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1.
Sensors (Basel) ; 21(12)2021 Jun 09.
Artículo en Inglés | MEDLINE | ID: mdl-34207543

RESUMEN

Forage dry matter is the main source of nutrients in the diet of ruminant animals. Thus, this trait is evaluated in most forage breeding programs with the objective of increasing the yield. Novel solutions combining unmanned aerial vehicles (UAVs) and computer vision are crucial to increase the efficiency of forage breeding programs, to support high-throughput phenotyping (HTP), aiming to estimate parameters correlated to important traits. The main goal of this study was to propose a convolutional neural network (CNN) approach using UAV-RGB imagery to estimate dry matter yield traits in a guineagrass breeding program. For this, an experiment composed of 330 plots of full-sib families and checks conducted at Embrapa Beef Cattle, Brazil, was used. The image dataset was composed of images obtained with an RGB sensor embedded in a Phantom 4 PRO. The traits leaf dry matter yield (LDMY) and total dry matter yield (TDMY) were obtained by conventional agronomic methodology and considered as the ground-truth data. Different CNN architectures were analyzed, such as AlexNet, ResNeXt50, DarkNet53, and two networks proposed recently for related tasks named MaCNN and LF-CNN. Pretrained AlexNet and ResNeXt50 architectures were also studied. Ten-fold cross-validation was used for training and testing the model. Estimates of DMY traits by each CNN architecture were considered as new HTP traits to compare with real traits. Pearson correlation coefficient r between real and HTP traits ranged from 0.62 to 0.79 for LDMY and from 0.60 to 0.76 for TDMY; root square mean error (RSME) ranged from 286.24 to 366.93 kg·ha-1 for LDMY and from 413.07 to 506.56 kg·ha-1 for TDMY. All the CNNs generated heritable HTP traits, except LF-CNN for LDMY and AlexNet for TDMY. Genetic correlations between real and HTP traits were high but varied according to the CNN architecture. HTP trait from ResNeXt50 pretrained achieved the best results for indirect selection regardless of the dry matter trait. This demonstrates that CNNs with remote sensing data are highly promising for HTP for dry matter yield traits in forage breeding programs.


Asunto(s)
Redes Neurales de la Computación , Tecnología de Sensores Remotos , Animales , Brasil , Bovinos , Fenotipo
2.
Sheng Li Xue Bao ; 73(3): 482-490, 2021 Jun 25.
Artículo en Chino | MEDLINE | ID: mdl-34230949

RESUMEN

S100 calcium binding protein A9 (S100A9) is involved in a variety of biological processes such as inflammation and tumor cell migration and invasion regulation. The purpose of this study was to construct S100A9 gene-edited mice by using CRISPR/Cas9 technology, thereby providing an animal model for exploring the biological functions of this gene. According to the S100A9 gene sequence, the single-stranded small guide RNA (sgRNA) targeting exons 2 and 3 was transcribed in vitro, and a mixture of Cas9 mRNA and candidate sgRNA was injected into mouse fertilized eggs by microinjection. Early embryos were obtained and transferred to surrogate mice, and F0 mice were obtained and identified by PCR identification and gene sequencing. F0 mice were further mated with wild-type C57BL/6 mice to obtain F1 heterozygous mice, and then homozygous offspring were obtained through F1 mice self-crossing. Real-time PCR, Western blot and immunohistochemistry (IHC) were used to verify the expression and distribution of S100A9. In order to observe the pathological changes of mouse lung tissue using HE staining, an allergic asthma model was induced by ovalbumin from chicken egg white (OVA). The results showed that the 2 492 bp of exons 2, 3 of the S100A9 gene was successfully knocked out, and S100A9-/- mice with stable inheritance were obtained. Furthermore, it was found that S100A9 gene was highly expressed in the lung and spleen of wild-type mice. The expression of S100A9 mRNA and protein was not detected in the lung and spleen of S100A9-/- mice. However, compared with wild-type mice, the lungs of S100A9-/- mice showed a significantly worse inflammatory phenotype, and the proportion of eosinophils in bronchoalveolar lavage fluid (BALF) was significantly increased in response to the treatment of OVA. These results suggest we have successfully constructed a new strain of S100A9-/- mice, and preliminarily confirmed that the lack of S100A9 function can aggravate airway inflammation in asthmatic mice, providing a new mouse model for further study of S100A9 gene function.


Asunto(s)
Sistemas CRISPR-Cas , Marcación de Gen , Animales , Líquido del Lavado Bronquioalveolar , Sistemas CRISPR-Cas/genética , Calgranulina B , Modelos Animales de Enfermedad , Técnicas de Inactivación de Genes , Pulmón , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Ovalbúmina , Fenotipo
3.
BMC Genomics ; 22(1): 498, 2021 Jul 03.
Artículo en Inglés | MEDLINE | ID: mdl-34217203

RESUMEN

BACKGROUND: Virescent mutation broadly exists in plants and is an ideal experimental material to investigate regulatory mechanisms underlying chlorophyll synthesis, photosynthesis and plant growth. Up to date, the molecular mechanisms in two virescent mutations have been clarified in cottons (Gossypiuma hirsutum). A virescent mutation has been found in the cotton strain Sumian 22, and the underlying molecular mechanisms have been studied. METHODS: The virescent mutant and wild type (WT) of Sumian 22 were cross-bred, and the F1 population were self-pollinated to calculate the segregation ratio. Green and yellow leaves from F2 populations were subjected to genome sequencing and bulked-segregant analysis was performed to screen mutations. Real-time quantitative PCR (RT-qPCR) were performed to identify genes in relations to chlorophyll synthesis. Intermediate products for chlorophyll synthesis were determined to validate the RT-qPCR results. RESULTS: The segregation ratio of green and virescent plants in F2 population complied with 3:1. Compared with WT, a 0.34 Mb highly mutated interval was identified on the chromosome D10 in mutant, which contained 31 genes. Among them, only ABCI1 displayed significantly lower levels in mutant than in WT. Meanwhile, the contents of Mg-protoporphyrin IX, protochlorophyllide, chlorophyll a and b were all significantly lower in mutant than in WT, which were consistent with the inhibited levels of ABCI1. In addition, a mutation from A to T at the -317 bp position from the start codon of ABCI1 was observed in the genome sequence of mutant. CONCLUSIONS: Inhibited transcription of ABCI1 might be the mechanism causing virescent mutation in Sumian 22 cotton, which reduced the transportation of protoporphyrin IX to plastid, and then inhibited Mg-protoporphyrin IX, Protochlorophyllide and finally chlorophyll synthesis. These results provided novel insights into the molecular mechanisms underlying virescent mutation in cotton.


Asunto(s)
Fitomejoramiento , Hojas de la Planta , Clorofila , Clorofila A , Mapeo Cromosómico , Mutación , Fenotipo
4.
BMC Genomics ; 22(1): 501, 2021 Jul 03.
Artículo en Inglés | MEDLINE | ID: mdl-34217223

RESUMEN

BACKGROUND: Improving feed efficiency (FE) is an important goal due to its economic and environmental significance for farm animal production. The FE phenotype is complex and based on the measurements of the individual feed consumption and average daily gain during a test period, which is costly and time-consuming. The identification of reliable predictors of FE is a strategy to reduce phenotyping efforts. RESULTS: Gene expression data of the whole blood from three independent experiments were combined and analyzed by machine learning algorithms to propose molecular biomarkers of FE traits in growing pigs. These datasets included Large White pigs from two lines divergently selected for residual feed intake (RFI), a measure of net FE, and in which individual feed conversion ratio (FCR) and blood microarray data were available. Merging the three datasets allowed considering FCR values (Mean = 2.85; Min = 1.92; Max = 5.00) for a total of n = 148 pigs, with a large range of body weight (15 to 115 kg) and different test period duration (2 to 9 weeks). Random forest (RF) and gradient tree boosting (GTB) were applied on the whole blood transcripts (26,687 annotated molecular probes) to identify the most important variables for binary classification on RFI groups and a quantitative prediction of FCR, respectively. The dataset was split into learning (n = 74) and validation sets (n = 74). With iterative steps for variable selection, about three hundred's (328 to 391) molecular probes participating in various biological pathways, were identified as important predictors of RFI or FCR. With the GTB algorithm, simpler models were proposed combining 34 expressed unique genes to classify pigs into RFI groups (100% of success), and 25 expressed unique genes to predict FCR values (R2 = 0.80, RMSE = 8%). The accuracy performance of RF models was slightly lower in classification and markedly lower in regression. CONCLUSION: From small subsets of genes expressed in the whole blood, it is possible to predict the binary class and the individual value of feed efficiency. These predictive models offer good perspectives to identify animals with higher feed efficiency in precision farming applications.


Asunto(s)
Alimentación Animal , Transcriptoma , Alimentación Animal/análisis , Animales , Biomarcadores , Biología Computacional , Ingestión de Alimentos , Fenotipo , Porcinos
5.
Int J Mol Sci ; 22(12)2021 Jun 14.
Artículo en Inglés | MEDLINE | ID: mdl-34198491

RESUMEN

Rare germline pathogenic TP53 missense variants often predispose to a wide spectrum of tumors characterized by Li-Fraumeni syndrome (LFS) but a subset of variants is also seen in families with exclusively hereditary breast cancer (HBC) outcomes. We have developed a logistic regression model with the aim of predicting LFS and HBC outcomes, based on the predicted effects of individual TP53 variants on aspects of protein conformation. A total of 48 missense variants either unique for LFS (n = 24) or exclusively reported in HBC (n = 24) were included. LFS-variants were over-represented in residues tending to be buried in the core of the tertiary structure of TP53 (p = 0.0014). The favored logistic regression model describes disease outcome in terms of explanatory variables related to the surface or buried status of residues as well as their propensity to contribute to protein compactness or protein-protein interactions. Reduced, internally validated models discriminated well between LFS and HBC (C-statistic = 0.78-0.84; equivalent to the area under the ROC (receiver operating characteristic) curve), had a low risk for over-fitting and were well calibrated in relation to the known outcome risk. In conclusion, this study presents a phenotypic prediction model of LFS and HBC risk for germline TP53 missense variants, in an attempt to provide a complementary tool for future decision making and clinical handling.


Asunto(s)
Neoplasias de la Mama/genética , Estudios de Asociación Genética , Predisposición Genética a la Enfermedad , Síndrome de Li-Fraumeni/genética , Mutación Missense/genética , Proteína p53 Supresora de Tumor/química , Proteína p53 Supresora de Tumor/genética , Secuencia de Aminoácidos , Femenino , Mutación de Línea Germinal/genética , Humanos , Modelos Logísticos , Análisis Multivariante , Fenotipo , Conformación Proteica
6.
Int J Mol Sci ; 22(11)2021 Jun 05.
Artículo en Inglés | MEDLINE | ID: mdl-34198873

RESUMEN

Nicotinamide nucleotide transhydrogenase (NNT) is a proton pump in the inner mitochondrial membrane that generates reducing equivalents in the form of NAPDH, which can be used for anabolic pathways or to remove reactive oxygen species (ROS). A number of studies have linked NNT dysfunction to cardiomyopathies and increased risk of atherosclerosis; however, biallelic mutations in humans commonly cause a phenotype of adrenal insufficiency, with rare occurrences of cardiac dysfunction and testicular tumours. Here, we compare the transcriptomes of the hearts, adrenals and testes from three mouse models: the C57BL/6N, which expresses NNT; the C57BL/6J, which lacks NNT; and a third mouse, expressing the wild-type NNT sequence on the C57BL/6J background. We saw enrichment of oxidative phosphorylation genes in the C57BL/B6J in the heart and adrenal, possibly indicative of an evolved response in this substrain to loss of Nnt. However, differential gene expression was mainly driven by mouse background with some changes seen in all three tissues, perhaps reflecting underlying genetic differences between the C57BL/B6J and -6N substrains.


Asunto(s)
Aterosclerosis/genética , Cardiomiopatías/genética , Miocardio/metabolismo , NADP Transhidrogenasa AB-Específica/genética , Fosforilación Oxidativa , Glándulas Suprarrenales/metabolismo , Animales , Aterosclerosis/metabolismo , Aterosclerosis/patología , Cardiomiopatías/patología , Modelos Animales de Enfermedad , Regulación de la Expresión Génica/genética , Humanos , Masculino , Ratones , Ratones Endogámicos C57BL , Mitocondrias/genética , Membranas Mitocondriales/metabolismo , Proteínas Mitocondriales/genética , Fenotipo , Especies Reactivas de Oxígeno/metabolismo , Testículo/metabolismo
7.
Int J Mol Sci ; 22(12)2021 Jun 15.
Artículo en Inglés | MEDLINE | ID: mdl-34203675

RESUMEN

Recently, we found that the deletion of TRPC5 leads to increased inflammation and pain-related behaviour in two animal models of arthritis. (-)-Englerin A (EA), an extract from the East African plant Phyllanthus engleri has been identified as a TRPC4/5 agonist. Here, we studied whether or not EA has any anti-inflammatory and analgesic properties via TRPC4/5 in the carrageenan model of inflammation. We found that EA treatment in CD1 mice inhibited thermal hyperalgesia and mechanical allodynia in a dose-dependent manner. Furthermore, EA significantly reduced the volume of carrageenan-induced paw oedema and the mass of the treated paws. Additionally, in dorsal root ganglion (DRG) neurons cultured from WT 129S1/SvIm mice, EA induced a dose-dependent cobalt uptake that was surprisingly preserved in cultured DRG neurons from 129S1/SvIm TRPC5 KO mice. Likewise, EA-induced anti-inflammatory and analgesic effects were preserved in the carrageenan model in animals lacking TRPC5 expression or in mice treated with TRPC4/5 antagonist ML204.This study demonstrates that while EA activates a sub-population of DRG neurons, it induces a novel TRPC4/5-independent analgesic and anti-inflammatory effect in vivo. Future studies are needed to elucidate the molecular and cellular mechanisms underlying EA's anti-inflammatory and analgesic effects.


Asunto(s)
Analgésicos/farmacología , Antiinflamatorios/farmacología , Sesquiterpenos de Guayano/farmacología , Canales Catiónicos TRPC/metabolismo , Analgésicos/uso terapéutico , Animales , Antiinflamatorios/uso terapéutico , Conducta Animal/efectos de los fármacos , Carragenina , Células Cultivadas , Cobalto/metabolismo , Modelos Animales de Enfermedad , Edema/patología , Ganglios Espinales/efectos de los fármacos , Ganglios Espinales/metabolismo , Hiperalgesia/tratamiento farmacológico , Inflamación/complicaciones , Inflamación/tratamiento farmacológico , Inflamación/patología , Masculino , Ratones Noqueados , Dolor/complicaciones , Dolor/tratamiento farmacológico , Dolor/patología , Fenotipo , Células Receptoras Sensoriales/efectos de los fármacos , Células Receptoras Sensoriales/metabolismo , Sesquiterpenos de Guayano/uso terapéutico
8.
Int J Mol Sci ; 22(12)2021 Jun 15.
Artículo en Inglés | MEDLINE | ID: mdl-34203775

RESUMEN

Mitochondrial disorders (MD) comprise a group of heterogeneous clinical disorders for which non-invasive diagnosis remains a challenge. Two protein biomarkers have so far emerged for MD detection, FGF-21 and GDF-15, but the identification of additional biomarkers capable of improving their diagnostic accuracy is highly relevant. Previous studies identified Gelsolin as a regulator of cell survival adaptations triggered by mitochondrial defects. Gelsolin presents a circulating plasma isoform (pGSN), whose altered levels could be a hallmark of mitochondrial dysfunction. Therefore, we investigated the diagnostic performance of pGSN for MD relative to FGF-21 and GDF-15. Using ELISA assays, we quantified plasma levels of pGSN, FGF-21, and GDF-15 in three age- and gender-matched adult cohorts: 60 genetically diagnosed MD patients, 56 healthy donors, and 41 patients with unrelated neuromuscular pathologies (non-MD). Clinical variables and biomarkers' plasma levels were compared between groups. Discrimination ability was calculated using the area under the ROC curve (AUC). Optimal cut-offs and the following diagnostic parameters were determined: sensitivity, specificity, positive and negative predictive values, positive and negative likelihood ratios, and efficiency. Comprehensive statistical analyses revealed significant discrimination ability for the three biomarkers to classify between MD and healthy individuals, with the best diagnostic performance for the GDF-15/pGSN combination. pGSN and GDF-15 preferentially discriminated between MD and non-MD patients under 50 years, whereas FGF-21 best classified older subjects. Conclusion: pGSN improves the diagnosis accuracy for MD provided by FGF-21 and GDF-15.


Asunto(s)
Factores de Crecimiento de Fibroblastos/sangre , Gelsolina/sangre , Factor 15 de Diferenciación de Crecimiento/sangre , Enfermedades Mitocondriales/sangre , Enfermedades Mitocondriales/diagnóstico , Adulto , Biomarcadores/sangre , Estudios de Casos y Controles , Femenino , Humanos , Masculino , Persona de Mediana Edad , Fenotipo
9.
Int J Mol Sci ; 22(12)2021 Jun 15.
Artículo en Inglés | MEDLINE | ID: mdl-34203883

RESUMEN

Variants of the TTLL5 gene, which encodes tubulin tyrosine ligase-like family member five, are a rare cause of cone dystrophy (COD) or cone-rod dystrophy (CORD). To date, only a few TTLL5 patients have been clinically and genetically described. In this study, we report five patients harbouring biallelic variants of TTLL5. Four adult patients presented either COD or CORD with onset in the late teenage years. The youngest patient had a phenotype of early onset severe retinal dystrophy (EOSRD). Genetic analysis was performed by targeted next generation sequencing of gene panels and assessment of copy number variants (CNV). We identified eight variants, of which six were novel, including two large multiexon deletions in patients with COD or CORD, while the EOSRD patient harboured the novel homozygous p.(Trp640*) variant and three distinct USH2A variants, which might explain the observed rod involvement. Our study highlights the role of TTLL5 in COD/CORD and the importance of large deletions. These findings suggest that COD or CORD patients lacking variants in known genes may harbour CNVs to be discovered in TTLL5, previously undetected by classical sequencing methods. In addition, variable phenotypes in TTLL5-associated patients might be due to the presence of additional gene defects.


Asunto(s)
Proteínas Portadoras/genética , Distrofias de Conos y Bastones/genética , Enfermedades Hereditarias del Ojo/genética , Estudios de Asociación Genética , Predisposición Genética a la Enfermedad , Mutación/genética , Distrofias Retinianas/genética , Adulto , Anciano , Niño , Puntos de Rotura del Cromosoma , Simulación por Computador , Distrofias de Conos y Bastones/fisiopatología , Variaciones en el Número de Copia de ADN/genética , Electrorretinografía , Enfermedades Hereditarias del Ojo/fisiopatología , Femenino , Genotipo , Humanos , Masculino , Persona de Mediana Edad , Fenotipo , Distrofias Retinianas/fisiopatología
10.
Int J Mol Sci ; 22(12)2021 Jun 15.
Artículo en Inglés | MEDLINE | ID: mdl-34203952

RESUMEN

Endocannabinoids play a role in adaptation to stress and regulate the release of glucocorticoids in stressed and unstressed conditions. We recently found that basal corticosterone pulsatility may significantly impact the vulnerability for developing post-traumatic-stress-disorder (PTSD), suggesting that the endocannabinoid system may contribute to its development. To examine this, we exposed rats to predator scent stress (PSS). Behavioral reactions were recorded seven days post-PSS. Cerebrospinal fluid (CSF) was collected from anesthetized rats shortly after PSS exposure to determine the levels of 2-arachidonoyl glycerol (2-AG) and anandamide (AEA). To correlate between endocannabinoids and corticosterone levels, rats were placed in metabolic cages for urine collection. To assess the levels of endocannabinoids in specific brain regions, rats' brains were harvested one day after behavioral analysis for staining and fluorescence quantification. Moreover, 2-AG was elevated in the CSF of PTSD-phenotype rats as compared with other groups and was inversely correlated with corticosterone urinary secretion. Eight days post-PSS exposure, hippocampal and hypothalamic 2-AG levels and hippocampal AEA levels were significantly more reduced in the PTSD-phenotype group compared to other groups. We posit that maladaptation to stress, which is propagated by an abnormal activation of endocannabinoids, mediates the subsequent stress-induced behavioral disruption, which, later, reduces neuronal the expression of endocannabinoids, contributing to PTSD symptomology.


Asunto(s)
Endocannabinoides/metabolismo , Sistema Hipotálamo-Hipofisario/fisiología , Sistema Hipófiso-Suprarrenal/patología , Trastornos por Estrés Postraumático/patología , Estrés Psicológico/complicaciones , Estrés Psicológico/metabolismo , Animales , Conducta Animal , Corticosterona/orina , Endocannabinoides/líquido cefalorraquídeo , Masculino , Fenotipo , Ratas Sprague-Dawley , Trastornos por Estrés Postraumático/orina , Estrés Psicológico/orina
11.
BMC Plant Biol ; 21(1): 326, 2021 Jul 06.
Artículo en Inglés | MEDLINE | ID: mdl-34229625

RESUMEN

BACKGROUND: Glycolate oxidase (GLO) is not only a key enzyme in photorespiration but also a major engine for H2O2 production in plants. Catalase (CAT)-dependent H2O2 decomposition has been previously reported to be involved in the regulation of IAA biosynthesis. However, it is still not known which mechanism contributed to the H2O2 production in IAA regulation. RESULTS: In this study, we found that in glo mutants of rice, as H2O2 levels decreased IAA contents significantly increased, whereas high CO2 abolished the difference in H2O2 and IAA contents between glo mutants and WT. Further analyses showed that tryptophan (Trp, the precursor for IAA biosynthesis in the Trp-dependent biosynthetic pathway) also accumulated due to increased tryptophan synthetase ß (TSB) activity. Moreover, expression of the genes involved in Trp-dependent IAA biosynthesis and IBA to IAA conversion were correspondingly up-regulated, further implicating that both pathways contribute to IAA biosynthesis as mediated by the GLO-dependent production of H2O2. CONCLUSION: We investigated the function of GLO in IAA signaling in different levels from transcription, enzyme activities to metabolic levels. The results suggest that GLO-dependent H2O2 signaling, essentially via photorespiration, confers regulation over IAA biosynthesis in rice plants.


Asunto(s)
Oxidorreductasas de Alcohol/metabolismo , Peróxido de Hidrógeno/metabolismo , Ácidos Indolacéticos/metabolismo , Oryza/enzimología , Oxidorreductasas de Alcohol/genética , Vías Biosintéticas/efectos de la radiación , Respiración de la Célula/efectos de la radiación , Regulación de la Expresión Génica de las Plantas/efectos de la radiación , Luz , Modelos Biológicos , Mutación/genética , Oryza/genética , Oryza/efectos de la radiación , Peroxisomas/metabolismo , Peroxisomas/efectos de la radiación , Fenotipo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Triptófano/metabolismo
12.
BMC Plant Biol ; 21(1): 327, 2021 Jul 07.
Artículo en Inglés | MEDLINE | ID: mdl-34233614

RESUMEN

BACKGROUND: Grapevine cultivars of the Pinot family represent clonally propagated mutants with major phenotypic and physiological differences, such as different colour or shifted ripening time, as well as changes in important viticultural traits. Specifically, the cultivars 'Pinot Noir' (PN) and 'Pinot Noir Precoce' (PNP, early ripening) flower at the same time, but vary in the beginning of berry ripening (veraison) and, consequently, harvest time. In addition to genotype, seasonal climatic conditions (i.e. high temperatures) also affect ripening times. To reveal possible regulatory genes that affect the timing of veraison onset, we investigated differences in gene expression profiles between PN and PNP throughout berry development with a closely meshed time series and over two separate years. RESULTS: The difference in the duration of berry formation between PN and PNP was quantified to be approximately two weeks under the growth conditions applied, using plant material with a proven PN and PNP clonal relationship. Clusters of co-expressed genes and differentially expressed genes (DEGs) were detected which reflect the shift in the timing of veraison onset. Functional annotation of these DEGs fit to observed phenotypic and physiological changes during berry development. In total, we observed 3,342 DEGs in 2014 and 2,745 DEGs in 2017 between PN and PNP, with 1,923 DEGs across both years. Among these, 388 DEGs were identified as veraison-specific and 12 were considered as berry ripening time regulatory candidates. The expression profiles revealed two candidate genes for ripening time control which we designated VviRTIC1 and VviRTIC2 (VIT_210s0071g01145 and VIT_200s0366g00020, respectively). These genes likely contribute the phenotypic differences observed between PN and PNP. CONCLUSIONS: Many of the 1,923 DEGs show highly similar expression profiles in both cultivars if the patterns are aligned according to developmental stage. In our work, putative genes differentially expressed between PNP and PN which could control ripening time as well as veraison-specific genes were identified. We point out connections of these genes to molecular events during berry development and discuss potential candidate genes which may control ripening time. Two of these candidates were observed to be differentially expressed in the early berry development phase. Several down-regulated genes during berry ripening are annotated as auxin response factors / ARFs. Conceivably, general changes in auxin signaling may cause the earlier ripening phenotype of PNP.


Asunto(s)
Frutas/crecimiento & desarrollo , Perfilación de la Expresión Génica , Regulación del Desarrollo de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Genes de Plantas , Vitis/crecimiento & desarrollo , Vitis/genética , Análisis por Conglomerados , Flores/genética , Flores/fisiología , Frutas/genética , Fenotipo , Análisis de Componente Principal , Factores de Tiempo
13.
Int J Mol Sci ; 22(12)2021 Jun 20.
Artículo en Inglés | MEDLINE | ID: mdl-34202990

RESUMEN

Proteins that contain the FYVE zinc-finger domain are recruited to PtdIns3P-containing membranes, participating in numerous biological processes such as membrane trafficking, cytoskeletal regulation, and receptor signaling. However, the genome-wide distribution, evolution, and biological functions of FYVE-containing proteins are rarely reported for oomycetes. By genome mining of Phytophthora sojae, two proteins (PsFP1 and PsFP2) with a combination of the FYVE domain and the PX domain (a major phosphoinositide binding module) were found. To clarify the functions of PsFP1 and PsFP2, the CRISPR/Cas9-mediated gene replacement system was used to knock out the two genes respectively. Only heterozygous deletion mutants of PsFP1 were recovered, and the expression level of PsFP1 in the heterozygous knockout transformants was significantly down-regulated. These PsFP1 mutants showed a decrease in mycelial growth and pathogenicity and were more sensitive to hydrogen peroxide. These phenotypes were recovered to the level of wild-type by overexpression PsFP1 gene in the PsFP1 heterozygous knockout transformant. In contrast, deletion of PsFP2 had no significant effect on vegetative growth, asexual and sexual reproduction, pathogenicity, or oxidative stress sensitivity. PsFP1 was primarily localized in vesicle-like structures and both the FYVE and PX domains are important for its localization. Overall, our results indicate that PsFP1 plays an important role in the vegetative growth and virulence of P. sojae.


Asunto(s)
Estrés Oxidativo , Phytophthora/fisiología , Proteínas/metabolismo , Dedos de Zinc , Secuencia de Aminoácidos , Expresión Génica , Fenotipo , Phytophthora/patogenicidad , Enfermedades de las Plantas/parasitología , Dominios Proteicos , Transporte de Proteínas , Proteínas/química , Proteínas/genética , Eliminación de Secuencia , Virulencia/genética
14.
Int J Mol Sci ; 22(12)2021 Jun 20.
Artículo en Inglés | MEDLINE | ID: mdl-34203082

RESUMEN

Ideal Plant Architecture 1 (IPA1) encodes SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 14 (SPL14) with a pleiotropic effect on regulating rice development and biotic stress responses. To investigate the role of IPA1 in early seedling development, we developed a pair of IPA1/ipal-NILs and found that seed germination and early seedling growth were retarded in the ipa1-NIL. Analysis of the soluble sugar content, activity of amylase, and expression of the α-amylase genes revealed that the starch metabolism was weakened in the ipa1-NIL germinating seeds. Additionally, the content of bioactive gibberellin (GA) was significantly lower than that in the IPA1-NIL seeds at 48 h of imbibition. Meanwhile, the expression of GA synthesis-related gene OsGA20ox1 was downregulated, whereas the expression of GA inactivation-related genes was upregulated in ipa1-NIL seeds. In addition, the expression of OsWRKY51 and OsWRKY71 was significantly upregulated in ipa1-NIL seeds. Using transient dual-luciferase and yeast one-hybrid assays, IPA1 was found to directly activate the expression of OsWRKY51 and OsWRKY71, which would interfere with the binding affinity of GA-induced transcription factor OsGAMYB to inhibit the expression of α-amylase genes. In summary, our results suggest that IPA1 negatively regulates seed germination and early seedling growth by interfering with starch metabolism via the GA and WRKY pathways.


Asunto(s)
Proteínas de Unión al ADN/metabolismo , Giberelinas/metabolismo , Oryza/fisiología , Desarrollo de la Planta , Plantones/crecimiento & desarrollo , Transducción de Señal , Almidón/metabolismo , Factores de Transcripción/metabolismo , Regulación de la Expresión Génica de las Plantas , Germinación/genética , Fenotipo , Unión Proteica , alfa-Amilasas/metabolismo
15.
Int J Mol Sci ; 22(11)2021 Jun 02.
Artículo en Inglés | MEDLINE | ID: mdl-34199520

RESUMEN

Autosomal dominant polycystic kidney disease (ADPKD) is caused by loss of function of PKD1 (polycystin 1) or PKD2 (polycystin 2). The Ca2+-activated Cl- channel TMEM16A has a central role in ADPKD. Expression and function of TMEM16A is upregulated in ADPKD which causes enhanced intracellular Ca2+ signaling, cell proliferation, and ion secretion. We analyzed kidneys from Pkd1 knockout mice and found a more pronounced phenotype in males compared to females, despite similar levels of expression for renal tubular TMEM16A. Cell proliferation, which is known to be enhanced with loss of Pkd1-/-, was larger in male when compared to female Pkd1-/- cells. This was paralleled by higher basal intracellular Ca2+ concentrations in primary renal epithelial cells isolated from Pkd1-/- males. The results suggest enhanced intracellular Ca2+ levels contributing to augmented cell proliferation and cyst development in male kidneys. Enhanced resting Ca2+ also caused larger basal chloride currents in male primary cells, as detected in patch clamp recordings. Incubation of mouse primary cells, mCCDcl1 collecting duct cells or M1 collecting duct cells with dihydrotestosterone (DHT) enhanced basal Ca2+ levels and increased basal and ATP-stimulated TMEM16A chloride currents. Taken together, the more severe cystic phenotype in males is likely to be caused by enhanced cell proliferation, possibly due to enhanced basal and ATP-induced intracellular Ca2+ levels, leading to enhanced TMEM16A currents. Augmented Ca2+ signaling is possibly due to enhanced expression of Ca2+ transporting/regulating proteins.


Asunto(s)
Anoctamina-1/genética , Enfermedades Renales Poliquísticas/genética , Canales Catiónicos TRPP/genética , Animales , Calcio/metabolismo , Señalización del Calcio/genética , Proliferación Celular/genética , Cloruros/metabolismo , Dihidrotestosterona/farmacología , Modelos Animales de Enfermedad , Femenino , Regulación de la Expresión Génica/efectos de los fármacos , Humanos , Riñón/metabolismo , Riñón/patología , Masculino , Ratones , Ratones Noqueados , Fenotipo , Enfermedades Renales Poliquísticas/metabolismo , Enfermedades Renales Poliquísticas/patología , Caracteres Sexuales
16.
Int J Mol Sci ; 22(11)2021 Jun 02.
Artículo en Inglés | MEDLINE | ID: mdl-34199672

RESUMEN

Large-scale RNA sequencing and genome-wide profiling data revealed the identification of a heterogeneous group of noncoding RNAs, known as long noncoding RNAs (lncRNAs). These lncRNAs play central roles in health and disease processes in diabetes and cancer. The critical association between aberrant expression of lncRNAs in diabetes and diabetic kidney disease have been reported. LncRNAs regulate diverse targets and can function as sponges for regulatory microRNAs, which influence disease phenotype in the kidneys. Importantly, lncRNAs and microRNAs may regulate bidirectional or crosstalk mechanisms, which need to be further investigated. These studies offer the novel possibility that lncRNAs may be used as potential therapeutic targets for diabetes and diabetic kidney diseases. Here, we discuss the functions and mechanisms of actions of lncRNAs, and their crosstalk interactions with microRNAs, which provide insight and promise as therapeutic targets, emphasizing their role in the pathogenesis of diabetes and diabetic kidney disease.


Asunto(s)
Diabetes Mellitus/genética , Nefropatías Diabéticas/genética , MicroARNs/genética , ARN Largo no Codificante/genética , Diabetes Mellitus/patología , Nefropatías Diabéticas/patología , Regulación de la Expresión Génica/genética , Humanos , Riñón/metabolismo , Riñón/patología , Fenotipo
17.
Sensors (Basel) ; 21(13)2021 Jun 25.
Artículo en Inglés | MEDLINE | ID: mdl-34202291

RESUMEN

Plant phenomics has been rapidly advancing over the past few years. This advancement is attributed to the increased innovation and availability of new technologies which can enable the high-throughput phenotyping of complex plant traits. The application of artificial intelligence in various domains of science has also grown exponentially in recent years. Notably, the computer vision, machine learning, and deep learning aspects of artificial intelligence have been successfully integrated into non-invasive imaging techniques. This integration is gradually improving the efficiency of data collection and analysis through the application of machine and deep learning for robust image analysis. In addition, artificial intelligence has fostered the development of software and tools applied in field phenotyping for data collection and management. These include open-source devices and tools which are enabling community driven research and data-sharing, thereby availing the large amounts of data required for the accurate study of phenotypes. This paper reviews more than one hundred current state-of-the-art papers concerning AI-applied plant phenotyping published between 2010 and 2020. It provides an overview of current phenotyping technologies and the ongoing integration of artificial intelligence into plant phenotyping. Lastly, the limitations of the current approaches/methods and future directions are discussed.


Asunto(s)
Inteligencia Artificial , Fenómica , Aprendizaje Automático , Fenotipo , Programas Informáticos
18.
BMC Infect Dis ; 21(1): 627, 2021 Jul 01.
Artículo en Inglés | MEDLINE | ID: mdl-34210263

RESUMEN

BACKGROUND AND OBJECTIVE: Carriage of virulence factors confers some evolutionary benefit to bacteria, which favors the resistant strains. We aimed to analyze whether antibiotic susceptibility of Staphylococcus aureus strains is affected by agr typing, biofilm formation ability, and virulence profiles. METHODS: A total of 123 S. aureus clinical isolates were subjected to antimicrobial susceptibility testing by disk diffusion method, biofilm formation by microtiter plate method, as well as polymerase chain reaction screening to identify virulence genes and the accessory gene regulator (agr) types I-IV. A P value < 0.05 was considered significant. RESULTS: The most prevalent virulence gene was staphyloxanthin crtN, followed by hemolysin genes, capsular cap8H, toxic shock toxin tst, and enterotoxin sea, respectively. Resistant isolates were more commonly found in the agr-negative group than in the agr-positive group. Isolates of agr type III were more virulent than agr I isolates. Strong biofilm producers showed more antibiotic susceptibility and carried more virulence genes than non-strong biofilm producers. Associations were found between the presence of virulence genes and susceptibility to antibiotics. Carriage of the virulence genes and agr was higher in the inpatients; while, resistance and strong biofilms were more prevalent in the outpatients. CONCLUSION: These findings indicated the presence of several virulence factors, biofilm production capacity, agr types and resistance to antibiotics in clinical S. aureus isolates. Considering the importance of S. aureus for human medicine, an understanding of virulence and resistance relationships would help to reduce the impact of S. aureus infections.


Asunto(s)
Proteínas Bacterianas , Biopelículas , Staphylococcus aureus/genética , Staphylococcus aureus/aislamiento & purificación , Staphylococcus aureus/fisiología , Staphylococcus aureus/patogenicidad , Transactivadores , Factores de Virulencia/genética , Toxinas Bacterianas/genética , Farmacorresistencia Bacteriana , Enterotoxinas/genética , Exfoliatinas/genética , Femenino , Proteínas Hemolisinas/genética , Humanos , Masculino , Pruebas de Sensibilidad Microbiana , Fenotipo , Reacción en Cadena de la Polimerasa , Superantígenos/genética , Xantófilas
19.
Biol Lett ; 17(7): 20210213, 2021 07.
Artículo en Inglés | MEDLINE | ID: mdl-34228940

RESUMEN

There has been an explosion of recent evidence that environments experienced by fathers or their ejaculates can influence offspring phenotypes (paternal effects). However, little is known about whether such effects are adaptive, which would have far-reaching implications for the many species facing rapidly changing environments. For example, some arguments suggest paternal effects might be a source of cross-generational plasticity, preparing offspring to face similar conditions to their father (anticipatory hypothesis). Alternatively, ejaculate-mediated effects on offspring may be non-adaptive by-products of stress. Here, we conduct an experiment to distinguish between these predictions, exposing ejaculates of the externally fertilizing mussel Mytilus galloprovincialis to ambient (19°C) and high (24°C) temperatures, then rearing offspring groups in temperatures that match and mismatch those of sperm. We find that, overall, high temperature-treated sperm induced higher rates of normal offspring development and higher success in transitioning to second-stage larvae, which may represent adaptive epigenetic changes or selection on sperm haplotypes. However, the progeny of high temperature-treated sperm did not perform better than those of ambient temperature-treated sperm when rearing temperatures were high. Overall, these findings offer little support for the anticipatory hypothesis and suggest instead that beneficial paternal effects may be eroded when offspring develop under stressful conditions.


Asunto(s)
Mytilus edulis , Herencia Paterna , Animales , Fertilización , Masculino , Fenotipo , Espermatozoides
20.
Rev Bras Ter Intensiva ; 33(2): 196-205, 2021.
Artículo en Portugués, Inglés | MEDLINE | ID: mdl-34231800

RESUMEN

OBJECTIVE: To identify more severe COVID-19 presentations. METHODS: Consecutive intensive care unit-admitted patients were subjected to a stepwise clustering method. RESULTS: Data from 147 patients who were on average 56 ± 16 years old with a Simplified Acute Physiological Score 3 of 72 ± 18, of which 103 (70%) needed mechanical ventilation and 46 (31%) died in the intensive care unit, were analyzed. From the clustering algorithm, two well-defined groups were found based on maximal heart rate [Cluster A: 104 (95%CI 99 - 109) beats per minute versus Cluster B: 159 (95%CI 155 - 163) beats per minute], maximal respiratory rate [Cluster A: 33 (95%CI 31 - 35) breaths per minute versus Cluster B: 50 (95%CI 47 - 53) breaths per minute], and maximal body temperature [Cluster A: 37.4 (95%CI 37.1 - 37.7)°C versus Cluster B: 39.3 (95%CI 39.1 - 39.5)°C] during the intensive care unit stay, as well as the oxygen partial pressure in the blood over the oxygen inspiratory fraction at intensive care unit admission [Cluster A: 116 (95%CI 99 - 133) mmHg versus Cluster B: 78 (95%CI 63 - 93) mmHg]. Subphenotypes were distinct in inflammation profiles, organ dysfunction, organ support, intensive care unit length of stay, and intensive care unit mortality (with a ratio of 4.2 between the groups). CONCLUSION: Our findings, based on common clinical data, revealed two distinct subphenotypes with different disease courses. These results could help health professionals allocate resources and select patients for testing novel therapies.


Asunto(s)
COVID-19/fisiopatología , Cuidados Críticos/métodos , Enfermedad Crítica/terapia , Unidades de Cuidados Intensivos , Respiración Artificial/estadística & datos numéricos , Adulto , Anciano , Algoritmos , COVID-19/mortalidad , COVID-19/terapia , Análisis por Conglomerados , Estudios de Cohortes , Femenino , Humanos , Tiempo de Internación , Masculino , Persona de Mediana Edad , Selección de Paciente , Fenotipo , Frecuencia Respiratoria/fisiología , Estudios Retrospectivos , Índice de Severidad de la Enfermedad
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