Analysis of Codon Usage Patterns in Giardia Duodenalis Based on Transcriptome Data from Giardiadb
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Insights Into Comparative Genomics, Codon Usage Bias, And
plants Article Insights into Comparative Genomics, Codon Usage Bias, and Phylogenetic Relationship of Species from Biebersteiniaceae and Nitrariaceae Based on Complete Chloroplast Genomes Xiaofeng Chi 1,2 , Faqi Zhang 1,2 , Qi Dong 1,* and Shilong Chen 1,2,* 1 Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; [email protected] (X.C.); [email protected] (F.Z.) 2 Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China * Correspondence: [email protected] (Q.D.); [email protected] (S.C.) Received: 29 October 2020; Accepted: 17 November 2020; Published: 18 November 2020 Abstract: Biebersteiniaceae and Nitrariaceae, two small families, were classified in Sapindales recently. Taxonomic and phylogenetic relationships within Sapindales are still poorly resolved and controversial. In current study, we compared the chloroplast genomes of five species (Biebersteinia heterostemon, Peganum harmala, Nitraria roborowskii, Nitraria sibirica, and Nitraria tangutorum) from Biebersteiniaceae and Nitrariaceae. High similarity was detected in the gene order, content and orientation of the five chloroplast genomes; 13 highly variable regions were identified among the five species. An accelerated substitution rate was found in the protein-coding genes, especially clpP. The effective number of codons (ENC), parity rule 2 (PR2), and neutrality plots together revealed that the codon usage bias is affected by mutation and selection. The phylogenetic analysis strongly supported (Nitrariaceae (Biebersteiniaceae + The Rest)) relationships in Sapindales. Our findings can provide useful information for analyzing phylogeny and molecular evolution within Biebersteiniaceae and Nitrariaceae. -
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. -
Mutation Bias Shapes Gene Evolution in Arabidopsis Thaliana
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.17.156752; this version posted June 18, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Mutation bias shapes gene evolution in Arabidopsis thaliana 1,2† 1 1 3,4 Monroe, J. Grey , Srikant, Thanvi , Carbonell-Bejerano, Pablo , Exposito-Alonso, Moises , 5 6 7 1† Weng, Mao-Lun , Rutter, Matthew T. , Fenster, Charles B. , Weigel, Detlef 1 Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany 2 Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA 3 Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA 4 Department of Biology, Stanford University, Stanford, CA 94305, USA 5 Department of Biology, Westfield State University, Westfield, MA 01086, USA 6 Department of Biology, College of Charleston, SC 29401, USA 7 Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA † corresponding authors: [email protected], [email protected] Classical evolutionary theory maintains that mutation rate variation between genes should be random with respect to fitness 1–4 and evolutionary optimization of genic 3,5 mutation rates remains controversial . However, it has now become known that cytogenetic (DNA sequence + epigenomic) features influence local mutation probabilities 6 , which is predicted by more recent theory to be a prerequisite for beneficial mutation 7 rates between different classes of genes to readily evolve . To test this possibility, we used de novo mutations in Arabidopsis thaliana to create a high resolution predictive model of mutation rates as a function of cytogenetic features across the genome. -
CKI and CKII Mediate the FREQUENCY-Dependent Phosphorylation of the WHITE COLLAR Complex to Close the Neurospora Circadian Negative Feedback Loop
Downloaded from genesdev.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press CKI and CKII mediate the FREQUENCY-dependent phosphorylation of the WHITE COLLAR complex to close the Neurospora circadian negative feedback loop Qun He,1,2 Joonseok Cha,1 Qiyang He,1,3 Heng-Chi Lee,1 Yuhong Yang,1,4 and Yi Liu1,5 1Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; 2State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100094, China The eukaryotic circadian oscillators consist of circadian negative feedback loops. In Neurospora,itwas proposed that the FREQUENCY (FRQ) protein promotes the phosphorylation of the WHITE COLLAR (WC) complex, thus inhibiting its activity. The kinase(s) involved in this process is not known. In this study, we show that the disruption of the interaction between FRQ and CK-1a (a casein kinase I homolog) results in the hypophosphorylation of FRQ, WC-1, and WC-2. In the ck-1aL strain, a knock-in mutant that carries a mutation equivalent to that of the Drosophila dbtL mutation, FRQ, WC-1, and WC-2 are hypophosphorylated. The mutant also exhibits ∼32 h circadian rhythms due to the increase of FRQ stability and the significant delay of FRQ progressive phosphorylation. In addition, the levels of WC-1 and WC-2 are low in the ck-1aL strain, indicating that CK-1a is also important for the circadian positive feedback loops. In spite of its low accumulation in the ck-1aL strain, the hypophosphorylated WCC efficiently binds to the C-box within the frq promoter, presumably because it cannot be inactivated through FRQ-mediated phosphorylation. -
Insights Into the Codon Usage Bias of 13 Severe Acute
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.01.019463; this version posted April 4, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Insights into The Codon Usage Bias of 13 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Isolates from Different Geo- locations Ali Mostafa Anwar *1, Saif M. Khodary 1 1 Department of Genetics, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt *Correspondence: [email protected] Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of Coronavirus disease 2019 (COVID-19) which is an infectious disease that spread throughout the world and was declared as a pandemic by the World Health Organization (WHO). In the present study, we analyzed genome-wide codon usage patterns in 13 SARS-CoV-2 isolates from different geo-locations (countries) by utilizing different CUB measurements. Nucleotide and di-nucleotide compositions displayed bias toward A/U content in all codon positions and CpU-ended codons preference, respectively. Relative Synonymous Codon Usage (RSCU) analysis revealed 8 common putative preferred codons among all the 13 isolates. Interestingly, all of the latter codons are A/U-ended (U-ended: 7, A-ended: 1). Cluster analysis (based on RSCU values) was performed and showed comparable results to the phylogenetic analysis (based on their whole genome sequences) indicating that the CUB pattern may reflect the evolutionary relationship between the tested isolates. -
Codon Usage and Adenovirus Fitness: Implications for Vaccine Development
fmicb-12-633946 February 8, 2021 Time: 11:48 # 1 REVIEW published: 10 February 2021 doi: 10.3389/fmicb.2021.633946 Codon Usage and Adenovirus Fitness: Implications for Vaccine Development Judit Giménez-Roig1, Estela Núñez-Manchón1, Ramon Alemany2, Eneko Villanueva3 and Cristina Fillat1,4,5* 1 Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain, 2 Procure Program, Institut Català d’Oncologia- Oncobell Program, IDIBELL, L’Hospitalet de Llobregat, Barcelona, Spain, 3 Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom, 4 Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain, 5 Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), Barcelona, Spain Vaccination is the most effective method to date to prevent viral diseases. It intends to mimic a naturally occurring infection while avoiding the disease, exposing our bodies to viral antigens to trigger an immune response that will protect us from future infections. Among different strategies for vaccine development, recombinant vaccines are one of the most efficient ones. Recombinant vaccines use safe viral vectors as vehicles and incorporate a transgenic antigen of the pathogen against which we intend to Edited by: Rosa Maria Pintó, generate an immune response. These vaccines can be based on replication-deficient University of Barcelona, Spain viruses or replication-competent viruses. While the most effective strategy involves Reviewed by: replication-competent viruses, they must be attenuated to prevent any health hazard Kai Li, Harbin Veterinary Research Institute, while guaranteeing a strong humoral and cellular immune response. Several attenuation Chinese Academy of Agricultural strategies for adenoviral-based vaccine development have been contemplated over Sciences, China time. -
Chapter 3. the Beginnings of Genomic Biology – Molecular
Chapter 3. The Beginnings of Genomic Biology – Molecular Genetics Contents 3. The beginnings of Genomic Biology – molecular genetics 3.1. DNA is the Genetic Material 3.6.5. Translation initiation, elongation, and termnation 3.2. Watson & Crick – The structure of DNA 3.6.6. Protein Sorting in Eukaryotes 3.3. Chromosome structure 3.7. Regulation of Eukaryotic Gene Expression 3.3.1. Prokaryotic chromosome structure 3.7.1. Transcriptional Control 3.3.2. Eukaryotic chromosome structure 3.7.2. Pre-mRNA Processing Control 3.3.3. Heterochromatin & Euchromatin 3.4. DNA Replication 3.7.3. mRNA Transport from the Nucleus 3.4.1. DNA replication is semiconservative 3.7.4. Translational Control 3.4.2. DNA polymerases 3.7.5. Protein Processing Control 3.4.3. Initiation of replication 3.7.6. Degradation of mRNA Control 3.4.4. DNA replication is semidiscontinuous 3.7.7. Protein Degradation Control 3.4.5. DNA replication in Eukaryotes. 3.8. Signaling and Signal Transduction 3.4.6. Replicating ends of chromosomes 3.8.1. Types of Cellular Signals 3.5. Transcription 3.8.2. Signal Recognition – Sensing the Environment 3.5.1. Cellular RNAs are transcribed from DNA 3.8.3. Signal transduction – Responding to the Environment 3.5.2. RNA polymerases catalyze transcription 3.5.3. Transcription in Prokaryotes 3.5.4. Transcription in Prokaryotes - Polycistronic mRNAs are produced from operons 3.5.5. Beyond Operons – Modification of expression in Prokaryotes 3.5.6. Transcriptions in Eukaryotes 3.5.7. Processing primary transcripts into mature mRNA 3.6. Translation 3.6.1. -
Codon Clusters with Biased Synonymous Codon Usage Represent
bioRxiv preprint doi: https://doi.org/10.1101/530345; this version posted January 25, 2019. 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. 1 Codon clusters with biased synonymous codon usage represent 2 hidden functional domains in protein-coding DNA sequences 3 4 Authors 5 Zhen Peng1*, Yehuda Ben-Shahar1 6 7 Affiliations 8 1Department of Biology, Washington University in St. Louis, MO 63130, USA. 9 *Correspondence to: Zhen Peng ([email protected]). 10 11 Outline 12 1. Abstract 13 2. Introduction 14 3. Results 15 3.1. Identifying putatively functional codon clusters (PFCCs) 16 3.2. Codon usage patterns of PFCCs are diverse 17 3.3. PFCC distribution is not restricted to specific regions of protein-coding sequences 18 3.4. Specific protein functional classes are overrepresented in genes carrying PFCCs while most PFCCs 19 are not associated with known protein domains 20 3.5. Voltage-gated sodium channels include a conserved rare-codon cluster associated with the 21 inactivation gate 22 4. Discussion 23 5. Materials and Methods 24 5.1. Reference genome and data pre-procession Page 1 of 28 bioRxiv preprint doi: https://doi.org/10.1101/530345; this version posted January 25, 2019. 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. 25 5.2. Identifying PFCCs 26 5.3. Calculating TCAI 27 5.4. K-mean clustering of PFCCs 28 5.5. -
"The" Genetic Code?
Evolutionary Anthropology 14:6–11 (2005) CROTCHETS & QUIDDITIES “The” Genetic Code? KENNETH M. WEISS AND ANNE V. BUCHANAN The DNA-based code for protein through messenger and transfer RNA is widely themselves, that carry the informa- regarded as the code of life. But genomes are littered with other kinds of coding tion. elements as well, and all of them probably came after a supercode for the tRNA Your life depends on the fidelity of system itself. these many codes. Aberrant codes re- lated to cell behavior can lead to dys- genesis or various metabolic diseases. Evolution and the diversification of Everyone knows of “the” genetic Anomalous cell-surface proteins can organisms are made possible by code, by which nucleotide triplets in cause autoimmune destruction, and vi- codes, or arbitrary assignments of DNA in the nucleus of cells specify the ruses are the Alan Turings of life that “meaning,” in multiple ways. Many amino acid (aa) sequence of proteins. evolve ways to break their receptor are not widely appreciated. Codes al- This is the code described in text- codes to gain illicit entry into cells (Fig. low the same system of components books as the heart of the genetic the- 1). to be used for multiple purposes. ory of life and its evolution. Discover- But there is an additional code, a These can be open-ended, the way the ies in recent years have made things code of codes, that makes all of this alphabet and vocabulary make this more complicated by showing that ge- possible, including “the” genetic code column possible, but the flexibility of nomes are littered with all sorts of itself, and may be the oldest and most a code can become constrained once a other kinds of coding elements. -
Designing Lentiviral Vectors for Gene Therapy of Genetic Diseases
viruses Review Designing Lentiviral Vectors for Gene Therapy of Genetic Diseases Valentina Poletti 1,2,3,* and Fulvio Mavilio 4 1 Department of Woman and Child Health, University of Padua, 35128 Padua, Italy 2 Harvard Medical School, Harvard University, Boston, MA 02115, USA 3 Pediatric Research Institute City of Hope, 35128 Padua, Italy 4 Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; [email protected] * Correspondence: [email protected] Abstract: Lentiviral vectors are the most frequently used tool to stably transfer and express genes in the context of gene therapy for monogenic diseases. The vast majority of clinical applications involves an ex vivo modality whereby lentiviral vectors are used to transduce autologous somatic cells, ob- tained from patients and re-delivered to patients after transduction. Examples are hematopoietic stem cells used in gene therapy for hematological or neurometabolic diseases or T cells for immunotherapy of cancer. We review the design and use of lentiviral vectors in gene therapy of monogenic diseases, with a focus on controlling gene expression by transcriptional or post-transcriptional mechanisms in the context of vectors that have already entered a clinical development phase. Keywords: lentiviral vectors; transcriptional regulation; post-transcriptional regulation; miRNA; promoters; retroviral integration; ex vivo gene therapy Citation: Poletti, V.; Mavilio, F. 1. Introduction Designing Lentiviral Vectors for Gene Therapy of Genetic Diseases. -
Robust Normalization of Luciferase Reporter Data
Technical Note Robust Normalization of Luciferase Reporter Data Andrea Repele † and Manu * Department of Biology, University of North Dakota, Grand Forks, ND 58202, USA * Correspondence: [email protected] † Current address: JMB—Center for Immunity and Immunotherapies, Seattle Children’s Hospital, Seattle, WA 98105, USA. Received: 17 June 2019; Accepted: 22 July 2019; Published: 25 July 2019 Abstract: Transient Luciferase reporter assays are widely used in the study of gene regulation and intracellular cell signaling. In order to control for sample-to-sample variation in luminescence arising from variability in transfection efficiency and other sources, an internal control reporter is co-transfected with the experimental reporter. The luminescence of the experimental reporter is normalized against the control by taking the ratio of the two. Here we show that this method of normalization, “ratiometric”, performs poorly when the transfection efficiency is low and leads to biased estimates of relative activity. We propose an alternative methodology based on linear regression that is much better suited for the normalization of reporter data, especially when transfection efficiency is low. We compare the ratiometric method against three regression methods on both simulated and empirical data. Our results suggest that robust errors-in-variables (REIV) regression performs the best in normalizing Luciferase reporter data. We have made the R code for Luciferase data normalization using REIV available on GitHub. Keywords: luciferase reporter; transfection efficiency; normalization; gene regulation; promoter; enhancer 1. Introduction Transient reporter assays are an important and widely used tool in the study of gene regulation [1–4], intracellular cell signaling [5–7], and other areas of molecular, cellular, and developmental biology [8–10]. -
Pressure Accelerates the Circadian Clock of Cyanobacteria
www.nature.com/scientificreports OPEN Pressure accelerates the circadian clock of cyanobacteria Ryo Kitahara 1,2, Katsuaki Oyama2, Takahiro Kawamura2, Keita Mitsuhashi2, Soichiro Kitazawa1, Kazuhiro Yasunaga1, Natsuno Sagara1, Megumi Fujimoto2 & Kazuki Terauchi2,3 Received: 12 April 2019 Although organisms are exposed to various pressure and temperature conditions, information remains Accepted: 7 August 2019 limited on how pressure afects biological rhythms. This study investigated how hydrostatic pressure Published: xx xx xxxx afects the circadian clock (KaiA, KaiB, and KaiC) of cyanobacteria. While the circadian rhythm is inherently robust to temperature change, KaiC phosphorylation cycles that were accelerated from 22 h at 1 bar to 14 h at 200 bars caused the circadian-period length to decline. This decline was caused by the pressure-induced enhancement of KaiC ATPase activity and allosteric efects. Because ATPase activity was elevated in the CI and CII domains of KaiC, while ATP hydrolysis had negative activation volumes (ΔV≠), both domains played key roles in determining the period length of the KaiC phosphorylation cycle. The thermodynamic contraction of the structure of the active site during the transition state might have positioned catalytic residues and lytic water molecules favourably to facilitate ATP hydrolysis. Internal cavities might represent sources of compaction and structural rearrangement in the active site. Overall, the data indicate that pressure diferences could alter the circadian rhythms of diverse organisms with evolved thermotolerance, as long as enzymatic reactions defning period length have a specifc activation volume. Circadian rhythms are endogenous timing systems that induce the circadian clock, resulting in numerous organisms, from cyanobacteria to higher animals, being adapted to the day-night cycle1,2.