The Alternative Regenerative Strategy of Bearded Dragon Unveils the Key
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Screening and Identification of Key Biomarkers in Clear Cell Renal Cell Carcinoma Based on Bioinformatics Analysis
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Screening and identification of key biomarkers in clear cell renal cell carcinoma based on bioinformatics analysis Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignancy of the urinary system. The pathogenesis and effective diagnosis of ccRCC have become popular topics for research in the previous decade. In the current study, an integrated bioinformatics analysis was performed to identify core genes associated in ccRCC. An expression dataset (GSE105261) was downloaded from the Gene Expression Omnibus database, and included 26 ccRCC and 9 normal kideny samples. Assessment of the microarray dataset led to the recognition of differentially expressed genes (DEGs), which was subsequently used for pathway and gene ontology (GO) enrichment analysis. -
Systematic Comparison of Sea Urchin and Sea Star Developmental Gene Regulatory Networks Explains How Novelty Is Incorporated in Early Development
ARTICLE https://doi.org/10.1038/s41467-020-20023-4 OPEN Systematic comparison of sea urchin and sea star developmental gene regulatory networks explains how novelty is incorporated in early development Gregory A. Cary 1,3,5, Brenna S. McCauley1,4,5, Olga Zueva1, Joseph Pattinato1, William Longabaugh2 & ✉ Veronica F. Hinman 1 1234567890():,; The extensive array of morphological diversity among animal taxa represents the product of millions of years of evolution. Morphology is the output of development, therefore phenotypic evolution arises from changes to the topology of the gene regulatory networks (GRNs) that control the highly coordinated process of embryogenesis. A particular challenge in under- standing the origins of animal diversity lies in determining how GRNs incorporate novelty while preserving the overall stability of the network, and hence, embryonic viability. Here we assemble a comprehensive GRN for endomesoderm specification in the sea star from zygote through gastrulation that corresponds to the GRN for sea urchin development of equivalent territories and stages. Comparison of the GRNs identifies how novelty is incorporated in early development. We show how the GRN is resilient to the introduction of a transcription factor, pmar1, the inclusion of which leads to a switch between two stable modes of Delta-Notch signaling. Signaling pathways can function in multiple modes and we propose that GRN changes that lead to switches between modes may be a common evolutionary mechanism for changes in embryogenesis. Our data additionally proposes a model in which evolutionarily conserved network motifs, or kernels, may function throughout development to stabilize these signaling transitions. 1 Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA. -
Transcription Profiles of Age-At-Maturity-Associated Genes Suggest Cell Fate Commitment Regulation As a Key Factor in the Atlant
INVESTIGATION Transcription Profiles of Age-at-Maturity- Associated Genes Suggest Cell Fate Commitment Regulation as a Key Factor in the Atlantic Salmon Maturation Process Johanna Kurko,*,† Paul V. Debes,*,† Andrew H. House,*,† Tutku Aykanat,*,† Jaakko Erkinaro,‡ and Craig R. Primmer*,†,1 *Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland, 00014, †Institute of Biotechnology, University of Helsinki, Helsinki, Finland, 00014, and ‡Natural Resources Institute Finland (Luke), Oulu, Finland, 90014 ORCID IDs: 0000-0002-4598-116X (J.K.); 0000-0003-4491-9564 (P.V.D.); 0000-0001-8705-0358 (A.H.H.); 0000-0002-4825-0231 (T.A.); 0000-0002-7843-0364 (J.E.); 0000-0002-3687-8435 (C.R.P.) ABSTRACT Despite recent taxonomic diversification in studies linking genotype with phenotype, KEYWORDS follow-up studies aimed at understanding the molecular processes of such genotype-phenotype Atlantic salmon associations remain rare. The age at which an individual reaches sexual maturity is an important fitness maturation trait in many wild species. However, the molecular mechanisms regulating maturation timing process processes remain obscure. A recent genome-wide association study in Atlantic salmon (Salmo salar) vgll3 identified large-effect age-at-maturity-associated chromosomal regions including genes vgll3, akap11 mRNA and six6, which have roles in adipogenesis, spermatogenesis and the hypothalamic-pituitary-gonadal expression (HPG) axis, respectively. Here, we determine expression patterns of these genes during salmon de- cell fate velopment and their potential molecular partners and pathways. Using Nanostring transcription pro- regulation filing technology, we show development- and tissue-specific mRNA expression patterns for vgll3, akap11 and six6. Correlated expression levels of vgll3 and akap11, which have adjacent chromosomal location, suggests they may have shared regulation. -
Lecture 2 – Bone
Oral Histology Summary Notes Enoch Ng Lecture 2 – Bone - Protection of brain, lungs, other internal organs - Structural support for heart, lungs, and marrow - Attachment sites for muscles - Mineral reservoir for calcium (99% of body’s) and phosphorous (85% of body’s) - Trap for dangerous minerals (ex:// lead) - Transduction of sound - Endocrine organ (osteocalcin regulates insulin signaling, glucose metabolism, and fat mass) Structure - Compact/Cortical o Diaphysis of long bone, “envelope” of cuboid bones (vertebrae) o 10% porosity, 70-80% calcified (4x mass of trabecular bone) o Protective, subject to bending/torsion/compressive forces o Has Haversian system structure - Trabecular/Cancellous o Metaphysis and epiphysis of long bone, cuboid bone o 3D branching lattice formed along areas of mechanical stress o 50-90% porosity, 15-25% calcified (1/4 mass of compact bone) o High surface area high cellular activity (has marrow) o Metabolic turnover 8x greater than cortical bone o Subject to compressive forces o Trabeculae lined with endosteum (contains osteoprogenitors, osteoblasts, osteoclasts) - Woven Bone o Immature/primitive, rapidly growing . Normally – embryos, newborns, fracture calluses, metaphyseal region of bone . Abnormally – tumors, osteogenesis imperfecta, Pagetic bone o Disorganized, no uniform orientation of collagen fibers, coarse fibers, cells randomly arranged, varying mineral content, isotropic mechanical behavior (behavior the same no matter direction of applied force) - Lamellar Bone o Mature bone, remodeling of woven -
Specialized Stem Cell Niche Enables Repetitive Renewal of Alligator Teeth
Specialized stem cell niche enables repetitive renewal PNAS PLUS of alligator teeth Ping Wua, Xiaoshan Wua,b, Ting-Xin Jianga, Ruth M. Elseyc, Bradley L. Templed, Stephen J. Diverse, Travis C. Glennd, Kuo Yuanf, Min-Huey Cheng,h, Randall B. Widelitza, and Cheng-Ming Chuonga,h,i,1 aDepartment of Pathology, University of Southern California, Los Angeles, CA 90033; bDepartment of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, Hunan 410008, China; cLouisiana Department of Wildlife and Fisheries, Rockefeller Wildlife Refuge, Grand Chenier, LA 70643; dEnvironmental Health Science and eDepartment of Small Animal Medicine and Surgery, University of Georgia, Athens, GA 30602; fDepartment of Dentistry and iResearch Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan City 70101, Taiwan; and gSchool of Dentistry and hResearch Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei 10617, Taiwan Edited by Edward M. De Robertis, Howard Hughes Medical Institute/University of California, Los Angeles, CA, and accepted by the Editorial Board March 28, 2013 (received for review July 31, 2012) Reptiles and fish have robust regenerative powers for tooth renewal. replaced from the dental lamina connected to the lingual side of However, extant mammals can either renew their teeth one time the deciduous tooth (15). Human teeth are only replaced one time; (diphyodont dentition) or not at all (monophyodont dentition). however, a remnant of the dental lamina still exists (16) and may Humans replace their milk teeth with permanent teeth and then become activated later in life to form odontogenic tumors (17). lose their ability for tooth renewal. -
Dlx3b/4B Is Required for Early-Born but Not Later-Forming Sensory Hair Cells
© 2017. Published by The Company of Biologists Ltd | Biology Open (2017) 6, 1270-1278 doi:10.1242/bio.026211 RESEARCH ARTICLE Dlx3b/4b is required for early-born but not later-forming sensory hair cells during zebrafish inner ear development Simone Schwarzer, Sandra Spieß, Michael Brand and Stefan Hans* ABSTRACT complex arrangement of mechanosensory hair cells, nonsensory Morpholino-mediated knockdown has shown that the homeodomain supporting cells and sensory neurons (Barald and Kelley, 2004; Raft transcription factors Dlx3b and Dlx4b are essential for proper and Groves, 2015; Whitfield, 2015). Inner ear formation is a induction of the otic-epibranchial progenitor domain (OEPD), as multistep process initiated by the establishment of the preplacodal well as subsequent formation of sensory hair cells in the developing region, a zone of ectoderm running around the anterior border of the zebrafish inner ear. However, increasing use of reverse genetic neural plate containing precursors for all sensory placodes (Streit, approaches has revealed poor correlation between morpholino- 2007). The preplacodal region is further specified into a common induced and mutant phenotypes. Using CRISPR/Cas9-mediated otic-epibranchial progenitor domain (OEPD) that in zebrafish also mutagenesis, we generated a defined deletion eliminating the entire contains the progenitors of the anterior lateral line ganglion (Chen open reading frames of dlx3b and dlx4b (dlx3b/4b) and investigated a and Streit, 2013; McCarroll et al., 2012; Hans et al., 2013). potential phenotypic -
Genome-Wide DNA Methylation Analysis of KRAS Mutant Cell Lines Ben Yi Tew1,5, Joel K
www.nature.com/scientificreports OPEN Genome-wide DNA methylation analysis of KRAS mutant cell lines Ben Yi Tew1,5, Joel K. Durand2,5, Kirsten L. Bryant2, Tikvah K. Hayes2, Sen Peng3, Nhan L. Tran4, Gerald C. Gooden1, David N. Buckley1, Channing J. Der2, Albert S. Baldwin2 ✉ & Bodour Salhia1 ✉ Oncogenic RAS mutations are associated with DNA methylation changes that alter gene expression to drive cancer. Recent studies suggest that DNA methylation changes may be stochastic in nature, while other groups propose distinct signaling pathways responsible for aberrant methylation. Better understanding of DNA methylation events associated with oncogenic KRAS expression could enhance therapeutic approaches. Here we analyzed the basal CpG methylation of 11 KRAS-mutant and dependent pancreatic cancer cell lines and observed strikingly similar methylation patterns. KRAS knockdown resulted in unique methylation changes with limited overlap between each cell line. In KRAS-mutant Pa16C pancreatic cancer cells, while KRAS knockdown resulted in over 8,000 diferentially methylated (DM) CpGs, treatment with the ERK1/2-selective inhibitor SCH772984 showed less than 40 DM CpGs, suggesting that ERK is not a broadly active driver of KRAS-associated DNA methylation. KRAS G12V overexpression in an isogenic lung model reveals >50,600 DM CpGs compared to non-transformed controls. In lung and pancreatic cells, gene ontology analyses of DM promoters show an enrichment for genes involved in diferentiation and development. Taken all together, KRAS-mediated DNA methylation are stochastic and independent of canonical downstream efector signaling. These epigenetically altered genes associated with KRAS expression could represent potential therapeutic targets in KRAS-driven cancer. Activating KRAS mutations can be found in nearly 25 percent of all cancers1. -
Basic Histology (23 Questions): Oral Histology (16 Questions
Board Question Breakdown (Anatomic Sciences section) The Anatomic Sciences portion of part I of the Dental Board exams consists of 100 test items. They are broken up into the following distribution: Gross Anatomy (50 questions): Head - 28 questions broken down in this fashion: - Oral cavity - 6 questions - Extraoral structures - 12 questions - Osteology - 6 questions - TMJ and muscles of mastication - 4 questions Neck - 5 questions Upper Limb - 3 questions Thoracic cavity - 5 questions Abdominopelvic cavity - 2 questions Neuroanatomy (CNS, ANS +) - 7 questions Basic Histology (23 questions): Ultrastructure (cell organelles) - 4 questions Basic tissues - 4 questions Bone, cartilage & joints - 3 questions Lymphatic & circulatory systems - 3 questions Endocrine system - 2 questions Respiratory system - 1 question Gastrointestinal system - 3 questions Genitouirinary systems - (reproductive & urinary) 2 questions Integument - 1 question Oral Histology (16 questions): Tooth & supporting structures - 9 questions Soft oral tissues (including dentin) - 5 questions Temporomandibular joint - 2 questions Developmental Biology (11 questions): Osteogenesis (bone formation) - 2 questions Tooth development, eruption & movement - 4 questions General embryology - 2 questions 2 National Board Part 1: Review questions for histology/oral histology (Answers follow at the end) 1. Normally most of the circulating white blood cells are a. basophilic leukocytes b. monocytes c. lymphocytes d. eosinophilic leukocytes e. neutrophilic leukocytes 2. Blood platelets are products of a. osteoclasts b. basophils c. red blood cells d. plasma cells e. megakaryocytes 3. Bacteria are frequently ingested by a. neutrophilic leukocytes b. basophilic leukocytes c. mast cells d. small lymphocytes e. fibrocytes 4. It is believed that worn out red cells are normally destroyed in the spleen by a. neutrophils b. -
Supplemental Figure 1. Recombination Pattern of Six3-Cre in the Adult Retina and Brain
Supplemental Figure 1. Recombination pattern of Six3-cre in the adult retina and brain. The conditional reporter line, R26R, commences expression of β-galactosidase upon Cre-mediated recombination. The recombination pattern of the Six3-cre transgene in the retina on P21 reveals widespread recombination in all layers (A-C). At the retinal margin, areas devoid of recombination are apparent, as depicted by gaps in the X-gal staining pattern in this region (C, arrowheads). Co- immunolabeling using anti-Isl1 and anti-β-galactosidase reveals that most Isll+ cells in the INL co-localize with Six3-cre's lineage (D-F), although several Isl1+ cells are devoid of detectable reporter expression (D-F, arrowheads). At the retinal margin, many more Isl1+ cells devoid of detectable reporter expression are encountered (G-I, arrowheads). The recombination pattern of Six3-cre in the brain of P21 animals reveals widespread recombination in the hypothalamus, septum and striatum (J). Scale bar equals 50 µm in B (applies to B-C), in F (applies to D-F), in I (applies to G-I), and 1mm in J. Supplemental Figure 2. Additional cell marker expression in the Isl1-null retina. Isl1-null retinas display a 71% reduction in the expression of the RGC marker Pou4f1 (B) compared to control (A; average number of Pou4f1+ cells ± standard deviation: controls: 35 ± 7, n=3; Isl1-nulls: 10 ± 2, n=3, p<0.01, Student's t test). A slight 17% increase in the numbers of the horizontal cell marker, Calbindin-28K, in Isl1-null retinas is observed, although this change is not significant (compare C to D; average number of Calbindin-28K+ cells ± standard deviation: controls: 10 ± 2, n=4; Isl1-nulls: 12 ± 1, n=4, p=0.05, Student's t test). -
Brain Region-Dependent Gene Networks Associated with Selective Breeding for Increased Voluntary Wheel-Running Behavior
UC Riverside UC Riverside Previously Published Works Title Brain region-dependent gene networks associated with selective breeding for increased voluntary wheel-running behavior. Permalink https://escholarship.org/uc/item/8c49g8fd Journal PloS one, 13(8) ISSN 1932-6203 Authors Zhang, Pan Rhodes, Justin S Garland, Theodore et al. Publication Date 2018 DOI 10.1371/journal.pone.0201773 Peer reviewed eScholarship.org Powered by the California Digital Library University of California RESEARCH ARTICLE Brain region-dependent gene networks associated with selective breeding for increased voluntary wheel-running behavior Pan Zhang1,2, Justin S. Rhodes3,4, Theodore Garland, Jr.5, Sam D. Perez3, Bruce R. Southey2, Sandra L. Rodriguez-Zas2,6,7* 1 Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America, 2 Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United a1111111111 States of America, 3 Beckman Institute for Advanced Science and Technology, Urbana, IL, United States of a1111111111 America, 4 Center for Nutrition, Learning and Memory, University of Illinois at Urbana-Champaign, Urbana, a1111111111 IL, United States of America, 5 Department of Evolution, Ecology, and Organismal Biology, University of a1111111111 California, Riverside, CA, United States of America, 6 Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America, 7 Carle Woese Institute for Genomic Biology, a1111111111 University of Illinois at Urbana-Champaign, Urbana, IL, United States of America * [email protected] OPEN ACCESS Abstract Citation: Zhang P, Rhodes JS, Garland T, Jr., Perez SD, Southey BR, Rodriguez-Zas SL (2018) Brain Mouse lines selectively bred for high voluntary wheel-running behavior are helpful models region-dependent gene networks associated with for uncovering gene networks associated with increased motivation for physical activity and selective breeding for increased voluntary wheel- other reward-dependent behaviors. -
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. -
Longitudinal Studies on Tooth Replacement in the Leopard
LONGITUDINAL STUDIES ON TOOTH REPLACEMENT IN THE LEOPARD GECKO by Andrew Carlton Edward Wong BMSc, DDS, The University of Alberta, 2011 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Craniofacial Science) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) July 2015 © Andrew Carlton Edward Wong, 2015 Abstract The leopard gecko is an emerging reptilian model for the molecular basis of indefinite tooth replacement. Here we characterize the tooth replacement frequency and pattern of tooth loss in the normal adult gecko. We chose to perturb the system of tooth replacement by activating the Wingless signaling pathway (Wnt). Misregulation of Wnt leads to supernumerary teeth in mice and humans. We hypothesized by activating Wnt signaling with LiCl, tooth replacement frequency would increase. To measure the rate of tooth loss and replacement, weekly dental wax bites of 3 leopard geckos were taken over a 35-week period. The present/absent tooth positions were recorded. During the experimental period, the palate was injected bilaterally with NaCl (control) and then with LiCl. The geckos were to be biological replicates. Symmetry was analyzed with parametric tests (repeated measures ANOVA, Tukey’s post-hoc), while time for emergence and total absent teeth per week were analyzed with non- parametric tests (Kruskal-Wallis ANOVA, Mann-Whitney U post-hoc and Bonferroni Correction). The average replacement frequency was 6-7 weeks and posterior-to-anterior waves of replacement were formed. Right to left symmetry between individual tooth positions was high (>80%) when all teeth were included but dropped to 50% when only absent teeth were included.