LIVIVO - Search results -

Search results

Result 1 - 10 of total 118

Search options

Article ; Online: The most exposed regions of SARS-CoV-2 structural proteins are subject to strong positive selection and gene overlap may locally modify this behavior.

Rubio, Alejandro / de Toro, Maria / Pérez-Pulido, Antonio J

mSystems

2023 Volume 9, Issue 1, Page(s) e0071323

Abstract: The SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic that emerged in 2019 has been an unprecedented event in international science, as it has been possible to sequence millions of genomes, tracking their evolution very closely. This ... ...

Abstract	The SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic that emerged in 2019 has been an unprecedented event in international science, as it has been possible to sequence millions of genomes, tracking their evolution very closely. This has enabled various types of secondary analyses of these genomes, including the measurement of their sequence selection pressure. In this work, we have been able to measure the selective pressure of all the described SARS-CoV-2 genes, even analyzed by sequence regions, and we show how this type of analysis allows us to separate the genes between those subject to positive selection (usually those that code for surface proteins or those exposed to the host immune system) and those subject to negative selection because they require greater conservation of their structure and function. We have also seen that when another gene with an overlapping reading frame appears within a gene sequence, the overlapping sequence between the two genes evolves under a stronger purifying selection than the average of the non-overlapping regions of the main gene. We propose this type of analysis as a useful tool for locating and analyzing all the genes of a viral genome when an adequate number of sequences are available.IMPORTANCEWe have analyzed the selection pressure of all severe acute respiratory syndrome coronavirus 2 genes by means of the nonsynonymous (Ka) to synonymous (Ks) substitution rate. We found that protein-coding genes are exposed to strong positive selection, especially in the regions of interaction with other molecules (host receptor and genome of the virus itself). However, overlapping coding regions are more protected and show negative selection. This suggests that this measure could be used to study viral gene function as well as overlapping genes.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19 ; Proteins ; Genome, Viral/genetics ; Genes, Viral/genetics
Chemical Substances	Proteins
Language	English
Publishing date	2023-12-14
Publishing country	United States
Document type	Journal Article
ISSN	2379-5077
ISSN (online)	2379-5077
DOI	10.1128/msystems.00713-23
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Assessment of selection pressure exerted on genes from complete pangenomes helps to improve the accuracy in the prediction of new genes.

Rubio, Alejandro / Jimenez, Juan / Pérez-Pulido, Antonio J

Briefings in bioinformatics

2022 Volume 23, Issue 2

Abstract: Bacterial genomes are massively sequenced, and they provide valuable data to better know the complete set of genes of a species. The analysis of thousands of bacterial strains can identify both shared genes and those appearing only in the pathogenic ones. ...

Abstract	Bacterial genomes are massively sequenced, and they provide valuable data to better know the complete set of genes of a species. The analysis of thousands of bacterial strains can identify both shared genes and those appearing only in the pathogenic ones. Current computational gene finders facilitate this task but often miss some existing genes. However, the present availability of different genomes from the same species is useful to estimate the selective pressure applied on genes of complete pangenomes. It may assist in evaluating gene predictions either by checking the certainty of a new gene or annotating it as a gene under positive selection. Here, we estimated the selective pressure of 19 271 genes that are part of the pangenome of the human opportunistic pathogen Acinetobacter baumannii and found that most genes in this bacterium are subject to negative selection. However, 23% of them showed values compatible with positive selection. These latter were mainly uncharacterized proteins or genes required to evade the host defence system including genes related to resistance and virulence whose changes may be favoured to acquire new functions. Finally, we evaluated the utility of measuring selection pressure in the detection of sequencing errors and the validation of gene prediction.
MeSH term(s)	Acinetobacter baumannii/genetics ; Acinetobacter baumannii/metabolism ; Bacteria/genetics ; Base Sequence ; Genome, Bacterial ; Humans ; Phylogeny ; Virulence/genetics
Language	English
Publishing date	2022-02-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbac010
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 6262: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: E-learning strategies from a bioinformatics postgraduate programme to improve student engagement and completion rate.

Garzón, Andrés / Rubio, Alejandro / Pérez-Pulido, Antonio J

Bioinformatics advances

2022 Volume 2, Issue 1, Page(s) vbac031

Abstract: Motivation: E-learning is the standard solution adopted in transnational study programmes for which multiple face-to-face learning places are not an option. Bioinformatics is compatible with e-learning because its resource requirements are low. Online ... ...

Abstract	Motivation: E-learning is the standard solution adopted in transnational study programmes for which multiple face-to-face learning places are not an option. Bioinformatics is compatible with e-learning because its resource requirements are low. Online learning, however, is usually associated with high dropout rates because students start from a very low computational level and/or they need support to conduct practical analyses on their own. Results: In this article, we analyse the academic results of an online bioinformatics educational programme based on learning communities. The programme has been offered by the Spanish Pablo de Olavide University for more than 5 years with a completion rate of close to 90%. Learning bioinformatics requires technical and operational competencies that can only be acquired through a practical methodology. We have thus developed a student-centred and problem-based constructivist learning model; the model uses faculty and peer mentoring to drive individual work and retain students. Regarding our innovative learning model, the recruitment level (i.e. the number of applicants per available places and international origin), the results obtained (i.e. the retention index and learning outcomes) as well as the satisfaction index expressed by students and faculty lead us to regard this programme as a successful strategy for online graduate learning in bioinformatics. Availability and implementation: All data and results for this article are available in the figures and supplementary files. The current syllabus (Supplementary File S7) and other details of the course are available at: https://www.upo.es/postgrado/Diploma-de-Especializacion-Analisis-Bioinformatico and https://www.upo.es/postgrado/Master-Analisis-Bioinformatico-Avanzado. Supplementary information: Supplementary data are available at
Language	English
Publishing date	2022-05-10
Publishing country	England
Document type	Journal Article
ISSN	2635-0041
ISSN (online)	2635-0041
DOI	10.1093/bioadv/vbac031
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Protein-Coding Genes of

Rubio, Alejandro / Pérez-Pulido, Antonio J

Genes

2021 Volume 12, Issue 3

Abstract: The current availability of complete genome sequences has allowed knowing that bacterial genomes can bear genes not present in the genome of all the strains from a specific species. So, the genes shared by all the strains comprise the core of the species, ...

Abstract	The current availability of complete genome sequences has allowed knowing that bacterial genomes can bear genes not present in the genome of all the strains from a specific species. So, the genes shared by all the strains comprise the core of the species, but the pangenome can be much greater and usually includes genes appearing in one only strain. Once the pangenome of a species is estimated, other studies can be undertaken to generate new knowledge, such as the study of the evolutionary selection for protein-coding genes. Most of the genes of a pangenome are expected to be subject to purifying selection that assures the conservation of function, especially those in the core group. However, some genes can be subject to selection pressure, such as genes involved in virulence that need to escape to the host immune system, which is more common in the accessory group of the pangenome. We analyzed 180 strains of
MeSH term(s)	Bacterial Proteins/genetics ; Computational Biology/methods ; Evolution, Molecular ; Helicobacter pylori/classification ; Helicobacter pylori/genetics ; Membrane Proteins/genetics ; Molecular Sequence Annotation ; Selection, Genetic ; Sequence Analysis, DNA ; Whole Genome Sequencing
Chemical Substances	Bacterial Proteins ; Membrane Proteins
Language	English
Publishing date	2021-03-06
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes12030377
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: ASACO: Automatic and Serial Analysis of CO-expression to discover gene modifiers with potential use in drug repurposing.

Moral-Turón, Cristina / Asencio-Cortés, Gualberto / Rodriguez-Diaz, Francesc / Rubio, Alejandro / Navarro, Alberto G / Brokate-Llanos, Ana M / Garzón, Andrés / Muñoz, Manuel J / Pérez-Pulido, Antonio J

Briefings in functional genomics

2024

Abstract: Massive gene expression analyses are widely used to find differentially expressed genes under specific conditions. The results of these experiments are often available in public databases that are undergoing a growth similar to that of molecular sequence ...

Abstract	Massive gene expression analyses are widely used to find differentially expressed genes under specific conditions. The results of these experiments are often available in public databases that are undergoing a growth similar to that of molecular sequence databases in the past. This now allows novel secondary computational tools to emerge that use such information to gain new knowledge. If several genes have a similar expression profile across heterogeneous transcriptomics experiments, they could be functionally related. These associations are usually useful for the annotation of uncharacterized genes. In addition, the search for genes with opposite expression profiles is useful for finding negative regulators and proposing inhibitory compounds in drug repurposing projects. Here we present a new web application, Automatic and Serial Analysis of CO-expression (ASACO), which has the potential to discover positive and negative correlator genes to a given query gene, based on thousands of public transcriptomics experiments. In addition, examples of use are presented, comparing with previous contrasted knowledge. The results obtained propose ASACO as a useful tool to improve knowledge about genes associated with human diseases and noncoding genes. ASACO is available at http://www.bioinfocabd.upo.es/asaco/.
Language	English
Publishing date	2024-02-29
Publishing country	England
Document type	Journal Article
ZDB-ID	2540916-5
ISSN	2041-2657 ; 2041-2649 ; 2041-2647
ISSN (online)	2041-2657
ISSN	2041-2649 ; 2041-2647
DOI	10.1093/bfgp/elae006
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 6076: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Influence of Agaricus bisporus establishment and fungicidal treatments on casing soil metataxonomy during mushroom cultivation.

Tello Martín, Maria Luisa / Lavega, Rebeca / Carrasco, Jaime Carrasco / Pérez, Margarita / Pérez-Pulido, Antonio J / Thon, Michael / Pérez Benito, Ernesto

BMC genomics

2022 Volume 23, Issue 1, Page(s) 442

Abstract: The cultivation of edible mushroom is an emerging sector with a potential yet to be discovered. Unlike plants, it is a less developed agriculture where many studies are lacking to optimize the cultivation. In this work we have employed high-throughput ... ...

Abstract	The cultivation of edible mushroom is an emerging sector with a potential yet to be discovered. Unlike plants, it is a less developed agriculture where many studies are lacking to optimize the cultivation. In this work we have employed high-throughput techniques by next generation sequencing to screen the microbial structure of casing soil employed in mushroom cultivation (Agaricus bisporus) while sequencing V3-V4 of the 16S rRNA gene for bacteria and the ITS2 region of rRNA for. In addition, the microbiota dynamics and evolution (bacterial and fungal communities) in peat-based casing along the process of incubation of A. bisporus have been studied, while comparing the effect of fungicide treatment (chlorothalonil and metrafenone). Statistically significant changes in populations of bacteria and fungi were observed. Microbial composition differed significantly based on incubation day, changing radically from the original communities in the raw material to a specific microbial composition driven by the A. bisporus mycelium growth. Chlorothalonil treatment seems to delay casing colonization by A. bisporus. Proteobacteria and Bacteroidota appeared as the most dominant bacterial phyla. We observed a great change in the structure of the bacteria populations between day 0 and the following days. Fungi populations changed more gradually, with A. bisporus displacing the rest of the species as the cultivation cycle progresses. A better understanding of the microbial communities in the casing will hopefully allow us to increase the biological efficiency of the crop.
MeSH term(s)	Agaricus/genetics ; Bacteria/genetics ; Fungi/genetics ; Fungicides, Industrial/pharmacology ; RNA, Ribosomal, 16S/genetics ; Soil
Chemical Substances	Fungicides, Industrial ; RNA, Ribosomal, 16S ; Soil
Language	English
Publishing date	2022-06-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2041499-7
ISSN	1471-2164 ; 1471-2164
ISSN (online)	1471-2164
ISSN	1471-2164
DOI	10.1186/s12864-022-08638-x
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Analysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systems.

Rubio, Alejandro / Sprang, Maximilian / Garzón, Andrés / Moreno-Rodriguez, Antonio / Pachón-Ibáñez, Maria Eugenia / Pachón, Jerónimo / Andrade-Navarro, Miguel A / Pérez-Pulido, Antonio J

Science advances

2023 Volume 9, Issue 12, Page(s) eadd8911

Abstract: CRISPR-Cas systems are prokaryotic acquired immunity mechanisms, which are found in 40% of bacterial genomes. They prevent viral infections through small DNA fragments called spacers. However, the vast majority of these spacers have not yet been ... ...

Abstract	CRISPR-Cas systems are prokaryotic acquired immunity mechanisms, which are found in 40% of bacterial genomes. They prevent viral infections through small DNA fragments called spacers. However, the vast majority of these spacers have not yet been associated with the virus they recognize, and it has been named CRISPR dark matter. By analyzing the spacers of tens of thousands of genomes from six bacterial species, we have been able to reduce the CRISPR dark matter from 80% to as low as 15% in some of the species. In addition, we have observed that, when a genome presents CRISPR-Cas systems, this is accompanied by particular sets of membrane proteins. Our results suggest that when bacteria present membrane proteins that make it compete better in its environment and these proteins are, in turn, receptors for specific phages, they would be forced to acquire CRISPR-Cas.
MeSH term(s)	CRISPR-Cas Systems/genetics ; Bacteria/genetics ; Genome, Bacterial ; Bacteriophages/genetics
Language	English
Publishing date	2023-03-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.add8911
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: Protein-Coding Genes of Helicobacter pylori Predominantly Present Purifying Selection though Many Membrane Proteins Suffer from Selection Pressure: A Proposal to Analyze Bacterial Pangenomes

Rubio, Alejandro / Pérez-Pulido, Antonio J

Genes. 2021 Mar. 06, v. 12, no. 3

2021

Abstract	The current availability of complete genome sequences has allowed knowing that bacterial genomes can bear genes not present in the genome of all the strains from a specific species. So, the genes shared by all the strains comprise the core of the species, but the pangenome can be much greater and usually includes genes appearing in one only strain. Once the pangenome of a species is estimated, other studies can be undertaken to generate new knowledge, such as the study of the evolutionary selection for protein-coding genes. Most of the genes of a pangenome are expected to be subject to purifying selection that assures the conservation of function, especially those in the core group. However, some genes can be subject to selection pressure, such as genes involved in virulence that need to escape to the host immune system, which is more common in the accessory group of the pangenome. We analyzed 180 strains of Helicobacter pylori, a bacterium that colonizes the gastric mucosa of half the world population and presents a low number of genes (around 1500 in a strain and 3000 in the pangenome). After the estimation of the pangenome, the evolutionary selection for each gene has been calculated, and we found that 85% of them are subject to purifying selection and the remaining genes present some grade of selection pressure. As expected, the latter group is enriched with genes encoding for membrane proteins putatively involved in interaction to host tissues. In addition, this group also presents a high number of uncharacterized genes and genes encoding for putative spurious proteins. It suggests that they could be false positives from the gene finders used for identifying them. All these results propose that this kind of analyses can be useful to validate gene predictions and functionally characterize proteins in complete genomes.
Keywords	Helicobacter pylori ; bacteria ; gastric mucosa ; genes ; immune system ; selection pressure ; virulence
Language	English
Dates of publication	2021-0306
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes12030377
Database	NAL-Catalogue (AGRICOLA)

Order via subito

Article ; Online: Ancient evolutionary signals of protein-coding sequences allow the discovery of new genes in the Drosophila melanogaster genome.

Casimiro-Soriguer, Carlos S / Rubio, Alejandro / Jimenez, Juan / Pérez-Pulido, Antonio J

BMC genomics

2020 Volume 21, Issue 1, Page(s) 210

Abstract: Background: The current growth in DNA sequencing techniques makes of genome annotation a crucial task in the genomic era. Traditional gene finders focus on protein-coding sequences, but they are far from being exhaustive. The number of this kind of ... ...

Abstract	Background: The current growth in DNA sequencing techniques makes of genome annotation a crucial task in the genomic era. Traditional gene finders focus on protein-coding sequences, but they are far from being exhaustive. The number of this kind of genes continuously increases due to new experimental data and development of improved bioinformatics algorithms. Results: In this context, AnABlast represents a novel in silico strategy, based on the accumulation of short evolutionary signals identified by protein sequence alignments of low score. This strategy potentially highlights protein-coding regions in genomic sequences regardless of traditional homology or translation signatures. Here, we analyze the evolutionary information that the accumulation of these short signals encloses. Using the Drosophila melanogaster genome, we stablish optimal parameters for the accurate gene prediction with AnABlast and show that this new strategy significantly contributes to add genes, exons and pseudogenes regions, yet to be discovered in both already annotated and new genomes. Conclusions: AnABlast can be freely used to analyze genomic regions of whole genomes where it contributes to complete the previous annotation.
MeSH term(s)	Algorithms ; Animals ; Computational Biology ; Computer Simulation ; Drosophila melanogaster/genetics ; Evolution, Molecular ; Exons/genetics ; Genes, Insect ; Genome ; Open Reading Frames/genetics ; Pseudogenes ; Sequence Alignment ; Sequence Analysis, DNA
Language	English
Publishing date	2020-03-05
Publishing country	England
Document type	Journal Article
ISSN	1471-2164
ISSN (online)	1471-2164
DOI	10.1186/s12864-020-6632-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Automated selection of homologs to track the evolutionary history of proteins.

Mier, Pablo / Pérez-Pulido, Antonio J / Andrade-Navarro, Miguel A

BMC bioinformatics

2018 Volume 19, Issue 1, Page(s) 431

Abstract: Background: The selection of distant homologs of a query protein under study is a usual and useful application of protein sequence databases. Such sets of homologs are often applied to investigate the function of a protein and the degree to which ... ...

Abstract	Background: The selection of distant homologs of a query protein under study is a usual and useful application of protein sequence databases. Such sets of homologs are often applied to investigate the function of a protein and the degree to which experimental results can be transferred from one organism to another. In particular, a variety of databases facilitates static browsing for orthologs. However, these resources have a limited power when identifying orthologs between taxonomically distant species. In addition, in some situations, for a given query protein, it is advantageous to compare the sets of orthologs from different specific organisms: this recursive step-wise search might give an idea of the evolutionary path of the protein as a series of consecutive steps, for example gaining or losing domains. However, a step-wise orthology search is a time-consuming task if the number of steps is high. Results: To illustrate a solution for this problem, we present the web tool ProteinPathTracker, which allows to track the evolutionary history of a query protein by locating homologs in selected proteomes along several evolutionary paths. Additional functionalities include locking a region of interest to follow its evolution in the discovered homologous sequences and the study of the protein function evolution by analysis of the annotations of the homologs. Conclusions: ProteinPathTracker is an easy-to-use web tool that automatises the practice of looking for selected homologs in distant species in a straightforward way for non-expert users.
MeSH term(s)	Databases, Protein ; Evolution, Molecular ; Humans ; Proteins/metabolism ; Proteome/analysis ; Software
Chemical Substances	Proteins ; Proteome
Language	English
Publishing date	2018-11-19
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-018-2457-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

To top

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito