scholarly journals Profiling of Wheat Class III Peroxidase Genes Derived from Powdery Mildew-Attacked Epidermis Reveals Distinct Sequence-Associated Expression Patterns

2005 ◽  
Vol 18 (7) ◽  
pp. 730-741 ◽  
Author(s):  
Guosheng Liu ◽  
Xiaoyan Sheng ◽  
David L. Greenshields ◽  
Adam Ogieglo ◽  
Susan Kaminskyj ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Differential Expression ◽  
Fluorescent Protein ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Amino Acid Sequences ◽  
Protein Fusion ◽  
Powdery Mildew Fungus ◽  
Mesophyll Cells ◽  
Signal Molecule

A cDNA library was constructed from leaf epidermis of diploid wheat (Triticum monococcum) infected with the powdery mildew fungus (Blumeria graminis f. sp. tritici) and was screened for genes encoding peroxidases. From 2,500 expressed sequence tags (ESTs), 36 cDNAs representing 10 peroxidase genes (designated TmPRX1 to TmPRX10) were isolated and further characterized. Alignment of the deduced amino acid sequences and phylogenetic clustering with peroxidases from other plant species demonstrated that these peroxidases fall into four distinct groups. Differential expression and tissue-specific localization among the members were observed during the B. graminis f. sp. tritici attack using Northern blots and reverse-transcriptase polymerase chain reaction analyses. Consistent with its abundance in the EST collection, TmPRX1 expression showed the highest induction during pathogen attack and fluctuated in response to the fungal parasitic stages. TmPRX1 to TmPRX6 were expressed predominantly in mesophyll cells, whereas TmPRX7 to TmPRX10, which feature a putative C-terminal propeptide, were detectable mainly in epidermal cells. Using TmPRX8 as a representative, we demonstrated that its C-terminal propeptide was sufficient to target a green fluorescent protein fusion protein to the vacuoles in onion cells. Finally, differential expression profiles of the TmPRXs after abiotic stresses and signal molecule treatments were used to dissect the potential role of these peroxidases in multiple stress and defense pathways.

scholarly journals Differential expression and correlation analysis of miRNA–mRNA profiles in swine testicular cells infected with porcine epidemic diarrhea virus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Xiaoqian Zhang ◽  
Chang Li ◽  
Bingzhou Zhang ◽  
Zhonghua Li ◽  
Wei Zeng ◽  
...  
Keyword(s):  
Differential Expression ◽  
Porcine Epidemic Diarrhea Virus ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Bacterial Invasion ◽  
Sequencing Data ◽  
Diarrhea Virus ◽  
Comparison Groups ◽  
Porcine Epidemic Diarrhea

AbstractThe variant virulent porcine epidemic diarrhea virus (PEDV) strain (YN15) can cause severe porcine epidemic diarrhea (PED); however, the attenuated vaccine-like PEDV strain (YN144) can induce immunity in piglets. To investigate the differences in pathogenesis and epigenetic mechanisms between the two strains, differential expression and correlation analyses of the microRNA (miRNA) and mRNA in swine testicular (ST) cells infected with YN15, YN144, and mock were performed on three comparison groups (YN15 vs Control, YN144 vs Control, and YN15 vs YN144). The mRNA and miRNA expression profiles were obtained using next-generation sequencing (NGS), and the differentially expressed (DE) (p-value < 0.05) mRNA and miRNA were obtained using DESeq R package. mRNAs targeted by DE miRNAs were predicted using the miRanda algortithm. 8039, 8631 and 3310 DE mRNAs, and 36, 36, and 22 DE miRNAs were identified in the three comparison groups, respectively. 14,140, 15,367 and 3771 DE miRNA–mRNA (targeted by DE miRNAs) interaction pairs with negatively correlated expression patterns were identified, and interaction networks were constructed using Cytoscape. Six DE miRNAs and six DE mRNAs were randomly selected to verify the sequencing data by real-time relative quantitative reverse transcription polymerase chain reaction (qRT-PCR). Based on bioinformatics analysis, we discovered the differences were mostly involved in host immune responses and viral pathogenicity, including NF-κB signaling pathway and bacterial invasion of epithelial cells, etc. This is the first comprehensive comparison of DE miRNA–mRNA pairs in YN15 and YN144 infection in vitro, which could provide novel strategies for the prevention and control of PED.

Fluorescent protein expression in temperature tolerant and susceptible reef-building corals

2021 ◽  
pp. 1-10
Author(s):  
Exequiel Gabriel S. Dizon ◽  
Jeric P. Da-Anoy ◽  
Melissa S. Roth ◽  
Cecilia Conaco
Keyword(s):  
Spectral Properties ◽  
Coral Species ◽  
Fluorescent Protein ◽  
Fluorescent Proteins ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Antioxidant Properties ◽  
Variable Expression ◽  
Acropora Digitifera ◽  
Insight Into

Abstract Fluorescent proteins (FPs) are reported to play an important role as photoprotectants and antioxidants in corals subjected to stressful conditions. Identifying the various FP genes expressed and FP gene expression patterns under stress in diverse coral species can provide insight into FP function. In this study, we identified 16 putative FP homologues from the transcriptomes of corals with varying susceptibility to elevated temperature, including Acropora digitifera, Favites colemani, Montipora digitata and Seriatopora caliendrum. Each coral expressed a different complement of FP transcripts, which were predicted to have distinct spectral properties. The most diverse and abundant repertoire of FP transcripts, including at least 6 green FPs, were expressed in the temperature-tolerant coral, F. colemani. In comparison, the other corals expressed fewer FP types. Specific FP transcripts exhibited variable expression profiles in coral fragments subjected to 32 ± 1 °C (treatment) or 28 ± 1 °C (control) for up to 72 h, suggesting that distinct FPs may have different roles. Further studies on the expression of the proteins encoded by these FP transcripts, their fluorescence activity, tissue localization, and possible antioxidant properties, are needed to reveal their contribution to thermal stress tolerance in certain species of corals.

scholarly journals Structure and Location Studies on Key Enzymes in Saponins Biosynthesis of Panax notoginseng

2019 ◽  
Vol 20 (24) ◽  
pp. 6121
Author(s):  
Pengguo Xia ◽  
Yujie Zheng ◽  
Zongsuo Liang
Keyword(s):  
Subcellular Localization ◽  
Fluorescent Protein ◽  
Expression Patterns ◽  
Three Dimensional ◽  
Panax Notoginseng ◽  
Squalene Epoxidase ◽  
Protein Fusion ◽  
Active Components ◽  
Key Enzymes ◽  
Saponin Biosynthesis

Panax notoginseng is one of the most widely used traditional herbs for the treatment of various diseases, in which saponins were the main active components. At present, the research of P. notoginseng mainly focused on the discovery of new compounds and pharmacology. However, there were few studies on the molecular mechanism of the synthesis of secondary metabolites of P. notoginseng. In our study, four coding sequences (CDS) encoding the key enzymes involved in saponin biosynthesis were cloned, namely farnesyl diphosphate synthase (FPS), squalene synthase (SS), squalene epoxidase (SE), and dammarenediol-II synthase (DS), which contained open reading frame (ORF) of 1029 bp, 1248 bp, 1614 bp, and 2310 bp, and coded 342, 415, 537, and 769 amino acids, respectively. At the same time, their domains, secondary structures, three-dimensional structures, and phylogenetics trees were analyzed by kinds of bioinformatics tools. Their phylogenetics relationships were also analyzed. In addition, GFP (Green fluorescent protein) fusion genes were constructed by the plasmid transformation system to determine the subcellular localization. The results of subcellular localization showed that FPS, SE, and DS were mainly located in cytomembrane and its surrounding, while SS was located both in cytoplasm and cytomembrane. Our findings provided data demonstrating the expression patterns of genes involved in saponin biosynthesis and would facilitate efforts to further elucidate the biosynthesis of the bioactive components in P. notoginseng.

scholarly journals RankerGUI: A Computational Framework to Compare Differential Gene Expression Profiles Using Rank Based Statistics

2019 ◽  
Vol 20 (23) ◽  
pp. 6098 ◽  
Author(s):  
Amarinder Singh Thind ◽  
Kumar Parijat Tripathi ◽  
Mario Rosario Guarracino
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Differential Gene Expression ◽  
Web Application ◽  
Cellular Response ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Experimental Conditions ◽  
Differential Gene

The comparison of high throughput gene expression datasets obtained from different experimental conditions is a challenging task. It provides an opportunity to explore the cellular response to various biological events such as disease, environmental conditions, and drugs. There is a need for tools that allow the integration and analysis of such data. We developed the “RankerGUI pipeline”, a user-friendly web application for the biological community. It allows users to use various rank based statistical approaches for the comparison of full differential gene expression profiles between the same or different biological states obtained from different sources. The pipeline modules are an integration of various open-source packages, a few of which are modified for extended functionality. The main modules include rank rank hypergeometric overlap, enriched rank rank hypergeometric overlap and distance calculations. Additionally, preprocessing steps such as merging differential expression profiles of multiple independent studies can be added before running the main modules. Output plots show the strength, pattern, and trends among complete differential expression profiles. In this paper, we describe the various modules and functionalities of the developed pipeline. We also present a case study that demonstrates how the pipeline can be used for the comparison of differential expression profiles obtained from multiple platforms’ data of the Gene Expression Omnibus. Using these comparisons, we investigate gene expression patterns in kidney and lung cancers.

scholarly journals Linked genetic variation and not genome structure causes widespread differential expression associated with chromosomal inversions

2018 ◽  
Vol 115 (21) ◽  
pp. 5492-5497 ◽  
Author(s):  
Iskander Said ◽  
Ashley Byrne ◽  
Victoria Serrano ◽  
Charis Cardeno ◽  
Christopher Vollmers ◽  
...  
Keyword(s):  
Gene Expression ◽  
Natural Selection ◽  
Differential Expression ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Genome Structure ◽  
Regulatory Domains ◽  
Chromosomal Inversions ◽  
Important Variation ◽  
Genome Wide

Chromosomal inversions are widely thought to be favored by natural selection because they suppress recombination between alleles that have higher fitness on the same genetic background or in similar environments. Nonetheless, few selected alleles have been characterized at the molecular level. Gene expression profiling provides a powerful way to identify functionally important variation associated with inversions and suggests candidate phenotypes. However, altered genome structure itself might also impact gene expression by influencing expression profiles of the genes proximal to inversion breakpoint regions or by modifying expression patterns genome-wide due to rearranging large regulatory domains. In natural inversions, genetic differentiation and genome structure are inextricably linked. Here, we characterize differential expression patterns associated with two chromosomal inversions found in natural Drosophila melanogaster populations. To isolate the impacts of genome structure, we engineered synthetic chromosomal inversions on controlled genetic backgrounds with breakpoints that closely match each natural inversion. We find that synthetic inversions have negligible effects on gene expression. Nonetheless, natural inversions have broad-reaching regulatory impacts in cis and trans. Furthermore, we find that differentially expressed genes associated with both natural inversions are enriched for loci associated with immune response to bacterial pathogens. Our results support the idea that inversions in D. melanogaster experience natural selection to maintain associations between functionally related alleles to produce complex phenotypic outcomes.

scholarly journals The Ambivalence of the Barley Mlo Locus: Mutations Conferring Resistance Against Powdery Mildew (Blumeria graminis f. sp. hordei) Enhance Susceptibility to the Rice Blast Fungus Magnaporthe grisea

1999 ◽  
Vol 12 (6) ◽  
pp. 508-514 ◽  
Author(s):  
Birgit Jarosch ◽  
Karl-Heinz Kogel ◽  
Ulrich Schaffrath
Keyword(s):  
Powdery Mildew ◽  
Rice Blast ◽  
Magnaporthe Grisea ◽  
Durable Resistance ◽  
Rice Blast Fungus ◽  
Blumeria Graminis ◽  
Negative Regulator ◽  
Powdery Mildew Fungus ◽  
Mesophyll Cells ◽  
Blast Fungus

Recessive alleles of the barley Mlo locus confer non-race-specific resistance against the powdery mildew fungus Blumeria graminis f. sp. hordei (Bgh). Recently the Mlo gene has been isolated and it was suggested that the Mlo product is a negative regulator of cell death. Thus, loss of function can precondition cells to a higher responsiveness for the onset of multiple defense functions. Here, we document an enhanced susceptibility of barley mlo mutants to the rice blast fungus Magnaporthe grisea. The disease phenotype is independent of the barley cultivar in which the mlo allele has been introgressed and occurs in equal amounts in barley backcross lines of cv. Ingrid carrying the mlo-1, mlo-3, or mlo-5 allele. Ror genes, which are required for the full expression of mlo resistance in barley against Bgh, do not affect the specific mlo-mediated phenotype observed after M. grisea infection. Formation of an effective papilla restricts blast development in epidermal cells of Mlo plants. In contrast, papillae are mostly penetrated in mlo mutants and, as a consequence, the fungus spreads into adjacent mesophyll cells. Both wild-type plants and mlo mutants did not differ in perception of a purified elicitor derived from M. grisea. Thus, we hypothesize that a functional Mlo protein is a prerequisite for penetration resistance of barley to fungal pathogens like M. grisea. The benefit of mlo alleles for durable resistance in barley and a proposed role of mlo-type-mutations in rice are discussed.

scholarly journals Genome-wide expression profiling in colorectal cancer focusing on lncRNAs in the adenoma-carcinoma transition

BMC Cancer ◽  
2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Alexandra Kalmár ◽  
Zsófia Brigitta Nagy ◽  
Orsolya Galamb ◽  
István Csabai ◽  
András Bodor ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Differential Expression ◽  
Colorectal Adenoma ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Aberrant Expression ◽  
Array Data ◽  
Lncrna Expression ◽  
Qrt Pcr ◽  
Mrna Targets

Abstract Background Long non-coding RNAs (lncRNAs) play a fundamental role in colorectal cancer (CRC) development, however, lncRNA expression profiles in CRC and its precancerous stages remain to be explored. We aimed to study whole genomic lncRNA expression patterns in colorectal adenoma–carcinoma transition and to analyze the underlying functional interactions of aberrantly expressed lncRNAs. Methods LncRNA expression levels of colonic biopsy samples (20 CRCs, 20 adenomas (Ad), 20 healthy controls (N)) were analyzed with Human Transcriptome Array (HTA) 2.0. Expression of a subset of candidates was verified by qRT-PCR and in situ hybridization (ISH) analyses. Furthermore, in silico validation was performed on an independent HTA 2.0, on HGU133Plus 2.0 array data and on the TCGA COAD dataset. MiRNA targets of lncRNAs were predicted with miRCODE and lncBase v2 algorithms and miRNA expression was analyzed on miRNA3.0 Array data. MiRNA-mRNA target prediction was performed using miRWALK and c-Met protein levels were analyzed by immunohistochemistry. Comprehensive lncRNA-mRNA-miRNA co-expression pattern analysis was also performed. Results Based on our HTA results, a subset of literature-based CRC-associated lncRNAs showed remarkable expression changes already in precancerous colonic lesions. In both Ad vs. normal and CRC vs. normal comparisons 16 lncRNAs, including downregulated LINC02023, MEG8, AC092834.1, and upregulated CCAT1, CASC19 were identified showing differential expression during early carcinogenesis that persisted until CRC formation (FDR-adjusted p < 0.05). The intersection of CRC vs. N and CRC vs. Ad comparisons defines lncRNAs characteristic of malignancy in colonic tumors, where significant downregulation of LINC01752 and overexpression of UCA1 and PCAT1 were found. Two candidates with the greatest increase in expression in the adenoma-carcinoma transition were further confirmed by qRT-PCR (UCA1, CCAT1) and by ISH (UCA1). In line with aberrant expression of certain lncRNAs in tumors, the expression of miRNA and mRNA targets showed systematic alterations. For example, UCA1 upregulation in CRC samples occurred in parallel with hsa-miR-1 downregulation, accompanied by c-Met target mRNA overexpression (p < 0.05). Conclusion The defined lncRNA sets may have a regulatory role in the colorectal adenoma-carcinoma transition. A subset of CRC-associated lncRNAs showed significantly differential expression in precancerous samples, raising the possibility of developing adenoma-specific markers for early detection of colonic lesions.

scholarly journals Characterization of the microRNA Expression Profiles in the Goat Kid Liver

2022 ◽  
Vol 12 ◽  
Author(s):  
Xiaodong Zhao ◽  
Zhibin Ji ◽  
Rong Xuan ◽  
Aili Wang ◽  
Qing Li ◽  
...  
Keyword(s):  
Differential Expression ◽  
Fatty Acid Synthase ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Metabolic Process ◽  
Liver Development ◽  
Hormone Synthesis ◽  
Liver Tissues

The liver is the largest digestive gland in goats with an important role in early metabolic function development. MicroRNAs (miRNA) are crucial for regulating the development and metabolism in the goat liver. In the study, we sequenced the miRNAs in the liver tissues of the goat kid to further research their regulation roles in early liver development. The liver tissues were procured at 5-time points from the Laiwu black goats of 1 day (D1), 2 weeks (W2), 4 weeks (W4), 8 weeks (W8), and 12 weeks (W12) after birth, respectively with five goats per time point, for a total of 25 goats. Our study identified 214 differential expression miRNAs, and the expression patterns of 15 randomly selected miRNAs were examined among all five age groups. The Gene ontology annotation results showed that differential expression miRNA (DE miRNA) target genes were significantly enriched in the fatty acid synthase activity, toxin metabolic process, cell surface, and antibiotic metabolic process. The KEGG analysis result was significantly enriched in steroid hormone synthesis and retinol metabolism pathways. Further miRNA-mRNA regulation network analysis reveals 9 differently expressed miRNA with important regulation roles. Overall, the DE miRNAs were mainly involved in liver development, lipid metabolism, toxin related metabolism-related biological process, and pathways. Our results provide new information about the molecular mechanisms and pathways in the goat kid liver development.

Chromosomal and cytoplasmic context determines predisposition to maternal age-related aneuploidy: brief overview and update on MCAK in mammalian oocytes

2010 ◽  
Vol 38 (6) ◽  
pp. 1681-1686 ◽  
Author(s):  
Ursula Eichenlaub-Ritter ◽  
Nora Staubach ◽  
Tom Trapphoff
Keyword(s):  
Cell Cycle ◽  
Chromosome Segregation ◽  
Maternal Age ◽  
Fluorescent Protein ◽  
Expression Patterns ◽  
Model Organisms ◽  
Aged Mouse ◽  
Protein Fusion ◽  
Mouse Oocytes ◽  
Age Related

It has been known for more than half a century that the risk of conceiving a child with trisomy increases with advanced maternal age. However, the origin of the high susceptibility to nondisjunction of whole chromosomes and precocious separation of sister chromatids, leading to aneuploidy in aged oocytes and embryos derived from them, cannot be traced back to a single disturbance and mechanism. Instead, analysis of recombination patterns of meiotic chromosomes of spread oocytes from embryonal ovary, and of origins and exchange patterns of extra chromosomes in trisomies, as well as morphological and molecular studies of oocytes and somatic cells from young and aged females, show chromosome-specific risk patterns and cellular aberrations related to the chronological age of the female. In addition, analysis of the function of meiotic- and cell-cycle-regulating genes in oogenesis, and the study of the spindle and chromosomal status of maturing oocytes, suggest that several events contribute synergistically to errors in chromosome segregation in aged oocytes in a chromosome-specific fashion. For instance, loss of cohesion may differentially predispose chromosomes with distal or pericentromeric chiasmata to nondisjunction. Studies on expression in young and aged oocytes from human or model organisms, like the mouse, indicate that the presence and functionality/activity of gene products involved in cell-cycle regulation, spindle formation and organelle integrity may be altered in aged oocytes, thus contributing to a high risk of error in chromosome segregation in meiosis I and II. Genes that are often altered in aged mouse oocytes include MCAK (mitotic-centromere-associated protein), a microtubule depolymerase, and AURKB (Aurora kinase B), a protein of the chromosomal passenger complex that has many targets and can also phosphorylate and regulate MCAK localization and activity. Therefore we explored the role of MCAK in maturing mouse oocytes by immunofluorescence, overexpression of a MCAK–EGFP (enhanced green fluorescent protein) fusion protein, knockdown of MCAK by RNAi (RNA interference) and inhibition of AURKB. The observations suggest that MCAK is involved in spindle regulation, chromosome congression and cell-cycle control, and that reductions in mRNA and protein in a context of permissive SAC (spindle assembly checkpoint) predispose to aneuploidy. Failure to recruit MCAK to centromeres and low expression patterns, as well as disturbances in regulation of enzyme localization and activity, e.g. due to alterations in activity of AURKB, may therefore contribute to maternal age-related rises in aneuploidy in mammalian oocytes.

scholarly journals A classifier driven approach to find biomarkers for affective disorders from transcription profiles in blood

2016 ◽  
Vol 1 (1) ◽  
pp. 34 ◽  
Author(s):  
Wiktor Mazin ◽  
Joseph A Tamm ◽  
Irina A Antonijevic ◽  
Aicha Abdourahman ◽  
Munish Das ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Affective Disorders ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Expression Levels ◽  
Control Subjects ◽  
Transcription Profiles

Gene expression profiles in blood are increasingly being used to identify biomarkers for different affective disorders. We have selected a set of 29 genes to generate expression profiles for healthy control subjects as well as for patients diagnosed with acute post-traumatic stress disorder (PTSD) and with borderline personality disorder (BPD). Measurements were performed by quantitative polymerase chain reaction (qPCR). Using the actual data in an anonym-ous form we constructed a series of artificial data sets with known gene expression profiles. These sets were used to test 14 classification algorithms and feature selection methods for their ability to identify the correct expression patterns. Application of the three most effective algorithms to the actual expression data showed that control subjects can be dis-tinguished from BPD patients based on differential expression levels of the gene transcripts Gi2, GR and MAPK14, targets that may have links to stress related diseases. Controls can also be distinguished from acute PTSD patients by differential expression levels of the transcripts for ERK2 and RGS2 that are known to be associated with mood disord-ers and social anxiety. We conclude that it is possible to identify informative transcription profiles in blood samples from individuals with affective disorders.

Sign in / Sign up

Export Citation Format

Share Document