A cluster of Ankyrin and Ankyrin-TPR repeat genes is associated with panicle branching diversity in rice

The number of grains per panicle is an important yield-related trait in cereals which depends in part on panicle branching complexity. One component of this complexity is the number of secondary branches per panicle. Previously, a GWAS site associated with secondary branch and spikelet numbers per panicle in rice was identified. Here we combined gene capture, bi-parental genetic population analysis, expression profiling and transgenic approaches in order to investigate the functional significance of a cluster of 6 ANK and ANK-TPR genes within the QTL. Four of the ANK and ANK-TPR genes present a differential expression associated with panicle secondary branch number in contrasted accessions. These differential expression patterns correlate in the different alleles of these genes with specific deletions of potential cis-regulatory sequences in their promoters. Two of these genes were confirmed through functional analysis as playing a role in the control of panicle architecture. Our findings indicate that secondary branching diversity in the rice panicle is governed in part by differentially expressed genes within this cluster encoding ANK and ANK-TPR domain proteins that may act as positive or negative regulators of panicle meristem’s identity transition from indeterminate to determinate state.

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Analysis of the Differential Expression Patterns of Sumoylation Enzymes E1, E2 and E3 in Ocular Cell Lines

Current Molecular Medicine ◽

10.2174/1566524019666190112143636 ◽

2019 ◽

Vol 18 (8) ◽

pp. 509-515 ◽

Cited By ~ 1

Author(s):

Qian Nie ◽

Jie Xie ◽

Xiaodong Gong ◽

Zhongwen Luo ◽

Ling Wang ◽

...

Keyword(s):

Differential Expression ◽

Cell Lines ◽

Expression Patterns

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

Scientific Reports ◽

10.1038/s41598-021-81189-5 ◽

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.

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P01.05 Differential expression patterns of the transforming growth factor (TGF)-beta receptors (TGF-bR) I ALK-1 and ALK-5 and TGF-bR II in glioblastoma

Neuro-Oncology ◽

10.1093/neuonc/now188.062 ◽

2016 ◽

Vol 18 (suppl_4) ◽

pp. iv19-iv19

Author(s):

I. Burghardt ◽

S. Krishnan

Keyword(s):

Growth Factor ◽

Differential Expression ◽

Transforming Growth Factor ◽

Expression Patterns ◽

Tgf Beta ◽

Beta Receptors ◽

Alk 5

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Migration of mouse antibody-secreting hybridoma cells from blood to genital tract and its regulation by sex hormones are associated with the differential expression patterns of adhesion molecules and chemokines in the tract rather than in the antibody-secreting cells

Journal of Reproductive Immunology ◽

10.1016/j.jri.2006.09.003 ◽

2007 ◽

Vol 74 (1-2) ◽

pp. 78-89 ◽

Cited By ~ 2

Author(s):

Mingcan Yu ◽

Xiaomei Cao ◽

Xiaolei Wang ◽

Jinju Xu ◽

Min Yang ◽

...

Keyword(s):

Differential Expression ◽

Adhesion Molecules ◽

Sex Hormones ◽

Genital Tract ◽

Expression Patterns ◽

Hybridoma Cells ◽

Mouse Antibody ◽

Antibody Secreting Cells

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Differential expression patterns of myogenic regulatory factors in the postnatal longissimus dorsi muscle of Jeju Native Pig and Berkshire breeds along with their co-expression with Pax7

Electronic Journal of Biotechnology ◽

10.1016/j.ejbt.2021.03.001 ◽

2021 ◽

Author(s):

Simrinder Singh Sodhi ◽

Neelesh Sharma ◽

Mrinmoy Ghosh ◽

Ram Saran Sethi ◽

Dong Kee Jeong ◽

...

Keyword(s):

Differential Expression ◽

Expression Patterns ◽

Longissimus Dorsi ◽

Myogenic Regulatory Factors ◽

Regulatory Factors ◽

Longissimus Dorsi Muscle ◽

Dorsi Muscle

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Differential expression patterns and a novel interaction factor of Damaged DNA Binding Protein 1A (DDB1A) and DDB1B in Arabidopsis thaliana

Journal of Plant Biology ◽

10.1007/s12374-014-0221-z ◽

2014 ◽

Vol 57 (4) ◽

pp. 239-244 ◽

Cited By ~ 2

Author(s):

Pei Hou ◽

Peng-fei Ren ◽

De-er Zeng ◽

Gui-rong Yu ◽

Wei Tang ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Dna Binding ◽

Differential Expression ◽

Binding Protein ◽

Expression Patterns ◽

Dna Binding Protein ◽

Interaction Factor ◽

Damaged Dna

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Differential Expression of Melanocytic Markers in Myoid, Lipomatous, and Vascular Components of Renal Angiomyolipomas

Archives of Pathology & Laboratory Medicine ◽

10.5858/2007-131-122-deommi ◽

2007 ◽

Vol 131 (1) ◽

pp. 122-125 ◽

Cited By ~ 1

Author(s):

Andres A. Roma ◽

Cristina Magi-Galluzzi ◽

Ming Zhou

Keyword(s):

Smooth Muscle ◽

Blood Vessel ◽

Blood Vessels ◽

Differential Expression ◽

Tumor Cells ◽

Tissue Microarray ◽

Expression Patterns ◽

Renal Angiomyolipoma ◽

Melanocytic Lesions ◽

Hmb 45

Abstract Context.—Renal angiomyolipoma is a tumor composed of varying amounts of fat, smooth muscle, and blood vessels. Characteristically, tumor cells express melanocytic markers such as HMB-45 and Melan-A. Recently, several other markers have been described as having excellent diagnostic sensitivity in cutaneous melanocytic lesions. Objectives.—To compare the sensitivities of 5 melanocytic markers in renal angiomyolipoma and to study the expression patterns of these markers in the 3 different components of angiomyolipoma. Design.—A tissue microarray of 20 renal angiomyolipomas was constructed. For each case, 3 cores containing fat, blood vessels, and smooth muscle were taken. The tissue microarray was then stained for HMB-45, Melan-A, tyrosinase, NK1-C3, and CD117. Results.—HMB-45 was positive in 95%, Melan-A in 85%, NK1-C3 in 70%, tyrosinase in 50%, and CD117 in 40% of the cases. All (20/20) were positive for HMB-45 and Melan-A combined. These 5 markers had different sensitivities in the 3 components. HMB-45 was positive in 90%, 85%, and 80% of fat, smooth muscle, and blood vessel components, respectively; Melan-A in 70%, 60%, and 40%; NK1-C3 in 55%, 55%, and 45%; tyrosinase in 30%, 40%, and 10%; and CD117 in 20%, 40%, and 10%, respectively, of these 3 components. Conclusions.—HMB-45 and Melan-A combined were positive in 100% of the renal angiomyolipomas. We recommend the use of these 2 markers in the workup of this entity, including those with predominantly 1 component. Other melanocytic markers are of limited use. A tissue block comprising predominantly fat or smooth muscle components should be used when performing melanocytic marker immunostain.

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Differential Expression of Cytokeratins 8 and 20 Distinguishes Craniopharyngioma From Rathke Cleft Cyst

Archives of Pathology & Laboratory Medicine ◽

10.5858/2002-126-1174-deocad ◽

2002 ◽

Vol 126 (10) ◽

pp. 1174-1178 ◽

Cited By ~ 6

Author(s):

Wei Xin ◽

Mark A. Rubin ◽

Paul E. McKeever

Keyword(s):

Molecular Weight ◽

Differential Expression ◽

Expression Patterns ◽

Primary Diagnosis ◽

Pars Intermedia ◽

Rathke Cleft Cyst ◽

Cytokeratin Expression ◽

Pituitary Glands ◽

Clinically Significant ◽

Difficult Cases

Abstract Background.—Craniopharyngiomas are epithelial neoplasms usually located in the sellar and suprasellar regions. Distinguishing craniopharyngioma from Rathke cleft cyst is sometimes difficult, and the distinction is clinically significant because Rathke cleft cysts have a better prognosis than craniopharyngiomas. Design.—We retrieved 10 cases with a primary diagnosis of craniopharyngioma and 5 cases with a diagnosis of Rathke cleft cyst for analysis. Five cases of normal pars intermedia of pituitary glands from autopsy served as controls. We evaluated the expression patterns of a broad range of low– to intermediate–molecular weight cytokeratins (CK7, CK8, CK10, CK17, CK18, CK19, and CK20) and high–molecular weight cytokeratins (K903: a combination of CK1, CK5, CK10, and CK14; and CK5/6) in these cases. Results.—Craniopharyngiomas had a cytokeratin expression pattern distinct from that of Rathke cleft cysts and pituitary gland pars intermedia: craniopharyngiomas did not express cytokeratins 8 and 20, whereas Rathke cleft cysts and pars intermedia of pituitary glands both expressed cytokeratins 8 and 20. Conclusion.—The differential expression of cytokeratins distinguishes between craniopharyngioma and Rathke cleft cyst, and this difference could be useful for identifying craniopharyngioma in difficult cases in which only a small biopsy is available. The different cytokeratin profiles of craniopharyngioma and Rathke cleft cyst suggest that these lesions do not come from the same origin, or that they come from a different developmental stage of the pouch epithelium.

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