LIVIVO - Search results -

Search results

Result 1 - 10 of total 28

Search options

Article ; Online: Selection of Reference Genes for Transcription Studies Considering Co-Regulation and Average Transcriptional Stability: Case Study on Adventitious Root Induction in Olive (Olea europaea L.) Microshoots

Noceda, Carlos / Peixe, Augusto / Arnholdt-Schmitt, Birgit

Agronomy. 2022 Dec. 16, v. 12, no. 12

2022

Abstract: Selection of reference genes (RGs) for normalization of PCR-gene expression data includes two crucial steps: determination of the between-sample transcriptionally more stable genes, and subsequent choosing of the most suitable genes as internal controls. ...

Abstract	Selection of reference genes (RGs) for normalization of PCR-gene expression data includes two crucial steps: determination of the between-sample transcriptionally more stable genes, and subsequent choosing of the most suitable genes as internal controls. Both steps can be carried out through generally accepted strategies, each having different strengths and weaknesses. The present study proposes reinforcement of the normalization of gene expression data by integrating analytical revision at critical steps of those accepted procedures. In vitro olive adventitious rooting was used as an experimental system. Candidate RGs were ranked according to transcriptional stability according to several methods. An algorithm of one of these programs (GeNorm) was adapted to allow for partial automatization of RG selection for any strategy of transcriptional-gene stability ordering. In order to choose the more appropriate set of RGs, the achieved results were analytically revised, with special emphasis on biasing effects such as co-regulation. The obtained putative RG sets were also tested for cases restricted to fewer variables. The set formed by the genes H2B, OUB and ACT is valid for normalization in transcriptional studies on olive microshoot rooting when comparing treatments, time points and assays. Such internal reference is now available for wider expression studies on any target gene in similar biological systems. The overall methodology aims to constitute a guide for general application.
Keywords	Olea europaea ; adventitious roots ; agronomy ; algorithms ; case studies ; gene expression ; genes ; olives ; rooting ; transcription (genetics)
Language	English
Dates of publication	2022-1216
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article ; Online
ZDB-ID	2607043-1
ISSN	2073-4395
ISSN	2073-4395
DOI	10.3390/agronomy12123201
Database	NAL-Catalogue (AGRICOLA)

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.

Article: Detection of hibiscus latent Fort Pierce virus in hibiscus (Hibiscus rosa-sinensis L.) and in a water source in Ecuador

Guevara, Fiama Estefany / Peredes, Estefany / Viera, William / Noceda, Carlos / Flores, Francisco Javier

Journal of plant pathology. 2022 Feb., v. 104, no. 1

2022

Abstract: Hibiscus latent Fort Pierce virus (HLFPV) is a member of the genus Tobamovirus (family Virgaviridae) and a common virus infecting members of the family Malvaceae. This research presents the first report of HLFPV detection in hibiscus plants with viral ... ...

Abstract	Hibiscus latent Fort Pierce virus (HLFPV) is a member of the genus Tobamovirus (family Virgaviridae) and a common virus infecting members of the family Malvaceae. This research presents the first report of HLFPV detection in hibiscus plants with viral symptoms and the use of high throughput sequencing (HTS) to detect this virus in a water source in Ecuador. The near complete genome (99.41%) of HLFPV was assembled.
Keywords	Hibiscus latent Fort Pierce virus ; Hibiscus rosa-sinensis ; genome ; plant pathology ; viruses ; Ecuador
Language	English
Dates of publication	2022-02
Size	p. 33-35.
Publishing place	Edizioni ETS
Document type	Article
ZDB-ID	1378427-4
ISSN	2239-7264 ; 1125-4653
ISSN (online)	2239-7264
ISSN	1125-4653
Database	NAL-Catalogue (AGRICOLA)

In stock of ZB MED Bonn / Germany

Z 6602: Show issues

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.

Details ▾
- See ZB MED holdings
- Order with fees

Article: Major Complex Trait for Early De Novo Programming 'CoV-MAC-TED' Detected in Human Nasal Epithelial Cells Infected by Two SARS-CoV-2 Variants Is Promising to Help in Designing Therapeutic Strategies.

Costa, José Hélio / Aziz, Shahid / Noceda, Carlos / Arnholdt-Schmitt, Birgit

Vaccines

2021 Volume 9, Issue 12

Abstract: Background: Early metabolic reorganization was only recently recognized as an essentially integrated part of immunology. In this context, unbalanced ROS/RNS levels connected to increased aerobic fermentation, which is linked to alpha-tubulin-based cell ... ...

Abstract	Background: Early metabolic reorganization was only recently recognized as an essentially integrated part of immunology. In this context, unbalanced ROS/RNS levels connected to increased aerobic fermentation, which is linked to alpha-tubulin-based cell restructuring and control of cell cycle progression, were identified as a major complex trait for early de novo programming ('CoV-MAC-TED') during SARS-CoV-2 infection. This trait was highlighted as a critical target for developing early anti-viral/anti-SARS-CoV-2 strategies. To obtain this result, analyses had been performed on transcriptome data from diverse experimental cell systems. A call was released for wide data collection of the defined set of genes for transcriptome analyses, named 'ReprogVirus', which should be based on strictly standardized protocols and data entry from diverse virus types and variants into the 'ReprogVirus Platform'. This platform is currently under development. However, so far, an in vitro cell system from primary target cells for virus attacks that could ideally serve for standardizing the data collection of early SARS-CoV-2 infection responses has not been defined. Results: Here, we demonstrate transcriptome-level profiles of the most critical 'ReprogVirus' gene sets for identifying 'CoV-MAC-TED' in cultured human nasal epithelial cells infected by two SARS-CoV-2 variants differing in disease severity. Our results (a) validate 'Cov-MAC-TED' as a crucial trait for early SARS-CoV-2 reprogramming for the tested virus variants and (b) demonstrate its relevance in cultured human nasal epithelial cells. Conclusion: In vitro-cultured human nasal epithelial cells proved to be appropriate for standardized transcriptome data collection in the 'ReprogVirus Platform'. Thus, this cell system is highly promising to advance integrative data analyses with the help of artificial intelligence methodologies for designing anti-SARS-CoV-2 strategies.
Language	English
Publishing date	2021-11-26
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2703319-3
ISSN	2076-393X
ISSN	2076-393X
DOI	10.3390/vaccines9121399
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: Transcriptome Analyses in Adult Olive Trees Indicate Acetaldehyde Release and Cyanide-Mediated Respiration Traits as Critical for Tolerance against

Arnholdt-Schmitt, Birgit / Sircar, Debabrata / Aziz, Shahid / Germano, Thais Andrade / Thiers, Karine Leitão Lima / Noceda, Carlos / Bharadwaj, Revuru / Mohanapriya, Gunasekaran / Costa, José Hélio

Pathogens (Basel, Switzerland)

2024 Volume 13, Issue 3

Abstract: ... Xylella ... ...

Abstract	Xylella fastidiosa
Language	English
Publishing date	2024-03-05
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens13030227
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: Metabolomics, a Powerful Tool for Understanding Plant Abiotic Stress

Carrera, Fredy P / Noceda, Carlos / Maridueña-Zavala, María G / Cevallos-Cevallos, Juan M

Agronomy. 2021 Apr. 22, v. 11, no. 5

2021

Abstract: Metabolomics is a technology that generates large amounts of data and contributes to obtaining wide and integral explanations of the biochemical state of a living organism. Plants are continuously affected by abiotic stresses such as water scarcity, high ...

Abstract	Metabolomics is a technology that generates large amounts of data and contributes to obtaining wide and integral explanations of the biochemical state of a living organism. Plants are continuously affected by abiotic stresses such as water scarcity, high temperatures and high salinity, and metabolomics has the potential for elucidating the response-to-stress mechanisms and develop resistance strategies in affected cultivars. This review describes the characteristics of each of the stages of metabolomic studies in plants and the role of metabolomics in the characterization of the response of various plant species to abiotic stresses.
Keywords	abiotic stress ; agronomy ; cultivars ; metabolomics ; salinity ; water shortages
Language	English
Dates of publication	2021-0422
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2607043-1
ISSN	2073-4395
ISSN	2073-4395
DOI	10.3390/agronomy11050824
Database	NAL-Catalogue (AGRICOLA)

Order via subito

Article ; Online: Polymorphisms in alternative oxidase genes from ecotypes of Arabidopsis and rice revealed an environment‐induced linkage to altitude and rainfall

Thiers, Karine Leitão Lima / da Silva, João Hermínio Martins / Vasconcelos, Disraeli Cavalcante Araújo / ʻAzīz, Shāhid / Noceda, Carlos / Arnholdt‐Schmitt, Birgit / Costa, José Hélio

Physiologia Plantarum. 2023 Jan., v. 175, no. 1 p.e13847-

2023

Abstract: We investigated SNPs in alternative oxidase (AOX) genes and their connection to ecotype origins (climate, altitude, and rainfall) by using genomic data sets of Arabidopsis and rice populations from 1190 and 90 ecotypes, respectively. Parameters were ... ...

Abstract	We investigated SNPs in alternative oxidase (AOX) genes and their connection to ecotype origins (climate, altitude, and rainfall) by using genomic data sets of Arabidopsis and rice populations from 1190 and 90 ecotypes, respectively. Parameters were defined to detect non‐synonymous SNPs in the AOX ORF, which revealed amino acid (AA) changes in AOX1c, AOX1d, and AOX2 from Arabidopsis and AOX1c from rice in comparison to AOX references from Columbia‐0 and Japonica ecotypes, respectively. Among these AA changes, Arabidopsis AOX1c_A161E&G165R and AOX1c_R242S revealed a link to high rainfall and high altitude, respectively, while all other changes in Arabidopsis and rice AOX was connected to high altitude and rainfall. Comparative 3D modeling showed that all mutant AOX presented structural differences in relation to the respective references. Molecular docking analysis uncovered lower binding affinity values between AOX and the substrate ubiquinol for most of the identified structures compared to their reference, indicating better enzyme‐substrate binding affinities. Thus, our in silico data suggest that the majority of the AA changes found in the available ecotypes will confer better enzyme‐subtract interactions and thus indicate environment‐related, more efficient AOX activity.
Keywords	Arabidopsis ; altitude ; amino acids ; climate ; computer simulation ; ecotypes ; enzyme substrates ; genomics ; mutants ; oxidoreductases ; rain ; rice
Language	English
Dates of publication	2023-01
Publishing place	Blackwell Publishing Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2020837-6
ISSN	1399-3054 ; 0031-9317
ISSN (online)	1399-3054
ISSN	0031-9317
DOI	10.1111/ppl.13847
Database	NAL-Catalogue (AGRICOLA)

Order via subito

Article ; Online: Polymorphisms in alternative oxidase genes from ecotypes of Arabidopsis and rice revealed an environment-induced linkage to altitude and rainfall.

Thiers, Karine Leitão Lima / da Silva, João Hermínio Martins / Vasconcelos, Disraeli Cavalcante Araújo / Aziz, Shahid / Noceda, Carlos / Arnholdt-Schmitt, Birgit / Costa, José Hélio

Physiologia plantarum

2022 Volume 175, Issue 1, Page(s) e13847

Abstract	We investigated SNPs in alternative oxidase (AOX) genes and their connection to ecotype origins (climate, altitude, and rainfall) by using genomic data sets of Arabidopsis and rice populations from 1190 and 90 ecotypes, respectively. Parameters were defined to detect non-synonymous SNPs in the AOX ORF, which revealed amino acid (AA) changes in AOX1c, AOX1d, and AOX2 from Arabidopsis and AOX1c from rice in comparison to AOX references from Columbia-0 and Japonica ecotypes, respectively. Among these AA changes, Arabidopsis AOX1c_A161E&G165R and AOX1c_R242S revealed a link to high rainfall and high altitude, respectively, while all other changes in Arabidopsis and rice AOX was connected to high altitude and rainfall. Comparative 3D modeling showed that all mutant AOX presented structural differences in relation to the respective references. Molecular docking analysis uncovered lower binding affinity values between AOX and the substrate ubiquinol for most of the identified structures compared to their reference, indicating better enzyme-substrate binding affinities. Thus, our in silico data suggest that the majority of the AA changes found in the available ecotypes will confer better enzyme-subtract interactions and thus indicate environment-related, more efficient AOX activity.
MeSH term(s)	Arabidopsis/metabolism ; Oryza/metabolism ; Ecotype ; Altitude ; Molecular Docking Simulation ; Plant Proteins/metabolism ; Mitochondrial Proteins/metabolism
Chemical Substances	alternative oxidase (EC 1.-) ; Plant Proteins ; Mitochondrial Proteins
Language	English
Publishing date	2022-12-23
Publishing country	Denmark
Document type	Journal Article
ZDB-ID	2020837-6
ISSN	1399-3054 ; 0031-9317
ISSN (online)	1399-3054
ISSN	0031-9317
DOI	10.1111/ppl.13847
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: Somatic embryogenesis and plant regeneration from leaf of the interspecific hybrid of mahogany (Swietenia macrophylla King × S. mahagoni (L.) Jacq.)

Quiala, Elisa / Barbón, Raúl / Mestanza, Saúl / La O, Mariana / Merlan, Gardenis / Nuñez-Ramos, Jenny / Pérez, Naivy / Leiva, Michel / Jiménez, Elio / Daniels, Dion / Noceda, Carlos

Trees. 2022 Feb., v. 36, no. 1

2022

Abstract: KEY MESSAGE : A protocol for somatic embryogenesis here described, open the possibility for the clonal propagation of selected trees of the natural hybrid of mahogany Swietenia macrophylla King × S. mahagoni (L.) Jacq. Young leaves were collected from ... ...

Abstract	KEY MESSAGE : A protocol for somatic embryogenesis here described, open the possibility for the clonal propagation of selected trees of the natural hybrid of mahogany Swietenia macrophylla King × S. mahagoni (L.) Jacq. Young leaves were collected from greenhouse plants cloned from epicormic shoots of a 35-year-old interspecific hybrid of mahogany (Swietenia macrophylla King × S. mahagoni (L.) Jacq.) tree. All explants formed calli when cultured on a medium containing Murashige and Skoog salts, 3% sucrose (Lobachemie), 0.3% Phytagel (Sigma) and 4.52 µM 2,4-dichlorophenoxyacetic acid and regardless of the concentration of kinetin used (4.65, 9.29 or 13.94 µM). After 3 months, the calli were separated from the leaf segments and subcultured on differentiation medium. The greatest number of calli (38–40%) forming somatic embryos, after 6 months of culture, was obtained on the differentiation media containing 4.44 or 6.66 µM benzyladenine (BA). Secondary or repetitive somatic embryogenesis was achieved when primary cotyledonary somatic embryos were subcultured on fresh medium of the same composition as differentiation medium containing 4.44 µM BA. Numerous cotyledonary somatic embryos were developed after 5 weeks of subculture on differentiation medium with decreased BA concentration (1.77 µM). Thereby, developed somatic embryos had different morphological features, which are described herein. The highest frequency of somatic embryo germination (62%) was obtained using half-strength MS medium supplemented with 0.27 µM of BA plus 0.145 µM of gibberellic acid. Twenty-five percent of the plantlets developed normally in the greenhouse. In this study, a somatic embryogenesis system was established from leaf explants of a natural hybrid of mahogany Swietenia macrophylla King × S. mahagoni (L.) Jacq was established, hence opening the possibility for the clonal propagation of selected trees of this natural hybrid.
Keywords	2,4-D ; Swietenia macrophylla ; benzyladenine ; callus ; epicormics ; germination ; gibberellic acid ; greenhouses ; hybrids ; kinetin ; leaves ; plantlets ; somatic embryogenesis ; sucrose ; trees
Language	English
Dates of publication	2022-02
Size	p. 167-178.
Publishing place	Springer Berlin Heidelberg
Document type	Article
ZDB-ID	90595-1
ISSN	1432-2285 ; 0931-1890
ISSN (online)	1432-2285
ISSN	0931-1890
DOI	10.1007/s00468-021-02192-x
Database	NAL-Catalogue (AGRICOLA)

In stock of ZB MED Bonn / Germany

Z 4635: Show issues

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.

Details ▾
- See ZB MED holdings
- Order with fees

Article: Changes in the Metabolite Profile during Micropropagation of Normal and Somaclonal Variants of Banana Musa AAA cv. Williams

Carrera, Fredy P / Noceda, Carlos / Maridueña-Zavala, María G / García, José A / Ruiz-Barzola, Omar / Cevallos-Cevallos, Juan M

Horticulturae. 2021 Feb. 26, v. 7, no. 3

2021

Abstract: Micropropagation techniques allow the mass production of banana plants but can cause somaclonal variations such as dwarfism. Changes in the metabolite profile during micropropagation of normal (NP) and dwarf (DP) banana plants have not been described. ... ...

Abstract	Micropropagation techniques allow the mass production of banana plants but can cause somaclonal variations such as dwarfism. Changes in the metabolite profile during micropropagation of normal (NP) and dwarf (DP) banana plants have not been described. Both, NPs and DPs of banana Musa AAA cv. Williams were micropropagated and the metabolite profile of vitroplants was assessed at the proliferation (PP), rooting (RP) and the second greenhouse-acclimatization (APII) phases of tissue culture. Metabolites from 10 DPs and 10 NPs meristems from each micropropagation phase were extracted and identified by gas chromatography coupled with mass spectrometry (GC-MS). Principal component analysis (PCA) and test of statistical significance were applied to detect differentially accumulated metabolites. The PCA showed a clear grouping of DPs separated from NPs in RP and APII. Among the differentially accumulated metabolites, various precursors of apoplast components including arabinose and galactose or deoxygalactose in both PP and RP, as well as mannose and fucose in APII were under-accumulated in DPs. Results suggest affected apoplast composition during micropropagation of DPs.
Keywords	Musa ; apoplast ; arabinose ; bananas ; dwarfing ; fucose ; galactose ; mannose ; meristems ; metabolites ; micropropagation ; principal component analysis ; tissue culture
Language	English
Dates of publication	2021-0226
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2813983-5
ISSN	2311-7524
ISSN	2311-7524
DOI	10.3390/horticulturae7030039
Database	NAL-Catalogue (AGRICOLA)

Order via subito

Article: Phylodynamics and Coat Protein Analysis of Babaco Mosaic Virus in Ecuador.

Mosquera-Yuqui, Francisco / Flores, Francisco J / Moncayo, Eduardo A / Garzón-Proaño, Brighitte A / Méndez, Miguel A / Guevara, Fiama E / Quito-Avila, Diego F / Viera, William / Cornejo-Franco, Juan F / Izquierdo, Andrés R / Noceda, Carlos

Plants (Basel, Switzerland)

2022 Volume 11, Issue 13

Abstract: Babaco is a fast-growing herbaceous shrub with great commercial potential because of the organoleptic properties of its fruit. Babaco mosaic virus (BabMV) is a potexvirus in the ... ...

Abstract	Babaco is a fast-growing herbaceous shrub with great commercial potential because of the organoleptic properties of its fruit. Babaco mosaic virus (BabMV) is a potexvirus in the family
Language	English
Publishing date	2022-06-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants11131646
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

To top

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Bonn / Germany

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

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

More links

Kategorien

In stock of ZB MED Bonn / Germany

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito