck ◽  
John S. Hawkins ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Biology ◽  
Large Scale ◽  
Control Gene ◽  
Specific Expression ◽  
Expression Phenotype ◽  
Control Gene Expression ◽  
Human Genes ◽  
A Genome ◽  
Multiple Cell

AbstractBiological phenotypes arise from the degrees to which genes are expressed, but the lack of tools to precisely control gene expression limits our ability to evaluate the underlying expression-phenotype relationships. Here, we describe a readily implementable approach to titrate expression of human genes using series of systematically compromised sgRNAs and CRISPR interference. We empirically characterize the activities of compromised sgRNAs using large-scale measurements across multiple cell models and derive the rules governing sgRNA activity using deep learning, enabling construction of a compact sgRNA library to titrate expression of ∼2,400 genes involved in central cell biology and a genome-wide in silico library. Staging cells along a continuum of gene expression levels combined with rich single-cell RNA-seq readout reveals gene-specific expression-phenotype relationships with expression level-specific responses. Our work provides a general tool to control gene expression, with applications ranging from tuning biochemical pathways to identifying suppressors for diseases of dysregulated gene expression.

scholarly journals Systematic Identification of Housekeeping Genes Possibly Used as References in Caenorhabditis elegans by Large-Scale Data Integration

Cells ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 786 ◽  
Author(s):  
Jingxin Tao ◽  
Youjin Hao ◽  
Xudong Li ◽  
Huachun Yin ◽  
Xiner Nie ◽  
...  
Keyword(s):  
Gene Expression ◽  
Caenorhabditis Elegans ◽  
Gene Expression Data ◽  
Reference Genes ◽  
Large Scale ◽  
Gene Array ◽  
Housekeeping Genes ◽  
Functional Enrichment ◽  
Expression Data ◽  
Data Types

For accurate gene expression quantification, normalization of gene expression data against reliable reference genes is required. It is known that the expression levels of commonly used reference genes vary considerably under different experimental conditions, and therefore, their use for data normalization is limited. In this study, an unbiased identification of reference genes in Caenorhabditis elegans was performed based on 145 microarray datasets (2296 gene array samples) covering different developmental stages, different tissues, drug treatments, lifestyle, and various stresses. As a result, thirteen housekeeping genes (rps-23, rps-26, rps-27, rps-16, rps-2, rps-4, rps-17, rpl-24.1, rpl-27, rpl-33, rpl-36, rpl-35, and rpl-15) with enhanced stability were comprehensively identified by using six popular normalization algorithms and RankAggreg method. Functional enrichment analysis revealed that these genes were significantly overrepresented in GO terms or KEGG pathways related to ribosomes. Validation analysis using recently published datasets revealed that the expressions of newly identified candidate reference genes were more stable than the commonly used reference genes. Based on the results, we recommended using rpl-33 and rps-26 as the optimal reference genes for microarray and rps-2 and rps-4 for RNA-sequencing data validation. More importantly, the most stable rps-23 should be a promising reference gene for both data types. This study, for the first time, successfully displays a large-scale microarray data driven genome-wide identification of stable reference genes for normalizing gene expression data and provides a potential guideline on the selection of universal internal reference genes in C. elegans, for quantitative gene expression analysis.

scholarly journals PPARγ

2008 ◽  
Vol 56 (2) ◽  
pp. 515-517 ◽  
Author(s):  
C. Michael Hart ◽  
Jesse Roman ◽  
Raju Reddy ◽  
Patricia J. Sime
Keyword(s):  
Cell Biology ◽  
Medical Center ◽  
Associate Professor ◽  
Background Information ◽  
Pulmonary Vascular Disease ◽  
Peroxisome Proliferator ◽  
Widespread Application ◽  
Emory University ◽  
The University

Interest in peroxisome proliferator-activated receptors (PPARs) has steadily increased over the past 15 years. The recognition that subclasses of this receptor played critical roles in regulation of metabolism led to the development of synthetic ligands and their widespread application in the treatment of type 2 diabetes. At the same time, emerging evidence demonstrated that the influence of PPARs extends well beyond metabolism and diabetes. A salient example of this can be seen in studies that explore the role of PPARs in lung cell biology. In fact, current literature suggests that PPAR receptors may well represent exciting new targets for treatment in a variety of lung disorders. In an attempt to keep the scientific and medical communities abreast of these developments, a symposium sponsored by the American Federation for Medical Research entitled "PPARγ: A Novel Molecular Target in Lung Disease" was convened on April 29, 2007, at the Experimental Biology Meeting in Washington, DC. During that symposium, 4 speakers reviewed the latest developments in basic and translational research as they relate to specific lung diseases. Jesse Roman, MD, professor and director of the Emory University Division of Pulmonary, Allergy, and Critical Care Medicine, reviewed the role of PPARγ in the pathogenesis of lung cancer and its implications for therapy. Raju Reddy, MD, assistant professor of Medicine at the University of Michigan, presented data regarding the immunomodulatory role of PPARγ in alveolar macrophages. Patricia J. Sime, MD, associate professor of Medicine, Environmental Medicine, and Oncology at the University of Rochester School of Medicine, discussed the antifibrogenic potential of PPARγ ligands in pulmonary fibrosis. Finally, C. Michael Hart, MD, professor of Medicine at Emory University and chief of the Atlanta Veterans Affairs Medical Center Pulmonary Section, reviewed the role of PPARγ in pulmonary vascular disease. This brief introduction to the symposium will provide background information about PPARs to facilitate the general reader's appreciation of the more in-depth and disease-specific discussions that follow.

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