scholarly journals Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 963
Author(s):  
Friedhelm Pfeiffer ◽  
Mike Dyall-Smith
Keyword(s):  
Protein Function ◽  
Halophilic Archaea ◽  
Haloferax Volcanii ◽  
Background Information ◽  
Strong Focus ◽  
Correct Function ◽  
Key Aspects ◽  
Species Being ◽  
Annotation Errors ◽  
Function Assignment

Background: Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases, the enzymes cannot be isofunctional. Here, we examined a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeon Haloferax volcanii. Results: Annotated proteins of Hfx. volcanii were identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence, but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We listed 50 of those cases, each with detailed background information, so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only the key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Materials. Conclusions: Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to systematically confirm (or disprove) our function predictions or to uncover yet more unexpected functions.

scholarly journals Open issues for protein function assignment in Haloferax volcanii and other halophilic archaea

2021 ◽  
Author(s):  
Friedhelm Pfeiffer ◽  
Mike Dyall-Smith
Keyword(s):  
Protein Function ◽  
Halophilic Archaea ◽  
Haloferax Volcanii ◽  
Background Information ◽  
Strong Focus ◽  
Correct Function ◽  
Key Aspects ◽  
Species Being ◽  
Annotation Errors ◽  
Function Assignment

Background: Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases the enzymes cannot be isofunctional. Here, we examine a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeon Haloferax volcanii. Results: Annotated proteins of Hfx. volcanii were identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We list 50 of those cases, each with detailed background information so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Material. Conclusions: Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to sytematically confirm (or disprove) our function predictions or to uncover yet unexpected functions.

Development and Application of a Simulation Tool for Biomass Gasification Based Processes

2008 ◽  
Vol 6 (1) ◽  
Author(s):  
Tobias Pröll ◽  
Hermann Hofbauer
Keyword(s):  
Background Information ◽  
Simulation Tool ◽  
Water Steam ◽  
Organic Mixtures ◽  
Ideal Gases ◽  
Dual Fluidized Bed ◽  
Modelling Environment ◽  
Model Equations ◽  
Key Aspects ◽  
Energy Balances

A simulation tool for gasification based processes is presented for an equation-oriented, steady state modelling environment. The approach aims at an adequate description of phenomena linked to gasification. Background information is provided regarding the structure of the framework, thermodynamic data processing, and on the formulation of the model equations. The implemented substance streams are water/steam, ideal gases, inorganic solids, and organic mixtures. The models are based upon mass and energy balances and feature thermodynamic considerations. The addition of correlations for fluid dynamics or chemical kinetics is generally possible but not within the focus of this paper. The key-aspects of the typical unit-models, like pumps, turbines, heat exchangers, separators and chemical reactors are highlighted. The model of a dual-fluidized bed biomass gasifier is presented in detail. In a final case study, the suitability of the simulation tool is demonstrated for the description of the gasification-based biomass combined heat and power plant in Güssing/Austria.

scholarly journals A Computational Strategy for Protein Function Assignment which Addresses the Multidomain Problem

2002 ◽  
Vol 3 (5) ◽  
pp. 423-440 ◽  
Author(s):  
A. J. Pérez ◽  
A. Rodríguez ◽  
O. Trelles ◽  
G. Thode
Keyword(s):  
Protein Function ◽  
Sequence Similarity ◽  
Protein Database ◽  
Specific Sequence ◽  
Functional Annotations ◽  
Cluster Set ◽  
Sequence Position ◽  
Computational Strategy ◽  
Function Assignment

A method for assigning functions to unknown sequences based on finding correlations between short signals and functional annotations in a protein database is presented. This approach is based on keyword (KW) and feature (FT) information stored in the SWISS-PROT database. The former refers to particular protein characteristics and the latter locates these characteristics at a specific sequence position. In this way, a certain keyword is only assigned to a sequence if sequence similarity is found in the position described by the FT field. Exhaustive tests performed over sequences with homologues (cluster set) and without homologues (singleton set) in the database show that assigning functions is much ’cleaner’ when information about domains (FT field) is used, than when only the keywords are used.

scholarly journals Molecular Factors of Hypochlorite Tolerance in the Hypersaline Archaeon Haloferax volcanii

Genes ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 562 ◽  
Author(s):  
Miguel Gomez ◽  
Whinkie Leung ◽  
Swathi Dantuluri ◽  
Alexander Pillai ◽  
Zyan Gani ◽  
...  
Keyword(s):  
Hypochlorous Acid ◽  
Insertion Site ◽  
Model Organism ◽  
Halophilic Archaea ◽  
Haloferax Volcanii ◽  
Polyamine Biosynthesis ◽  
Active Compounds ◽  
Redox Active ◽  
High Concentrations ◽  
High Doses

Halophilic archaea thrive in hypersaline conditions associated with desiccation, ultraviolet (UV) irradiation and redox active compounds, and thus are naturally tolerant to a variety of stresses. Here, we identified mutations that promote enhanced tolerance of halophilic archaea to redox-active compounds using Haloferax volcanii as a model organism. The strains were isolated from a library of random transposon mutants for growth on high doses of sodium hypochlorite (NaOCl), an agent that forms hypochlorous acid (HOCl) and other redox acid compounds common to aqueous environments of high concentrations of chloride. The transposon insertion site in each of twenty isolated clones was mapped using the following: (i) inverse nested two-step PCR (INT-PCR) and (ii) semi-random two-step PCR (ST-PCR). Genes that were found to be disrupted in hypertolerant strains were associated with lysine deacetylation, proteasomes, transporters, polyamine biosynthesis, electron transfer, and other cellular processes. Further analysis revealed a ΔpsmA1 (α1) markerless deletion strain that produces only the α2 and β proteins of 20S proteasomes was hypertolerant to hypochlorite stress compared with wild type, which produces α1, α2, and β proteins. The results of this study provide new insights into archaeal tolerance of redox active compounds such as hypochlorite.

Dizziness

2021 ◽  
Author(s):  
Kevin A. Kerber ◽  
Robert W. Baloh
Keyword(s):  
Vestibular System ◽  
Clinical Medicine ◽  
Background Information ◽  
History Taking ◽  
Symptom Presentation ◽  
Anatomy And Physiology ◽  
Common Causes ◽  
History Of ◽  
Specific Disorders ◽  
Key Aspects

Dizziness is the quintessential symptom presentation in all of clinical medicine. It is a common reason that patients present to a physician. This chapter provides background information about the vestibular system, then reviews key aspects of history-taking and examination of the patient, then discusses specific disorders and common presentation types. Throughout the chapter the focus is on neurologic and vestibular disorders. Normal vestibular anatomy and physiology are discussed, followed by recommendations for history-taking and the physical examination. Specific disorders that cause dizziness are explored, along with common causes of non-specific dizziness. Common presentations are discussed, including acute severe dizziness, recurrent attacks, and recurrent positional vertigo. Finally, the chapter looks at laboratory investigations in diagnosis and management. Figures include population prevalence of dizziness symptoms, the anatomy of inner structures, primary afferent vestibular nerve activity, the head thrust test, the Dix-Hallpike maneuver, the supine positional test, the canalith repositioning procedure, and the barbecue roll maneuver. Tables list physiologic properties and clinical features of the components of the peripheral vestibular system, information to be acquired from history of the present illness, common symptoms patients report as dizziness, examination components, distinguishing among common peripheral and central vertigo syndromes, common causes of nonspecific dizziness, types of dizziness presentations, relevant imaging abnormalities on neuroimaging studies, vestibular testing components, and medical therapy for symptomatic dizziness. This review contains 8 highly rendered figures, 11 tables, and 69 references.

Dizziness

2021 ◽  
Author(s):  
Kevin A. Kerber ◽  
Robert W. Baloh
Keyword(s):  
Vestibular System ◽  
Clinical Medicine ◽  
Background Information ◽  
History Taking ◽  
Symptom Presentation ◽  
Anatomy And Physiology ◽  
Common Causes ◽  
History Of ◽  
Specific Disorders ◽  
Key Aspects

Dizziness is the quintessential symptom presentation in all of clinical medicine. It is a common reason that patients present to a physician. This chapter provides background information about the vestibular system, then reviews key aspects of history-taking and examination of the patient, then discusses specific disorders and common presentation types. Throughout the chapter the focus is on neurologic and vestibular disorders. Normal vestibular anatomy and physiology are discussed, followed by recommendations for history-taking and the physical examination. Specific disorders that cause dizziness are explored, along with common causes of non-specific dizziness. Common presentations are discussed, including acute severe dizziness, recurrent attacks, and recurrent positional vertigo. Finally, the chapter looks at laboratory investigations in diagnosis and management. Figures include population prevalence of dizziness symptoms, the anatomy of inner structures, primary afferent vestibular nerve activity, the head thrust test, the Dix-Hallpike maneuver, the supine positional test, the canalith repositioning procedure, and the barbecue roll maneuver. Tables list physiologic properties and clinical features of the components of the peripheral vestibular system, information to be acquired from history of the present illness, common symptoms patients report as dizziness, examination components, distinguishing among common peripheral and central vertigo syndromes, common causes of nonspecific dizziness, types of dizziness presentations, relevant imaging abnormalities on neuroimaging studies, vestibular testing components, and medical therapy for symptomatic dizziness. This review contains 8 highly rendered figures, 11 tables, and 69 references.

scholarly journals Morphological Stasis and Proteome Innovation in Cephalochordates

Genes ◽  
2018 ◽  
Vol 9 (7) ◽  
pp. 353 ◽  
Author(s):  
László Bányai ◽  
Krisztina Kerekes ◽  
Mária Trexler ◽  
László Patthy
Keyword(s):  
Morphological Evolution ◽  
Gene Prediction ◽  
Domain Architecture ◽  
Morphological Stasis ◽  
Branchiostoma Belcheri ◽  
Branchiostoma Lanceolatum ◽  
The Given ◽  
Species Being ◽  
Annotation Errors

Lancelets, extant representatives of basal chordates, are prototypic examples of evolutionary stasis; they preserved a morphology and body-plan most similar to the fossil chordates from the early Cambrian. Such a low level of morphological evolution is in harmony with a low rate of amino acid substitution; cephalochordate proteins were shown to evolve slower than those of the slowest evolving vertebrate, the elephant shark. Surprisingly, a study comparing the predicted proteomes of Chinese amphioxus, Branchiostoma belcheri and the Florida amphioxus, Branchiostoma floridae has led to the conclusion that the rate of creation of novel domain combinations is orders of magnitude greater in lancelets than in any other Metazoa, a finding that contradicts the notion that high rates of protein innovation are usually associated with major evolutionary innovations. Our earlier studies on a representative sample of proteins have provided evidence suggesting that the differences in the domain architectures of predicted proteins of these two lancelet species reflect annotation errors, rather than true innovations. In the present work, we have extended these studies to include a larger sample of genes and two additional lancelet species, Asymmetron lucayanum and Branchiostoma lanceolatum. These analyses have confirmed that the domain architecture differences of orthologous proteins of the four lancelet species are because of errors of gene prediction, the error rate in the given species being inversely related to the quality of the transcriptome dataset that was used to aid gene prediction.

scholarly journals Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons

2020 ◽  
Vol 36 (16) ◽  
pp. 4383-4388 ◽  
Author(s):  
Xiaoqiong Wei ◽  
Chengxin Zhang ◽  
Peter L Freddolino ◽  
Yang Zhang
Keyword(s):  
Gene Ontology ◽  
Protein Function ◽  
Large Scale ◽  
Structural Similarity ◽  
Supplementary Information ◽  
Specific Rate ◽  
New Developments ◽  
Detection Approach ◽  
Taxonomic Groups ◽  
Annotation Errors

Abstract Motivation Many protein function databases are built on automated or semi-automated curations and can contain various annotation errors. The correction of such misannotations is critical to improving the accuracy and reliability of the databases. Results We proposed a new approach to detect potentially incorrect Gene Ontology (GO) annotations by comparing the ratio of annotation rates (RAR) for the same GO term across different taxonomic groups, where those with a relatively low RAR usually correspond to incorrect annotations. As an illustration, we applied the approach to 20 commonly studied species in two recent UniProt-GOA releases and identified 250 potential misannotations in the 2018-11-6 release, where only 25% of them were corrected in the 2019-6-3 release. Importantly, 56% of the misannotations are ‘Inferred from Biological aspect of Ancestor (IBA)’ which is in contradiction with previous observations that attributed misannotations mainly to ‘Inferred from Sequence or structural Similarity (ISS)’, probably reflecting an error source shift due to the new developments of function annotation databases. The results demonstrated a simple but efficient misannotation detection approach that is useful for large-scale comparative protein function studies. Availability and implementation https://zhanglab.ccmb.med.umich.edu/RAR. Supplementary information Supplementary data are available at Bioinformatics online.

Sign in / Sign up

Export Citation Format

Share Document