A Novel Interleukin-1 Receptor-Associated Kinase-4 from Thick Shell Mussel Mytilus Coruscus Is Involved in Inflammatory Response T
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CO2-Induced Ph Reduction Increases Physiological Toxicity of Nano-Tio2
www.nature.com/scientificreports OPEN CO2-induced pH reduction increases physiological toxicity of nano-TiO2 in the mussel Mytilus coruscus Received: 27 July 2016 Menghong Hu1,2,*, Daohui Lin2,3,*, Yueyong Shang1, Yi Hu3, Weiqun Lu1, Xizhi Huang1, Accepted: 02 December 2016 Ke Ning1, Yimin Chen1 & Youji Wang1,2 Published: 05 January 2017 The increasing usage of nanoparticles has caused their considerable release into the aquatic environment. Meanwhile, anthropogenic CO2 emissions have caused a reduction of seawater pH. However, their combined effects on marine species have not been experimentally evaluated. This study estimated the physiological toxicity of nano-TiO2 in the mussel Mytilus coruscus under high pCO2 (2500–2600 μatm). We found that respiration rate (RR), food absorption efficiency (AE), clearance rate (CR), scope for growth (SFG) and O:N ratio were significantly reduced by nano-TiO2, whereas faecal organic weight rate and ammonia excretion rate (ER) were increased under nano-TiO2 conditions. High pCO2 exerted lower effects on CR, RR, ER and O:N ratio than nano-TiO2. Despite this, significant interactions of CO2-induced pH change and nano-TiO2 were found in RR, ER and O:N ratio. PCA showed close relationships among most test parameters, i.e., RR, CR, AE, SFG and O:N ratio. The normal physiological responses were strongly correlated to a positive SFG with normal pH and no/low nano- TiO2 conditions. Our results indicate that physiological functions of M. coruscus are more severely impaired by the combination of nano-TiO2 and high pCO2. Increasing production of engineered nanoparticles (NPs) has raised concern about their potential biological and 1 ecological effects . -
The Prevalence of MADH4 and BMPR1A Mutations in Juvenile Polyposis and Absence of BMPR2, BMPR1B, and ACVR1 Mutations
484 ORIGINAL ARTICLE J Med Genet: first published as 10.1136/jmg.2004.018598 on 2 July 2004. Downloaded from The prevalence of MADH4 and BMPR1A mutations in juvenile polyposis and absence of BMPR2, BMPR1B, and ACVR1 mutations J R Howe, M G Sayed, A F Ahmed, J Ringold, J Larsen-Haidle, A Merg, F A Mitros, C A Vaccaro, G M Petersen, F M Giardiello, S T Tinley, L A Aaltonen, H T Lynch ............................................................................................................................... J Med Genet 2004;41:484–491. doi: 10.1136/jmg.2004.018598 Background: Juvenile polyposis (JP) is an autosomal dominant syndrome predisposing to colorectal and gastric cancer. We have identified mutations in two genes causing JP, MADH4 and bone morphogenetic protein receptor 1A (BMPR1A): both are involved in bone morphogenetic protein (BMP) mediated signalling and are members of the TGF-b superfamily. This study determined the prevalence of mutations See end of article for in MADH4 and BMPR1A, as well as three other BMP/activin pathway candidate genes in a large number authors’ affiliations ....................... of JP patients. Methods: DNA was extracted from the blood of JP patients and used for PCR amplification of each exon of Correspondence to: these five genes, using primers flanking each intron–exon boundary. Mutations were determined by Dr J R Howe, Department of Surgery, 4644 JCP, comparison to wild type sequences using sequence analysis software. A total of 77 JP cases were University of Iowa College sequenced for mutations in the MADH4, BMPR1A, BMPR1B, BMPR2, and/or ACVR1 (activin A receptor) of Medicine, 200 Hawkins genes. The latter three genes were analysed when MADH4 and BMPR1A sequencing found no mutations. -
Two Toll-Like Receptors Identified in the Mantle of Mytilus Coruscus Are
Fish and Shellfish Immunology 90 (2019) 134–140 Contents lists available at ScienceDirect Fish and Shellfish Immunology journal homepage: www.elsevier.com/locate/fsi Short sequence report Two toll-like receptors identified in the mantle of Mytilus coruscus are abundant in haemocytes T Yi-Feng Lia,b,c,1, Yu-Zhu Liua,b,1, Yan-Wen Chena,b, Ke Chena,b, Frederico M. Batistad, João C.R. Cardosod, Yu-Ru Chena,b, Li-Hua Penga,b, Ya Zhanga,b, You-Ting Zhua,b,c, ∗∗ ∗ Xiao Lianga,b,c, Deborah M. Powera,b,d, , Jin-Long Yanga,b,c, a International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China b Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China c National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China d Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal ARTICLE INFO ABSTRACT Keywords: Toll-like receptors (TLRs) are a large family of pattern recognition receptors (PRRs) that play a critical role in Mytilus coruscus innate immunity. TLRs are activated when they recognize microbial associated molecular patterns (MAMPs) of Toll-like receptors bacteria, viruses, or fungus. In the present study, two TLRs were isolated from the mantle of the hard-shelled Haemocytes mussel (Mytilus coruscus) and designated McTLR2 and McTLR3 based on their sequence similarity and phylo- Mantle genetic clustering with Crassostrea gigas, CgiTLR2 and CgiTLR3, respectively. Quantitative RT-PCR analysis demonstrated that McTLR2 and McTLR3 were constitutively expressed in many tissues but at low abundance. -
Nanopore Sequencing and Hi-C Based De Novo Assembly of Trachidermus Fasciatus Genome
G C A T T A C G G C A T genes Article Nanopore Sequencing and Hi-C Based De Novo Assembly of Trachidermus fasciatus Genome Gangcai Xie 1,* , Xu Zhang 2,3, Feng Lv 4, Mengmeng Sang 1, Hairong Hu 5, Jinqiu Wang 5,* and Dong Liu 2,3,* 1 Institute of Reproductive Medicine, Medical School, Nantong University, Nantong 226001, China; [email protected] 2 Nantong Laboratory of Development and Diseases, School of Life Science, Nantong University, Nantong 226001, China; [email protected] 3 Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neu-Roregeneration, Nantong University, Nantong 226001, China 4 Nantong College of Science and Technology, Qingnian Middle Road 136, Nantong 226006, China; [email protected] 5 State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China; [email protected] * Correspondence: [email protected] (G.X.); [email protected] (J.W.); [email protected] (D.L.) Abstract: Trachidermus fasciatus is a roughskin sculpin fish widespread across the coastal areas of East Asia. Due to environmental destruction and overfishing, the population of this species is under threat. In order to protect this endangered species, it is important to have the genome sequenced. Reference genomes are essential for studying population genetics, domestic farming, and genetic resource protection. However, currently, no reference genome is available for Trachidermus fasciatus, and this has greatly hindered the research on this species. In this study, we integrated nanopore long-read sequencing, Illumina short-read sequencing, and Hi-C methods to thoroughly assemble the Trachidermus fasciatus genome. -
Casein Kinase 1 Isoforms in Degenerative Disorders
CASEIN KINASE 1 ISOFORMS IN DEGENERATIVE DISORDERS DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Theresa Joseph Kannanayakal, M.Sc., M.S. * * * * * The Ohio State University 2004 Dissertation Committee: Approved by Professor Jeff A. Kuret, Adviser Professor John D. Oberdick Professor Dale D. Vandre Adviser Professor Mike X. Zhu Biophysics Graduate Program ABSTRACT Casein Kinase 1 (CK1) enzyme is one of the largest family of Serine/Threonine protein kinases. CK1 has a wide distribution spanning many eukaryotic families. In cells, its kinase activity has been found in various sub-cellular compartments enabling it to phosphorylate many proteins involved in cellular maintenance and disease pathogenesis. Tau is one such substrate whose hyperphosphorylation results in degeneration of neurons in Alzheimer’s disease (AD). AD is a slow neuroprogessive disorder histopathologically characterized by Granulovacuolar degeneration bodies (GVBs) and intraneuronal accumulation of tau in Neurofibrillary Tangles (NFTs). The level of CK1 isoforms, CK1α, CK1δ and CK1ε has been shown to be elevated in AD. Previous studies of the correlation of CK1δ with lesions had demonstrated its importance in tau hyperphosphorylation. Hence we investigated distribution of CK1α and CK1ε with the lesions to understand if they would play role in tau hyperphosphorylation similar to CK1δ. The kinase results were also compared with lesion correlation studies of peptidyl cis/trans prolyl isomerase (Pin1) and caspase-3. Our results showed that among the enzymes investigated, CK1 isoforms have the greatest extent of colocalization with the lesions. We have also investigated the distribution of CK1α with different stages of NFTs that follow AD progression. -
Evolutionary Genomics of a Plastic Life History Trait: Galaxias Maculatus Amphidromous and Resident Populations
EVOLUTIONARY GENOMICS OF A PLASTIC LIFE HISTORY TRAIT: GALAXIAS MACULATUS AMPHIDROMOUS AND RESIDENT POPULATIONS by María Lisette Delgado Aquije Submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy at Dalhousie University Halifax, Nova Scotia August 2021 Dalhousie University is located in Mi'kma'ki, the ancestral and unceded territory of the Mi'kmaq. We are all Treaty people. © Copyright by María Lisette Delgado Aquije, 2021 I dedicate this work to my parents, María and José, my brothers JR and Eduardo for their unconditional love and support and for always encouraging me to pursue my dreams, and to my grandparents Victoria, Estela, Jesús, and Pepe whose example of perseverance and hard work allowed me to reach this point. ii TABLE OF CONTENTS LIST OF TABLES ............................................................................................................ vii LIST OF FIGURES ........................................................................................................... ix ABSTRACT ...................................................................................................................... xii LIST OF ABBREVIATION USED ................................................................................ xiii ACKNOWLEDGMENTS ................................................................................................ xv CHAPTER 1. INTRODUCTION ....................................................................................... 1 1.1 Galaxias maculatus .................................................................................................. -
RAF Protein-Serine/Threonine Kinases: Structure and Regulation
Biochemical and Biophysical Research Communications 399 (2010) 313–317 Contents lists available at ScienceDirect Biochemical and Biophysical Research Communications journal homepage: www.elsevier.com/locate/ybbrc Mini Review RAF protein-serine/threonine kinases: Structure and regulation Robert Roskoski Jr. * Blue Ridge Institute for Medical Research, 3754 Brevard Road, Suite 116, Box 19, Horse Shoe, NC 28742, USA article info abstract Article history: A-RAF, B-RAF, and C-RAF are a family of three protein-serine/threonine kinases that participate in the Received 12 July 2010 RAS-RAF-MEK-ERK signal transduction cascade. This cascade participates in the regulation of a large vari- Available online 30 July 2010 ety of processes including apoptosis, cell cycle progression, differentiation, proliferation, and transforma- tion to the cancerous state. RAS mutations occur in 15–30% of all human cancers, and B-RAF mutations Keywords: occur in 30–60% of melanomas, 30–50% of thyroid cancers, and 5–20% of colorectal cancers. Activation 14-3-3 of the RAF kinases requires their interaction with RAS-GTP along with dephosphorylation and also phos- ERK phorylation by SRC family protein-tyrosine kinases and other protein-serine/threonine kinases. The for- GDC-0879 mation of unique side-to-side RAF dimers is required for full kinase activity. RAF kinase inhibitors are MEK Melanoma effective in blocking MEK1/2 and ERK1/2 activation in cells containing the oncogenic B-RAF Val600Glu PLX4032 activating mutation. RAF kinase inhibitors lead to the paradoxical increase in RAF kinase activity in cells PLX4720 containing wild-type B-RAF and wild-type or activated mutant RAS. -
Analysis of Protein Kinase Domain and Tyrosine Kinase Or Serine/Threonine Kinase Signatures Involved in Lung Cancer
Analysis of Protein Kinase Domain and Tyrosine Kinase Or serine/Threonine Kinase Signatures Involved In Lung Cancer Lung cancer results when normal check and balance system of cell division is disrupted and ultimately the cells divide and proliferate in an uncontrollable manner forming a mass of cells in our body, known as tumor. Frequent mutations in Protein Kinase Domain alter the process of phosphorylation which results in abnormality in regulations of cell apoptosis and differentiation. Tyrosine Protein kinases and Serine/Threonine Protein Kinases are the two s t broad classes of protein kinases in accordance to their substrate specificity. The study of n i r Tyrosine protein kinase and serine Kinase coding regions have the importance of sequence P and structure determinants of cancer-causing mutations from mutation-dependent activation e r P process. In the present study, we analyzed huge amounts of data extracted from various biological databases and NCBI. Out of the 534 proteins that may play a role in lung cancer, 71 proteins were selected that are likely to be actively involved in lung cancer. These proteins were evaluated by employing Multiple Sequence Alignment and a Phylogenetic tree was constructed using Neighbor-Joining Algorithm. From the constructed phylogenetic tree, protein kinase domain and motif study was performed. The results of this study revealed that the presence of Protein Kinase Domain and Tyrosine or Serine/Threonine Kinase signatures in some of the proteins are mutated, which play a dominant role in the pathogenesis of Lung Cancer and these may be addressed with the help of inhibitors to develop an efficient anticancer drugs. -
Development of Microsatellite Markers for a Hard-Shelled Mussel, Mytilus Coruscus, and Cross-Species Transfer J.H
Development of microsatellite markers for a hard-shelled mussel, Mytilus coruscus, and cross-species transfer J.H. Kang1, Y.K. Kim1, J.Y. Park1, E.S. Noh1, J.E. Jeong2, Y.S. Lee2 and T.J. Choi3 1Biotechnology Research Division, National Fisheries Research and Development Institute, Busan, Republic of Korea 2Department of Life Science and Biotechnology, Soonchunhyang University, Asan, Republic of Korea 3Department of Microbiology, Pukyong National University, Busan, Republic of Korea Corresponding author: T.J. Choi E-mail: [email protected] Genet. Mol. Res. 12 (3): 4009-4017 (2013) Received February 18, 2013 Accepted July 5, 2013 Published September 27, 2013 DOI http://dx.doi.org/10.4238/2013.September.27.2 ABSTRACT. The Korean mussel Mytilus coruscus, an endemic marine bivalve mollusk, is economically important. Its population is currently decreasing due to overexploitation and invasion of a more competitive species, Mytilus galloprovincialis. In this study, microsatellite markers for M. coruscus were developed using a cost-effective pyrosequencing technique. Among the 33,859 dinucleotide microsatellite sequences identified, 176 loci that contained more than 8 CA, CT, or AT repeats were selected for primer synthesis. Sixty-four (36.4%) primer sets were produced from the 100- to 200-bp polymerase chain reaction products obtained from 2 M. coruscus individuals. Twenty of these were chosen to amplify DNA from 82 M. coruscus individuals, and 18 polymorphic loci and 2 monomorphic loci were selected as microsatellite markers. The number of alleles and the allele richness of the polymorphic loci ranged from 2 to 22 and from 2.0 to 19.7 with means of 10.8 and 10.1, Genetics and Molecular Research 12 (3): 4009-4017 (2013) ©FUNPEC-RP www.funpecrp.com.br J.H. -
Two Novel Disease-Causing Variants in BMPR1B Are Associated with Brachydactyly Type A1
European Journal of Human Genetics (2015) 23, 1640–1645 & 2015 Macmillan Publishers Limited All rights reserved 1018-4813/15 www.nature.com/ejhg ARTICLE Two novel disease-causing variants in BMPR1B are associated with brachydactyly type A1 Lemuel Racacho1,2, Ashley M Byrnes1,3, Heather MacDonald3, Helen J Dranse4, Sarah M Nikkel5,6, Judith Allanson6, Elisabeth Rosser7, T Michael Underhill4 and Dennis E Bulman*,1,2,5 Brachydactyly type A1 is an autosomal dominant disorder primarily characterized by hypoplasia/aplasia of the middle phalanges of digits 2–5. Human and mouse genetic perturbations in the BMP-SMAD signaling pathway have been associated with many brachymesophalangies, including BDA1, as causative mutations in IHH and GDF5 have been previously identified. GDF5 interacts directly as the preferred ligand for the BMP type-1 receptor BMPR1B and is important for both chondrogenesis and digit formation. We report pathogenic variants in BMPR1B that are associated with complex BDA1. A c.975A4C (p. (Lys325Asn)) was identified in the first patient displaying absent middle phalanges and shortened distal phalanges of the toes in addition to the significant shortening of middle phalanges in digits 2, 3 and 5 of the hands. The second patient displayed a combination of brachydactyly and arachnodactyly. The sequencing of BMPR1B in this individual revealed a novel c.447-1G4A at a canonical acceptor splice site of exon 8, which is predicted to create a novel acceptor site, thus leading to a translational reading frameshift. Both mutations are most likely to act in a dominant-negative manner, similar to the effects observed in BMPR1B mutations that cause BDA2. -
Kinase-Targeted Cancer Therapies: Progress, Challenges and Future Directions Khushwant S
Bhullar et al. Molecular Cancer (2018) 17:48 https://doi.org/10.1186/s12943-018-0804-2 REVIEW Open Access Kinase-targeted cancer therapies: progress, challenges and future directions Khushwant S. Bhullar1, Naiara Orrego Lagarón2, Eileen M. McGowan3, Indu Parmar4, Amitabh Jha5, Basil P. Hubbard1 and H. P. Vasantha Rupasinghe6,7* Abstract The human genome encodes 538 protein kinases that transfer a γ-phosphate group from ATP to serine, threonine, or tyrosine residues. Many of these kinases are associated with human cancer initiation and progression. The recent development of small-molecule kinase inhibitors for the treatment of diverse types of cancer has proven successful in clinical therapy. Significantly, protein kinases are the second most targeted group of drug targets, after the G-protein- coupled receptors. Since the development of the first protein kinase inhibitor, in the early 1980s, 37 kinase inhibitors have received FDA approval for treatment of malignancies such as breast and lung cancer. Furthermore, about 150 kinase-targeted drugs are in clinical phase trials, and many kinase-specific inhibitors are in the preclinical stage of drug development. Nevertheless, many factors confound the clinical efficacy of these molecules. Specific tumor genetics, tumor microenvironment, drug resistance, and pharmacogenomics determine how useful a compound will be in the treatment of a given cancer. This review provides an overview of kinase-targeted drug discovery and development in relation to oncology and highlights the challenges and future potential for kinase-targeted cancer therapies. Keywords: Kinases, Kinase inhibition, Small-molecule drugs, Cancer, Oncology Background Recent advances in our understanding of the fundamen- Kinases are enzymes that transfer a phosphate group to a tal molecular mechanisms underlying cancer cell signaling protein while phosphatases remove a phosphate group have elucidated a crucial role for kinases in the carcino- from protein. -
Ecological Effects of the First Dam on Yangtze Main Stream and Future Conservation Recommendations: a Review of the Past 60 Years
Zhang et al.: Ecological effects of the first dam on Yangtze main stream - 2081 - ECOLOGICAL EFFECTS OF THE FIRST DAM ON YANGTZE MAIN STREAM AND FUTURE CONSERVATION RECOMMENDATIONS: A REVIEW OF THE PAST 60 YEARS ZHANG, H.1 – LI, J. Y.1 – WU, J. M.1 – WANG, C. Y.1 – DU, H.1 – WEI, Q. W.1* – KANG, M.2* 1Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China; Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei Province, P. R. China (phone: +86-27-8178-0118; fax: +86-27-8178-0118) 2Department of Maritime Police and Production System / The Institute of Marine Industry, Gyeongsang National University, Cheondaegukchi-Gil 38, Tongyeong-si, Gyeongsangnam-do, 53064, South Korea (phone: +82-55-772-9187; fax: +82-55-772-9189) *Corresponding authors e-mail: [email protected]; [email protected] (Received 21st Jul 2017; accepted 27th Oct 2017) Abstract. The Gezhouba Dam was the first and lowermost dam on the major stem of the Yangtze River. Up to now, the dam has been operating for more than 35 years. The time period was a fast economic development stage in the Yangtze basin. Therefore, the entire Yangtze aquatic ecosystem has been highly affected by various anthropogenic activities. Especially, the fish population and distribution in the Yangtze River have been largely altered. This study reviews the ecological effects of the Gezhouba Dam to the Yangtze aquatic biodiversity for the past 60 years based on literatures. It was concluded that the pre-assessment of the Gezhouba Dam on Yangtze fishes in 1970s was appropriate.