scholarly journals Extending the classification of bacterial transcription factors beyond the helix-turn-helix motif as an alternative approach to discover new cis/trans relationships

2004 ◽  
Vol 32 (11) ◽  
pp. 3418-3426 ◽  
Author(s):  
S. Rigali
Keyword(s):  
Transcription Factors ◽  
Bacterial Transcription ◽  
Alternative Approach

scholarly journals PredicTF: a tool to predict bacterial transcription factors in complex microbial communities

2021 ◽  
Author(s):  
Lummy Maria Oliveira Monteiro ◽  
Joao Saraiva ◽  
Rodolfo Brizola Toscan ◽  
Peter F Stadler ◽  
Rafael Silva-Rocha ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Microbial Communities ◽  
Open Source ◽  
Genetic Information ◽  
Environmental Isolate ◽  
Ammonium Oxidation ◽  
Cellular Gene ◽  
Bacterial Transcription

AbstractTranscription Factors (TFs) are proteins that control the flow of genetic information by regulating cellular gene expression. Here we describe PredicTF, a first platform supporting the prediction and classification of novel bacterial TF in complex microbial communities. We evaluated PredicTF using a two-step approach. First, we tested PredictTF’s ability to predict TFs for the genome of an environmental isolate. In the second evaluation step, PredicTF was used to predict TFs in a metagenome and 11 metatranscriptomes recovered from a community performing anaerobic ammonium oxidation (anammox) in a bioreactor. PredicTF is open source pipeline available at https://github.com/mdsufz/PredicTF.

CNN-based Classification of Degraded Images

2020 ◽  
Vol 2020 (10) ◽  
pp. 28-1-28-7 ◽  
Author(s):  
Kazuki Endo ◽  
Masayuki Tanaka ◽  
Masatoshi Okutomi
Keyword(s):  
Neural Networks ◽  
Image Restoration ◽  
Image Classification ◽  
Convolutional Neural Networks ◽  
Deep Convolutional Neural Networks ◽  
Alternative Approach ◽  
Degraded Image ◽  
Degraded Images ◽  
Straightforward Approach

Classification of degraded images is very important in practice because images are usually degraded by compression, noise, blurring, etc. Nevertheless, most of the research in image classification only focuses on clean images without any degradation. Some papers have already proposed deep convolutional neural networks composed of an image restoration network and a classification network to classify degraded images. This paper proposes an alternative approach in which we use a degraded image and an additional degradation parameter for classification. The proposed classification network has two inputs which are the degraded image and the degradation parameter. The estimation network of degradation parameters is also incorporated if degradation parameters of degraded images are unknown. The experimental results showed that the proposed method outperforms a straightforward approach where the classification network is trained with degraded images only.

scholarly journals Bacterial transcription factors involved in global regulation

1999 ◽  
Vol 33 (1) ◽  
pp. 8-17 ◽  
Author(s):  
Miguel Vicente ◽  
Keith F. Chater ◽  
Victor de Lorenzo
Keyword(s):  
Transcription Factors ◽  
Global Regulation ◽  
Bacterial Transcription

scholarly journals In the Case of Protosemiosis: Indexicality vs. Iconicity of Proteins

Biosemiotics ◽  
2020 ◽  
Author(s):  
Dan Faltýnek ◽  
Ľudmila Lacková
Keyword(s):  
Lower Organism ◽  
Low Level ◽  
Alternative Approach ◽  
Typological Characteristic

AbstractThe concept of protosemiosis or semiosis at the lower levels of the living goes back to Giorgio Prodi, Thomas A. Sebeok and others. More recently, a typology of proto-signs was introduced by Sharov and Vehkavaara. Kull uses the term of vegetative semiosis, defined by iconicity, when referring to plants and lower organism semiosis. The criteria for the typology of proto-signs by Sharov and Vehkavaara are mostly based on two important presuppositions: agency and a lack of representation in low-level semiosis. We would like to focus on an alternative approach to protosign classification. In particular, we aim to provide a sign-typological characteristic of proteins (in analogy to Maran’ s classification of environmental signs). Our approach is focused on representation, that is, we only consider the relation between a sign and its object. We are considering representation independently from the role of interpretant and interpretation (which is an epiphenomenon of agency). Two hypotheses are investigated and accordingly evaluated in this paper: (I) Proteins are indexical protosigns. (II) Proteins are iconic protosigns. The conclusion our argumentation leads to supports the hypothesis (II).

scholarly journals Structure and functional implications of WYL-domain-containing transcription factor PafBC involved in the mycobacterial DNA damage response

2019 ◽  
Author(s):  
Andreas U. Müller ◽  
Marc Leibundgut ◽  
Nenad Ban ◽  
Eilika Weber-Ban
Keyword(s):  
Dna Damage ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Structural Information ◽  
Rna Molecules ◽  
Bacterial Transcription ◽  
Arthrobacter Aurescens

AbstractIn mycobacteria, transcriptional activator PafBC is responsible for upregulating the majority of genes induced by DNA damage. Understanding the mechanism of PafBC activation is impeded by a lack of structural information on this transcription factor that contains a widespread, but poorly understood WYL domain frequently encountered in bacterial transcription factors. Here, we determined the crystal structure ofArthrobacter aurescensPafBC. The protein consists of two modules, each harboring an N-terminal helix-turn-helix DNA binding domain followed by a central WYL and a C-terminal extension (WCX) domain. The WYL domains exhibit Sm-folds, while the WCX domains adopt ferredoxin-like folds, both characteristic for RNA binding proteins. Our results suggest a mechanism of regulation in which WYL domain-containing transcription factors may be activated by binding RNA molecules. Using anin vivomutational screen inMycobacterium smegmatis, we identify potential co-activator binding sites on PafBC.

scholarly journals An Alternative Approach to Classify Illegal Logging: The Case in Vietnam

2020 ◽  
Vol 9 (3) ◽  
pp. 130-143
Author(s):  
Huu Nam Nguyen ◽  
Ngoc Anh Cao
Keyword(s):  
Illegal Logging ◽  
Alternative Approach

This article examines the different kinds of illegal logging that takes place in Vietnam, challenging the typical approaches to understanding and classifying the various criminal activities involved. We argue that either overlooking the classification of illegal logging or relying solely on illegal timber volumes and legal descriptions to categorise the crime is not sufficient to comprehend its diverse nature. This leads to inappropriate measures to tackle the crime. Instead, this study suggests that illegal logging should be categorised into three types, which are fundamentally distinctive, not only with regard to the volumes of illicit timber and the legislative definitions of the crime, but also (and more importantly) with reference to the attributes of harvesters, the degree of their involvement and their motivations, and the level of organisation involved in criminal commissions.

scholarly journals Taxonomic classification of algae by the use of chlorophyll a fluorescence

2017 ◽  
Vol 26 (4) ◽  
pp. 470-480
Author(s):  
Nikodem Szymański ◽  
Piotr Dąbrowski ◽  
Hazem Kalaji ◽  
Detlev Lohse ◽  
Balaji Panchal ◽  
...  
Keyword(s):  
Algal Blooms ◽  
Continuous Monitoring ◽  
Algal Species ◽  
Fluorescence Analysis ◽  
Traditional Group ◽  
Non Invasive ◽  
Alternative Approach ◽  
Chlorophyll Fluorescence Analysis

Natural water reservoirs are very important ecosystems thus they should be under continuous monitoring and protection. In water of low quality, the algal blooms develop develops vastly. The knowledge of algal species composition is necessary for understanding this process. There are a few traditional group-specific methods of microalgae classification, but they are often labour-intense and time-consuming. Moreover, the samples must be prepared and/or collected before getting any results. Non-invasive chlorophyll fluorescence analysis offers an alternative approach and potentially allows in situ estimation of algal concentration. In this work the fluorometric methods to estimate algae content in water and to differentiate algal populations is presented.

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