Biochemistry Commons^™

Pharmacological Correction Of Obesity-Induced Autophagy Arrest Using Calcium Channel Blockers, Hwan-Woo Park, Haeli Park, Ian A. Semple, Insook Jang, Seung-Hyun Ro, Myungjin Kim, Victor A. Cazares, Edward L. Stuenkel, Jung-Jae Kim, Jeong Sig Kim, Jun Hee Lee

Department of Biochemistry: Faculty Publications

Autophagy deregulation during obesity contributes to the pathogenesis of diverse metabolic disorders. However, without understanding the molecular mechanism of obesity interference in autophagy, development of therapeutic strategies for correcting such defects in obese individuals is challenging. Here we show that a chronic increase of the cytosolic calcium concentration in hepatocytes during obesity and lipotoxicity attenuates autophagic flux by preventing the fusion between autophagosomes and lysosomes. As a pharmacological approach to restore cytosolic calcium homeostasis in vivo, we administered the clinically approved calcium channel blocker verapamil to obese mice. Such treatment successfully increases autophagosome–lysosome fusion in liver, preventing accumulation of …

Hepatoprotective Role Of Sestrin2 Against Chronic Er Stress, Hwan-Woo Park, Haeli Park, Seung-Hyun Ro, Insook Jang, Ian A. Semple, David N. Kim, Myungjin Kim, Myeongjin Nam, Deqiang Zhang, Lei Yin, Jun Hee Lee

Department of Biochemistry: Faculty Publications

Upon prolonged endoplasmic reticulum (ER) stress, cells attenuate protein translation to prevent accumulation of unfolded proteins. Here we show that Sestrin2 is critical for this process. Sestrin2 expression is induced by an ER stress-activated transcription factor CCAATenhancer- binding protein beta (c/EBPβ). Once induced, Sestrin2 halts protein synthesis by inhibiting mammalian target of rapamycin complex 1 (mTORC1). As Sestrin2-deficient cells continue to translate a large amount of proteins during ER stress, they are highly susceptible to ER stress-associated cell death. Accordingly, dietary or genetically induced obesity, which does not lead to any pathological indication other than simple fat accumulation in the …

Evaluations Of A Mechanistic Hypothesis For The Influence Of Extracellular Ions On Electroporation Due To High-Intensity, Nanosecond Pulsing, V. Sridhara, R. P. Joshi

Electrical & Computer Engineering Faculty Publications

The effect of ions present in the extracellular medium on electroporation by high-intensity, short-duration pulsing is studied through molecular dynamic simulations. Our simulation results indicate that mobile ions in the medium might play a role in creating stronger local electric fields across membranes that then reinforce and strengthen electroporation. Much faster pore formation is predicted in higher conductivity media. However, the impact of extracellular conductivity on cellular inflows, which depend on transport processes such as electrophoresis, could be different as discussed here. Our simulation results also show that interactions between cations (Na+ in this case) and the carbonyl oxygen of …

The Effects Of Salinity, Ph, Temperature, And Dissolved Oxygen On Sensitivity Of Pcr Identification Of T4 Bacteriophage, Joesph F. Cannon, Nicholas A. Thurn, Paul E. Richardson

Journal of the South Carolina Academy of Science

Bacteriophages are used as indicators of pathogenic bacteria in drinking, and wastewaters. They also show potential in limiting aquatic bacterial populations through their lytic properties. The effect of different water characteristics (salinity, pH, dissolved oxygen, and temperature) on the sensitivity of the PCR identification of virus particles were analyzed to determine at what levels bacteriophage can be detected in environmental samples. Results from this preliminary study indicate that a PCR bacteriophage detection technique has potential as a relatively efficient and economical indicator of coliform contamination in multiple aquatic environments. While further evaluation is needed, the protocol appears to function in …

Biochemical Assay Optimization And Computational Screening Efforts To Identify Potential Luxs Inhibitors, Keeshia Q. Wang

Master's Theses

Quorum sensing (QS) is a process of coordination of bacterial gene expression in response to cell population. System two QS is regulated by the small signaling molecule autoinducer-2 (AI-2) and is implicated in the infectious behaviors of various bacterial species. AI-2 is biosynthesized from S-ribosylhomocysteine (SRH) by the enzyme LuxS and induces interspecies cell-to-cell communication. Inhibition of LuxS would therefore inhibit interspecies QS. Herein, a search for novel molecular species that will competitively bind with SRH in the LuxS binding site is performed in silico. Computational screening results are then validated in vitro using an optimized LuxS inhibition …

Mutational Analysis Of The Rotavirus Nsp4 Enterotoxic Domain That Binds To Caveolin-1, Judith M. Ball, Megan E. Schroeder, Cecelia V. Williams, Friedhelm Schroeder, Rebecca D. Parr

Faculty Publications

Background: Rotavirus (RV) nonstructural protein 4 (NSP4) is the first described viral enterotoxin, which induces early secretory diarrhea in neonatal rodents. Our previous data show a direct interaction between RV NSP4 and the structural protein of caveolae, caveolin-1 (cav-1), in yeast and mammalian cells. The binding site of cav-1 mapped to the NSP4 amphipathic helix, and led us to examine which helical face was responsible for the interaction.

Methods: A panel of NSP4 mutants were prepared and tested for binding to cav-1 by yeast two hybrid and direct binding assays. The charged residues of the NSP4 amphipathic helix were changed …

Development Of A Metabolomic Method To Define The Phenylalanome In Arabidopsis Thaliana, Cole G. Wunderlich, Clint Chapple, Xu Li

The Summer Undergraduate Research Fellowship (SURF) Symposium

In the study of metabolomics, one of the greatest challenges can be accurately identifying compounds detected in biological extracts, especially when standards are not readily available. Current metabolomic methods are also limited in that they provide little to no information about a compound’s metabolic origin. In this study, we sought to address these issues by developing a novel metabolomic method that employs stable isotope feeding, LC-MS, Xcms, and an analytical software algorithm to study the ‘phenylalanome’ of Arabidopsis thaliana. Using this approach we were able to develop a method that, based on current results, is capable of detecting over …

The Creation Of Α2nc1 Transgenic Drosophila Melanogaster, Jordan Olberding

Mahurin Honors College Capstone Experience/Thesis Projects

The α2 isoform of collagen IV’s noncollagenous 1 domain (α2NC1 or canstatin) has shown promise as an anti-cancer molecule, possessing both angiostatic and pro-apoptotic properties. This work aims to further the knowledge of α2NC1 by conducting a truly in vivo study in which the Gal4-induced endogenous overexpression of α2NC1 in Drosophila melanogaster will be used to assess the effects of α2NC1 upon normal development as well as tumorigenesis. To this end, transgenic fly lines capable of overexpressing α2NC1 were created. Initial overexpression studies indicated no developmental phenotype was caused by abundance of α2NC1. However, future overexpression studies in which α2NC1 …

Preservation Of Biosignature Molecules In Potential Sample Return Container Of The Mars 2020 Mission, Kimberly E. Lykens, Fei Chen Ph.D

STAR Program Research Presentations

Preservation of Biosignature Molecules in Potential Sample Return Container of the Mars 2020 Mission

Kimberly Lykens¹ and Fei Chen²

¹Wittenberg University, Springfield, Ohio 45501 ²Jet Propulsion Laboratory, Pasadena, California, 91109

One requirement for sustainable life on terrestrial planets includes the presence of organic polymers, compounds that are essential for major biological functions such as replication and catalysis. An identified goal of the Mars mission in the year 2020 is to implement a sample-return to identify and validate signs of life on Mars through the discovery of biosignature molecules in Martian core samples. Martian core samples recovered …

Cytochrome B5 Reductase Encoded By Cbr1 Is Essential For A Functional Male Gametophyte In Arabidopsis, Laura L. Wayne, James G. Wallis, Rajesh Kumar, Jennifer E. Markham, John Browse

Department of Biochemistry: Faculty Publications

In all eukaryotes, NADH:cytochrome b5 reductase provides electrons, via cytochrome b5, for a range of biochemical reactions in cellular metabolism, including for fatty acid desaturation in the endoplasmic reticulum. Studies in mammals, yeast, and in vitro plant systems have shown that cytochrome b5 can, at least in some circumstances, also accept electrons from NADPH:cytochrome P450 reductase, potentially allowing for redundancy in reductase function. Here, we report characterization of three T-DNA insertional mutants of the gene encoding cytochrome b5 reductase in Arabidopsis thaliana, CBR1. The progeny of plants heterozygous for the cbr1-2 allele segregated 6% homozygous mutants, while cbr1-3 and cbr1-4 …

Influence Of Media Composition On The Growth Rate Of Chlorella Vulgaris And Scenedesmus Acutus Utilized For Co2 Mitigation, Czarena L. Crofcheck, Xinyi E, Aubrey Shea, Michael D. Montross, Mark Crocker, Rodney Andrews

Biosystems and Agricultural Engineering Faculty Publications

Atmospheric carbon dioxide levels have increased since the industrial revolution due to increasing combustion of fossil fuels. One possible CO₂ mitigation strategy is the use of microalgae for mitigation of CO₂. This paper focuses on the influence of media composition on the growth rate of two microalgae strains, Chlorella vulgaris and Scenedesmus actus. A KNO₃ based medium was found to work better for Chlorella, while a urea based equivalent worked better for Scenedesmus. The urea based media investigated here resulted in growth similar to that found with previously reported KNO₃ based media. …

Diversity Of Plant Methionine Sulfoxide Reductases B And Evolution Of A Form Specific For Free Methionine Sulfoxide, Dung Tien Le, Lionel Tarrago, Yasuko Watanabe, Alaattin Kaya, Byung Cheon Lee, Uyen Tran, Rie Nishiyama, Dmitri E. Fomenko, Vadim N. Gladyshev, Lam-Son Phan Tran

Department of Biochemistry: Faculty Publications

Methionine can be reversibly oxidized to methionine sulfoxide (MetO) under physiological conditions. Organisms evolved two distinct methionine sulfoxide reductase families (MSRA & MSRB) to repair oxidized methionine residues. We found that 5 MSRB genes exist in the soybean genome, including GmMSRB1 and two segmentally duplicated gene pairs (GmMSRB2 and GmMSRB5, GmMSRB3 and GmMSRB4). GmMSRB2 and GmMSRB4 proteins showed MSRB activity toward protein-based MetO with either DTT or thioredoxin (TRX) as reductants, whereas GmMSRB1 was active only with DTT. GmMSRB2 had a typical MSRB mechanism with Cys121 and Cys 68 as catalytic and resolving residues, respectively. Surprisingly, this enzyme also possessed …

Validation Of Antibodies Used To Study Hypoxia Inducible Factors In Two Species Of Fundulus, Jenna D. Hill

LSU New Orleans Theses and Dissertations

Hypoxia inducible factors (HIFs) are transcription factors and the master regulators of oxygen-dependent gene expression in animals. The focus of this thesis is the distribution of HIF protein in tissues of the fish Fundulus heteroclitus and F. grandis, two widespread species that occur in naturally hypoxic waters. Polyclonal antibodies against HIF-1α, HIF-2α, and HIF-3α were tested on proteins made in vitro and on extracts made from several tissues of normoxic and hypoxic fish. Antibodies against HIF-1α and 3α bound specifically to full length protein made in vitro, and produced bands on western blots of nuclear extracts of near …

Regulation Of The Target Of Rapamycin Signaling Pathway In Saccharomyces Cerevisiae, Tammy Pracheil

LSU New Orleans Theses and Dissertations

An integrative, biochemical, genetic, and molecular biology approach utilizing gene manipulation, gene knock outs, plasmid based protein expression, and in vivo protein localization of fluorescence tagged proteins was employed to determine the function of an essential protein, Lst8, in TORC1 and TORC2 signaling and a previously uncharacterized complex, the Far3-7-8-9-10-11 complex (Far complex) in the budding yeast, Saccharomyces cerevisiae. Mutations in SAC7 and FAR11 suppressed lethality of both lst8 and tor2-21 mutations but not TORC1 inactivation, suggesting that the essential function of Lst8 is linked only to TORC2.

Far11, a component of a six-member complex, was found to interact …

Aerobic Degradation Of Α-, Β-, Γ-Hexachlorocyclohexane By Narragansett Bay Bacterioplankton, Ian M. Rambo

Senior Honors Projects

Hexachlorocyclohexanes (HCHs) are a family of chlorinated organic compounds that were previously used as agricultural insecticides. HCHs are recognized as persistent organic pollutants due to their toxicity, recalcitrant properties, and tendency to bioaccumulate in food webs. Although HCH was first synthesized in 1825, its use was not widespread until the discovery of the insecticidal activity of the γ-HCH isomer in 1942. γ-HCH and its toxic waste isomers α-HCH and β-HCH were banned from production and use by the United Nations in 2009, yet these chemicals still present environmental problems due to their persistence in soils and surface waters. HCHs continue …

A Cell Simulator Platform: The Cell Collective, Tomáš Helikar, B. Kowal, J. A. Rogers

Department of Biochemistry: Faculty Publications

Diseases are often a result of multiple malfunctions in complex, nonlinear biological/biochemical networks. As such, these processes are far more complicated to understand because they tend to give rise to functions that are emergent in nature, i.e., higher-level (mal)functions that are more than the sum of their parts. Systems biology provides a new approach to understanding biological systems and diseases from a holistic perspective.

Expression, Production, And Purification Of Novel Therapeutic Proteins, Mckinzie Shea Fruchtl

Graduate Theses and Dissertations

Interest in the production of recombinant proteins consisting of collagen binding domain (CBD) fused to a bioactive material has increased due to the targeting/attachment capabilities of CBD. For example, CBD fusions can be applied to the reversing of bone density loss and the repair of the eardrum, specifically, by choosing an appropriate fusion partner (parathyroid hormone or epidermal growth factor). The production of CBD fusions was examined using batch and fed-batch culturing of Escherichia coli to express the fusion proteins, and affinity chromatography to isolate the final product.

Different medium formulations, feeding strategies, and induction methods were tested in order …

Disocvering Ionic Liquid Resistant Genes, Bree Person, Douglass Higgins, Michael Thelen

STAR Program Research Presentations

: Plant biomass is a rich source of sugars that can be converted to biofuels by engineered microbes. However, because the lignocellulose in biomass is insoluble in aqueous conditions and recalcitrant to enzymatic degradation, thermochemical treatment is required to break apart the lignin and cellulose polymers before sugars can be released. The most effective chemicals for doing this are known as ionic liquids, which are salts that are molten at temperatures below 100° C. Although these solvents have many unique properties that are ideal for solubilizing lignocellulose, they have been found to inhibit the growth of bacterial strains used to …

Proline Mechanisms Of Stress Survival, Xinwen Liang, Lu Zhang, Sathish Kumar Natarajan, Donald F. Becker

Department of Biochemistry: Faculty Publications

Significance: The imino acid proline is utilized by different organisms to offset cellular imbalances caused by environmental stress. The wide use in nature of proline as a stress adaptor molecule indicates that proline has a fundamental biological role in stress response. Understanding the mechanisms by which proline enhances abiotic/biotic stress response will facilitate agricultural crop research and improve human health. Recent Advances: It is now recognized that proline metabolism propels cellular signaling processes that promote cellular apoptosis or survival. Studies have shown that proline metabolism influences signaling pathways by increasing reactive oxygen species (ROS) formation in the mitochondria …

Comparative Metabolic Profiling Of Haberlea Rhodopensis, Thellungiella Halophyla, And Arabidopsis Thaliana Exposed To Low Temperature, Maria Benina, Toshihiro Obata, Nikolay Mehterov, Ivan Ivanov, Veselin Petrov, Valentina Toneva, Alisdair R. Fernie, Tsanko S. Gechev

Department of Biochemistry: Faculty Publications

Haberlea rhodopensis is a resurrection species with extreme resistance to drought stress and desiccation but also with ability to withstand low temperatures and freezing stress. In order to identify biochemical strategies which contribute to Haberlea's remarkable stress tolerance, the metabolic reconfiguration of H. rhodopensis during low temperature (4^◦C) and subsequent return to optimal temperatures (21^◦C) was investigated and compared with that of the stress tolerant Thellungiella halophyla and the stress sensitive Arabidopsis thaliana. Metabolic analysis by GC-MS revealed intrinsic differences in the metabolite levels of the three species even at 21^◦C. H. rhodopensis …

The Hyaluronan Receptor For Endocytosis (Hare) Activates Nf-Κb-Mediated Gene Expression In Response To 40–400-Kda, But Not Smaller Or Larger, Hyaluronans, Madhu S. Pandey, Bruce A. Baggenstoss, Jennifer Washburn, Edward N. Harris, Paul H. Weigel

Department of Biochemistry: Faculty Publications

Background: HARE mediates systemic clearance of hyaluronan (HA), which turns over continuously in tissues.

Results: HARE uptake of 40–400-kDa, but not larger or smaller, HA stimulated NF-κB activation.

Conclusion: HA-HARE signal complexes activate NF-κB and gene transcription only with optimally sized HA.

Significance: HARE responsiveness to a narrow size range ofHAdegradation products may be a sensing system to detect tissue ECM stress.

Towards Elucidation Of A Viral Dna Packaging Motor, Chad T. Schwartz

Theses and Dissertations--Pharmacy

Previously, gp16, the ATPase protein of phi29 DNA packaging motor, was an enigma due to its tendency to form multiple oligomeric states. Recently we employed new methodologies to decipher both its stoichiometry and also the mechanism in which the protein functions to hydrolyze ATP and provide the driving force for DNA packaging. The oligomeric states were determined by biochemical and biophysical approaches. Contrary to many reported intriguing models of viral DNA packaging, it was found that phi29 DNA packaging motor permits the translocation of DNA unidirectionally and driven cooperatively by three rings of defined shape. The mechanism for the generation …

A Comprehensive, Multi-Scale Dynamical Model Of Erbb Receptor Signal Transduction In Human Mammary Epithelial Cells, Tomáš Helikar, Naomi Kochi, Bryan Kowal, Manjari Dimri, Mayumi Naramura, Srikumar M. Raja, Vimla Band, Hamid Band, Jim A. Rogers

Department of Biochemistry: Faculty Publications

The non-receptor tyrosine kinase Src and receptor tyrosine kinase epidermal growth factor receptor (EGFR/ErbB1) have been established as collaborators in cellular signaling and their combined dysregulation plays key roles in human cancers, including breast cancer. In part due to the complexity of the biochemical network associated with the regulation of these proteins as well as their cellular functions, the role of Src in EGFR regulation remains unclear. Herein we present a new comprehensive, multi-scale dynamical model of ErbB receptor signal transduction in human mammary epithelial cells. This model, constructed manually from published biochemical literature, consists of 245 nodes representing proteins …

Functional Convergence Of Structurally Distinct Thioesterases From Cyanobacteria And Plants Involved In Phylloquinone Biosynthesis, Fabienne Furt, William J. Allen, Joshua R. Widhalm, Peter Madzelan, Robert C. Rizzo, Gilles J. Basset, Mark A. Wilson

Department of Biochemistry: Faculty Publications

The synthesis of phylloquinone (vitamin K₁) in photosynthetic organisms requires a thioesterase that hydrolyzes 1,4-dihydroxy- 2-naphthoyl-CoA (DHNA-CoA) to release 1,4- dihydroxy-2-naphthoate (DHNA). Cyanobacteria and plants contain distantly related hotdog-fold thioesterases that catalyze this reaction, although the structural basis of these convergent enzymatic activities is unknown. To investigate this, the crystal structures of hotdog-fold DHNA-CoA thioesterases from the cyanobacterium Synechocystis (Slr0204) and the flowering plant Arabidopsis thaliana (AtDHNAT1) were determined. These enzymes form distinct homotetramers and use different active sites to catalyze hydrolysis of DHNACoA, similar to the 4-hydroxybenzoyl-CoA (4-HBA-CoA) thioesterases from Pseudomonas and Arthrobacter. Like the 4-HBA-CoA …

Rapid Detection And Quantification Of Triacylglycerol By Hplc–Elsd In Chlamydomonas Reinhardtii And Chlorella Strains, Naoko Kobayashi, Eric A. Noel, Austin Barnes, Julian Rosenberg, Concetta C. Dirusso, Paul N. Black, George A. Oyler

Department of Biochemistry: Faculty Publications

Triacylglycerol (TAG) analysis and quantification are commonly performed by first obtaining a purified TAG fraction from a total neutral lipid extract using thinlayer chromatography (TLC), and then analyzing the fatty

acid composition of the purified TAG fraction by gas chromatography (GC). This process is time-consuming, labor

intensive and is not suitable for analysis of small sample sizes or large numbers. A rapid and efficient method for monitoring oil accumulation in algae using high performance liquid chromatography for separation of all lipid classes combined with detection by evaporative light scattering (HPLC–ELSD) was developed and compared to the conventional TLC/GC method. TAG …

Probing Arabidopsis Chloroplast Diacylglycerol Pools By Selectively Targeting Bacterial Diacylglycerol Kinase To Suborganellar Membranes, Bagyalakshmi Muthan, Rebecca Roston, John E. Froehlich, Christoph Benning

Department of Biochemistry: Faculty Publications

Diacylglycerol (DAG) is an intermediate in metabolism of both triacylglycerols and membrane lipids. Probing the steady-state pools of DAG and understanding how they contribute to the synthesis of different lipids is important when designing plants with altered lipid metabolism. However, traditional methods of assaying DAG pools are difficult, because its abundance is low and because fractionation of subcellular membranes affects DAG pools. To manipulate and probe DAG pools in an in vivo context, we generated multiple stable transgenic lines of Arabidopsis (Arabidopsis thaliana) that target an Escherichia coli DAGkinase (DAGK) to each leaflet of each chloroplast envelope membrane. …

Reporters For The Analysis Of N-Glycosylation In Candida Albicans, Shahida Shahana, Hector M. Mora-Montes, Luis Castillo, Iryna Bohovych, Chirag C. Sheth, Frank C. Odds, Neil A.R. Gow, Alistair J.P. Brown

Department of Biochemistry: Faculty Publications

A large proportion of Candida albicans cell surface proteins are decorated post-translationally by glycosylation. Indeed N-glycosylation is critical for cell wall biogenesis in this major fungal pathogen and for its interactions with host cells. A detailed understanding of N-glycosylation will yield deeper insights into host-pathogen interactions. However, the analysis of N-glycosylation is extremely challenging because of the complexity and heterogeneity of these structures. Therefore, in an attempt to reduce this complexity and facilitate the analysis of N-glycosylation, we have developed new synthetic C. albicans reporters that carry a single N-linked glycosylation site derived from Saccharomyces cerevisiae Suc₂. These …

Microrna Function In Human Diseases, Sathish Kumar Natarajan, Mary Anne Smith, Cody J. Wehrkamp, Ashley M. Mohr, Justin L. Mott

Department of Biochemistry: Faculty Publications

MicroRNAs are emerging as a hot topic in research, and rightfully so. They show great promise as targets of treatment and as markers for common human diseases, such as cancer and metabolic diseases. In this review, we address some of the basic questions regarding micro- RNA function in human disease and the clinical significance of microRNAs. Specifically, micro- RNAs in epigenetics, cancer, and metabolic diseases are discussed, with examples taken from cholangiocarcinoma and nonalcoholic fatty liver disease.

Sbml Qualitative Models: A Model Representation Format And Infrastructure To Foster Interactions Between Qualitative Modelling Formalisms And Tools, Claudine Chaouiya, Duncan Bérenguier, Sarah M. Keating, Aurélien Naldi, Martijn P. Van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan Kowal, Benjamin Wicks, Emanuel Gonçalves, Julien Dorier, Michel Page, Pedro T. Monteiro, Axel Von Kamp, Ioannis Xenarios, Hidde De Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomáš Helikar

Department of Biochemistry: Faculty Publications

Background: Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, and that they are well-suited for studies of large networks. While numerous groups have developed specific computational tools that provide original methods to analyse qualitative models, a standard format to exchange qualitative models has been missing.

Results: We present the Systems Biology Markup Language (SBML) Qualitative Models Package (“qual”), an extension of the SBML Level 3 standard designed for computer representation of qualitative …

Selenodb 2.0: Annotation Of Selenoprotein Genes In Animals And Their Genetic Diversity In Humans, Frederic Romagne, Didac Santesmasses, Louise White, Gaurab K. Sarangi, Marco Mariotti, Ron Hübler, Antje Weihmann, Genis Parra, Vadim N. Gladyshev, Roderic Guigo, Sergi Castellano

Department of Biochemistry: Faculty Publications

SelenoDB (http://www.selenodb.org) aims to provide high-quality annotations of selenoprotein genes, proteins and SECIS elements. Selenoproteins are proteins that contain the amino acid selenocysteine (Sec) and the first release of the database included annotations for eight species. Since the release of SelenoDB 1.0 many new animal genomes have been sequenced. The annotations of selenoproteins in new genomes usually contain many errors in major databases. For this reason, we have now fully annotated selenoprotein genes in 58 animal genomes. We provide manually curated annotations for human selenoproteins, whereas we use an automatic annotation pipeline to annotate selenoprotein genes in other animal genomes. …