scholarly journals Microbial genome analysis: the COG approach

2017 ◽  
Vol 20 (4) ◽  
pp. 1063-1070 ◽  
Author(s):  
Michael Y Galperin ◽  
David M Kristensen ◽  
Kira S Makarova ◽  
Yuri I Wolf ◽  
Eugene V Koonin
Keyword(s):  
Genome Analysis ◽  
Metabolic Pathways ◽  
Genome Annotation ◽  
Functional Characterization ◽  
Microbial Genome ◽  
Functional Categories ◽  
Orthologous Genes ◽  
Microbial Genomes ◽  
The Past

Abstract For the past 20 years, the Clusters of Orthologous Genes (COG) database had been a popular tool for microbial genome annotation and comparative genomics. Initially created for the purpose of evolutionary classification of protein families, the COG have been used, apart from straightforward functional annotation of sequenced genomes, for such tasks as (i) unification of genome annotation in groups of related organisms; (ii) identification of missing and/or undetected genes in complete microbial genomes; (iii) analysis of genomic neighborhoods, in many cases allowing prediction of novel functional systems; (iv) analysis of metabolic pathways and prediction of alternative forms of enzymes; (v) comparison of organisms by COG functional categories; and (vi) prioritization of targets for structural and functional characterization. Here we review the principles of the COG approach and discuss its key advantages and drawbacks in microbial genome analysis.

scholarly journals Using comparative genome analysis to identify problems in annotated microbial genomes

Microbiology ◽  
2010 ◽  
Vol 156 (7) ◽  
pp. 1909-1917 ◽  
Author(s):  
Maria S. Poptsova ◽  
J. Peter Gogarten
Keyword(s):  
Genome Analysis ◽  
Genome Annotation ◽  
Comparative Genome Analysis ◽  
Multiple Gene ◽  
Comparative Genome ◽  
Microbial Genomes ◽  
Automated Annotation ◽  
Sequencing Technologies ◽  
Automated Methods ◽  
Better Than

Genome annotation is a tedious task that is mostly done by automated methods; however, the accuracy of these approaches has been questioned since the beginning of the sequencing era. Genome annotation is a multilevel process, and errors can emerge at different stages: during sequencing, as a result of gene-calling procedures, and in the process of assigning gene functions. Missed or wrongly annotated genes differentially impact different types of analyses. Here we discuss and demonstrate how the methods of comparative genome analysis can refine annotations by locating missing orthologues. We also discuss possible reasons for errors and show that the second-generation annotation systems, which combine multiple gene-calling programs with similarity-based methods, perform much better than the first annotation tools. Since old errors may propagate to the newly sequenced genomes, we emphasize that the problem of continuously updating popular public databases is an urgent and unresolved one. Due to the progress in genome-sequencing technologies, automated annotation techniques will remain the main approach in the future. Researchers need to be aware of the existing errors in the annotation of even well-studied genomes, such as Escherichia coli, and consider additional quality control for their results.

Second international scientific conference «Present fundamental problems of vegetation classification» (Yalta, 15–20 September 2019)

2019 ◽  
pp. 135-142
Author(s):  
K. V. Ivanova ◽  
A. M. Lapina ◽  
V. V. Neshataev
Keyword(s):  
Plant Communities ◽  
National Archive ◽  
Botanical Garden ◽  
Vegetation Classification ◽  
Scientific Conference ◽  
Scientific Journals ◽  
Time Dynamics ◽  
The Past ◽  
Research Organizations

The 2nd international scientific conference «Fundamental problems of vegetation classification» took place at the Nikitskiy Botanical Garden (Yalta, Republic of Crimea, Russia) on 15–20 September 2019. There were 56 participants from 33 cities and 43 research organizations in Russia. The conference was mostly focused on reviewing the success in classification of the vegetation done by Russian scientists in the past three years. The reports covered various topics such as classification, description of new syntaxonomical units, geobotanical mapping for different territories and types of vegetation, studies of space-time dynamics of plant communities. The final discussion on the last day covered problems yet to be solved: establishment of the Russian Prodromus and the National archive of vegetation, complications of higher education in the profile of geobotany, and the issue of the data leakage to foreign scientific journals. In conclusion, it was announced that the 3rd conference in Nikitskiy Botanical Garden will be held in 2022.

The Poetry and Music of Science

2019 ◽  
Author(s):  
Tom McLeish
Keyword(s):  
School Leaver ◽  
Creative People ◽  
Creative Processes ◽  
Arts And Sciences ◽  
The Past ◽  
The Arts ◽  
The Two Cultures ◽  
Personal Accounts ◽  
Poetry And Music

‘I could not see any place in science for my creativity or imagination’, was the explanation, of a bright school leaver to the author, of why she had abandoned all study of science. Yet as any scientist knows, the imagination is essential to the immense task of re-creating a shared model of nature from the scale of the cosmos, through biological complexity, to the smallest subatomic structures. Encounters like that one inspired this book, which takes a journey through the creative process in the arts as well as sciences. Visiting great creative people of the past, it also draws on personal accounts of scientists, artists, mathematicians, writers, and musicians today to explore the commonalities and differences in creation. Tom McLeish finds that the ‘Two Cultures’ division between the arts and the sciences is not after all, the best classification of creative processes, for all creation calls on the power of the imagination within the constraints of form. Instead, the three modes of visual, textual, and abstract imagination have woven the stories of the arts and sciences together, but using different tools. As well as panoramic assessments of creativity, calling on ideas from the ancient world, medieval thought, and twentieth-century philosophy and theology, The Poetry and Music of Science illustrates its emerging story by specific close-up explorations of musical (Schumann), literary (James, Woolf, Goethe) mathematical (Wiles), and scientific (Humboldt, Einstein) creation. The book concludes by asking how creativity contributes to what it means to be human.

scholarly journals Cytokinin N-glucosides: Occurrence, Metabolism and Biological Activities in Plants

Biomolecules ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 24
Author(s):  
Eva Pokorná ◽  
Tomáš Hluska ◽  
Petr Galuszka ◽  
H. Tucker Hallmark ◽  
Petre I. Dobrev ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Growth And Development ◽  
Biological Activities ◽  
Physiological Effects ◽  
Inhibitory Effects ◽  
Plant Growth And Development ◽  
The Past ◽  
Complex Process ◽  
Considerable Impact ◽  
Physiological Impact

Cytokinins (CKs) are a class of phytohormones affecting many aspects of plant growth and development. In the complex process of CK homeostasis in plants, N-glucosylation represents one of the essential metabolic pathways. Its products, CK N7- and N9-glucosides, have been largely overlooked in the past as irreversible and inactive CK products lacking any relevant physiological impact. In this work, we report a widespread distribution of CK N-glucosides across the plant kingdom proceeding from evolutionary older to younger plants with different proportions between N7- and N9-glucosides in the total CK pool. We show dramatic changes in their profiles as well as in expression levels of the UGT76C1 and UGT76C2 genes during Arabidopsis ontogenesis. We also demonstrate specific physiological effects of CK N-glucosides in CK bioassays including their antisenescent activities, inhibitory effects on root development, and activation of the CK signaling pathway visualized by the CK-responsive YFP reporter line, TCSv2::3XVENUS. Last but not least, we present the considerable impact of CK N7- and N9-glucosides on the expression of CK-related genes in maize and their stimulatory effects on CK oxidase/dehydrogenase activity in oats. Our findings revise the apparent irreversibility and inactivity of CK N7- and N9-glucosides and indicate their involvement in CK evolution while suggesting their unique function(s) in plants.

scholarly journals ANCA Status or Clinical Phenotype — What Counts More?

2021 ◽  
Vol 23 (6) ◽  
Author(s):  
Martin Windpessl ◽  
Erica L. Bettac ◽  
Philipp Gauckler ◽  
Jae Il Shin ◽  
Duvuru Geetha ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Granulomatosis With Polyangiitis ◽  
Clinical Phenotype ◽  
Antineutrophil Cytoplasmic Antibody ◽  
Cardiovascular Death ◽  
Genetic Associations ◽  
Ongoing Debate ◽  
The Past ◽  
Anca Associated Vasculitis

Abstract Purpose of Review There is ongoing debate concerning the classification of antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis. That is, whether classification should be based on the serotype (proteinase 3 (PR3)- or myeloperoxidase (MPO)-ANCA) or on the clinical phenotype (granulomatosis with polyangiitis (GPA) or microscopic polyangiitis (MPA)). To add clarity, this review focused on integration of the most recent literature. Recent Findings Large clinical trials have provided evidence that a serology-based risk assessment for relapses is more predictive than distinction based on the phenotype. Research conducted in the past decade indicated that a serology-based approach more closely resembles the genetic associations, the clinical presentation (i.e., lung involvement), biomarker biology, treatment response, and is also predicting comorbidities (such as cardiovascular death). Summary Our review highlights that a serology-based approach could replace a phenotype-based approach to classify ANCA-associated vasculitides. In future, clinical trials and observational studies will presumably focus on this distinction and, as such, translate into a “personalized medicine.”

scholarly journals Morphological Characteristics, Classifications and Difficulties in the Use of Diagnostic Criteria for Serrated Lesions of the Large Intestine

2021 ◽  
Author(s):  
Cesar de Souza Bastos Junior ◽  
Vera Lucia Nunes Pannain ◽  
Adriana Caroli-Bottino
Keyword(s):  
Diagnostic Criteria ◽  
Morphological Characteristics ◽  
World Health ◽  
Diagnostic Tools ◽  
Serrated Adenoma ◽  
The Past ◽  
The World ◽  
Serrated Lesions ◽  
Health Organization

Abstract Introduction Colorectal carcinoma (CRC) is the most common gastrointestinal neoplasm in the world, accounting for 15% of cancer-related deaths. This condition is related to different molecular pathways, among them the recently described serrated pathway, whose characteristic entities, serrated lesions, have undergone important changes in their names and diagnostic criteria in the past thirty years. The multiplicity of denominations and criteria over the last years may be responsible for the low interobserver concordance (IOC) described in the literature. Objectives The present study aims to describe the evolution in classification of serrated lesions, based on the last three publications of the World Health Organization (WHO) and the reproducibility of these criteria by pathologists, based on the evaluation of the IOC. Methods A search was conducted in the PubMed, ResearchGate and Portal Capes databases, with the following terms: sessile serrated lesion; serrated lesions; serrated adenoma; interobserver concordance; and reproducibility. Articles published since 1990 were researched. Results and Discussion The classification of serrated lesions in the past thirty years showed different denominations and diagnostic criteria. The reproducibility and IOC of these criteria in the literature, based on the kappa coefficient, varied in most studies, from very poor to moderate. Conclusions Interobserver concordance and the reproducibility of microscopic criteria may represent a limitation for the diagnosis and appropriate management of these lesions. It is necessary to investigate diagnostic tools to improve the performance of the pathologist's evaluation, for better concordance, and, consequently, adequate diagnosis and treatment.

scholarly journals Application of Artificial Intelligence in Food Industry—a Guideline

2021 ◽  
Author(s):  
Nidhi Rajesh Mavani ◽  
Jarinah Mohd Ali ◽  
Suhaili Othman ◽  
M. A. Hussain ◽  
Haslaniza Hashim ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Intelligent Systems ◽  
Food Industry ◽  
Near Infrared ◽  
Vision System ◽  
Electronic Tongue ◽  
World Population ◽  
Computer Vision System ◽  
The Past

AbstractArtificial intelligence (AI) has embodied the recent technology in the food industry over the past few decades due to the rising of food demands in line with the increasing of the world population. The capability of the said intelligent systems in various tasks such as food quality determination, control tools, classification of food, and prediction purposes has intensified their demand in the food industry. Therefore, this paper reviews those diverse applications in comparing their advantages, limitations, and formulations as a guideline for selecting the most appropriate methods in enhancing future AI- and food industry–related developments. Furthermore, the integration of this system with other devices such as electronic nose, electronic tongue, computer vision system, and near infrared spectroscopy (NIR) is also emphasized, all of which will benefit both the industry players and consumers.

scholarly journals Species Boundaries and Molecular Markers for the Classification of 16SrI Phytoplasmas Inferred by Genome Analysis

2020 ◽  
Vol 11 ◽  
Author(s):  
Shu-Ting Cho ◽  
Hung-Jui Kung ◽  
Weijie Huang ◽  
Saskia A. Hogenhout ◽  
Chih-Horng Kuo
Keyword(s):  
Molecular Markers ◽  
Genome Analysis ◽  
Species Boundaries

Small Bowel Obstruction

2010 ◽  
Vol 21 (2) ◽  
pp. 187-194
Author(s):  
Colleen Trevino
Keyword(s):  
Small Bowel ◽  
Physical Examination ◽  
Surgical Intervention ◽  
Signs And Symptoms ◽  
Bowel Ischemia ◽  
Key Factors ◽  
The Past ◽  
Factors Influencing ◽  
Imaging Response

Strategies for the management of small bowel obstructions have changed significantly over the years. Nonoperative medical management has become the mainstay of treatment of many small bowel obstructions. However, the key to the management of small bowel obstructions is identifying those patients who need surgical intervention. Identification of those at risk for bowel ischemia and bowel death is an art as much as it is a science. Using the current literature and the past knowledge regarding small bowel obstructions, the clinician must carefully identify the signs and symptoms that suggest the need for operative intervention. Classification of the obstruction, history and physical examination, imaging, response to decompression and resuscitation, and resolution or progression of symptoms are the key factors influencing the management of small bowel obstructions.

scholarly journals Conjuring up a ghost: structural and functional characterization of FhuF, a ferric siderophore reductase from E. coli

2021 ◽  
Author(s):  
I. B. Trindade ◽  
G. Hernandez ◽  
E. Lebègue ◽  
F. Barrière ◽  
T. Cordeiro ◽  
...  
Keyword(s):  
Functional Characterization ◽  
Paramagnetic Nmr ◽  
E Coli ◽  
The Past ◽  
Internal Cavities ◽  
Structural Differences ◽  
Bond Strengths ◽  
Redox Bohr Effect ◽  
Micromolar Range

AbstractIron is a fundamental element for virtually all forms of life. Despite its abundance, its bioavailability is limited, and thus, microbes developed siderophores, small molecules, which are synthesized inside the cell and then released outside for iron scavenging. Once inside the cell, iron removal does not occur spontaneously, instead this process is mediated by siderophore-interacting proteins (SIP) and/or by ferric-siderophore reductases (FSR). In the past two decades, representatives of the SIP subfamily have been structurally and biochemically characterized; however, the same was not achieved for the FSR subfamily. Here, we initiate the structural and functional characterization of FhuF, the first and only FSR ever isolated. FhuF is a globular monomeric protein mainly composed by α-helices sheltering internal cavities in a fold resembling the “palm” domain found in siderophore biosynthetic enzymes. Paramagnetic NMR spectroscopy revealed that the core of the cluster has electronic properties in line with those of previously characterized 2Fe–2S ferredoxins and differences appear to be confined to the coordination of Fe(III) in the reduced protein. In particular, the two cysteines coordinating this iron appear to have substantially different bond strengths. In similarity with the proteins from the SIP subfamily, FhuF binds both the iron-loaded and the apo forms of ferrichrome in the micromolar range and cyclic voltammetry reveals the presence of redox-Bohr effect, which broadens the range of ferric-siderophore substrates that can be thermodynamically accessible for reduction. This study suggests that despite the structural differences between FSR and SIP proteins, mechanistic similarities exist between the two classes of proteins. Graphic abstract

Sign in / Sign up

Export Citation Format

Share Document