Genotyping of Breech Flystrike Resource – Update
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Influencers on Thyroid Cancer Onset: Molecular Genetic Basis
G C A T T A C G G C A T genes Review Influencers on Thyroid Cancer Onset: Molecular Genetic Basis Berta Luzón-Toro 1,2, Raquel María Fernández 1,2, Leticia Villalba-Benito 1,2, Ana Torroglosa 1,2, Guillermo Antiñolo 1,2 and Salud Borrego 1,2,* 1 Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; [email protected] (B.L.-T.); [email protected] (R.M.F.); [email protected] (L.V.-B.); [email protected] (A.T.); [email protected] (G.A.) 2 Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain * Correspondence: [email protected]; Tel.: +34-955-012641 Received: 3 September 2019; Accepted: 6 November 2019; Published: 8 November 2019 Abstract: Thyroid cancer, a cancerous tumor or growth located within the thyroid gland, is the most common endocrine cancer. It is one of the few cancers whereby incidence rates have increased in recent years. It occurs in all age groups, from children through to seniors. Most studies are focused on dissecting its genetic basis, since our current knowledge of the genetic background of the different forms of thyroid cancer is far from complete, which poses a challenge for diagnosis and prognosis of the disease. In this review, we describe prevailing advances and update our understanding of the molecular genetics of thyroid cancer, focusing on the main genes related with the pathology, including the different noncoding RNAs associated with the disease. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Genome-Wide Analysis of ATP-Binding
Tian et al. BMC Genomics (2017) 18:330 DOI 10.1186/s12864-017-3706-6 RESEARCH ARTICLE Open Access Genome-wide analysis of ATP-binding cassette (ABC) transporters in the sweetpotato whitefly, Bemisia tabaci Lixia Tian1, Tianxue Song2, Rongjun He1, Yang Zeng1, Wen Xie1, Qingjun Wu1, Shaoli Wang1, Xuguo Zhou3* and Youjun Zhang1* Abstract Background: ABC transporter superfamily is one of the largest and ubiquitous groups of proteins. Because of their role in detoxification, insect ABC transporters have gained more attention in recent years. In this study, we annotated ABC transporters from a newly sequenced sweetpotato whitefly genome. Bemisia tabaci Q biotype is an emerging global invasive species that has caused extensive damages to field crops as well as ornamental plants. Results: A total of 55 ABC transporters containing all eight described subfamilies (A to H) were identified in the B. tabaci Q genome, including 8 ABCAs, 3 ABCBs, 6 ABCCs, 2 ABCDs, 1 ABCE, 3 ABCFs, 23 ABCGs and 9 ABCHs. In comparison to other species, subfamilies G and H in both phloem- and blood-sucking arthropods are expanded. The temporal expression profiles of these 55 ABC transporters throughout B. tabaci developmental stages and their responses to imidacloprid, a neonicotinoid insecticide, were investigated using RNA-seq analysis. Furthermore, the mRNA expression of 24 ABC transporters (44% of the total) representing all eight subfamilies was confirmed by the quantitative real-time PCR (RT-qPCR). Furthermore, mRNA expression levels estimated by RT-qPCR and RNA-seq analyses were significantly correlated (r =0.684,p <0.01). Conclusions: It is the first genome-wide analysis of the entire repertoire of ABC transporters in B. -
5' Untranslated Region Elements Show High Abundance and Great
International Journal of Molecular Sciences Article 0 5 Untranslated Region Elements Show High Abundance and Great Variability in Homologous ABCA Subfamily Genes Pavel Dvorak 1,2,* , Viktor Hlavac 2,3 and Pavel Soucek 2,3 1 Department of Biology, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic 2 Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; [email protected] (V.H.); [email protected] (P.S.) 3 Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic * Correspondence: [email protected]; Tel.: +420-377593263 Received: 7 October 2020; Accepted: 20 November 2020; Published: 23 November 2020 Abstract: The 12 members of the ABCA subfamily in humans are known for their ability to transport cholesterol and its derivatives, vitamins, and xenobiotics across biomembranes. Several ABCA genes are causatively linked to inborn diseases, and the role in cancer progression and metastasis is studied intensively. The regulation of translation initiation is implicated as the major mechanism in the processes of post-transcriptional modifications determining final protein levels. In the current bioinformatics study, we mapped the features of the 50 untranslated regions (50UTR) known to have the potential to regulate translation, such as the length of 50UTRs, upstream ATG codons, upstream open-reading frames, introns, RNA G-quadruplex-forming sequences, stem loops, and Kozak consensus motifs, in the DNA sequences of all members of the subfamily. Subsequently, the conservation of the features, correlations among them, ribosome profiling data as well as protein levels in normal human tissues were examined. The 50UTRs of ABCA genes contain above-average numbers of upstream ATGs, open-reading frames and introns, as well as conserved ones, and these elements probably play important biological roles in this subfamily, unlike RG4s. -
Evaluation of Variability in Human Kidney Organoids
ARTICLES https://doi.org/10.1038/s41592-018-0253-2 Evaluation of variability in human kidney organoids Belinda Phipson 1, Pei X. Er1, Alexander N. Combes1,2, Thomas A. Forbes1,3,4, Sara E. Howden1,2, Luke Zappia1,5, Hsan-Jan Yen1, Kynan T. Lawlor1, Lorna J. Hale1,4, Jane Sun6, Ernst Wolvetang6, Minoru Takasato1,7, Alicia Oshlack1,5 and Melissa H. Little 1,2,4* The utility of human pluripotent stem cell–derived kidney organoids relies implicitly on the robustness and transferability of the protocol. Here we analyze the sources of transcriptional variation in a specific kidney organoid protocol. Although individ- ual organoids within a differentiation batch showed strong transcriptional correlation, we noted significant variation between experimental batches, particularly in genes associated with temporal maturation. Single-cell profiling revealed shifts in neph- ron patterning and proportions of component cells. Distinct induced pluripotent stem cell clones showed congruent transcrip- tional programs, with interexperimental and interclonal variation also strongly associated with nephron patterning. Epithelial cells isolated from organoids aligned with total organoids at the same day of differentiation, again implicating relative matura- tion as a confounder. This understanding of experimental variation facilitated an optimized analysis of organoid-based disease modeling, thereby increasing the utility of kidney organoids for personalized medicine and functional genomics. he ability to derive induced pluripotent stem cells (iPSCs) In this study, we provide a comprehensive transcriptional from the somatic cells of patients1, together with directed dif- and morphological evaluation of our kidney organoid protocol. Tferentiation protocols, provides a capacity to model the cell Applying RNA sequencing (RNA-seq) to 57 whole organoids and types affected by disease. -
Nephrin Mutations Can Cause Childhood-Onset Steroid-Resistant Nephrotic Syndrome
BRIEF COMMUNICATION www.jasn.org Nephrin Mutations Can Cause Childhood-Onset Steroid-Resistant Nephrotic Syndrome Aure´lie Philippe,*† Fabien Nevo,*† Ernie L. Esquivel,*† Dalia Reklaityte,*† ʈ Olivier Gribouval,*† Marie-Jose`phe Teˆte,*‡ Chantal Loirat,§ Jacques Dantal, Michel Fischbach,¶ Claire Pouteil-Noble,** Ste´phane Decramer,†† Martin Hoehne,‡‡ Thomas Benzing,‡‡ Marina Charbit,‡ Patrick Niaudet,*†‡ and Corinne Antignac*†§§ † *Inserm U574, Hoˆpital Necker-Enfants Malades, Universite´ Paris Descartes, Faculte´deMe´ decine Rene´ Descartes, BRIEF COMMUNICATION ‡Pediatric Nephrology and §§Department of Genetics, Hoˆpital Necker-Enfants Malades, Assistance Publique-Hoˆpitaux de Paris, and §Pediatric Nephrology Department, Universite´ Paris VII, Assistance Publique-Hoˆpitaux de Paris, Hoˆpital ʈ Robert Debre´, Paris, ITERT, Department of Nephrology and Clinical Immunology, CHU Nantes, Nantes, ¶Nephrology Dialysis Transplantation Children’s Unit, Hoˆpital de Hautepierre, Strasbourg, **Transplantation and Nephrology Unit, Centre Hospitalier Lyon-Sud, Pierre-Be´nite, and ††Department of Pediatric Nephrology, Hoˆpital des Enfants, and Inserm, U858/I2MR, Department of Renal and Cardiac Remodeling, Toulouse, France; and ‡‡Department of Medicine IV, University of Cologne, Cologne, Germany ABSTRACT Classically, infants with mutations in NPHS1, which encodes nephrin, present with but has since been described in other nephrotic syndrome within the first 3 mo of life (congenital nephrotic syndrome of populations.3–5 Nephrin is a single-pass the Finnish-type), and children with mutations in NPHS2, which encodes podocin, transmembrane protein consisting of present later with steroid-resistant nephrotic syndrome. Recently, however, eight extracellular Ig-like modules, a fi- NPHS2 mutations have been identified in children with congenital nephrotic syn- bronectin type III–like motif, and a cy- drome. Whether NPHS1 mutations similarly account for some cases of childhood tosolic C-terminal tail. -
NPHS2 Antibody (Podocin) (R30382)
NPHS2 Antibody (Podocin) (R30382) Catalog No. Formulation Size R30382 0.5mg/ml if reconstituted with 0.2ml sterile DI water 100 ug Bulk quote request Availability 1-3 business days Species Reactivity Human, Mouse, Rat Format Antigen affinity purified Clonality Polyclonal (rabbit origin) Isotype Rabbit IgG Purity Antigen affinity Buffer Lyophilized from 1X PBS with 2.5% BSA and 0.025% sodium azide/thimerosal UniProt Q9NP85 Applications Western blot : 0.5-1ug/ml Limitations This NPHS2 antibody is available for research use only. Western blot testing of NPHS2 antibody and rat kidney tissue lysate. Predicted molecular weight ~42kDa. Description NPHS2, also called Podocin (PDCN), is a protein which lines the podocytes and assists in maintaining the barrier at the glomerular basement membrane. NPHS2 is a causative gene for Familial idiopathic nephrotic syndromes, which represents a heterogeneous group of kidney disorders, and include autosomal recessive steroid-resistant nephrotic syndrome, which is characterized by early childhood onset of proteinuria, rapid progression to end-stage renal disease and focal segmental glomerulosclerosis. By positional cloning, it was mapped to 1q25-31. It is almost exclusively expressed in the podocytes of fetal and mature kidney glomeruli, and encodes a new integral membrane protein, podocin, belonging to the stomatin protein family. Boute et al.(2000) found ten different NPHS2 mutations, comprising nonsense, frameshift and missense mutations, to segregate with the disease, demonstrating a crucial role for podocin in the function of the glomerular filtration barrier. Application Notes The stated application concentrations are suggested starting amounts. Titration of the NPHS2 antibody may be required due to differences in protocols and secondary/substrate sensitivity. -
NPHS2 Gene Mutation, Atopy, and Gender As Risk Factors for Steroid-Resistant Nephrotic Syndrome in Indonesians
Paediatrica Indonesiana VOLUME 51 September NUMBER 5 Original Article NPHS2 gene mutation, atopy, and gender as risk factors for steroid-resistant nephrotic syndrome in Indonesians Dedi Rachmadi, Dany Hilmanto, Ponpon Idjradinata, Abdurahman Sukadi Abstract QUHFHQW\HDUVPROHFXODUJHQHWLFVWXGLHVKDYH Background 6WHURLGUHVLVWDQWQHSKURWLFV\QGURPH 6516 RIWHQ EHHQZHOOGHYHORSHGLQFOXGLQJVWXGLHVIRU GHYHORSVLQWRHQGVWDJHUHQDOGLVHDVH3UHYLRXVVWXGLHVKDYH JHQHVLQYROYHGLQWKHSDWKRJHQHVLVRIQHSKURWLF reported that NPHS2JHQHPXWDWLRQJHQGHUDQGDWRSLFKLVWRU\ V\QGURPH2ISDUWLFXODULQWHUHVWLVWKHJHQH DUHULVNIDFWRUVDVVRFLDWHGZLWK6516,QWHUHWKQLFVRFLRFXOWXUDO I DQGHQYLURQPHQWDOGLIIHUHQFHVKDYHDOVREHHQVXJJHVWHGWRDIIHFW encoding a protein that maintains the diaphragm slit WKHVHPXWDWLRQV RISRGRF\WHV*HQHPXWDWLRQDQDO\VLVLVLPSRUWDQW Objective7RDQDO\]HSRVVLEOHULVNIDFWRUVIRU6516LQFOXGLQJ with regards to phenotype and predicting the severity NPHS2JHQHPXWDWLRQV &o7DQGGHO* JHQGHUDQG RIFOLQLFDOPDQLIHVWDWLRQV The NPHS2 gene encodes DWRSLFKLVWRU\LQ,QGRQHVLDQVXEMHFWVZLWK6516 the podocin protein and is located on chromosome Methods$FDVHFRQWUROVWXG\ZLWKVXEMHFWVFRQVLVWLQJRI 6516SDWLHQWVDQGFRQWUROVXEMHFWVZDVXQGHUWDNHQLQ T0XWDWLRQRIWKLVJHQHKDVEHHQDVVRFLDWHG ,QGRQHVLDQWHDFKLQJFHQWUHKRVSLWDOVIURP6HSWHPEHUWR ZLWKSRRUVWHURLGUHVSRQVHLQWUHDWPHQWRIQHSKURWLF 'HFHPEHU$QDO\VLVRIWKHNPHS2JHQHPXWDWLRQLQ V\QGURPH 16 3UHYLRXVVWXGLHVKDYHVKRZQWKDW &o7ZDVSHUIRUPHGE\DPSOLILFDWLRQUHIUDFWRU\PXWDWLRQV\VWHP SRNS patients with an NPHS2JHQHPXWDWLRQKDG SRO\PHUDVHFKDLQUHDFWLRQ $5063&5 ZKLOHWKDWIRUWKH NPHS2JHQHPXWDWLRQLQGHO*ZDVSHUIRUPHGE\UHVWULFWLRQ -
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. -
CG/CA Genotypes Represent Novel Markers in the NPHS2 Gene Region Associated with Nephrotic Syndrome
Journal of Genetics (2020)99:33 Ó Indian Academy of Sciences https://doi.org/10.1007/s12041-020-1188-9 (0123456789().,-volV)(0123456789().,-volV) RESEARCH ARTICLE CG/CA genotypes represent novel markers in the NPHS2 gene region associated with nephrotic syndrome LEILA ESMAELI CHAMGORDANI, NASIM EBRAHIMI, FARZANE AMIRMAHANI and SADEQ VALLIAN* Genetics Division, Faculty of Biological Sciences and Technologies, Department of Cellular and Molecular Biology and Microbiology, University of Isfahan, Isfahan, Iran *For correspondence. E-mail: [email protected]. Received 15 November 2019; revised 10 January 2020; accepted 14 January 2020 Abstract. Nephrotic syndrome (NS) is considered as a primary disease of the kidney that represents a heterogeneous group of glomerular disorders occurring mainly in children. It is generally divided into steroid-sensitive and steroid-resistant forms, depending upon the patient’s response to steroid therapy. Among the genes involved, the NPHS2 gene has been reported as the causative gene in steroid resistant form of nephrotic syndrome. In the present study, heterozygosity rate, allelic frequency and linkage of rs2274625 and rs3829795 markers were investigated in the NPHS2 gene region. To determine the SNP alleles, tetra-primer ARMS PCR was used. After genotyping rs2274625 and rs3829795 polymorphic markers in 120 unrelated individuals and nine trios families, the data were analysed using various computer programs such as UCSC Genome Browser, dbSNP and SNPper. Based on the statistical analysis of the results, for rs2274625 marker, allele frequency for C and T alleles was 97% and 3%, respectively. For rs3829795 marker allele frequency for G and A alleles was 55% and 45%, respectively. -
Role and Regulation of the P53-Homolog P73 in the Transformation of Normal Human Fibroblasts
Role and regulation of the p53-homolog p73 in the transformation of normal human fibroblasts Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Bayerischen Julius-Maximilians-Universität Würzburg vorgelegt von Lars Hofmann aus Aschaffenburg Würzburg 2007 Eingereicht am Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Dr. Martin J. Müller Gutachter: Prof. Dr. Michael P. Schön Gutachter : Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am Erklärung Hiermit erkläre ich, dass ich die vorliegende Arbeit selbständig angefertigt und keine anderen als die angegebenen Hilfsmittel und Quellen verwendet habe. Diese Arbeit wurde weder in gleicher noch in ähnlicher Form in einem anderen Prüfungsverfahren vorgelegt. Ich habe früher, außer den mit dem Zulassungsgesuch urkundlichen Graden, keine weiteren akademischen Grade erworben und zu erwerben gesucht. Würzburg, Lars Hofmann Content SUMMARY ................................................................................................................ IV ZUSAMMENFASSUNG ............................................................................................. V 1. INTRODUCTION ................................................................................................. 1 1.1. Molecular basics of cancer .......................................................................................... 1 1.2. Early research on tumorigenesis ................................................................................. 3 1.3. Developing -
ABCA5 (NM 018672) Human Tagged ORF Clone – RC213865 | Origene
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for RC213865 ABCA5 (NM_018672) Human Tagged ORF Clone Product data: Product Type: Expression Plasmids Product Name: ABCA5 (NM_018672) Human Tagged ORF Clone Tag: Myc-DDK Symbol: ABCA5 Synonyms: ABC13; EST90625; HTC3 Vector: pCMV6-Entry (PS100001) E. coli Selection: Kanamycin (25 ug/mL) Cell Selection: Neomycin ORF Nucleotide >RC213865 representing NM_018672 Sequence: Red=Cloning site Blue=ORF Green=Tags(s) TTTTGTAATACGACTCACTATAGGGCGGCCGGGAATTCGTCGACTGGATCCGGTACCGAGGAGATCTGCC GCCGCGATCGCC ATGTCCACTGCAATTAGGGAGGTAGGAGTTTGGAGACAGACCAGAACACTTCTACTGAAGAATTACTTAA TTAAATGCAGAACCAAAAAGAGTAGTGTTCAGGAAATTCTTTTTCCACTATTTTTTTTATTTTGGTTAAT ATTAATTAGCATGATGCATCCAAATAAGAAATATGAAGAAGTGCCTAATATAGAACTCAATCCTATGGAC AAGTTTACTCTTTCTAATCTAATTCTTGGATATACTCCAGTGACTAATATTACAAGCAGCATCATGCAGA AAGTGTCTACTGATCATCTACCTGATGTCATAATTACTGAAGAATATACAAATGAAAAAGAAATGTTAAC ATCCAGTCTCTCTAAGCCGAGCAACTTTGTAGGTGTGGTTTTCAAAGACTCCATGTCCTATGAACTTCGT TTTTTTCCTGATATGATTCCAGTATCTTCTATTTATATGGATTCAAGAGCTGGCTGTTCAAAATCATGTG AGGCTGCTCAGTACTGGTCCTCAGGTTTCACAGTTTTACAAGCATCCATAGATGCTGCCATTATACAGTT GAAGACCAATGTTTCTCTTTGGAAGGAGCTGGAGTCAACTAAAGCTGTTATTATGGGAGAAACTGCTGTT GTAGAAATAGATACCTTTCCCCGAGGAGTAATTTTAATATACCTAGTTATAGCATTTTCACCTTTTGGAT ACTTTTTGGCAATTCATATCGTAGCAGAAAAAGAAAAAAAAATAAAAGAATTTTTAAAGATAATGGGACT TCATGATACTGCCTTTTGGCTTTCCTGGGTTCTTCTATATACAAGTTTAATTTTTCTTATGTCCCTTCTT ATGGCAGTCATTGCGACAGCTTCTTTGTTATTTCCTCAAAGTAGCAGCATTGTGATATTTCTGCTTTTTT