scholarly journals Eucalyptus grandis THIOREDOXINS, DIVERSITY AND GENE EXPRESSION

2019 ◽  
Vol 43 (6) ◽  
Author(s):  
Vitória Régia Alves Cavalcante ◽  
Fabiana Silva de Araújo ◽  
Diego Gomes Teixeira ◽  
Paulo Marinho
Keyword(s):  
Gene Expression ◽  
Active Sites ◽  
Expression Patterns ◽  
Eucalyptus Grandis ◽  
Gene Encoding ◽  
Gene Characterization ◽  
Biochemical Processes ◽  
Multigenic Family ◽  
Oxidoreductase Enzymes ◽  
Gene Structure And Expression

ABSTRACT Tree genomes have been sequenced in recent years providing a source of basic information on multigenic family characterization. Comparative genomics based on those complete genome sequences available in public database is an important tool providing useful information to progress on functional gene characterization. In this work, we focus on gene encoding for Thioredoxins (Trxs) in Eucalyptus grandis genome, which are oxidoreductase enzymes, involved in significant biochemical processes, above all the maintenance of cellular homeostasis. Here we investigate the diversity, structure and expression of these genes in eucalyptus. For this purpose, bioinformatics tools were employed, using public platforms data, to identify coding sequences and validate gene expression. Specific softwares were employed to characterize gene structure and expression. RT-PCR assays were carried out to specifically verify the expression of 4 cytoplasmic thioredoxin genes, observed in silico from leaf, phloem, xylem and apical meristem tissues. Twenty-two Trxs with characteristic and canonic active sites were identified, confirming the presence of all types of the three main groups already defined as plastidial (m, f, x, y, z) cytoplasmatic (h) and mitochondrial (o). However, differences in the number of genes per group were observed when compared with other tree genomes. The expression of these thioredoxin genes compared to some homologous genes presented divergent expression patterns compared to Arabidopis thaliana suggesting a functional specificity in eucalyptus, such as in the case of Eucgr.F01604 gene encoding an h1 cytoplasmic Trx, which presents a strong expression in conductor tissues.

scholarly journals microRNA-138 modulates cardiac patterning during embryonic development

2008 ◽  
Vol 105 (46) ◽  
pp. 17830-17835 ◽  
Author(s):  
Sarah U. Morton ◽  
Paul J. Scherz ◽  
Kimberly R. Cordes ◽  
Kathryn N. Ivey ◽  
Didier Y. R. Stainier ◽  
...  
Keyword(s):  
Gene Expression ◽  
Retinoic Acid ◽  
Embryonic Development ◽  
Expression Patterns ◽  
Acid Synthesis ◽  
Specific Gene ◽  
Protein Activity ◽  
Gene Encoding ◽  
Small Noncoding Rnas ◽  
Discrete Domains

Organ patterning during embryonic development requires precise temporal and spatial regulation of protein activity. microRNAs (miRNAs), small noncoding RNAs that typically inhibit protein expression, are broadly important for proper development, but their individual functions during organogenesis are largely unknown. We report that miR-138 is expressed in specific domains in the zebrafish heart and is required to establish appropriate chamber-specific gene expression patterns. Disruption of miR-138 function led to ventricular expansion of gene expression normally restricted to the atrio-ventricular valve region and, ultimately, to disrupted ventricular cardiomyocyte morphology and cardiac function. Temporal-specific knockdown of miR-138 by antagomiRs showed miR-138 function was required during a discrete developmental window, 24–34 h post-fertilization (hpf). miR-138 functioned partially by repressing the retinoic acid synthesis enzyme, aldehyde dehydrogenase-1a2, in the ventricle. This activity was complemented by miR-138-mediated ventricular repression of the gene encoding versican (cspg2), which was positively regulated by retinoic-acid signaling. Our findings demonstrate that miR-138 helps establish discrete domains of gene expression during cardiac morphogenesis by targeting multiple members of a common pathway, and also establish the use of antagomiRs in fish for temporal knockdown of miRNA function.

scholarly journals Acute Systemic Inflammatory Response Alters Transcription Profile of Genes Related to Immune Response and Ca2+ Homeostasis in Hippocampus; Relevance to Neurodegenerative Disorders

2020 ◽  
Vol 21 (21) ◽  
pp. 7838
Author(s):  
Grzegorz A. Czapski ◽  
Yuhai Zhao ◽  
Walter J. Lukiw ◽  
Joanna B. Strosznajder
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Inflammatory Response ◽  
Histone Deacetylases ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Systemic Inflammatory Response ◽  
Lipocalin 2 ◽  
Gene Encoding ◽  
Expression Of Genes

Acute systemic inflammatory response (SIR) triggers an alteration in the transcription of brain genes related to neuroinflammation, oxidative stress and cells death. These changes are also characteristic for Alzheimer’s disease (AD) neuropathology. Our aim was to evaluate gene expression patterns in the mouse hippocampus (MH) by using microarray technology 12 and 96 h after SIR evoked by lipopolysaccharide (LPS). The results were compared with microarray analysis of human postmortem hippocampal AD tissues. It was found that 12 h after LPS administration the expression of 231 genes in MH was significantly altered (FC > 2.0); however, after 96 h only the S100a8 gene encoding calgranulin A was activated (FC = 2.9). Gene ontology enrichment analysis demonstrated the alteration of gene expression related mostly to the immune-response including the gene Lcn2 for Lipocalin 2 (FC = 237.8), involved in glia neurotoxicity. The expression of genes coding proteins involved in epigenetic regulation, histone deacetylases (Hdac4,5,8,9,11) and bromo- and extraterminal domain protein Brd3 were downregulated; however, Brd2 was found to be upregulated. Remarkably, the significant increase in expression of Lcn2, S100a8, S100a9 and also Saa3 and Ch25h, was found in AD brains suggesting that early changes of immune-response genes evoked by mild SIR could be crucial in AD pathogenesis.

scholarly journals Aspergillus nigercitrate exporter revealed by comparison of two alternative citrate producing conditions

2018 ◽  
Author(s):  
Dorett I Odoni ◽  
Thanaporn Laothanachareon ◽  
Marta Vazquez-Vilar ◽  
Merlijn P van Gaal ◽  
Tom Schonewille ◽  
...  
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Aspergillus Niger ◽  
Expression Patterns ◽  
Cell Factory ◽  
Complex Interplay ◽  
Gene Encoding ◽  
Organic Acid Production ◽  
Combining Data ◽  
Citrate Accumulation

AbstractCurrently, there is no consensus regarding the mechanism underlyingAspergillus nigercitrate biosynthesis and secretion, although it is amongst the most studied biotechnological production processes. Carbon excess relative to various other medium constituents is key, but the complex interplay between the limiting factors required for extracellular citrate accumulation remains elusive. It is thought that one of the industrial bottlenecks for citrate production is citrate export, however, noA. nigercitrate exporter has yet been identified. Here, we show that the phenotype of increased extracellular citrate accumulation can have fundamentally different underlying mechanisms, depending on how this response is triggered, and that combining gene expression analyses of the different conditions can lead to the compilation of a shortlist of the most promising citrate exporter candidates. Specifically, we found that varying the amount and type of supplement of an arginine auxotrophicA. nigerstrain shows down-regulation of citrate metabolising enzymes in the condition in which more citrate is accumulated extracellularly. This contrasts with the transcriptional adaptations triggered by iron limitation, which also induces increasedA. nigercitrate production. By combining data obtained from these two manners of inducing comparatively high extracellular citrate accumulation, we were able to compile a shortlist of the most likely citrate transporter candidates. Two of the most promising candidates were tested in the yeastSaccharomyces cerevisiae, one of which showed the ability to secrete citrate. Deletion of the endogenousA. nigergene encoding the corresponding transporter abolished the ability of this fungus to secrete citrate. Instead, under conditions that usually favourA. nigercitrate production, we found increased accumulation of extracellular oxalate. Our findings provide steps in untangling the complex interplay of different mechanisms underlyingA. nigercitrate accumulation, and we identify, for the first time, a fungal citrate exporter, offering a valuable tool for improvement ofA. nigeras biotechnological cell-factory for organic acid production.Author SummaryCitrate is widely applied as acidifier, flavouring and chelating agent. Industrial citrate production currently relies on the filamentous fungusAspergillus niger. Although the industrial production process usingA. niger has vastly improved since initiated almost 100 years ago, citrate export remains a bottleneck. Here, we studied the gene expression pattern ofA. nigerunder various citrate producing conditions. Using these expression patterns and different computational approaches, we compiled a shortlist of putative citrate exporter candidates. In this way, we were able to identify a gene encoding a transporter protein capable of citrate export. We show that the yeastSaccharomyces cerevisiae, normally a citrate non-producer, secretes detectable amounts of citrate when harbouring this gene. In addition, we verify the biological function of this gene inA. nigeritself, as removing this gene resulted in a citrate non-producing phenotype, which is atypical for this fungus. This finding is particularly exciting, as it is the first identification of a eukaryotic citrate exporter. With this, we not only provide a tool for improvement of industrial citrate production, but knowledge of this gene should help develop new methods for improvement ofA. nigeras biotechnological cell-factory for the production of other organic acids.

scholarly journals Characterization and expression of Cm-AAT1 gene encoding alcohol acyl-transferase in melon fruit (Cucumis melo L.) ‘Hikapel’

2020 ◽  
Vol 21 (7) ◽  
Author(s):  
WIKO ARIF WIBOWO ◽  
MUHAMMAD IMAM FATKHUROHMAN ◽  
BUDI SETIADI DARYONO
Keyword(s):  
Gene Expression ◽  
Cucumis Melo ◽  
Complex Mixture ◽  
Storage Period ◽  
Acyl Transferase ◽  
Gene Encoding ◽  
Distinctive Character ◽  
Gene Characterization ◽  
Cucumis Melo L ◽  
Melon Fruit

Abstract. Wibowo WA, Fatkhurohman MI, Daryono BS. 2020. Characterization and expression of Cm-AAT1 gene encoding alcohol acyl-transferase in melon fruit (Cucumis melo L.) ‘Hikapel’. Biodiversitas 21: 3041-3046. Melon (Cucumis melo L.) is one of the horticulture commodities that have high economic value and its needs increase continuously. Many new melon cultivars have been assembled to produce a higher quality melon. Melon 'Hikapel' developed by the Laboratory of Genetics and Breeding, Faculty of Biology UGM has distinctive character in the form of a strong aroma. This aroma is a complex mixture of various kinds of volatile compound. One of the main determinant compounds is a volatile ester, synthesized by the alcohol acyl-transferase enzyme encoded by the Cm-AAT1 gene. Characterization of Cm-AAT1 began with isolation of melon rinds to get total RNAs. Synthesis cDNA was conducted with oligo-dT primer, followed by detection of Cm-AAT1 using specific primers. A specific band was sequenced to perform phylogenetic tree. Gene expression from 4 melon cultivars, ‘Hikapel’, ‘Hikadi’, ‘Sun Lady’, and ‘Luna’ analysis was performed using relative quantitative Real-Time PCR. The results of this study showed that Cm-AAT1 owned not only by aromatic cultivars ‘Hikapel’ and ‘Hikadi’, but also owned by non-aromatic cultivars ‘Sun Lady’ and ‘Luna’. Phylogenetic analysis shows a high similarity between Cm-AAT1 on 'Hikapel' and 'Hikadi'. Gene expression analysis on 'Hikapel' increases as the process of fruit ripening during the storage period and it is in contrast to 'Hikadi' at decrease when the fruit began to enter the decay process on day 7th. Expression of Cm-AAT1 on ‘Hikapel’ was higher than ‘Hikadi’ at the peak of fruit maturity.

scholarly journals Modulating gene expression in breast cancer via DNA secondary structure and the CRISPR toolbox

NAR Cancer ◽  
2021 ◽  
Vol 3 (4) ◽  
Author(s):  
Jessica A Kretzmann ◽  
Kelly L Irving ◽  
Nicole M Smith ◽  
Cameron W Evans
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Transcription Factors ◽  
Active Sites ◽  
Early Stage ◽  
Expression Patterns ◽  
Significant Risk ◽  
Metastatic Breast ◽  
Survival Prognosis ◽  
Disease Heterogeneity

Abstract Breast cancer is the most commonly diagnosed malignancy in women, and while the survival prognosis of patients with early-stage, non-metastatic disease is ∼75%, recurrence poses a significant risk and advanced and/or metastatic breast cancer is incurable. A distinctive feature of advanced breast cancer is an unstable genome and altered gene expression patterns that result in disease heterogeneity. Transcription factors represent a unique therapeutic opportunity in breast cancer, since they are known regulators of gene expression, including gene expression involved in differentiation and cell death, which are themselves often mutated or dysregulated in cancer. While transcription factors have traditionally been viewed as ‘undruggable’, progress has been made in the development of small-molecule therapeutics to target relevant protein–protein, protein–DNA and enzymatic active sites, with varying levels of success. However, non-traditional approaches such as epigenetic editing, transcriptional control via CRISPR/dCas9 systems, and gene regulation through non-canonical nucleic acid secondary structures represent new directions yet to be fully explored. Here, we discuss these new approaches and current limitations in light of new therapeutic opportunities for breast cancers.

Gene expression patterns in blood predict future severe endpoints in community acquired pneumonia

Pneumologie ◽  
2018 ◽  
Vol 72 (S 01) ◽  
pp. S8-S9
Author(s):  
M Bauer ◽  
H Kirsten ◽  
E Grunow ◽  
P Ahnert ◽  
M Kiehntopf ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Community Acquired Pneumonia ◽  
Gene Expression Patterns

Identification of Differentially Expressed Genes Using cDNA-AFLP During Six Days In Vitro Tuberization of Potato

Zuriat ◽  
2015 ◽  
Vol 14 (1) ◽  
Author(s):  
Nono Carsono ◽  
Christian Bachem
Keyword(s):  
Gene Expression ◽  
Developmental Process ◽  
Expression Patterns ◽  
Induction Medium ◽  
In Vitro Tuberization ◽  
Storage Organ ◽  
Developmentally Regulated ◽  
Study Gene Expression ◽  
Differential Pattern

Tuberization in potato is a complex developmental process resulting in the differentiation of stolon into the storage organ, tuber. During tuberization, change in gene expression has been known to occur. To study gene expression during tuberization over the time, in vitro tuberization system provides a suitable tool, due to its synchronous in tuber formation. An early six days axillary bud growing on tuber induction medium is a crucial development since a large number of genes change in their expression patterns during this period. In order to identify, isolate and sequencing the genes which displaying differential pattern between tuberizing and non-tuberizing potato explants during six days in vitro tuberization, cDNA-AFLP fingerprint, method for the visualization of gene expression using cDNA as template which is amplified to generate an RNA-fingerprinting, was used in this experiment. Seventeen primer combinations were chosen based on their expression profile from cDNA-AFLP fingerprint. Forty five TDFs (transcript derived fragment), which displayed differential expressions, were obtained. Tuberizing explants had much more TDFs, which developmentally regulated, than those from non tuberizing explants. Seven TDFs were isolated, cloned and then sequenced. One TDF did not find similarity in the current databases. The nucleotide sequence of TDF F showed best similarity to invertase ezymes from the databases. The homology of six TDFs with known sequences is discussed in this paper.

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