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1.
BMC Plant Biol ; 24(1): 215, 2024 Mar 26.
Artículo en Inglés | MEDLINE | ID: mdl-38532331

RESUMEN

BACKGROUND: Seed dormancy is a biological mechanism that prevents germination until favorable conditions for the subsequent generation of plants are encountered. Therefore, this mechanism must be effectively established during seed maturation. Studies investigating the transcriptome and miRNAome of rice embryos and endosperms at various maturation stages to evaluate seed dormancy are limited. This study aimed to compare the transcriptome and miRNAome of rice seeds during seed maturation. RESULTS: Oryza sativa L. cv. Nipponbare seeds were sampled for embryos and endosperms at three maturation stages: 30, 45, and 60 days after heading (DAH). The pre-harvest sprouting (PHS) assay was conducted to assess the level of dormancy in the seeds at each maturation stage. At 60 DAH, the PHS rate was significantly increased compared to those at 30 and 45 DAH, indicating that the dormancy is broken during the later maturation stage (45 DAH to 60 DAH). However, the largest number of differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRs) were identified between 30 and 60 DAH in the embryo and endosperm, implying that the gradual changes in genes and miRNAs from 30 to 60 DAH may play a significant role in breaking seed dormancy. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses confirmed that DEGs related to plant hormones were most abundant in the embryo during 45 DAH to 60 DAH and 30 DAH to 60 DAH transitions. Alternatively, most of the DEGs in the endosperm were related to energy and abiotic stress. MapMan analysis and quantitative real-time polymerase chain reaction identified four newly profiled auxin-related genes (OsSAUR6/12/23/25) and one ethylene-related gene (OsERF087), which may be involved in seed dormancy during maturation. Additionally, miRNA target prediction (psRNATarget) and degradome dataset (TarDB) indicated a potential association between osa-miR531b and ethylene biosynthesis gene (OsACO4), along with osa-miR390-5p and the abscisic acid (ABA) exporter-related gene (OsMATE19) as factors involved in seed dormancy. CONCLUSIONS: Analysis of the transcriptome and miRNAome of rice embryos and endosperms during seed maturation provided new insights into seed dormancy, particularly its relationship with plant hormones such as ABA, auxin, and ethylene.


Asunto(s)
MicroARNs , Oryza , Latencia en las Plantas/genética , Oryza/genética , Transcriptoma , Reguladores del Crecimiento de las Plantas/metabolismo , Germinación/genética , Semillas/genética , Ácido Abscísico/metabolismo , Etilenos/metabolismo , Ácidos Indolacéticos/metabolismo , MicroARNs/metabolismo , Regulación de la Expresión Génica de las Plantas
2.
BMC Genomics ; 24(1): 36, 2023 Jan 20.
Artículo en Inglés | MEDLINE | ID: mdl-36658480

RESUMEN

BACKGROUND: Several studies showed genome-wide DNA methylation during Arabidopsis embryogenesis and germination. Although it has been known that the change of DNA methylation mainly occurs at CHH context mediated by small RNA-directed DNA methylation pathway during seed ripening and germination, the causality of the methylation difference exhibited in natural Arabidopsis ecotypes has not been thoroughly studied. RESULTS: In this study we compared DNA methylation difference using comparative pairwise multi-omics dynamics in Columbia-0 (Col) and Cape Verde Island (Cvi) ecotypes. Arabidopsis genome was divided into two regions, common regions in both ecotypes and Col-specific regions, depending on the reads mapping of whole genome bisulfite sequencing libraries from both ecotypes. Ecotype comparison was conducted within common regions and the levels of DNA methylation on common regions and Col-specific regions were also compared. we confirmed transcriptome were relatively dynamic in stage-wise whereas the DNA methylome and small RNAome were more ecotype-dependent. While the global CG methylation remains steady during maturation and germination, we found genic CG methylation differs the most between the two accessions. We also found that ecotype-specific differentially methylated regions (eDMR) are positively correlated with ecotype-specifically expressed 24-nt small RNA clusters. In addition, we discovered that Col-specific regions enriched with transposable elements (TEs) and structural variants that tend to become hypermethylated, and TEs in Col-specific regions were longer in size, more pericentromeric, and more hypermethylated than those in the common regions. Through the analysis of RdDM machinery mutants, we confirmed methylation on Col-specific region as well as on eDMRs in common region are contributed by RdDM pathway. Lastly, we demonstrated that highly variable sequences between ecotypes (HOT regions) were also affected by RdDM-mediated regulation. CONCLUSIONS: Through ecotype comparison, we revealed differences and similarities of their transcriptome, methylome and small RNAome both in global and local regions. We validated the contribution of RdDM causing differential methylation of common regions. Hypermethylated ecotype-specific regions contributed by RNA-directed DNA methylation pathway largely depend on the presence of TEs and copy-gain structural variations. These ecotype-specific regions are frequently associated with HOT regions, providing evolutionary insights into the epigenome dynamics within a species.


Asunto(s)
Proteínas de Arabidopsis , Arabidopsis , Arabidopsis/genética , Arabidopsis/metabolismo , Ecotipo , Silenciador del Gen , Metilación de ADN , Proteínas de Arabidopsis/genética , ARN Interferente Pequeño/genética , Regulación de la Expresión Génica de las Plantas
3.
J Med Virol ; 95(1): e28247, 2023 01.
Artículo en Inglés | MEDLINE | ID: mdl-36271493

RESUMEN

Monkeypox virus (MPXV) is a zoonotic orthopoxvirus within the Poxviridae family. MPXV is endemic to Central and West Africa. However, the world is currently witnessing an international outbreak with no clear epidemiological links to travel or animal exposure and with ever-increasing numbers of reported cases worldwide. Here, we evaluated and validated a new, sensitive, and specific real-time PCR-assay for MPXV diagnosis in humans and compare the performance of this novel assay against a Food & Drug Administration-cleared pan-Orthopox RT-PCR assay. We determined specificity, sensitivity, and analytic performance of the PKamp™ Monkeypox Virus RT-PCR assay targeting the viral F3L-gene. In addition, we further evaluated MPXV-PCR-positive specimens by viral culture, electron microscopy, and viral inactivation assays. The limit of detection was established at 7.2 genome copies/reaction, and MPXV was successfully identified in 20 clinical specimens with 100% correlation against the reference method with 100% sensitivity and specificity. Our results demonstrated the validity of this rapid, robust, and reliable RT-PCR assay for specific and accurate diagnosis of MPXV infection in human specimens collected both as dry swabs and in viral transport media. This assay has been approved by NYS Department of Health for clinical use.


Asunto(s)
Monkeypox virus , Mpox , Animales , Humanos , Monkeypox virus/genética , Mpox/epidemiología , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Técnicas de Amplificación de Ácido Nucleico/métodos , Reacción en Cadena en Tiempo Real de la Polimerasa
4.
J Med Internet Res ; 25: e40778, 2023 01 30.
Artículo en Inglés | MEDLINE | ID: mdl-36716080

RESUMEN

BACKGROUND: With widespread use of the internet and mobile devices, many people have gained improved access to health-related information online for health promotion and disease management. As the health information acquired online can affect health-related behaviors, health care providers need to take into account how each individual's online health literacy (eHealth literacy) can affect health-related behaviors. OBJECTIVE: To determine whether an individual's level of eHealth literacy affects actual health-related behaviors, the correlation between eHealth literacy and health-related behaviors was identified in an integrated manner through a systematic literature review and meta-analysis. METHODS: The MEDLINE, Embase, Cochrane, KoreaMed, and Research Information Sharing Service databases were systematically searched for studies published up to March 19, 2021, which suggested the relationship between eHealth literacy and health-related behaviors. Studies were eligible if they were conducted with the general population, presented eHealth literacy according to validated tools, used no specific control condition, and measured health-related behaviors as the outcomes. A meta-analysis was performed on the studies that could be quantitatively synthesized using a random effect model. A pooled correlation coefficient was generated by integrating the correlation coefficients, and the risk of bias was assessed using the modified Newcastle-Ottawa Scale. RESULTS: Among 1922 eHealth literacy-related papers, 29 studies suggesting an association between eHealth literacy and health-related behaviors were included. All retrieved studies were cross-sectional studies, and most of them used the eHealth Literacy Scale (eHEALS) as a measurement tool for eHealth literacy. Of the 29 studies, 22 presented positive associations between eHealth literacy and health-related behaviors. The meta-analysis was performed on 14 studies that presented the correlation coefficient for the relationship between eHealth literacy and health-related behaviors. When the meta-analysis was conducted by age, morbidity status, and type of health-related behavior, the pooled correlation coefficients were 0.37 (95% CI 0.29-0.44) for older adults (aged ≥65 years), 0.28 (95% CI 0.17-0.39) for individuals with diseases, and 0.36 (95% CI 0.27-0.41) for health-promoting behavior. The overall estimate of the correlation between eHealth literacy and health-related behaviors was 0.31 (95% CI 0.25-0.34), which indicated a moderate correlation between eHealth literacy and health-related behaviors. CONCLUSIONS: Our results of a positive correlation between eHealth literacy and health-related behaviors indicate that eHealth literacy can be a mediator in the process by which health-related information leads to changes in health-related behaviors. Larger-scale studies with stronger validity are needed to evaluate the detailed relationship between the proficiency level of eHealth literacy and health-related behaviors for health promotion in the future.


Asunto(s)
Alfabetización en Salud , Telemedicina , Humanos , Anciano , Encuestas y Cuestionarios , Alfabetización en Salud/métodos , Conductas Relacionadas con la Salud , Telemedicina/métodos , Promoción de la Salud
5.
Medicina (Kaunas) ; 59(3)2023 Feb 22.
Artículo en Inglés | MEDLINE | ID: mdl-36984432

RESUMEN

Background and Objectives: With the increased prevalence of patients with cancer, the demand for preparing cytotoxic drugs was increased by health-system pharmacists. To reduce the workload and contamination of work areas in pharmacies, compounding robots preparing cytotoxic drugs have been introduced, and the use of the robots has been expanded in recent years. As reports on the comprehensive and quantitative evaluation of compounding robots remain lacking, a systematic review and meta-analysis were conducted to provide descriptive and quantitative evaluations of the accuracy of preparing injectable cytotoxic drugs. Materials and Methods: A systematic review and meta-analysis were conducted using published studies up to 2020. To identify eligible studies, PubMed, EMBASE, and Cochrane Library were used. All studies reporting the outcomes relevant to drug-compounding robots such as accuracy, safety, and drug contamination were included. Outcomes from included studies were descriptively summarized. Drug contamination by the robot was quantitatively analyzed using the odds ratio (OR) with a 95% confidence interval (CI). The risk of bias was assessed using the Risk of Bias Assessment tool for Non-randomized Studies (RoBANS). Results: A total of 14 compounding robot studies were eligible for review and 4 studies were included in the meta-analysis. Robotic compounding showed failure rates of 0.9-16.75%, while the accuracy range was set at 5%. Two studies reported that robotic compounding needed more time than manual compounding, two reported that robotic compounding needed less time, and one just reported preparation time without a control group. In a meta-analysis regarding the contamination of the compounding area, manual compounding was associated with lower contamination, although the result was not statistically significant (OR 4.251, 95% CI 0.439-51.772). For the contamination of infusion bags, the robot was associated with lower contamination (OR 0.176, 95% CI 0.084-0.365). Conclusions: Robotic compounding showed better accuracy than manual compounding and, without control groups, showed a high accuracy rate and also reduced the risk of drug contamination and compounding workload. The preparation time of the robot was not consistent because the type of robot and introduced system were different. In conclusion, robotic compounding showed mixed results compared to the manual compounding of drugs, so the system should be introduced considering the risks and benefits of robots.


Asunto(s)
Antineoplásicos , Procedimientos Quirúrgicos Robotizados , Robótica , Humanos , Composición de Medicamentos/métodos , Antineoplásicos/uso terapéutico , Robótica/métodos
6.
Hum Genomics ; 15(1): 28, 2021 05 10.
Artículo en Inglés | MEDLINE | ID: mdl-33971976

RESUMEN

BACKGROUND: Rare diseases are pathologies that affect less than 1 in 2000 people. They are difficult to diagnose due to their low frequency and their often highly heterogeneous symptoms. Rare diseases have in general a high impact on the quality of life and life expectancy of patients, which are in general children or young people. The advent of high-throughput sequencing techniques has improved diagnosis in several different areas, from pediatrics, achieving a diagnostic rate of 41% with whole genome sequencing (WGS) and 36% with whole exome sequencing, to neurology, achieving a diagnostic rate between 47 and 48.5% with WGS. This evidence has encouraged our group to pursue a molecular diagnosis using WGS for this and several other patients with rare diseases. RESULTS: We used whole genome sequencing to achieve a molecular diagnosis of a 7-year-old girl with a severe panvascular artery disease that remained for several years undiagnosed. We found a frameshift variant in one copy and a large deletion involving two exons in the other copy of a gene called YY1AP1. This gene is related to Grange syndrome, a recessive rare disease, whose symptoms include stenosis or occlusion of multiple arteries, congenital heart defects, brachydactyly, syndactyly, bone fragility, and learning disabilities. Bioinformatic analyses propose these mutations as the most likely cause of the disease, according to its frequency, in silico predictors, conservation analyses, and effect on the protein product. Additionally, we confirmed one mutation in each parent, supporting a compound heterozygous status in the child. CONCLUSIONS: In general, we think that this finding can contribute to the use of whole genome sequencing as a diagnosis tool of rare diseases, and in particular, it can enhance the set of known mutations associated with different diseases.


Asunto(s)
Arteriopatías Oclusivas/genética , Proteínas de Ciclo Celular/genética , Cardiopatías Congénitas/genética , Enfermedades Raras/genética , Factores de Transcripción/genética , Arteriopatías Oclusivas/diagnóstico , Arteriopatías Oclusivas/patología , Arterias/diagnóstico por imagen , Arterias/patología , Niño , Femenino , Mutación del Sistema de Lectura/genética , Cardiopatías Congénitas/diagnóstico , Cardiopatías Congénitas/patología , Homocigoto , Humanos , Linaje , Enfermedades Raras/diagnóstico , Enfermedades Raras/patología , Secuenciación Completa del Genoma
7.
Endocr Pract ; 28(4): 420-424, 2022 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-35217191

RESUMEN

OBJECTIVE: Gender-affirming surgeries are becoming increasingly common in the United States. For many transgender and gender-diverse patients, gender-affirming surgery is a critical aspect of their overall health and wellness and has a significant impact on their social functioning. Although often the role of the primary care provider, endocrinology specialists may also need to counsel their patients and collaborate with surgical teams. METHODS: This narrative review provides an overview of the preoperative assessment and perioperative management for the most common gender-affirming surgeries. RESULTS: Preoperative assessment prior to gender-affirming surgeries can resemble assessment for other surgeries. CONCLUSION: In the absence of data specific to gender-affirming surgeries, risk stratification and amelioration must use surrogate data from other populations.


Asunto(s)
Cirugía de Reasignación de Sexo , Personas Transgénero , Transexualidad , Identidad de Género , Humanos , Atención Perioperativa , Cirugía de Reasignación de Sexo/métodos , Transexualidad/cirugía , Estados Unidos
8.
Int J Mol Sci ; 22(17)2021 Aug 30.
Artículo en Inglés | MEDLINE | ID: mdl-34502341

RESUMEN

Clubroot caused by Plasmodiophora brassicae is a severe disease of cruciferous crops that decreases crop quality and productivity. Several clubroot resistance-related quantitative trait loci and candidate genes have been identified. However, the underlying regulatory mechanism, the interrelationships among genes, and how genes are regulated remain unexplored. MicroRNAs (miRNAs) are attracting attention as regulators of gene expression, including during biotic stress responses. The main objective of this study was to understand how miRNAs regulate clubroot resistance-related genes in P. brassicae-infected Brassica rapa. Two Brassica miRNAs, Bra-miR1885a and Bra-miR1885b, were revealed to target TIR-NBS genes. In non-infected plants, both miRNAs were expressed at low levels to maintain the balance between plant development and basal immunity. However, their expression levels increased in P. brassicae-infected plants. Both miRNAs down-regulated the expression of the TIR-NBS genes Bra019412 and Bra019410, which are located at a clubroot resistance-related quantitative trait locus. The Bra-miR1885-mediated down-regulation of both genes was detected for up to 15 days post-inoculation in the clubroot-resistant line CR Shinki and in the clubroot-susceptible line 94SK. A qRT-PCR analysis revealed Bra019412 expression was negatively regulated by miR1885. Both Bra019412 and Bra019410 were more highly expressed in CR Shinki than in 94SK; the same expression pattern was detected in multiple clubroot-resistant and clubroot-susceptible inbred lines. A 5' rapid amplification of cDNA ends analysis confirmed the cleavage of Bra019412 by Bra-miR1885b. Thus, miR1885s potentially regulate TIR-NBS gene expression during P. brassicae infections of B. rapa.


Asunto(s)
Brassica rapa/inmunología , Resistencia a la Enfermedad/inmunología , Regulación de la Expresión Génica de las Plantas , MicroARNs/genética , Enfermedades de las Plantas/inmunología , Proteínas de Plantas/metabolismo , Plasmodiophorida/fisiología , Brassica rapa/genética , Brassica rapa/parasitología , Resistencia a la Enfermedad/genética , Enfermedades de las Plantas/genética , Enfermedades de las Plantas/parasitología , Proteínas de Plantas/genética
9.
Medicina (Kaunas) ; 56(4)2020 Apr 19.
Artículo en Inglés | MEDLINE | ID: mdl-32325902

RESUMEN

Background and Objectives: Recent evidence suggests that oral health is associated with various systemic diseases including psychiatric illnesses. This study examined the association between depression and access to dental care in Korean adults. Materials and Methods: A cross-sectional evaluation was performed using data from the Sixth Korea National Health and Nutrition Examination Survey 2014. The general characteristics of the participants, the current depression status, and issues with access to dental care were collected to evaluate the factors for not being able to make dental visits according to care needs. Results: The study population comprised a total of 5976 participants who were 19 years of age and older and represented 40.7 million Koreans. A multivariable logistic regression analysis with weighted observations revealed that participants with current depressive illness were about two times more likely to express that they could not make dental visits in spite of their perceived care needs (adjusted odds ratio (OR) = 2.097; 95% confidence interval (CI) 1.046-4.203). The reasons for not making dental visits included financial problems, perceived importance of the dental problem, and fear of visiting dental professionals. Conclusions: Korean adults with current depressive illness were less likely to make dental visits when they had dental care needs. To improve dental health accessibility for patients with depressive illness, coordinated efforts can be considered involving multidisciplinary health care professionals.


Asunto(s)
Atención Odontológica/estadística & datos numéricos , Depresión/epidemiología , Accesibilidad a los Servicios de Salud/estadística & datos numéricos , Adulto , Anciano , Estudios Transversales , Atención Odontológica/psicología , Femenino , Encuestas Epidemiológicas , Humanos , Masculino , Persona de Mediana Edad , Salud Bucal/estadística & datos numéricos , República de Corea/epidemiología
10.
Plant Physiol ; 177(3): 1050-1065, 2018 07.
Artículo en Inglés | MEDLINE | ID: mdl-29769325

RESUMEN

Algae undergo a complete metabolic transformation under stress by arresting cell growth, inducing autophagy and hyper-accumulating biofuel precursors such as triacylglycerols and starch. However, the regulatory mechanisms behind this stress-induced transformation are still unclear. Here, we use biochemical, mutational, and "omics" approaches to demonstrate that PI3K signaling mediates the homeostasis of energy molecules and influences carbon metabolism in algae. In Chlamydomonas reinhardtii, the inhibition and knockdown (KD) of algal class III PI3K led to significantly decreased cell growth, altered cell morphology, and higher lipid and starch contents. Lipid profiling of wild-type and PI3K KD lines showed significantly reduced membrane lipid breakdown under nitrogen starvation (-N) in the KD. RNA-seq and network analyses showed that under -N conditions, the KD line carried out lipogenesis rather than lipid hydrolysis by initiating de novo fatty acid biosynthesis, which was supported by tricarboxylic acid cycle down-regulation and via acetyl-CoA synthesis from glycolysis. Remarkably, autophagic responses did not have primacy over inositide signaling in algae, unlike in mammals and vascular plants. The mutant displayed a fundamental shift in intracellular energy flux, analogous to that in tumor cells. The high free fatty acid levels and reduced mitochondrial ATP generation led to decreased cell viability. These results indicate that the PI3K signal transduction pathway is the metabolic gatekeeper restraining biofuel yields, thus maintaining fitness and viability under stress in algae. This study demonstrates the existence of homeostasis between starch and lipid synthesis controlled by lipid signaling in algae and expands our understanding of such processes, with biotechnological and evolutionary implications.


Asunto(s)
Carbono/metabolismo , Chlamydomonas reinhardtii/metabolismo , Metabolismo Energético/fisiología , Fosfatidilinositol 3-Quinasas/metabolismo , Proteínas de Plantas/metabolismo , Adenosina Trifosfato/metabolismo , Autofagia/fisiología , Chlamydomonas reinhardtii/efectos de los fármacos , Chlamydomonas reinhardtii/genética , Inhibidores Enzimáticos/farmacología , Técnicas de Silenciamiento del Gen , Metabolismo de los Lípidos/genética , Lípidos de la Membrana/genética , Lípidos de la Membrana/metabolismo , Mutación , Fosfatidilinositol 3-Quinasas/genética , Inhibidores de las Quinasa Fosfoinosítidos-3 , Filogenia , Proteínas de Plantas/genética , Scenedesmus/efectos de los fármacos , Scenedesmus/metabolismo , Transducción de Señal , Almidón/genética , Almidón/metabolismo
11.
Nucleic Acids Res ; 45(4): 1569-1583, 2017 02 28.
Artículo en Inglés | MEDLINE | ID: mdl-28119422

RESUMEN

Although much is known about microRNA (miRNA) biogenesis and the mechanism by which miRNAs regulate their targets, little is known about the regulation of miRNA stability. Mature miRNAs are stabilized by binding to Argonaute (Ago) proteins, the core components of the RNA-induced silencing complex (RISC). Recent studies suggest that interactions between miRNAs and their highly complementary target RNAs promote release of miRNAs from Ago proteins, and this in turn can lead to destabilization of miRNAs. However, the physiological triggers of miRNA destabilization with molecular mechanisms remain largely unknown. Here, using an in vitro system that consists of a minimal human Ago2-RISC in HEK293T cell lysates, we sought to understand how miRNAs are destabilized by their targets. Strikingly, we showed that miRNA destabilization is dramatically enhanced by an interaction with seedless, non-canonical targets. We then showed that this process entails not only unloading of miRNAs from Ago, but also 3΄ end destabilization of miRNAs occurred within Ago. Furthermore, our mutation analysis indicates that conformational changes in the hinge region of the Ago PAZ domain are likely to be the main driving force of the miRNA destabilization. Our collective results suggest that non-canonical targets may provide a stability control mechanism in the regulation of miRNAs in humans.


Asunto(s)
Proteínas Argonautas/metabolismo , Regulación de la Expresión Génica , MicroARNs/genética , Interferencia de ARN , ARN Mensajero/genética , Emparejamiento Base , Células HEK293 , Células HeLa , Humanos , Modelos Biológicos , Unión Proteica , Estabilidad del ARN
12.
BMC Genomics ; 19(1): 532, 2018 Jul 13.
Artículo en Inglés | MEDLINE | ID: mdl-30005603

RESUMEN

BACKGROUND: Nitrogen (N) is a key macronutrient essential for plant growth, and its availability has a strong influence on crop development. The application of synthetic N fertilizers on crops has increased substantially in recent decades; however, the applied N is not fully utilized due to the low N use efficiency of crops. To overcome this limitation, it is important to understand the genome-wide responses and functions of key genes and potential regulatory factors in N metabolism. RESULTS: Here, we characterized changes in the rice (Oryza sativa) transcriptome, including genes, newly identified putative long non-coding RNAs (lncRNAs), and microRNAs (miRNAs) and their target mRNAs in response to N starvation using four different transcriptome approaches. Analysis of rice genes involved in N metabolism and/or transport using strand-specific RNA-Seq identified 2588 novel putative lncRNA encoding loci. Analysis of previously published RNA-Seq datasets revealed a group of N starvation-responsive lncRNAs showing differential expression under other abiotic stress conditions. Poly A-primed sequencing (2P-Seq) revealed alternatively polyadenylated isoforms of N starvation-responsive lncRNAs and provided precise 3' end information on the transcript models of these lncRNAs. Analysis of small RNA-Seq data identified N starvation-responsive miRNAs and down-regulation of miR169 family members, causing de-repression of NF-YA, as confirmed by strand-specific RNA-Seq and qRT-PCR. Moreover, we profiled the N starvation-responsive down-regulation of root-specific miRNA, osa-miR444a.4-3p, and Degradome sequencing confirmed MADS25 as a novel target gene. CONCLUSIONS: In this study, we used a combination of multiple RNA-Seq analyses to extensively profile the expression of genes, newly identified lncRNAs, and microRNAs in N-starved rice roots and shoots. Data generated in this study provide an in-depth understanding of the regulatory pathways modulated by N starvation-responsive miRNAs. The results of comprehensive, large-scale data analysis provide valuable information on multiple aspects of the rice transcriptome, which may be useful in understanding the responses of rice plants to changes in the N supply status of soil.


Asunto(s)
Nitrógeno/deficiencia , Oryza/genética , ARN no Traducido/genética , Transcriptoma , Perfilación de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , MicroARNs/genética , MicroARNs/metabolismo , Oryza/metabolismo , Fosfatos/metabolismo , Raíces de Plantas/genética , Raíces de Plantas/metabolismo , Brotes de la Planta/genética , Brotes de la Planta/metabolismo , ARN Largo no Codificante/genética , ARN Largo no Codificante/metabolismo , ARN no Traducido/metabolismo , Análisis de Secuencia de ARN , Estrés Fisiológico
13.
BMC Genomics ; 16: 680, 2015 Sep 04.
Artículo en Inglés | MEDLINE | ID: mdl-26341079

RESUMEN

BACKGROUND: Long non-coding RNAs (lncRNAs) are a class of RNAs that do not encode proteins. Recently, lncRNAs have gained special attention for their roles in various biological process and diseases. RESULTS: In an attempt to identify long intergenic non-coding RNAs (lincRNAs) and their possible involvement in honey bee development and diseases, we analyzed RNA-seq datasets generated from Asian honey bee (Apis cerana) and western honey bee (Apis mellifera). We identified 2470 lincRNAs with an average length of 1011 bp from A. cerana and 1514 lincRNAs with an average length of 790 bp in A. mellifera. Comparative analysis revealed that 5 % of the total lincRNAs derived from both species are unique in each species. Our comparative digital gene expression analysis revealed a high degree of tissue-specific expression among the seven major tissues of honey bee, different from mRNA expression patterns. A total of 863 (57 %) and 464 (18 %) lincRNAs showed tissue-dependent expression in A. mellifera and A. cerana, respectively, most preferentially in ovary and fat body tissues. Importantly, we identified 11 lincRNAs that are specifically regulated upon viral infection in honey bees, and 10 of them appear to play roles during infection with various viruses. CONCLUSIONS: This study provides the first comprehensive set of lincRNAs for honey bees and opens the door to discover lincRNAs associated with biological and hormone signaling pathways as well as various diseases of honey bee.


Asunto(s)
Abejas/genética , Abejas/virología , Genoma de los Insectos , Estudio de Asociación del Genoma Completo , ARN Largo no Codificante/genética , Animales , Análisis por Conglomerados , Biología Computacional/métodos , Expresión Génica , Perfilación de la Expresión Génica , Especificidad de Órganos/genética , Reproducibilidad de los Resultados , Análisis de Secuencia de ARN
14.
Int J Syst Evol Microbiol ; 63(Pt 12): 4519-4523, 2013 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-23859945

RESUMEN

A Gram-stain-negative, aerobic, motile by gliding, non-spore-forming, rod-shaped, orange-pigmented bacterium, designated strain H32-4(T), was isolated from 32 m deep water of Daechung reservoir in Daejeon, Republic of Korea. Based on the nucleotide sequence of the 16S rRNA gene, the closest neighbouring type strain was Lacibacter cauensis NJ-8(T) with which strain H32-4(T) shared 98.9% sequence similarity. The most abundant fatty acids in whole cells of strain H32-4(T) were C15 : 0 iso (40.6 %), C17 : 0 iso 3-OH (22.4%), summed feature 3 (C16:1ω7c and/or C16:1ω6c; 9.3%) and C15:0 (6.6 %). The predominant menaquinone was MK-7. The G+C content of the genomic DNA of strain H32-4(T) was 45.7 mol%. Thus, these combined genotypic and phenotypic data supported the conclusion that strain H32-4(T) represents a novel species of the genus Lacibacter, for which the name Lacibacter daechungensis sp. nov. is proposed. The type strain is H32-4(T) ( = KCTC 32395(T) = JCM 19172(T)).


Asunto(s)
Bacteroidetes/clasificación , Agua Dulce/microbiología , Filogenia , Técnicas de Tipificación Bacteriana , Bacteroidetes/genética , Bacteroidetes/aislamiento & purificación , Composición de Base , ADN Bacteriano/genética , Ácidos Grasos/química , Datos de Secuencia Molecular , ARN Ribosómico 16S/genética , República de Corea , Análisis de Secuencia de ADN , Vitamina K 2/análogos & derivados , Vitamina K 2/química
15.
Front Plant Sci ; 14: 1204279, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37360705

RESUMEN

CHH methylation (mCHH) increases gradually during embryogenesis across dicotyledonous plants, indicating conserved mechanisms of targeting and conferral. Although it is suggested that methylation increase during embryogenesis enhances transposable element silencing, the detailed epigenetic pathways underlying this process remain unclear. In Arabidopsis, mCHH is regulated by both small RNA-dependent DNA methylation (RdDM) and RNA-independent Chromomethylase 2 (CMT2) pathways. Here, we conducted DNA methylome profiling at five stages of Arabidopsis embryogenesis, and classified mCHH regions into groups based on their dependency on different methylation pathways. Our analysis revealed that the gradual increase in mCHH in embryos coincided with the expansion of small RNA expression and regional mCHH spreading to nearby sites at numerous loci. We identified distinct methylation dynamics in different groups of mCHH targets, which vary according to transposon length, location, and cytosine frequency. Finally, we highlight the characteristics of transposable element loci that are targeted by different mCHH machinery, showing that short, heterochromatic TEs with lower mCHG levels are enriched in loci that switch from CMT2 regulation in leaves, to RdDM regulation during embryogenesis. Our findings highlight the interplay between the length, location, and cytosine frequency of transposons and the mCHH machinery in modulating mCHH dynamics during embryogenesis.

16.
Front Pharmacol ; 13: 773454, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35185558

RESUMEN

Background: Prescription medication sharing is an inappropriate medication use behavior that can lead to medication errors and adverse drug events, posing a public health threat. The reported prevalence of prescription medication lending and borrowing varies by country, ranging from 6%-23% and 5%-52%, respectively. However, research on medication sharing is scant in Asian countries. Therefore, this study aimed to describe the rate of prescription medication sharing practices and investigate the associated behavioral factors, types of shared medications, and reasons for sharing among adults in South Korea. Methods: A cross-sectional study was conducted using an online self-administered survey of 1,000 adults (aged 19-69 years; November 2020). A stratified sampling method was used to select survey participants from a nationwide consumer panel, which ensured a representative distribution of the Korean population by age, gender, and region. Descriptive and logistic regression analyses were used to evaluate the information related to sharing behavior. Results: A total of 1,000 respondents participated in this study. The mean age of the respondents was 44.7 years (standard deviation [SD], 13.4), ranging from 20 to 69 years. The rate of medication sharing was 52.4%. The most prevalently shared medications were analgesic, antipyretic, and antimigraine medications. Prescription medications were shared mostly between family and relatives. Older age was a predictive factor for sharing analgesics. Lower educational level was a predictive factor for sharing ophthalmic medications. Conclusions: Approximately one in two respondents in our study have experienced medication sharing in their lifetime. Future studies are needed to establish evidence-based strategies for patient education and improve the medication use process. Healthcare professionals should assess patients' needs for accessing medications and be ready to educate and guide them with specific action plans. Policymakers should consider patient empowerment strategies including public education and campaigns to avoid potential adverse outcomes of medication sharing.

17.
J Rheumatol ; 49(6 Suppl 1): 40-43, 2022 06.
Artículo en Inglés | MEDLINE | ID: mdl-35365577

RESUMEN

The International Dermatology Outcome Measures (IDEOM) initiative presented an update on their progress related to instruments for psoriasis (PsO) and psoriatic arthritis (PsA) patient-centered outcome measures at the 2021 annual meeting of the Group for Research and Assessment of Psoriasis and Psoriatic Arthritis (GRAPPA). The Treatment Satisfaction working group presented the development of a 7-item treatment satisfaction questionnaire specific for dermatological conditions. The group is beginning by assessing the validity and reliability of the instrument in PsO patient populations, with the ultimate goal of validating it for use in multiple dermatological diseases. The Musculoskeletal Symptoms working group discussed how implementation of a screening measurement tool in patients with PsO can help identify unknown diagnoses of PsA or prevent worsening of symptoms.


Asunto(s)
Artritis Psoriásica , Dermatología , Psoriasis , Reumatología , Artritis Psoriásica/diagnóstico , Artritis Psoriásica/terapia , Humanos , Psoriasis/diagnóstico , Psoriasis/terapia , Reproducibilidad de los Resultados , Piel
18.
Transgend Health ; 7(5): 449-452, 2022 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-36644486

RESUMEN

Purpose: Although medical care for transgender and gender nonbinary (TGNB) individuals is rapidly expanding, numerous gaps in the organization of quality care for TGNB individuals remain. In 2018, the Mount Sinai Center for Transgender Medicine and Surgery (CTMS) expanded its unified care approach to integrate services with an interdisciplinary inpatient team for surgical patients as part of the program. The inpatient team connected with the existing interdisciplinary ambulatory team with all pertinent medical and psychosocial information shared between the teams. The format enabled the hospital team to better prepare in advance of a patient's arrival and facilitated discharge planning as well. We sought to assess patient satisfaction with inpatient care after implementation of the interdisciplinary operation. Methods: The standard Press Ganey survey tool used by the Mount Sinai Health System to measure patient satisfaction with care was queried before and after implementation of the interdisciplinary inpatient care team. Results: Patient ratings of inpatient care rose dramatically. Relative to other institutions nationally, Press Ganey scores rose into the 98th or 99th percentiles across all domains. The new scores represented a rise of 25% for communication with nurses, 3% for hospital environment, 25% for care transition, and 100% for willingness to recommend. The discharge information score represented a 30-fold improvement. Conclusion: An interdisciplinary inpatient health care team can significantly improve patient satisfaction for TGNB patients. Such an approach might be considered for other TGNB health care programs along with health care delivery in other areas of medicine.

19.
Front Plant Sci ; 12: 727302, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34421977

RESUMEN

Pre-harvest sprouting (PHS) is one of the primary problems associated with seed dormancy in rice (Oryza sativa L.). It causes yield loss and reduces grain quality under unpredictable humid conditions at the ripening stage, thus affecting the economic value of the rice crop. To resolve this issue, understanding the molecular mechanism underlying seed dormancy in rice is important. Recent studies have shown that seed dormancy is affected by a large number of genes associated with plant hormone regulation. However, understanding regarding the effect of heat stress on seed dormancy and plant hormones is limited. This study compared the transcriptome and small RNAome of the seed embryo and endosperm of two contrasting japonica rice accessions, PHS susceptible (with low seed dormancy) and PHS resistant (with high seed dormancy), at three different maturation stages. We found that 9,068 genes and 35 microRNAs (miRNAs) were differentially expressed in the embryo, whereas 360 genes were differentially expressed in the endosperm. Furthermore, we identified and verified the candidate genes associated with seed dormancy and heat stress-related responses in rice using quantitative real-time PCR. We newly discovered eight hormone-related genes, four heat shock protein-related genes, and two miRNAs potentially involved in PHS. These findings provide a strong foundation for understanding the dynamics of transcriptome and small RNAome of hormone- and heat stress-related genes, which affect PHS during seed maturation.

20.
J Clin Endocrinol Metab ; 106(4): e1586-e1590, 2021 03 25.
Artículo en Inglés | MEDLINE | ID: mdl-33417686

RESUMEN

BACKGROUND: Both surgery and exogenous estrogen use are associated with increased risk of venous thromboembolism (VTE). However, it is not known whether estrogen hormone therapy (HT) exacerbates the surgery-associated risk among transgender and gender nonbinary (TGNB) individuals. The lack of published data has contributed to heterogeneity in perioperative protocols regarding estrogen HT administration for TGNB patients undergoing gender-affirming surgery. METHODS: A single-center retrospective chart review was performed on all TGNB patients who underwent gender-affirming surgery between November 2015 and August 2019. Surgery type, preoperative HT regimen, perioperative HT regimen, VTE prophylaxis management, outcomes, and demographic data were recorded. RESULTS: A total of 919 TGNB patients underwent 1858 surgical procedures representing 1396 unique cases, of which 407 cases were transfeminine patients undergoing primary vaginoplasty. Of the latter, 190 cases were performed with estrogen suspended for 1 week prior to surgery, and 212 cases were performed with HT continued throughout. Of all cases, 1 patient presented with VTE, from the cohort of transfeminine patients whose estrogen HT was suspended prior to surgery. No VTE events were noted among those who continued HT. Mean postoperative follow-up was 285 days. CONCLUSIONS: Perioperative VTE was not a significant risk in a large, homogenously treated cohort of TGNB patients independent of whether HT was suspended or not prior to surgery.


Asunto(s)
Estrógenos/efectos adversos , Cirugía de Reasignación de Sexo/efectos adversos , Tromboembolia Venosa/etiología , Adulto , Femenino , Humanos , Masculino , Persona de Mediana Edad , Estudios Retrospectivos , Medición de Riesgo , Personas Transgénero , Resultado del Tratamiento
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