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Article ; Online: An Integrated Affinity Chromatography-Based Approach to Unravel the sRNA Interactome in Nitrogen-Fixing Rhizobia.

García-Tomsig, Natalia Isabel / Lagares, Antonio / Becker, Anke / Valverde, Claudio / Jiménez-Zurdo, José Ignacio

Methods in molecular biology (Clifton, N.J.)

2024 Volume 2741, Page(s) 363–380

Abstract: The activity mechanism and function of bacterial base-pairing small non-coding RNA regulators (sRNAs) are largely shaped by their main interacting cellular partners, i.e., proteins and mRNAs. We describe here an MS2 affinity chromatography-based ... ...

Abstract	The activity mechanism and function of bacterial base-pairing small non-coding RNA regulators (sRNAs) are largely shaped by their main interacting cellular partners, i.e., proteins and mRNAs. We describe here an MS2 affinity chromatography-based procedure adapted to unravel the sRNA interactome in nitrogen-fixing legume endosymbiotic bacteria. The method consists of tagging of the bait sRNA at its 5'-end with the MS2 aptamer followed by pulse overexpression and immobilization of the chimeric transcript from cell lysates by an MS2-MBP fusion protein conjugated to an amylose resin. The sRNA-binding proteins and target mRNAs are further profiled by mass spectrometry and RNAseq, respectively.
MeSH term(s)	RNA, Small Untranslated/genetics ; Rhizobium/genetics ; Rhizobium/metabolism ; Nitrogen/metabolism ; Bacteria/genetics ; Nitrogen-Fixing Bacteria/genetics ; Chromatography, Affinity/methods ; RNA, Bacterial/genetics ; Gene Expression Regulation, Bacterial
Chemical Substances	RNA, Small Untranslated ; Nitrogen (N762921K75) ; RNA, Bacterial
Language	English
Publishing date	2024-01-13
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-3565-0_19
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Article ; Online: Analysis of hospital costs by morbidity group for patients with severe mental illness.

Caballer-Tarazona, Vicent / Zúñiga-Lagares, Antonio / Reyes-Santias, Francisco

Annals of medicine

2022 Volume 54, Issue 1, Page(s) 858–866

Abstract: Objectives: The goal of this study is to analyse hospital costs and length of stay of patients admitted to psychiatric units in hospitals in a European region of the Mediterranean Arc. The aim is to identify the effects of comorbidities and other ... ...

Abstract	Objectives: The goal of this study is to analyse hospital costs and length of stay of patients admitted to psychiatric units in hospitals in a European region of the Mediterranean Arc. The aim is to identify the effects of comorbidities and other variables in order to create an explanatory cost model. Methods: In order to carry out the study, the Ministry of Health was asked to provide data on access to the mental health facilities of all hospitals in the region. Among other questions, this database identifies the most important diagnostic variables related to admission, like comorbidities, age and gender. The method used, based on the Manning-Mullahy algorithm, was linear regression. The results were measured by the statistical significance of the independent variables to determine which of them were valid to explain the cost of hospitalization. Results: Psychiatric inpatients can be divided into three main groups (psychotic, organic and neurotic), which have statistically significant differences in costs. The independent variables that were statistically significant ( Conclusions: Unlike most health services, access to psychiatric facilities does not correlate with comorbidities due to the specific nature of this specialization. Patients admitted to psychosis had higher costs and a higher number of average staysKEY MESSAGESThe highest average hospital expenditure occurred in patients admitted for psychotic disorders.Due to the particularities of psychiatry units and unlike other medical specialties, the number of comorbidities did not influence the number of hospital stays or hospital expenditure.Apart from the main diagnostic group, the variables that were useful to explain hospital expenditure were the presence of poisoning and injuries as comorbidity, diseases of circulatory system as comorbidity, history of substance abuse and readmission.
MeSH term(s)	Hospital Costs ; Hospitals ; Humans ; Length of Stay ; Mental Disorders/epidemiology ; Morbidity ; Substance-Related Disorders
Language	English
Publishing date	2022-03-23
Publishing country	England
Document type	Journal Article
ZDB-ID	1004226-x
ISSN	1365-2060 ; 1651-2219 ; 0785-3890 ; 1743-1387
ISSN (online)	1365-2060 ; 1651-2219
ISSN	0785-3890 ; 1743-1387
DOI	10.1080/07853890.2022.2048884
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Article ; Online: Guidelines for Inferring and Characterizing a Family of Bacterial trans-Acting Small Noncoding RNAs.

Lagares, Antonio / Valverde, Claudio

Methods in molecular biology (Clifton, N.J.)

2018 Volume 1737, Page(s) 31–45

Abstract: So far, every sequenced bacterial transcriptome encompasses hundreds of small regulatory noncoding RNAs (sRNAs). From those sRNAs that have been already characterized, we learned that their regulatory functions could span over almost every bacterial ... ...

Abstract	So far, every sequenced bacterial transcriptome encompasses hundreds of small regulatory noncoding RNAs (sRNAs). From those sRNAs that have been already characterized, we learned that their regulatory functions could span over almost every bacterial process, mostly acting at the posttranscriptional control of gene expression (Wagner and Romby, Adv Genet 90:133-208, 2015). Canonical molecular mechanisms of sRNA action have been described to rely on both sequence and/or structural traits of the RNA molecule. As for protein-coding genes, the conservation of sRNAs among species suggests conserved and adjusted functions across evolution. Knowing the phylogenetic distribution of an sRNA gene and how its functional traits have evolved may help to get a broad picture of its biological role in each single species. Here, we present a simple computational workflow to identify close and distant sRNA homologs present in sequenced bacterial genomes, which allows defining novel sRNA families. This strategy is based on the use of Covariance Models (CM) and assumes the conservation of sequence and structure of functional sRNA genes throughout evolution. Moreover, by carefully inspecting the conservation of the close genomic context of every member of the RNA family and how the patterns of microsynteny follow the path of species evolution, it is possible to define subgroups of sRNA orthologs, which in turn enables the definition of RNA subfamilies.
MeSH term(s)	Bacteria/genetics ; Computational Biology/methods ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Genome, Bacterial ; Guidelines as Topic ; Molecular Sequence Annotation ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Small Untranslated/genetics ; Sequence Analysis, RNA/methods ; Trans-Activators/genetics
Chemical Substances	RNA, Bacterial ; RNA, Small Untranslated ; Trans-Activators
Language	English
Publishing date	2018-02-26
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-7634-8_2
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Article ; Online: Characterization of an accessory plasmid of Sinorhizobium meliloti and its two replication-modules.

Luchetti, Abril / Castellani, Lucas G / Toscani, Andrés Martin / Lagares, Antonio / Del Papa, María Florencia / Torres Tejerizo, Gonzalo / Pistorio, Mariano

PloS one

2023 Volume 18, Issue 5, Page(s) e0285505

Abstract: Rhizobia are Gram-negative bacteria known for their ability to fix atmospheric N2 in symbiosis with leguminous plants. Current evidence shows that rhizobia carry in most cases a variable number of plasmids, containing genes necessary for symbiosis or ... ...

Abstract	Rhizobia are Gram-negative bacteria known for their ability to fix atmospheric N2 in symbiosis with leguminous plants. Current evidence shows that rhizobia carry in most cases a variable number of plasmids, containing genes necessary for symbiosis or free-living, a common feature being the presence of several plasmid replicons within the same strain. For many years, we have been studying the mobilization properties of pSmeLPU88b from the strain Sinorhizobium meliloti LPU88, an isolate from Argentina. To advance in the characterization of pSmeLPU88b plasmid, the full sequence was obtained. pSmeLPU88b is 35.9 kb in size, had an average GC % of 58.6 and 31 CDS. Two replication modules were identified in silico: one belonging to the repABC type, and the other to the repC. The replication modules presented high DNA identity to the replication modules from plasmid pMBA9a present in an S. meliloti isolate from Canada. In addition, three CDS presenting identity with recombinases and with toxin-antitoxin systems were found downstream of the repABC system. It is noteworthy that these CDS present the same genetic structure in pSmeLPU88b and in other rhizobial plasmids. Moreover, in all cases they are found downstream of the repABC operon. By cloning each replication system in suicide plasmids, we demonstrated that each of them can support plasmid replication in the S. meliloti genetic background, but with different stability behavior. Interestingly, while incompatibility analysis of the cloned rep systems results in the loss of the parental module, both obtained plasmids can coexist together.
MeSH term(s)	Humans ; Sinorhizobium meliloti/genetics ; Plasmids/genetics ; DNA, Bacterial/genetics ; Replicon/genetics ; DNA Replication/genetics ; Rhizobium/genetics ; Bacterial Proteins/genetics
Chemical Substances	DNA, Bacterial ; Bacterial Proteins
Language	English
Publishing date	2023-05-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0285505
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Article ; Online: Quantification of Bacterial Polyhydroxybutyrate Content by Flow Cytometry.

Lagares, Antonio / Valverde, Claudio

Bio-protocol

2017 Volume 7, Issue 23, Page(s) e2638

Abstract: We describe here a detailed protocol for the quantification of the intracellular content of polyhydroxybutyrate (PHB) in a population of bacterial cells by flow cytometry, which is based on a consensus of several previously reported works. ...

Abstract	We describe here a detailed protocol for the quantification of the intracellular content of polyhydroxybutyrate (PHB) in a population of bacterial cells by flow cytometry, which is based on a consensus of several previously reported works.
Language	English
Publishing date	2017-12-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2833269-6
ISSN	2331-8325 ; 2331-8325
ISSN (online)	2331-8325
ISSN	2331-8325
DOI	10.21769/BioProtoc.2638
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Article: Diversity, Genomics and Symbiotic Characteristics of Sinorhizobia That Nodulate

Zuber, Nicolás Emilio / Fornasero, Laura Viviana / Erdozain Bagolín, Sofía Agostina / Lozano, Mauricio Javier / Sanjuán, Juan / Del Papa, María Florencia / Lagares, Antonio

Biology

2023 Volume 12, Issue 7

Abstract: ... ...

Abstract	Desmanthus
Language	English
Publishing date	2023-07-04
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2661517-4
ISSN	2079-7737
ISSN	2079-7737
DOI	10.3390/biology12070958
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Article ; Online: Comparative Proteomic Analysis Revealing ActJ-Regulated Proteins in

Albicoro, Francisco Javier / Vacca, Carolina / Cafiero, Juan Hilario / Draghi, Walter Omar / Martini, María Carla / Goulian, Mark / Lagares, Antonio / Del Papa, María Florencia

Journal of proteome research

2023 Volume 22, Issue 6, Page(s) 1682–1694

Abstract: To adapt to different environmental conditions, ...

Abstract	To adapt to different environmental conditions,
MeSH term(s)	Sinorhizobium meliloti/genetics ; Sinorhizobium meliloti/metabolism ; Proteomics ; Proteome/genetics ; Proteome/metabolism ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Gene Expression Regulation, Bacterial ; Symbiosis/genetics
Chemical Substances	Proteome ; Bacterial Proteins
Language	English
Publishing date	2023-04-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.2c00731
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Article ; Online: Diversity, Genomics and Symbiotic Characteristics of Sinorhizobia That Nodulate Desmanthus spp. in Northwest Argentina

Zuber, Nicolás Emilio / Fornasero, Laura Viviana / Erdozain Bagolín, Sofía Agostina / Lozano, Mauricio Javier / Sanjuán, Juan / Del Papa, María Florencia / Lagares, Antonio

Biology (Basel). 2023 July 04, v. 12, no. 7

2023

Abstract: Desmanthus spp. are legumes with the ability to associate with diverse α-proteobacteria—a microsymbiont—in order to establish nitrogen-fixing root nodules. A previous investigation from our laboratory revealed that the main bacteria associated with ... ...

Abstract	Desmanthus spp. are legumes with the ability to associate with diverse α-proteobacteria—a microsymbiont—in order to establish nitrogen-fixing root nodules. A previous investigation from our laboratory revealed that the main bacteria associated with Desmanthus paspalaceus in symbiosis in central Argentina (Province of Santa Fe) were quite diverse and belonged to the genera Rhizobium and Mesorhizobium. To achieve a more extensive view of the local microsymbionts associated with Desmanthus spp., we sampled three different sites in Jujuy and Salta, in northwest Argentina. Matrix-assisted Laser-Desorption-Ionization Time-of-Flight mass spectrometry (MALDI-TOF) typing, 16S-rDNA analysis, and genome sequencing demonstrated that the dominant root-nodule microsymbionts belonged to the genus Sinorhizobium, with some sequenced genomes related to Sinorhizobium mexicanum, Sinorhizobium chiapanecum, and Sinorhizobium psoraleae. An analysis of nodA and nodC markers indicated that, in some of the isolates, horizontal gene transfer appeared to be responsible for the lack of congruence between the phylogenies of the chromosome and of the symbiotic region. These results revealed diverse evolutionary strategies for reaching the current Desmanthus-microsymbiont diversity. What is remarkable beside their observed genetic diversity is that the tolerance profiles of these isolates to abiotic stresses (temperature, salt concentration, pH) were quite coincident with the separation of the sinorhizobia according to place of origin, suggesting possible ecoedaphic adaptations. This observation, together with the higher aerial dry-weight matter that some isolates generated in Desmanthus virgatus cv. Marc when compared to the biomass generated by the commercial strain Sinorhizobium terangae CB3126, distinguish the collected sinorhizobia as constituting valuable germplasm for evaluation in local fields to select for more efficient symbiotic pairs.
Keywords	Desmanthus virgatus ; Mesorhizobium ; Rhizobium ; Sinorhizobium terangae ; biomass ; chromosomes ; genetic variation ; genome ; genomics ; germplasm ; horizontal gene transfer ; mass spectrometry ; microsymbionts ; nitrogen fixation ; pH ; phylogeny ; root nodules ; salt concentration ; symbiosis ; temperature ; Argentina
Language	English
Dates of publication	2023-0704
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article ; Online
ZDB-ID	2661517-4
ISSN	2079-7737
ISSN	2079-7737
DOI	10.3390/biology12070958
Database	NAL-Catalogue (AGRICOLA)

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Article: Curtobacterium, A Foliar Pathogen Isolated from Maize in Central Argentina

López-Ramírez, Viviana / Ruíz, Marcos / Rossi, Ezequiel / Zuber, Nicolás / Lagares, Antonio / Balzarini, Mónica / Bonamico, Natalia / Fischer, Sonia

Current microbiology. 2022 Sept., v. 79, no. 9

2022

Abstract: Plant pathogens, such as fungi, bacteria, and viruses, can cause serious damage to crops and significantly reduce yield and quality. Bacterial diseases of agronomic crops, however, have been little studied. The present study aims to isolate and identify ... ...

Abstract	Plant pathogens, such as fungi, bacteria, and viruses, can cause serious damage to crops and significantly reduce yield and quality. Bacterial diseases of agronomic crops, however, have been little studied. The present study aims to isolate and identify bacteria recovered from symptomatic maize (Zea mays) leaves collected from field samples in the province of Cordoba, Argentina. Bacterial strains were identified using whole-cell matrix-assisted laser-desorption-ionization–time-off light mass spectrometry and 16S rDNA sequencing. Members of the genera Exiguobacterium and Curtobacterium were dominant in the studied vegetal material. Two strains (RC18-1/2 and RC18-3/1) were selected for further studies. The pathogenicity test showed that plants inoculated with Curtobacterium sp. RC18-1/2 exhibited the same symptoms as those previously detected in the field. To our knowledge, this study provides the first evidence about the isolation of a Curtobacterium pathogenic strain in maize. Effective crop disease management will require the use of integrated strategies, such as resistant cultivars and/or biocontrol agents.
Keywords	Curtobacterium ; Exiguobacterium ; Zea mays ; biological control ; corn ; cultivars ; disease control ; mass spectrometry ; pathogenicity ; virulent strains ; Argentina
Language	English
Dates of publication	2022-09
Size	p. 261.
Publishing place	Springer US
Document type	Article
ZDB-ID	134238-1
ISSN	1432-0991 ; 0343-8651
ISSN (online)	1432-0991
ISSN	0343-8651
DOI	10.1007/s00284-022-02953-y
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Modular Low-Copy-Number Plasmid Vectors for Rhodobacterales with Extended Host Range in Alphaproteobacteria.

Körner, Désirée / Schäfer, Niklas M / Lagares, Antonio / Birmes, Lukas / Oehlmann, Niels N / Addison, Holly / Pöhl, Sebastian / Thanbichler, Martin / Rebelein, Johannes G / Petersen, Jörn / Becker, Anke

ACS synthetic biology

2024 Volume 13, Issue 5, Page(s) 1537–1548

Abstract: Members of the alphaproteobacterial order Rhodobacterales are metabolically diverse and highly abundant in the ocean. They are becoming increasingly interesting for marine biotechnology, due to their ecological adaptability, wealth of versatile low-copy- ... ...

Abstract	Members of the alphaproteobacterial order Rhodobacterales are metabolically diverse and highly abundant in the ocean. They are becoming increasingly interesting for marine biotechnology, due to their ecological adaptability, wealth of versatile low-copy-number plasmids, and their ability to produce secondary metabolites. However, molecular tools for engineering strains of this bacterial lineage are limited. Here, we expand the genetic toolbox by establishing standardized, modular
MeSH term(s)	Plasmids/genetics ; Genetic Vectors/genetics ; Alphaproteobacteria/genetics ; Host Specificity/genetics
Language	English
Publishing date	2024-05-08
Publishing country	United States
Document type	Journal Article
ISSN	2161-5063
ISSN (online)	2161-5063
DOI	10.1021/acssynbio.4c00062
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