Small RNA expression patterns in seminal plasma exosomes isolated from semen containing spermatozoa with cytoplasmic droplets versus regular exosomes in boar semen

AbstractWe present the Small RNA Expression Atlas (SEA), a web application that allows for the interactive querying, visualization, and analysis of known and novel small RNAs across ten organisms. It contains sRNA and pathogen expression information for over 4,200 published samples with standardized search terms and ontologies. In addition, SEA allows for the interactive visualization and re-analysis of 879 differential expression and 514 classification comparisons. SEA’s user model enables sRNA researchers to compare and re-analyze user-specific and published datasets, highlighting common and distinct sRNA expression patterns.We provide evidence for SEA’s fidelity by (i) generating a set of 591 tissue specific miRNAs across 30 tissues, (ii) finding known and novel bacterial and viral infections across diseases, and (iii) determining a Parkinson’s disease-specific blood biomarker signature using novel data.We believe that SEA’s simple semantic search interface, the flexible interactive reports, and the user model with rich analysis capabilities will enable researchers to better understand the potential function and diagnostic value of sRNAs or pathogens across tissues, diseases, and organisms.Availability and ImplementationSEA is implemented in Java, J2EE, spring, Django, html5, css3, JavaScript, Bootstrap, Vue.js, D3, mongodb and neo4j. It is freely available at http://sea.ims.bio/.

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SEAweb: the small RNA Expression Atlas web application

Nucleic Acids Research ◽

10.1093/nar/gkz869 ◽

2019 ◽

Vol 48 (D1) ◽

pp. D204-D219

Author(s):

Raza-Ur Rahman ◽

Anna-Maria Liebhoff ◽

Vikas Bansal ◽

Maksims Fiosins ◽

Ashish Rajput ◽

...

Keyword(s):

Small Rna ◽

Web Application ◽

Viral Infections ◽

Expression Patterns ◽

Diagnostic Value ◽

User Model ◽

Rna Expression ◽

Search Terms ◽

Expression Atlas ◽

Biomarker Signature

Abstract We present the Small RNA Expression Atlas (SEAweb), a web application that allows for the interactive querying, visualization and analysis of known and novel small RNAs across 10 organisms. It contains sRNA and pathogen expression information for over 4200 published samples with standardized search terms and ontologies. In addition, SEAweb allows for the interactive visualization and re-analysis of 879 differential expression and 514 classification comparisons. SEAweb's user model enables sRNA researchers to compare and re-analyze user-specific and published datasets, highlighting common and distinct sRNA expression patterns. We provide evidence for SEAweb's fidelity by (i) generating a set of 591 tissue specific miRNAs across 29 tissues, (ii) finding known and novel bacterial and viral infections across diseases and (iii) determining a Parkinson's disease-specific blood biomarker signature using novel data. We believe that SEAweb's simple semantic search interface, the flexible interactive reports and the user model with rich analysis capabilities will enable researchers to better understand the potential function and diagnostic value of sRNAs or pathogens across tissues, diseases and organisms.

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Genetic and epigenetic concept of SARS-CoV-2 targets in different renal cancer subtypes

Turkish Journal of Biochemistry ◽

10.1515/tjb-2020-0233 ◽

2021 ◽

Vol 0 (0) ◽

Author(s):

Dilara Fatma Akin-Bali ◽

Rahşan Ilikci Sagkan

Keyword(s):

Renal Cancer ◽

Promoter Methylation ◽

Target Genes ◽

Expression Patterns ◽

Rna Expression ◽

Total Rate ◽

Cancer Subtypes ◽

Genetic Landscape ◽

Healthy Control ◽

Genetic Anomaly

AbstractObjectivesRecent advances in defining the genetic landscape of has shown the host cell- SARS-CoV-2 interaction via ACE2 protein and the presence of at least three additional virus invasion genes including TMPRSS2, FURIN, CD147/BSG. In current study, we investigated the mutation and m-RNA expression patterns of target genes by evaluating the associations between genetic and epigenetic mechanisms in the target genes and susceptibility of SARS-CoV-2 infection of renal cancer subtypes.MethodsWe investigated the mutation and m-RNA expression patterns of our target genes. The promoter methylation profiles of target genes were tested in the UALCAN database.ResultsThe total rate of carrying genetic anomaly in the target genes including was 1.6% and seven mutations, one of which had a pathogenic feature, were detected. The expression analysis results in renal cancer groups showed that while the KIRC and KIRP patients had a lower level of TMPRSS2 than the healthy control, their ACE2 level was high. KICH patients had a higher level of CD147/BSG expression than the healthy group. The promoter methylation levels of ACE2 in KIRC and KIRP were reduced.ConclusionsWe concluded that renal cancer patients may be more sensitive to SARS-CoV-2 infection, which may worsen the prognosis.

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Thawing boar semen in the presence of seminal plasma improves motility, modifies subpopulation patterns and reduces chromatin alterations

Reproduction Fertility and Development ◽

10.1071/rd15530 ◽

2017 ◽

Vol 29 (8) ◽

pp. 1576 ◽

Cited By ~ 8

Author(s):

Rocío Fernández-Gago ◽

Manuel Álvarez-Rodríguez ◽

Marta E. Alonso ◽

J. Ramiro González ◽

Beatriz Alegre ◽

...

Keyword(s):

Seminal Plasma ◽

Chromatin Structure ◽

Sperm Chromatin ◽

Chromatin Compaction ◽

Sperm Analysis ◽

Positive Effects ◽

Fragmentation Index ◽

Non Linear ◽

Boar Semen ◽

Dna Fragmentation Index

Seminal plasma could have positive effects on boar semen after thawing. In the present study we investigated changes in the motility and chromatin structure in spermatozoa over 4 h incubation (37°C) of boar semen thawed in the presence of 0%, 10% or 50% seminal plasma from good-fertility boars. Cryopreserved doses were used from seven males, three of which were identified as susceptible to post-thawing chromatin alterations. Motility was analysed by computer-aided sperm analysis every hour, and data were used in a two-step clustering, yielding three subpopulations of spermatozoa (slow non-linear, fast non-linear, fast linear). Chromatin structure was analysed using a sperm chromatin structure assay and flow cytometry to determine the DNA fragmentation index (%DFI) as a percentage, the standard deviation of the DFI (SD-DFI) and the percentage of high DNA stainability (%HDS), indicating chromatin compaction. Thawing without seminal plasma resulted in a rapid loss of motility, whereas seminal plasma helped maintain motility throughout the incubation period and preserved the subpopulation comprising fast and linear spermatozoa. The incidence of chromatin alterations was very low in samples from non-susceptible males, whereas samples from males susceptible to post-thawing chromatin alterations exhibited marked alterations in %DFI and %HDS. Seminal plasma partly prevented these alterations in samples from susceptible males. Overall, 50% seminal plasma was the most efficient concentration to protect motility and chromatin. Some changes were concomitant with physiological events reported previously (e.g., semen thawed with 50% seminal plasma increased the production of reactive oxygen species and yielded higher fertility after AI). Thawing in the presence of seminal plasma could be particularly useful in the case of samples susceptible to post-thawing chromatin damage.

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Spermatozoa and seminal plasma small extracellular vesicles miRNAs as biomarkers of boar semen cryotolerance

Theriogenology ◽

10.1016/j.theriogenology.2021.07.022 ◽

2021 ◽

Author(s):

Ana Carolina Pedrosa ◽

Mariana A. Torres ◽

Diego V. Alkmin ◽

Jorge E.P. Pinzon ◽

Simone Maria M.K. Martins ◽

...

Keyword(s):

Extracellular Vesicles ◽

Seminal Plasma ◽

Boar Semen

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xMD-miRNA-seq to generate near in vivo miRNA expression estimates in colon epithelial cells

10.1101/333658 ◽

2018 ◽

Author(s):

Avi Z. Rosenberg ◽

Carrie Wright ◽

Karen Fox-Talbot ◽

Anandita Rajpurohit ◽

Courtney Williams ◽

...

Keyword(s):

Epithelial Cells ◽

Small Rna ◽

Mirna Expression ◽

Low Cost ◽

Expression Patterns ◽

Small Rna Sequencing ◽

Rna Seq ◽

Cell Type

AbstractAccurate, RNA-seq based, microRNA (miRNA) expression estimates from primary cells have recently been described. However, this in vitro data is mainly obtained from cell culture, which is known to alter cell maturity/differentiation status, significantly changing miRNA levels. What is needed is a robust method to obtain in vivo miRNA expression values directly from cells. We introduce expression microdissection miRNA small RNA sequencing (xMD-miRNA-seq), a method to isolate cells directly from formalin fixed paraffin-embedded (FFPE) tissues. xMD-miRNA-seq is a low-cost, high-throughput, immunohistochemistry-based method to capture any cell type of interest. As a proof-of-concept, we isolated colon epithelial cells from two specimens and performed low-input small RNA-seq. We generated up to 600,000 miRNA reads from the samples. Isolated epithelial cells, had abundant epithelial-enriched miRNA expression (miR-192; miR-194; miR-200b; miR-200c; miR-215; miR-375) and overall similar miRNA expression patterns to other epithelial cell populations (colonic enteroids and flow-isolated colon epithelium). xMD-derived epithelial cells were generally not contaminated by other adjacent cells of the colon as noted by t-SNE analysis. xMD-miRNA-seq allows for simple, economical, and efficient identification of cell-specific miRNA expression estimates. Further development will enhance rapid identification of cell-specific miRNA expression estimates in health and disease for nearly any cell type using archival FFPE material.

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Genome-wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L.

DNA Research ◽

10.1093/dnares/dsy021 ◽

2018 ◽

Vol 25 (5) ◽

pp. 511-520 ◽

Cited By ~ 7

Author(s):

Satoshi Takahashi ◽

Kenji Osabe ◽

Naoki Fukushima ◽

Shohei Takuno ◽

Naomi Miyaji ◽

...

Keyword(s):

Dna Methylation ◽

Brassica Rapa ◽

Small Rna ◽

Histone H3 ◽

Rna Expression ◽

Genome Wide

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Seasonal changes of steroid concentrations in seminal plasma of a European wild boar

Acta Endocrinologica ◽

10.1530/acta.0.1070425 ◽

1984 ◽

Vol 107 (3) ◽

pp. 425-427 ◽

Cited By ~ 15

Author(s):

D. Schopper ◽

J. Gaus ◽

R. Claus ◽

H. Bader

Keyword(s):

Wild Boar ◽

Seminal Plasma ◽

Seasonal Pattern ◽

Plasma Concentrations ◽

Boar Taint ◽

Steroid Production ◽

European Wild Boar ◽

Clear Seasonal Pattern ◽

Boar Semen ◽

Low Levels

Abstract. The influence of season on testicular steroid production as a parameter of testicular function has been studied in a wild boar. Semen was collected once weekly while it served the dummy. In seminal plasma concentrations of the following steroids were determined by radioimmunoassay: unconjugated testosterone, conjugated testosterone, unconjugated total oestrogens, conjugated total oestrogens and 5α-androst-16-en-3-one ('boar-taint steroid'). All steroids showed a clear seasonal pattern with highest concentrations in autumn and early winter and low levels from January to July. Maxima during the rutting season were 10–25 times greater than average values out of season. During a 2-month-period (mid-July until mid-September) libido was abolished and the wild boar refused to mount the dummy. These results indicate that the seasonal variation in testicular steroid production by the wild boar, regulated by photoperiod, are similar to those of the domestic boar.

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Efflux pump gene expression study using RNA-seq in multidrug-resistant TB

The International Journal of Tuberculosis and Lung Disease ◽

10.5588/ijtld.21.0117 ◽

2021 ◽

Vol 25 (12) ◽

pp. 974-981

Author(s):

J. J. Lee ◽

H. Y. Kang ◽

W-I. Lee ◽

S. Y. Cho ◽

Y. J. Kim ◽

...

Keyword(s):

Wild Type Strain ◽

Efflux Pump ◽

Expression Patterns ◽

Resistance Mechanism ◽

Multidrug Resistant ◽

Regulatory Genes ◽

Control Group ◽

Rna Expression ◽

Rna Seq ◽

Expression Study

BACKGROUND: The mechanism underlying kanamycin (KM) resistance in Mycobacterium tuberculosis is not well understood, although efflux pump proteins are thought to play a role. This study used RNA-seq data to investigate changes in the expression levels of efflux pump genes following exposure to KM.METHODS: RNA expression of efflux pump and regulatory genes following exposure to different concentrations of KM (minimum inhibitory concentration MIC 25 and MIC50) in rrs wild-type strain and rrs A1401G mutated strain were compared with the control group.RESULTS: The selected strains had differential RNA expression patterns. Among the 71 putative efflux pump and regulatory genes, 46 had significant fold changes, and 12 genes (Rv0842, Rv1146, Rv1258c, Rv1473, Rv1686c, Rv1687c, Rv1877, Rv2038c, Rv3065, Rv3197a, Rv3728 and Rv3789) that were overexpressed following exposure to KM were thought to contribute to drug resistance. Rv3197A (whiB7) showed a distinct fold change based on the concentration of KM.CONCLUSION: The significant changes in the expression of the efflux pump and regulatory genes following exposure to KM may provide insights into the identification of a new resistance mechanism.

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