Direct Reprogramming of Oligodendrocyte Precursor Cells Into Gabaergic Inhibitory Neurons by a Single Homeodomain Transcription Factor Dlx2 Linda L
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Implications of Zonal Architecture on Differential Gene Expression
www.nature.com/scientificreports OPEN Implications of zonal architecture on diferential gene expression profling and altered pathway expressions in mandibular condylar cartilage Aisha M. Basudan1*, Mohammad Azhar Aziz2 & Yanqi Yang3 Mandibular condylar cartilage (MCC) is a multi-zonal heterogeneous fbrocartilage containing diferent types of cells, but the factors/mechanisms governing the phenotypic transition across the zones have not been fully understood. The reliability of molecular studies heavily rely on the procurement of pure cell populations from the heterogeneous tissue. We used a combined laser-capture microdissection and microarray analysis approach which allowed identifcation of diferential zone-specifc gene expression profling and altered pathways in the MCC of 5-week-old rats. The bioinformatics analysis demonstrated that the MCC cells clearly exhibited distinguishable phenotypes from the articular chondrocytes. Additionally, a set of genes has been determined as potential markers to identify each MCC zone individually; Crab1 gene showed the highest enrichment while Clec3a was the most downregulated gene at the superfcial layer, which consists of fbrous (FZ) and proliferative zones (PZ). Ingenuity Pathway Analysis revealed numerous altered signaling pathways; Leukocyte extravasation signaling pathway was predicted to be activated at all MCC zones, in particular mature and hypertrophic chondrocytes zones (MZ&HZ), when compared with femoral condylar cartilage (FCC). Whereas Superpathway of Cholesterol Biosynthesis showed predicted activation in both FZ and PZ as compared with deep MCC zones and FCC. Determining novel zone-specifc diferences of large group of potential genes, upstream regulators and pathways in healthy MCC would improve our understanding of molecular mechanisms on regional (zonal) basis, and provide new insights for future therapeutic strategies. -
Crayfish Escape Behavior and Central Synapses
Crayfish Escape Behavior and Central Synapses. III. Electrical Junctions and Dendrite Spikes in Fast Flexor Motoneurons ROBERT S. ZUCKER Department of Biological Sciences and Program in the Neurological Sciences, Stanford University, Stanford, California 94305 THE LATERAL giant fiber is the decision fiber and fast flexor motoneurons are located in for a behavioral response in crayfish in- the dorsal neuropil of each abdominal gan- volving rapid tail flexion in response to glion. Dye injections and anatomical recon- abdominal tactile stimulation (27). Each structions of ‘identified motoneurons reveal lateral giant impulse is followed by a rapid that only those motoneurons which have tail flexion or tail flip, and when the giant dentritic branches in contact with a giant fiber does not fire in response to such stim- fiber are activated by that giant fiber (12, uli, the movement does not occur. 21). All of tl ie fast flexor motoneurons are The afferent limb of the reflex exciting excited by the ipsilateral giant; all but F4, the lateral giant has been described (28), F5 and F7 are also excited by the contra- and the habituation of the behavior has latkral giant (21 a). been explained in terms of the properties The excitation of these motoneurons, of this part of the neural circuit (29). seen as depolarizing potentials in their The properties of the neuromuscular somata, does not always reach threshold for junctions between the fast flexor motoneu- generating a spike which propagates out the rons and the phasic flexor muscles have also axon to the periphery (14). Indeed, only t,he been described (13). -
Long-Term Adult Human Brain Slice Cultures As a Model System to Study
TOOLS AND RESOURCES Long-term adult human brain slice cultures as a model system to study human CNS circuitry and disease Niklas Schwarz1, Betu¨ l Uysal1, Marc Welzer2,3, Jacqueline C Bahr1, Nikolas Layer1, Heidi Lo¨ ffler1, Kornelijus Stanaitis1, Harshad PA1, Yvonne G Weber1,4, Ulrike BS Hedrich1, Ju¨ rgen B Honegger4, Angelos Skodras2,3, Albert J Becker5, Thomas V Wuttke1,4†*, Henner Koch1†* 1Department of Neurology and Epileptology, Hertie-Institute for Clinical Brain Research, University of Tu¨ bingen, Tu¨ bingen, Germany; 2Department of Cellular Neurology, Hertie-Institute for Clinical Brain Research, University of Tu¨ bingen, Tu¨ bingen, Germany; 3German Center for Neurodegenerative Diseases (DZNE), Tu¨ bingen, Germany; 4Department of Neurosurgery, University of Tu¨ bingen, Tu¨ bingen, Germany; 5Department of Neuropathology, Section for Translational Epilepsy Research, University Bonn Medical Center, Bonn, Germany Abstract Most of our knowledge on human CNS circuitry and related disorders originates from model organisms. How well such data translate to the human CNS remains largely to be determined. Human brain slice cultures derived from neurosurgical resections may offer novel avenues to approach this translational gap. We now demonstrate robust preservation of the complex neuronal cytoarchitecture and electrophysiological properties of human pyramidal neurons *For correspondence: in long-term brain slice cultures. Further experiments delineate the optimal conditions for efficient [email protected] viral transduction of cultures, enabling ‘high throughput’ fluorescence-mediated 3D reconstruction tuebingen.de (TVW); of genetically targeted neurons at comparable quality to state-of-the-art biocytin fillings, and [email protected] demonstrate feasibility of long term live cell imaging of human cells in vitro. -
Supplemental Materials ZNF281 Enhances Cardiac Reprogramming
Supplemental Materials ZNF281 enhances cardiac reprogramming by modulating cardiac and inflammatory gene expression Huanyu Zhou, Maria Gabriela Morales, Hisayuki Hashimoto, Matthew E. Dickson, Kunhua Song, Wenduo Ye, Min S. Kim, Hanspeter Niederstrasser, Zhaoning Wang, Beibei Chen, Bruce A. Posner, Rhonda Bassel-Duby and Eric N. Olson Supplemental Table 1; related to Figure 1. Supplemental Table 2; related to Figure 1. Supplemental Table 3; related to the “quantitative mRNA measurement” in Materials and Methods section. Supplemental Table 4; related to the “ChIP-seq, gene ontology and pathway analysis” and “RNA-seq” and gene ontology analysis” in Materials and Methods section. Supplemental Figure S1; related to Figure 1. Supplemental Figure S2; related to Figure 2. Supplemental Figure S3; related to Figure 3. Supplemental Figure S4; related to Figure 4. Supplemental Figure S5; related to Figure 6. Supplemental Table S1. Genes included in human retroviral ORF cDNA library. Gene Gene Gene Gene Gene Gene Gene Gene Symbol Symbol Symbol Symbol Symbol Symbol Symbol Symbol AATF BMP8A CEBPE CTNNB1 ESR2 GDF3 HOXA5 IL17D ADIPOQ BRPF1 CEBPG CUX1 ESRRA GDF6 HOXA6 IL17F ADNP BRPF3 CERS1 CX3CL1 ETS1 GIN1 HOXA7 IL18 AEBP1 BUD31 CERS2 CXCL10 ETS2 GLIS3 HOXB1 IL19 AFF4 C17ORF77 CERS4 CXCL11 ETV3 GMEB1 HOXB13 IL1A AHR C1QTNF4 CFL2 CXCL12 ETV7 GPBP1 HOXB5 IL1B AIMP1 C21ORF66 CHIA CXCL13 FAM3B GPER HOXB6 IL1F3 ALS2CR8 CBFA2T2 CIR1 CXCL14 FAM3D GPI HOXB7 IL1F5 ALX1 CBFA2T3 CITED1 CXCL16 FASLG GREM1 HOXB9 IL1F6 ARGFX CBFB CITED2 CXCL3 FBLN1 GREM2 HOXC4 IL1F7 -
SUPPLEMENTARY MATERIAL Bone Morphogenetic Protein 4 Promotes
www.intjdevbiol.com doi: 10.1387/ijdb.160040mk SUPPLEMENTARY MATERIAL corresponding to: Bone morphogenetic protein 4 promotes craniofacial neural crest induction from human pluripotent stem cells SUMIYO MIMURA, MIKA SUGA, KAORI OKADA, MASAKI KINEHARA, HIROKI NIKAWA and MIHO K. FURUE* *Address correspondence to: Miho Kusuda Furue. Laboratory of Stem Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Saito-Asagi, Ibaraki, Osaka 567-0085, Japan. Tel: 81-72-641-9819. Fax: 81-72-641-9812. E-mail: [email protected] Full text for this paper is available at: http://dx.doi.org/10.1387/ijdb.160040mk TABLE S1 PRIMER LIST FOR QRT-PCR Gene forward reverse AP2α AATTTCTCAACCGACAACATT ATCTGTTTTGTAGCCAGGAGC CDX2 CTGGAGCTGGAGAAGGAGTTTC ATTTTAACCTGCCTCTCAGAGAGC DLX1 AGTTTGCAGTTGCAGGCTTT CCCTGCTTCATCAGCTTCTT FOXD3 CAGCGGTTCGGCGGGAGG TGAGTGAGAGGTTGTGGCGGATG GAPDH CAAAGTTGTCATGGATGACC CCATGGAGAAGGCTGGGG MSX1 GGATCAGACTTCGGAGAGTGAACT GCCTTCCCTTTAACCCTCACA NANOG TGAACCTCAGCTACAAACAG TGGTGGTAGGAAGAGTAAAG OCT4 GACAGGGGGAGGGGAGGAGCTAGG CTTCCCTCCAACCAGTTGCCCCAAA PAX3 TTGCAATGGCCTCTCAC AGGGGAGAGCGCGTAATC PAX6 GTCCATCTTTGCTTGGGAAA TAGCCAGGTTGCGAAGAACT p75 TCATCCCTGTCTATTGCTCCA TGTTCTGCTTGCAGCTGTTC SOX9 AATGGAGCAGCGAAATCAAC CAGAGAGATTTAGCACACTGATC SOX10 GACCAGTACCCGCACCTG CGCTTGTCACTTTCGTTCAG Suppl. Fig. S1. Comparison of the gene expression profiles of the ES cells and the cells induced by NC and NC-B condition. Scatter plots compares the normalized expression of every gene on the array (refer to Table S3). The central line -
The Narrowing of Dendrite Branches Across Nodes Follows a Well-Defined Scaling Law
The narrowing of dendrite branches across nodes follows a well-defined scaling law Maijia Liaoa, Xin Liangb, and Jonathon Howarda,1 aDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520; and bTsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China Edited by Yuh Nung Jan, Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, and approved May 17, 2021 (received for review October 28, 2020) The systematic variation of diameters in branched networks has minimized. Da Vinci’s law has been reformulated as the “pipe tantalized biologists since the discovery of da Vinci’s rule for trees. model” for plants, in which a fixed cross-section of stems and Da Vinci’s rule can be formulated as a power law with exponent branches is required to support each unit amount of leaves (13). two: The square of the mother branch’s diameter is equal to the Experimental support for scaling laws, however, is scarce because sum of the squares of those of the daughters. Power laws, with of the difficulties of imaging entire branched networks and because different exponents, have been proposed for branching in circula- intrinsic anatomical variability may obscure precise laws (14). Thus, tory systems (Murray’s law with exponent 3) and in neurons (Rall’s it is an open question whether scaling laws such as Eq. 1 apply in law with exponent 3/2). The laws have been derived theoretically, biological systems. based on optimality arguments, but, for the most part, have not To quantitatively test diameter-scaling laws in neurons, it is been tested rigorously. -
Transcriptional Regulatory Networks in Neocortical Development
Review From trans to cis: transcriptional regulatory networks in neocortical development 1 1 1,2 Mikihito Shibata , Forrest O. Gulden , and Nenad Sestan 1 Department of Neurobiology and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA 2 Department of Psychiatry and Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, New Haven, CT 06510, USA Transcriptional mechanisms mediated by the binding of tions among TFs and CREs form the central core of tran- transcription factors (TFs) to cis-acting regulatory ele- scriptional regulatory networks (TRNs) (Box 1) [1]. ments (CREs) in DNA play crucial roles in directing gene Interactions between TFs and CREs are complex, dynam- expression. While TFs have been extensively studied, ic,andmodulatedbyvariousepigeneticprocesses[12].While less effort has gone towards the identification and func- individual CREs may be regulated by the competitive or tional characterization of CREs and associated epigenet- cooperative binding of many TFs, multiple CREs may also ic modulation. However, owing to methodological and confer transcriptional control over the expression of any analytical advances, more comprehensive studies of single gene [12]. Furthermore, TFs and CREs regulate regulatory elements and mechanisms are now possible. transcription together with their cognate transcriptional We summarize recent progress in integrative analyses of cofactors, chromatin regulators, epigenetic modifications, these regulatory components in the development of the RNA-binding proteins, and non-coding RNAs [2,13]. This cerebral neocortex, the part of the brain involved in combinatorial and multi-level transcriptional regulation cognition and complex behavior. These studies are greatly increases the complexity of gene expression regula- uncovering not only the underlying transcriptional reg- tion, facilitating the unique spatio-temporal patterns nec- ulatory networks, but also how these networks are essary for tissue development and function [3]. -
Up-Regulation of Homeodomain Genes, DLX1 and DLX2, by FLT3 Signaling
SUPPLEMENTARY APPENDIX Up-regulation of homeodomain genes, DLX1 and DLX2, by FLT3 signaling Julia Starkova,1,3 Sharvari Gadgil,2 Yi Hua Qiu,4 Nianxiang Zhang,4 Ivana Hermanova,3 Steven M. Kornblau,4 and Harry A. Drabkin1,3 1Division of Hematology-Oncology, Medical University of South Carolina, Charleston, SC, USA; 2Division of Medical Oncology, University of Colorado Health Sciences Center, Aurora, CO, USA; 3Department of Paediatric Haematology/Oncology, 2nd Faculty of Medicine, Charles University Prague, Czech Republic, and 4Department of Stem Cell Transplantation and Cellular Therapy, Section of Molecular Hematology and Therapy, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA Citation: Starkova J, Gadgil S, Hua Qiu Y, Zhang N, Hermanova I, Kornblau SM, and Drabkin HA. Up-regulation of homeodomain genes, DLX1 and DLX2, by FLT3 signaling. Haematologica 2011;96(6):820-828. doi:10.3324/haematol.2010.031179 Online Supplementary Figure S1. Specificity and non-toxicity of PKC412 in MV4;11 cells (A) Results from flow cytometry analysis are shown as a percentage of cells in subG1, G1-G0, S and G2-M phases of the cell cycle after 0, 2, 5 and 24 h treatment of MV4;11 cells with PKC412. (B) Graph shows fold-change of DLX1 gene expression in MV4;11 cells after imatinib treatment. A B Online Supplementary Figure S2. AP1-binding site in the DLX1 promoter. Online Supplementary Figure S3. Diagram of the described interaction between FLT3 and DLX1. Online Supplementary Table S1. Primes sequences. Online Supplementary Table S2. DDCt values of normalized HOX gene expression in MV4; II cells after PKC412 treatment. -
Transcriptional and Post-Transcriptional Regulation of ATP-Binding Cassette Transporter Expression
Transcriptional and Post-transcriptional Regulation of ATP-binding Cassette Transporter Expression by Aparna Chhibber DISSERTATION Submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in Pharmaceutical Sciences and Pbarmacogenomies in the Copyright 2014 by Aparna Chhibber ii Acknowledgements First and foremost, I would like to thank my advisor, Dr. Deanna Kroetz. More than just a research advisor, Deanna has clearly made it a priority to guide her students to become better scientists, and I am grateful for the countless hours she has spent editing papers, developing presentations, discussing research, and so much more. I would not have made it this far without her support and guidance. My thesis committee has provided valuable advice through the years. Dr. Nadav Ahituv in particular has been a source of support from my first year in the graduate program as my academic advisor, qualifying exam committee chair, and finally thesis committee member. Dr. Kathy Giacomini graciously stepped in as a member of my thesis committee in my 3rd year, and Dr. Steven Brenner provided valuable input as thesis committee member in my 2nd year. My labmates over the past five years have been incredible colleagues and friends. Dr. Svetlana Markova first welcomed me into the lab and taught me numerous laboratory techniques, and has always been willing to act as a sounding board. Michael Martin has been my partner-in-crime in the lab from the beginning, and has made my days in lab fly by. Dr. Yingmei Lui has made the lab run smoothly, and has always been willing to jump in to help me at a moment’s notice. -
NEURAL CONNECTIONS: Some You Use, Some You Lose
NEURAL CONNECTIONS: Some You Use, Some You Lose by JOHN T. BRUER SOURCE: Phi Delta Kappan 81 no4 264-77 D 1999 . The magazine publisher is the copyright holder of this article and it is reproduced with permission. Further reproduction of this article in violation of the copyright is prohibited JOHN T. BRUER is president of the James S. McDonnell Foundation, St. Louis. This article is adapted from his new book, The Myth of the First Three Years (Free Press, 1999), and is reprinted by arrangement with The Free Press, a division of Simon Schuster Inc. ©1999, John T. Bruer . OVER 20 YEARS AGO, neuroscientists discovered that humans and other animals experience a rapid increase in brain connectivity -- an exuberant burst of synapse formation -- early in development. They have studied this process most carefully in the brain's outer layer, or cortex, which is essentially our gray matter. In these studies, neuroscientists have documented that over our life spans the number of synapses per unit area or unit volume of cortical tissue changes, as does the number of synapses per neuron. Neuroscientists refer to the number of synapses per unit of cortical tissue as the brain's synaptic density. Over our lifetimes, our brain's synaptic density changes in an interesting, patterned way. This pattern of synaptic change and what it might mean is the first neurobiological strand of the Myth of the First Three Years. (The second strand of the Myth deals with the notion of critical periods, and the third takes up the matter of enriched, or complex, environments.) Popular discussions of the new brain science trade heavily on what happens to synapses during infancy and childhood. -
(12) Patent Application Publication (10) Pub. No.: US 2017/0145518 A1 Hessels Et Al
US 20170145518A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2017/0145518 A1 Hessels et al. (43) Pub. Date: May 25, 2017 (54) METHOD FOR PREDICTING AND (52) U.S. Cl. TREATING CLINICALLY SIGNIFICANT CPC ..... CI2O 1/6886 (2013.01); C12O 2600/158 PROSTATE CANCER (2013.01) Applicant: MDxHealth Research B.V., Nijmegen (57) ABSTRACT (71) The present invention relates to methods, devices, combi (NL) nations, kits, and systems for predicting and treating clini cally significant prostate cancer in a urine sample of an (72) Inventors: Daphne Hessels, Nijmegen (NL); individual Suspected of Suffering from prostate cancer based Franciscus Petrus Smit, Nijmegen on expression analysis of normalised prostate tumour mark (NL); Jack A. Schalken, Nijmegen ers. The present methods, devices, combinations, kits, and (NL) systems are especially suitable for predicting and treating prostate cancer with a Gleason score of seven or more in (73) Assignee: MDxHealth Research B.V., Nijmegen individuals with a serum prostate-specific antigen (SPSA) (NL) level lower than 15 ng/ml. Specifically, the present invention relates to methods, devices, combinations, kits, and systems for predicting and treating clinically significant prostate (21) Appl. No.: 15/357,342 cancer in a urine sample of an individual Suspected of Suffering from prostate cancer, the method comprises the (22) Filed: Nov. 21, 2016 steps of: a) determining mRNA expression levels of one or more of the genes DLX1, HOXC6, TDRD1 and KLK3 in a Related U.S. Application Data urine sample of said individual; b) normalizing the mRNA expression levels of one ore more of DLX1, HOXC6, and (60) Provisional application No. -
How Do Dendrites Take Their Shape?
© 2001 Nature Publishing Group http://neurosci.nature.com review How do dendrites take their shape? Ethan K. Scott1 and Liqun Luo1,2 1 Department of Biological Sciences, Stanford University, Stanford, California 94305, USA 2 Neurosciences Program, Stanford University, Stanford, California 94305, USA Correspondence should be addressed to L.L. ([email protected]) Recent technical advances have made possible the visualization and genetic manipulation of individual dendritic trees. These studies have led to the identification and characterization of molecules that are important for different aspects of dendritic development. Although much remains to be learned, the existing knowledge has allowed us to take initial steps toward a comprehensive understanding of how complex dendritic trees are built. In this review, we describe recent advances in our understanding of the molecular mechanisms underlying dendritic morphogenesis, and discuss their cell-biological implications. With their great complexity and variety, dendrites (Fig. 1) are won- added advantage, can be used to study loss-of-function muta- ders of nature’s design. Built to receive and integrate inputs to neu- tions. Much of the progress reviewed in this article would not rons, dendrites occupy much of the brain’s volume and have been have been possible without these technological advances. the subject of studies since the days of Golgi and Cajal1. Over the course of much of the twentieth century, the prevailing belief that Breaking down complex dendritic trees axons take the more active role in wiring the brain and in estab- Although the processes used to build dendritic trees are complex lishing synaptic specificity led researchers to focus on the develop- and diverse (Fig.