scholarly journals Stem transcriptome of cold stressed Eucalyptus globulus and E. urograndis

2018 ◽  
Vol 1 (2) ◽  
Author(s):  
Pedro Araújo
Keyword(s):  
Eucalyptus Globulus ◽  
Plant Biotechnology ◽  
Eucalyptus Species ◽  
Transcript Analysis ◽  
Rna Seq ◽  
Gene Profile ◽  
Regulatory Pathways ◽  
Cultivated Plant ◽  
Cold Condition ◽  
Eucalyptus Urograndis

Eucalyptus is an important source of cellulose and a widely cultivated plant. Biotechnology tools can save time spent in breeding and transcriptomic approaches generate a gene profile that allows the identification of candidates involved in processes of interest. RNA-seq is a commonly used technology for transcript analysis and it provides an overview of regulatory pathways. Here, we selected two contrasting Eucalyptus species for cold acclimatization and focused in responsive genes under cold condition aiming woody properties – lignin and cellulose. The number of differentially expressed genes identified in stem sections were 3.300 in Eucalyptus globulus and 1370 in Eucalyptus urograndis. We listed genes with expression higher than 10 times including NAC, MYB and DUF family members. The GO analysis indicates increased oxidative process for E. urograndis. This data can provide information for more detailed analyses for breeding, especially in perennial plants.

scholarly journals Integrated genomic analysis reveals regulatory pathways and dynamic landscapes of the tRNA transcriptome

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zefang Sun ◽  
Jia Tan ◽  
Minqiong Zhao ◽  
Qiyao Peng ◽  
Mingqing Zhou ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Genomic Analysis ◽  
Rna Seq ◽  
Regulatory Pathways ◽  
Cellular Processes ◽  
Dynamic Landscapes ◽  
Rna Fragments ◽  
A Cell ◽  
Considerable Impact ◽  
New Algorithms

AbstracttRNAs and tRNA-derived RNA fragments (tRFs) play various roles in many cellular processes outside of protein synthesis. However, comprehensive investigations of tRNA/tRF regulation are rare. In this study, we used new algorithms to extensively analyze the publicly available data from 1332 ChIP-Seq and 42 small-RNA-Seq experiments in human cell lines and tissues to investigate the transcriptional and posttranscriptional regulatory mechanisms of tRNAs. We found that histone acetylation, cAMP, and pluripotency pathways play important roles in the regulation of the tRNA gene transcription in a cell-specific manner. Analysis of RNA-Seq data identified 950 high-confidence tRFs, and the results suggested that tRNA pools are dramatically distinct across the samples in terms of expression profiles and tRF composition. The mismatch analysis identified new potential modification sites and specific modification patterns in tRNA families. The results also show that RNA library preparation technologies have a considerable impact on tRNA profiling and need to be optimized in the future.

scholarly journals Antimicrobial Activity of Several Cineole-Rich Western Australian Eucalyptus Essential Oils

2018 ◽  
Vol 6 (4) ◽  
pp. 122 ◽  
Author(s):  
Fahad Aldoghaim ◽  
Gavin Flematti ◽  
Katherine Hammer
Keyword(s):  
Mass Spectrometry ◽  
Antimicrobial Activity ◽  
Essential Oils ◽  
Eucalyptus Globulus ◽  
Antimicrobial Agents ◽  
Gas Chromatography Mass Spectrometry ◽  
Eucalyptus Species ◽  
Broth Microdilution ◽  
Main Component ◽  
Western Australian

Essential oils from the Western Australian (WA) Eucalyptus mallee species Eucalyptus loxophleba, Eucalyptus polybractea, and Eucalyptus kochii subsp. plenissima and subsp. borealis were hydrodistilled from the leaves and then analysed by gas chromatography–mass spectrometry in addition to a commercial Eucalyptus globulus oil and 1,8-cineole. The main component of all oils was 1,8-cineole at 97.32% for E. kochii subsp. borealis, 96.55% for E. kochii subsp. plenissima, 82.95% for E. polybractea, 78.78% for E. loxophleba 2, 77.02% for E. globulus, and 66.93% for E. loxophleba 1. The Eucalyptus oils exhibited variable antimicrobial activity determined by broth microdilution, with E. globulus and E. polybractea oils showing the highest activities. The majority of microorganisms were inhibited or killed at concentrations ranging from 0.25% to 8.0% (v/v). Enterococcus faecalis and Candida albicans were the least susceptible organisms, whilst Acinetobacter baumannii was the most sensitive. In conclusion, all oils from WA Eucalyptus species showed microorganism inhibitory activity, although this varied according to both the Eucalyptus species and the microorganism tested. These data demonstrate that WA Eucalyptus oils show activity against a range of medically important pathogens and therefore have potential as antimicrobial agents.

scholarly journals Transcriptomic Analysis Reveals Hormonal Control of Shoot Branching in Salix matsudana

Forests ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 287
Author(s):  
Juanjuan Liu ◽  
Bingbing Ni ◽  
Yanfei Zeng ◽  
Caiyun He ◽  
Jianguo Zhang
Keyword(s):  
Molecular Level ◽  
Hormonal Control ◽  
Molecular Techniques ◽  
Differentially Expressed ◽  
Shoot Branching ◽  
Rna Seq ◽  
Comprehensive Understanding ◽  
Regulatory Pathways ◽  
Salix Matsudana ◽  
Transcriptome Expression

Shoot branching is regulated by axillary bud activities, which subsequently grow into branches. Phytohormones play a central role in shoot branching control, particularly with regard to auxin, cytokinins (CKs), strigolactones (SLs), and gibberellins (GAs). To further study the molecular basis for the shoot branching in Salix matsudana, how shoot branching responds to hormones and regulatory pathways was investigated, and potential genes involved in the regulation of shoot branching were identified. However, how these positive and inhibitory processes work on the molecular level remains unknown. RNA-Seq transcriptome expression analysis was used to elucidate the mechanisms underlying shoot branching. In total, 102 genes related to auxin, CKs, SLs, and GAs were differentially expressed in willow development. A majority of the potential genes associated with branching were differentially expressed at the time of shoot branching in S. matsudana, which have more number of branching. These findings are consistent with the growth and physiological results. A regulatory network model was proposed to explain the interaction between the four hormones that control shoot branching. Collectively, the results presented here contribute to a more comprehensive understanding of the hormonal effects on shoot branching in S. matsudana. In the future, these findings will help uncover the interactions among auxin, SLs, CKs, and GAs that control shoot branching in willow, which could help improve plant structures through the implementation of molecular techniques in targeted breeding.

scholarly journals HYPSOMETRY AND VOLUMETRY OF Eucalyptus urograndis IN A CROP-FOREST INTEGRATION SYSTEM

FLORESTA ◽  
2022 ◽  
Vol 52 (1) ◽  
pp. 159
Author(s):  
Stephany Diolino Cunha ◽  
Vagner Santiago Do Vale ◽  
Tatiana Vieira Ramos ◽  
Matheus Da Silva Araújo
Keyword(s):  
Positive Impact ◽  
Eucalyptus Grandis ◽  
Coefficient Of Determination ◽  
Eucalyptus Species ◽  
Total System ◽  
Volume Data ◽  
Volumetric Models ◽  
Best Fit ◽  
Full Height ◽  
Eucalyptus Urograndis

Due to the positive impact that the eucalyptus species has on the Brazilian economy, it is currently the most used forest essence. The objective of this work was to evaluate different hypsometric and volumetric models for Eucalyptus urograndis clones (Eucalyptus urophylla S.T. Blak and Eucalyptus grandis W. Hill ex Maiden) in a Crop-Forest Integration (CFI) system. The trees were evaluated at 7 years of age and arranged in double rows, occupying 20.76% of the total system area. The individuals were subjected to rigorous volumetric cubing according to the Smalian method at intervals of one meter up to full height. The following models were evaluated for the collected height data: Linear, Trorey, Stofels, Curtis, Henriksen, Prodan, Chapman & Richards, Petterson and Bailey & Clutter. Furthermore, the Spurr, Hohenald-Krenn, Stoate, Schumacher Hall, Meyer, Husch, Ogaya and Takata models were used for volume data. The results were determined through the coefficient of determination (R2), standard error of the estimate in percentage (Syx%), significance of the regression coefficients (𝛽) and graphical distribution. The hypsometric model which best fit the database among tested models was the Prodan equation, with a coefficient of determination (R²) of 0.89, while the best result for volumetric models was found using the Meyer model, with a coefficient of determination (R²) of 0.99. All evaluated models were efficient in estimating the height and volume of the Crop-Forest Integration (CFI) system, thus demonstrating that GG100 eucalyptus is a good option in integrated systems.

scholarly journals RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism

2019 ◽  
Vol 21 (1) ◽  
pp. 167 ◽  
Author(s):  
Isiaka Ibrahim Muhammad ◽  
Sze Ling Kong ◽  
Siti Nor Akmar Abdullah ◽  
Umaiyal Munusamy
Keyword(s):  
Transcriptional Regulation ◽  
Regulatory Networks ◽  
Data Sets ◽  
Rna Seq ◽  
Transcriptional Regulatory Networks ◽  
Regulatory Pathways ◽  
Specific Biological Process ◽  
Transcriptional Regulatory ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Sequencing Platforms

The availability of data produced from various sequencing platforms offer the possibility to answer complex questions in plant research. However, drawbacks can arise when there are gaps in the information generated, and complementary platforms are essential to obtain more comprehensive data sets relating to specific biological process, such as responses to environmental perturbations in plant systems. The investigation of transcriptional regulation raises different challenges, particularly in associating differentially expressed transcription factors with their downstream responsive genes. In this paper, we discuss the integration of transcriptional factor studies through RNA sequencing (RNA-seq) and Chromatin Immunoprecipitation sequencing (ChIP-seq). We show how the data from ChIP-seq can strengthen information generated from RNA-seq in elucidating gene regulatory mechanisms. In particular, we discuss how integration of ChIP-seq and RNA-seq data can help to unravel transcriptional regulatory networks. This review discusses recent advances in methods for studying transcriptional regulation using these two methods. It also provides guidelines for making choices in selecting specific protocols in RNA-seq pipelines for genome-wide analysis to achieve more detailed characterization of specific transcription regulatory pathways via ChIP-seq.

scholarly journals PfAP2-G2 Is Associated to Production and Maturation of Gametocytes in Plasmodium falciparum via Regulating the Expression of PfMDV-1

2021 ◽  
Vol 11 ◽  
Author(s):  
Yaozheng Xu ◽  
Dan Qiao ◽  
Yuhao Wen ◽  
Yifei Bi ◽  
Yuxi Chen ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Chromatin Immunoprecipitation ◽  
Transcriptional Start Site ◽  
Immunofluorescence Assay ◽  
Mosquito Vector ◽  
Schizont Stage ◽  
Ring Stage ◽  
Rna Seq ◽  
Regulatory Pathways ◽  
Qpcr Analysis

Gametocyte is the sole form of the Plasmodium falciparum which is transmissible to the mosquito vector. Here, we report that an Apicomplexan Apetala2 (ApiAP2) family transcription factor, PfAP2-G2 (Pf3D7_1408200), plays a role in the development of gametocytes in P. falciparum by regulating the expression of PfMDV-1 (Pf3D7_1216500). Reverse transcriptase-quantitative PCR (RT-qPCR) analysis showed that PfAP2-G2 was highly expressed in the ring stage. Indirect immunofluorescence assay showed nuclear localization of PfAP2-G2 in asexual stages. The knockout of PfAP2-G2 led to a ~95% decrease in the number of mature gametocytes with a more substantial influence on the production and maturation of the male gametocytes, resulting in a higher female/male gametocyte ratio. To test the mechanism of this phenotype, RNA-seq and RT-qPCR showed that disruption of PfAP2-G2 led to the down-regulation of male development gene-1 (PfMDV-1) in asexual stages. We further found that PfAP2-G2 was enriched at the transcriptional start site (TSS) of PfMDV-1 by chromatin immunoprecipitation and qPCR assay in both ring stage and schizont stage, which demonstrated that PfMDV-1 is one of the targets of PfAP2-G2. In addition, RT-qPCR also showed that PfAP2-G (Pf3D7_1222600), the master regulator for sexual commitment, was also down-regulated in the PfAP2-G2 knockout parasites in the schizont stage, but no change in the ring stage. This phenomenon suggested that PfAP2-G2 played a role at the asexual stage for the development of parasite gametocytes and warrants further investigations in regulatory pathways of PfAP2-G2.

scholarly journals Behavioral and Gene Expression Analysis of Stxbp6-Knockout Mice

2021 ◽  
Vol 11 (4) ◽  
pp. 436
Author(s):  
Cong Liu ◽  
Qian Hu ◽  
Yan Chen ◽  
Lingqian Wu ◽  
Xionghao Liu ◽  
...  
Keyword(s):  
Nervous System ◽  
Enrichment Analysis ◽  
Rna Seq ◽  
Regulatory Pathways ◽  
The Past ◽  
Protein Receptor ◽  
Normal Behavior ◽  
Sensitive Factor ◽  
The Central Nervous System ◽  
Underlying Mechanisms

Since the first report that Stxbp6, a brain-enriched protein, regulates the assembly of soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complexes, little has been discovered about its functions over the past two decades. To determine the effects of Stxbp6 loss on nervous-system-associated phenotypes and underlying mechanisms, we constructed a global Stxbp6-knockout mouse. We found that Stxbp6-null mice survive normally, with normal behavior, but gained less weight relative to age- and sex-matched wildtype mice. RNA-seq analysis of the cerebral cortex of Stxbp6-null mice relative to wildtype controls identified 126 differentially expressed genes. Of these, 57 were upregulated and 69 were downregulated. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the most significant enriched KEGG term was “complement and coagulation cascades”. Our results suggest some potential regulatory pathways of Stxbp6 in the central nervous system, providing a remarkable new resource for understanding Stxbp6 function at the organism level.

scholarly journals Integrative genomic and transcriptomic analysis in plasmablastic lymphoma identifies disruption of key regulatory pathways

2021 ◽  
Author(s):  
Hanno M. Witte ◽  
Axel Künstner ◽  
Nadine Hertel ◽  
Heinz-Wolfram Bernd ◽  
Veronica Bernard ◽  
...  
Keyword(s):  
B Cell ◽  
Antigen Processing ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Janus Kinase ◽  
Plasmablastic Lymphoma ◽  
Rna Seq ◽  
Transcription Activator ◽  
Class I Mhc ◽  
Regulatory Pathways

Plasmablastic-lymphoma (PBL) represents a clinically heterogeneous subtype of aggressive-B-cell-non-Hodgkin-lymphoma. Although targeted-sequencing-studies and a single-center whole-exome-sequencing (WES) study in HIV+ patients recently revealed several genes, associated with PBL-pathogenesis, the global mutational-landscape and transcriptional-profile of PBL remain elusive. To inform on disease-associated mutational-drivers, mutational-patterns and perturbed pathways in HIV+ and HIV-PBL we performed WES and transcriptome sequencing (RNA-seq) of 33 PBL-tumors. Integrative analysis of somatic-mutations and gene-expression-profiles were performed to acquire insights into the divergent genotype-phenotype-correlation in EBV+ and EBV-PBL. We describe a significant accumulation of mutations in the Janus-kinase-signal-transducer and transcription-activator (OSMR, STAT3, PIM1, SOCS1) as well as receptor tyrosine-kinase RAS-pathways (ERBB3, NRAS, PDGFRB, NTRK). We provide further evidence of frequent perturbance of nuclear-factor κB (NFκB) signaling (NFKB2, BTK). Induced pathways, identified by RNA-seq closely resemble the mutational-profile regarding alterations accentuated in IL-6/JAK/STAT-signaling, NFκB-activity and MYC-signaling. Moreover, class I-MHC mediated antigen-processing and cell-cycle-regulation were significantly impacted by the EBV-status. An almost exclusive upregulation of PI3K/AKT/MTOR-signaling in EBV+ PBL and a significantly induced expression of NTRK3 in concert with recurrent oncogenic-mutations in EBV- PBL, hints at specific therapeutically targetable-mechanism in PBL-subgroups. Our characterization of a mutational and transcriptomic-landscape in PBL, distinct from DLBCL and MM substantiates the pathobiological-independence of PBL in the spectrum of B-cell-malignancies and thereby refines the taxonomy for aggressive-lymphomas.

scholarly journals A competence-regulated toxin-antitoxin system in Haemophilus influenzae

2018 ◽  
Author(s):  
Hailey Findlay Black ◽  
Scott Mastromatteo ◽  
Sunita Sinha ◽  
Rachel L. Ehrlich ◽  
Corey Nislow ◽  
...  
Keyword(s):  
Genetic Information ◽  
Carbon Sources ◽  
Toxin Gene ◽  
Dna Uptake ◽  
Transcript Analysis ◽  
Rna Seq ◽  
Negative Bacterium ◽  
Natural Competence ◽  
Starvation Conditions ◽  
Species Deletion

ABSTRACTNatural competence allows bacteria to respond to environmental and nutritional cues by taking up free DNA from their surroundings, thus gaining nutrients and genetic information. In the Gram-negative bacterium Haemophilus influenae, the DNA uptake machinery is induced by the CRP and Sxy transcription factors in response to lack of preferred carbon sources and nucleotide precursors. Here we show that HI0659—which is absolutely required for DNA uptake— encodes the antitoxin of a competence-regulated toxin-antitoxin operon (‘toxTA’), likely acquired by horizontal gene transfer from a Streptococcus species. Deletion of the toxin restores uptake to the antitoxin mutant. In addition to the expected Sxy-and CRP-dependent-competence promoter, transcript analysis using RNA-seq identified an internal antitoxin-repressed promoter whose transcription starts within toxT and will yield nonfunctional protein. We present evidence that the most likely effect of unopposed toxin expression is non-specific cleavage of mRNAs and arrest or death of competent cells in the culture, and we show that the toxin gene has been inactivated by deletion in many H. influenzae strains. We suggest that this competence-regulated toxin-antitoxin system may facilitate downregulation of protein synthesis and recycling of nucleotides under starvation conditions, or alternatively be a simple genetic parasite.

Abstract 17503: ETV2 Functions as a Pioneer Factor and Regulates the Endothelial Lineage

Circulation ◽  
2020 ◽  
Vol 142 (Suppl_3) ◽  
Author(s):  
Wuming Gong ◽  
Satyabrata Das ◽  
Javier Sierra-Pagan ◽  
Mary G Garry ◽  
Daniel J Garry
Keyword(s):  
Marker Genes ◽  
Cardiovascular Development ◽  
Rna Seq ◽  
Regulatory Pathways ◽  
Cardiovascular Regeneration ◽  
Multipotent Progenitors ◽  
Cellular Context ◽  
Pioneer Factor ◽  
Pioneer Factors ◽  
Endothelial Lineage

Background: Genetic mutations perturb the multipotent progenitors, which results in congenital cardiovascular disease. Therefore, it is essential to decipher the pioneer factors and the regulatory pathways that govern the specification and differentiation of mesodermal progenitors and use this information to develop targeted therapies to promote cardiovascular regeneration. Etv2 as an essential transcription factor for the development of cardiac, endothelial and hematopoietic lineages. In the present study, we used ES/EB differentiation and MEF reprogramming systems, to define Etv2 as a novel pioneer factor that relaxes the closed chromatin and drives endothelial development. Results: Using the iHA-Etv2 ES cell line, we engineered a mouse that inducibly overexpresses ETV2. The bulk RNA-seq, single cell RNA-seq data and ATAC-seq experiments showed that inducing Etv2 in MEFs and ES/EBs activated the downstream endothelial marker genes and promoted the development of endothelial lineages, supporting the notion that Etv2 functioned as a master regulator to drive the endothelial lineage development in different cellular contexts. We found that similar to other known pioneer factors, Etv2 was intrinsically able to target and bind the nucleosomes, and this capability appeared to be independent of the cellular context. To further define the mechanism, we performed Etv2, Brg1 and H3K27ac ChIP-seq analyses during MEF reprogramming and ES/EB differentiation. We found that Brg1 maintains and stabilizes the binding of Etv2 on the nucleosome, and Etv2 requires Brg1 to activate downstream genes during reprograming. Conclusion: In these studies, we defined Etv2 as a novel pioneer factor that relaxed the closed chromatin and promoted the endothelial lineage in both ES/EB differentiation and MEF reprogramming. The definition of these mechanisms will enhance our understanding of cardiovascular development and regeneration and serve as a platform for therapeutic applications for patients with congenital or aging related cardiovascular diseases.

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