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"Carmona, José"
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Genome-Wide Analysis of MIKCC-Type MADS Box Genes in Grapevine
by
Díaz-Riquelme, José
,
Carmona, María José
,
Martínez-Zapater, José M
in
Arabidopsis thaliana
,
asexual reproduction
,
Biological and medical sciences
2009
MIKCC-type MADS box genes encode transcription factors that play crucial roles in plant growth and development. Analysis of the grapevine (Vitis vinifera) genome revealed up to 38 MIKCC-type genes. We report here a complete analysis of this gene family regarding their phylogenetic relationships with homologous genes identified in other sequenced dicot genomes, their genome location, and gene structure and expression. The grapevine genes cluster in 13 subfamilies with their Arabidopsis (Arabidopsis thaliana) and poplar (Populus trichocarpa) counterparts. The lack of recent whole genome duplications in grapevine allows assigning the gene diversification processes observed within each subfamily either to an ancestral polyploidization event predating the divergence of those three species or to later duplication events within each lineage. Expression profiles of MIKCC-type genes in vegetative and reproductive organs as well as during flower and tendril development show conserved expression domains for specific subfamilies but also reflect characteristic features of grapevine development. Expression analyses in latent buds and during flower development reveal common features previously described in other plant systems as well as possible new roles for members of some subfamilies during flowering transition. The analysis of MIKCC-type genes in grapevine helps in understanding the origin of gene diversification within each subfamily and provides the basis for functional analyses to uncover the role of these MADS box genes in grapevine development.
Journal Article
Experimental evolution of bet hedging in rotifer diapause traits as a response to environmental unpredictability
by
Carmona Navarro, María José
,
García Roger, Eduardo M.
,
Tarazona, Eva
in
Brachionus plicatilis
,
Diapause
,
directed evolution
2017
The adaptive response of organisms to unpredictable environments is increasingly recognized as a central topic in fundamental and applied evolutionary ecology. Selection due to environmental unpredictability can act on multiple traits of an organism's life cycle to reduce the impact of high environmental variance. The aim of this research was to study how unpredictability selects for diapause traits: 1) the timing of sex (a proxy of the timing of diapausing egg production), and 2) the diapausing egg hatching fraction (a proxy of diapause duration). We used an experimental evolution approach with the facultative sexual rotifer Brachionus plicatilis. Laboratory populations experiencing two contrasting regimes of environmental fluctuation (predictable versus unpredictable) evolved divergently over a short time span (< 77 days). The populations under the unpredictable regime showed an earlier initiation of sexual reproduction and a lower hatching fraction of diapausing eggs than populations under the predictable regime. These findings demonstrate empirically the existence of bet-hedging strategies in B. plicatilis regarding both traits, consistent with theoretical predictions of bet-hedging evolution under conditions of unpredictable environmental variance. Given that scenarios of increased environmental variability are expected to occur in the near future, a comprehensive understanding of the role of bet-hedging strategies is necessary for predicting population responses to environmental change.
Journal Article
Adaptation in response to environmental unpredictability
by
Serra Galindo, Manuel
,
Franch-Gras, L.
,
Carmona Navarro, María José
in
Animals
,
Bet Hedging
,
Biological Evolution
2017
Understanding how organisms adaptively respond to environmental fluctuations is a fundamental question in evolutionary biology. The Mediterranean region typically exhibits levels of environmental unpredictability that vary greatly in habitats over small geographical scales. In cyclically parthenogenetic rotifers, clonal proliferation occurs along with occasional bouts of sex. These bouts contribute to the production of diapausing eggs, which allows survival between growing seasons. Here,we studied two diapause-related traits in rotifers using clones from nine Brachionus plicatilis natural populations that vary in the degree of environmental unpredictability.We tested the hypothesis that the level of environmental unpredictability is directly related to the propensity for sex and inversely related to the hatching fraction of diapausing eggs.We found significant levels of genetic variation within populations for both traits. Interestingly, a positive correlation between pond unpredictability¿quantified in a previous study from satellite imagery¿and the propensity for sex was found. This correlation suggests a conservative, bet-hedging strategy that provides protection against unexpectedly short growing seasons. By contrast, the hatching fraction of diapausing eggswas not related to the level of environmental predictability. Our results highlight the ability of rotifer populations to locally adapt to time-varying environments, providing an evolutionarily relevant step forward in relating life-history traits to a quantitative measure of environmental unpredictability.
Journal Article
A survey of the kinome pharmacopeia reveals multiple scaffolds and targets for the development of novel anthelmintics
by
Zuercher, William
,
Carmona-Negrón, José A.
,
Knox, Jessica
in
631/92/275
,
631/92/507
,
631/92/555
2021
Over one billion people are currently infected with a parasitic nematode. Symptoms can include anemia, malnutrition, developmental delay, and in severe cases, death. Resistance is emerging to the anthelmintics currently used to treat nematode infection, prompting the need to develop new anthelmintics. Towards this end, we identified a set of kinases that may be targeted in a nematode-selective manner. We first screened 2040 inhibitors of vertebrate kinases for those that impair the model nematode
Caenorhabditis elegans
. By determining whether the terminal phenotype induced by each kinase inhibitor matched that of the predicted target mutant in
C. elegans
, we identified 17 druggable nematode kinase targets. Of these, we found that nematode EGFR, MEK1, and PLK1 kinases have diverged from vertebrates within their drug-binding pocket. For each of these targets, we identified small molecule scaffolds that may be further modified to develop nematode-selective inhibitors. Nematode EGFR, MEK1, and PLK1 therefore represent key targets for the development of new anthelmintic medicines.
Journal Article
Analysis of Global Research on Malaria and Plasmodium vivax
by
Manzano Agugliaro, Francisco Rogelio
,
Mesa Valle, Concepción
,
González Cerón, Lilia
in
Bibliographic data bases
,
Bibliometrics
,
chloroquine
2019
Background: Malaria is one of the infectious diseases of greatest interest to the scientific community and of greatest concern to international health authorities. Traditionally, the focus has been on Plasmodium falciparum, the parasite that causes the most severe form of the disease in Africa. However, in the last twenty years, the Plasmodium vivax parasite, responsible for a large number of cases in Latin America, the Middle East, South and Southeast Asia, the Horn of Africa, and Oceania, has also generated enormous interest due, among other things, to the published evidence that it can cause severe malaria. Methods: In this paper, the international scientific publication on malaria and P. vivax has been analyzed using the Scopus database to try to define global trends in this field of study. Results: It has been shown that events such as the emergence of resistance to certain drugs can break a trend. The important role of non-malaria-endemic countries such as the USA or Switzerland in malaria research is also evident. Conclusions: International cooperation will be essential for the eradication of the disease. Moreover, in this sense, the general vision given by the bibliometric analysis of malaria caused by P. vivax is fundamental to paint the picture regarding the current situation and encourage international cooperation and control efforts.
Journal Article
Structural and functional annotation of the MADS-box transcription factor family in grapevine
by
Grimplet, Jérôme
,
Carmona, María José
,
Martínez-Zapater, José Miguel
in
Animal Genetics and Genomics
,
Biomedical and Life Sciences
,
Gene Expression Regulation, Plant - genetics
2016
Background
MADS-box genes encode transcription factors that are involved in developmental control and signal transduction in eukaryotes. In plants, they are associated to numerous development processes most notably those related to reproductive development: flowering induction, specification of inflorescence and flower meristems, establishment of flower organ identity, as well as regulation of fruit, seed and embryo development. Genomic analyses of MADS-box genes in different plant species are providing new relevant information on the function and evolution of this transcriptional factor family. We have performed a true genome-wide analysis of the complete set of MADS-box genes in grapevine (
Vitis vinifera
), analyzed their expression pattern and establish their phylogenetic relationships (including MIKC* and type I MADS-box) with genes from 16 other plant species. This study was integrated to previous works on the family in grapevine.
Results
A total of 90 MADS-box genes were detected in the grapevine reference genome by completing current gene annotations with a genome-wide analysis based on sequence similarity. We performed a thorough in-depth curation of all gene models and combined the results with gene expression information including RNAseq data to clarifying the expression of newly identified genes and improve their functional characterization. Curated data were uploaded to the ORCAE database for grapevine in the frame of the grapevine genome curation effort. This approach resulted in the identification of 30 additional MADS box genes. Among them, ten new MIKC
C
genes were identified, including a potential new group of short proteins similar to the SVP protein subfamily. The MIKC* subgroup contains six genes in grapevine that can be grouped in the S (4 genes) and P (2 genes) clades, showing less redundancy than that observed in
Arabidopsis thaliana
. Expression pattern of these genes in grapevine is compatible with a role in male gametophyte development. Most of the identified new genes belong to the type I MADS-box genes and were classified as members of the Mα and Mγ subclasses. Ours analyses indicate that only few members of type I genes in grapevine have homology in other species and that species-specific clades appeared both in the Mα and Mγ subclasses. On the other hand, as deduced from the phylogenetic analysis with other plant species, genes that can be crucial for development of central cell, endosperm and embryos seems to be conserved in plants.
Conclusions
The genome analysis of MADS-box genes in grapevine, the characterization of their pattern of expression and the phylogenetic analysis with other plant species allowed the identification of new MADS-box genes not yet described in other plant species as well as basic characterization of their possible role, particularly in the case of type I and MIKC* genes.
Journal Article
Effect of the Welan Gum Concentration on the Rheological and Structural Behaviour of Biocomposite Hydrogels with Sepiolite as Filler
by
Calero, Nuria
,
Ramírez, Pablo
,
Carmona, José A.
in
Biocompatibility
,
Biomedical materials
,
Biopolymers
2022
A very positive and effective approach to tuning the mechanical properties of polymers has been the development of composites. This paper deals with novel biocomposite hydrogels composed by two biocompatible materials: welan gum as biopolymer matrix and sepiolite as filler. Welan gum content was studied as a tuning parameter to control the rheological properties of the developed biocomposites. The rheological and microstructural behaviour of the composites was investigated by mean of steady-state flow curves, creep-recovery tests, small amplitude oscillatory shear tests, and electron microscopy. An increase in welan gum content provoked the progressive disappearance of the shear-thinningzero-shear-thinning behaviour with a yield point which was clearly defined, characteristic of sepiolite gels, leading to a conventional shear-thinning behaviour, typical of polymeric systems. Also, a higher content of biopolymer in the mixtures led to a more elastic and compact structure characterized by higher values of both G’ and G”. The fundamental novelty was based on taking the flowability provided by the biopolymer as the main objective and reinforcing the viscosity yielded by welan gum with sepiolite, which contributed to increasing the biocomposite consistency. Thus, rheological properties can be adjusted, taking into account the balance of the components to adapt them to the requirements of each application.
Journal Article
Gene expression in diapausing rotifer eggs in response to divergent environmental predictability regimes
by
Carmona, María José
,
Lucas-Lledó, J. Ignacio
,
García-Roger, Eduardo M.
in
631/114
,
631/158
,
631/181
2020
In unpredictable environments in which reliable cues for predicting environmental variation are lacking, a diversifying bet-hedging strategy for diapause exit is expected to evolve, whereby only a portion of diapausing forms will resume development at the first occurrence of suitable conditions. This study focused on diapause termination in the rotifer
Brachionus plicatilis
s.s., addressing the transcriptional profile of diapausing eggs from environments differing in the level of predictability and the relationship of such profiles with hatching patterns. RNA-Seq analyses revealed significant differences in gene expression between diapausing eggs produced in the laboratory under combinations of two contrasting selective regimes of environmental fluctuation (predictable vs unpredictable) and two different diapause conditions (passing or not passing through forced diapause). The results showed that the selective regime was more important than the diapause condition in driving differences in the transcriptome profile. Most of the differentially expressed genes were upregulated in the predictable regime and mostly associated with molecular functions involved in embryo morphological development and hatching readiness. This was in concordance with observations of earlier, higher, and more synchronous hatching in diapausing eggs produced under the predictable regime.
Journal Article
3-Ferrocenyl-estra-1,3,5 (10)-triene-17-one: Synthesis, Crystal Structure, Hirshfeld Surface Analysis, DFT Studies, and Its Binding to Human Serum Albumin Studied through Fluorescence Quenching and In Silico Docking Studies
by
Carmona-Negrón, José A.
,
Meléndez, Enrique
,
Rheingold, Arnold L.
in
Albumin
,
Breast cancer
,
Crystal structure
2023
3-ferrocenyl-estra-1,3,5 (10)-triene-17-one (2), [Fe(C5H5)(C24H25O3)], crystallizes in the monoclinic space group C2. The cyclopentadienyl (Cp) rings adopt a nearly eclipsed conformation, and the Cp plane is tilted by 87.66° with respect to the substituted phenyl plane. An average Fe-C(Cp) bond length of 2.040(13) Å was determined, similar to the one reported for ferrocene. Hirshfeld surfaces and two-dimensional fingerprint plots were generated to analyze weak intermolecular C-H···π and C-H···O interactions. Density functional theory studies revealed a 1.15 kcal/mol rotational barrier for the C3-O1 single bound. Fluorescence quenching studies and in silico docking studies suggest that human serum albumin forms a complex with 2 via a static mechanism dominated by van der Waals interactions and hydrogen bonding interactions.
Journal Article
Effects of Single Low Dose of Dexamethasone before Noncardiac and Nonneurologic Surgery and General Anesthesia on Postoperative Cognitive Dysfunction—A Phase III Double Blind, Randomized Clinical Trial
by
Souza, Diogo O.
,
Pereira, Valeria Fontenelle Angelim
,
Vissoci, João Ricardo Nickenig
in
Aged
,
Anesthesia
,
Anesthesiology
2016
Postoperative cognitive dysfunction (POCD) is a multifactorial adverse event most frequently in elderly patients. This study evaluated the effect of dexamethasone on POCD incidence after noncardiac and nonneurologic surgery.
One hundred and forty patients (ASA I-II; age 60-87 years) took part in a prospective phase III, double blind, randomized study involving the administration or not of 8 mg of IV dexamethasone before general anesthesia under bispectral index (BIS) between 35-45 or 46-55. Neuropsychological tests were applied preoperatively and on the 3rd, 7th, 21st, 90th and 180th days after surgery and compared with normative data. S100β was evaluated before and 12 hours after induction of anesthesia. The generalized estimating equations (GEE) method was applied, followed by the posthoc Bonferroni test considering P<0.05 as significant.
On the 3rd postoperative day, POCD was diagnosed in 25.2% and 15.3% of patients receiving dexamethasone, BIS 35-45, and BIS 46-55 groups, respectively. Meanwhile, POCD was present in 68.2% and 27.2% of patients without dexamethasone, BIS 35-45 and BIS 46-55 groups (p<0.0001). Neuropsychological tests showed that dexamethasone associated to BIS 46-55 decreased the incidence of POCD, especially memory and executive function. The administration of dexamethasone might have prevented the postoperative increase in S100β serum levels.
Dexamethasone can reduce the incidence of POCD in elderly patients undergoing surgery, especially when associated with BIS 46-55. The effect of dexamethasone on S100β might be related with some degree of neuroprotection.
www.clinicaltrials.gov NCT01332812.
Journal Article