scholarly journals Circulating miRNA repertoire as a biomarker of metabolic and reproductive states in rainbow trout

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Emilie Cardona ◽  
Cervin Guyomar ◽  
Thomas Desvignes ◽  
Jérôme Montfort ◽  
Samia Guendouz ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Blood Plasma ◽  
Biological Fluid ◽  
Biological Fluids ◽  
Expression Profiles ◽  
Rna Seq ◽  
Ovarian Fluid ◽  
Non Invasive ◽  
Metabolic States ◽  
Evolutionarily Conserved

Abstract Background Circulating miRNAs (c-miRNAs) are found in most, if not all, biological fluids and are becoming well-established non-invasive biomarkers of many human pathologies. However, their features in non-pathological contexts and whether their expression profiles reflect normal life history events have received little attention, especially in non-mammalian species. The aim of the present study was to investigate the potential of c-miRNAs to serve as biomarkers of reproductive and metabolic states in fish. Results The blood plasma was sampled throughout the reproductive cycle of female rainbow trout subjected to two different feeding regimes that triggered contrasting metabolic states. In addition, ovarian fluid was sampled at ovulation, and all samples were subjected to small RNA-seq analysis, leading to the establishment of a comprehensive miRNA repertoire (i.e., miRNAome) and enabling subsequent comparative analyses to a panel of RNA-seq libraries from a wide variety of tissues and organs. We showed that biological fluid miRNAomes are complex and encompass a high proportion of the overall rainbow trout miRNAome. While sharing a high proportion of common miRNAs, the blood plasma and ovarian fluid miRNAomes exhibited strong fluid-specific signatures. We further revealed that the blood plasma miRNAome significantly changed depending on metabolic and reproductive states. We subsequently identified three evolutionarily conserved muscle-specific miRNAs or myomiRs (miR-1-1/2-3p, miR-133a-1/2-3p, and miR-206-3p) that accumulated in the blood plasma in response to high feeding rates, making these myomiRs strong candidate biomarkers of active myogenesis. We also identified miR-202-5p as a candidate biomarker for reproductive success that could be used to predict ovulation and/or egg quality. Conclusions Together, these promising results reveal the high potential of c-miRNAs, including evolutionarily conserved myomiRs, as physiologically relevant biomarker candidates and pave the way for the use of c-miRNAs for non-invasive phenotyping in various fish species.

scholarly journals Circulating miRNA diversity, origin and response to changing metabolic and reproductive states, new insights from the rainbow trout

2021 ◽  
Author(s):  
E Emilie Cardona ◽  
C Cervin Guyomar ◽  
Thomas Desvignes ◽  
J Jérôme Montfort ◽  
Samia Guendouz ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Egg Quality ◽  
Biological Fluids ◽  
Rna Seq ◽  
Feeding Rates ◽  
Ovarian Fluid ◽  
Non Invasive ◽  
Metabolic States ◽  
Evolutionarily Conserved ◽  
Strong Candidate

AbstractCirculating miRNAs (c-miRNAs) are found in most, if not all, biological fluids and are becoming well established biomarkers of many human pathologies. The aim of the present study was to investigate the potential of c-miRNAs as biomarkers of reproductive and metabolic states in fish, a question that has received little attention. Plasma was collected throughout the reproductive cycle from rainbow trout females subjected to two different feeding levels to trigger contrasting metabolic states; ovarian fluid was sample at ovulation. Fluid samples were subjected to small RNA-seq analysis followed by quantitative PCR validation for a subset of promising c-miRNA biomarkers. A comprehensive miRNA repertoire, which was lacking in trout, was first established to allow subsequent analysis. We first showed that biological fluids miRNAomes are complex and encompass a high proportion of the overall species miRNAome. While sharing a high proportion of common miRNAs, plasma and ovarian fluid miRNAomes exhibited strong fluid-specific signatures. We further showed that the plasma miRNAome exhibited major significant changes depending on metabolic and reproductive state. We subsequently identified three (miR-1-1/2-3p, miR-133-a-1/2-3p and miR-206-3p) evolutionarily conserved muscle-specific miRNA that accumulate in the plasma in response to high feeding rates, making these myomiRs strong candidate biomarkers of active myogenesis. We also identified miR-202-5p as a candidate biomarker for reproductive success that could be used to predict ovulation and/or egg quality. These highly promising results reveal the high potential of c-miRNAs as physiologically relevant biomarkers and pave the way for the use of c-miRNAs for non-invasive phenotyping in various fish species.

scholarly journals Extraction of Exosomes from Glioblastoma Multiforme Patients’ Blood Plasma

2019 ◽  
Vol 9 (3) ◽  
pp. 234-238
Author(s):  
I. F. Gareev ◽  
O. A. Beylerli ◽  
Sh. Zhao ◽  
G. Yang ◽  
J. Sun ◽  
...  
Keyword(s):  
Glioblastoma Multiforme ◽  
Blood Plasma ◽  
Biological Fluids ◽  
Morphological Characteristics ◽  
Spherical Shape ◽  
Experimental Protocol ◽  
Malignant Brain Tumour ◽  
Non Invasive ◽  
Diagnosis And Prognosis

Introduction. Glioblastoma multiforme (GBM) is the most common and aggressive form of primary malignant brain tumour in adults associated with a poor prognosis. Exosomes have been shown to be useful non-invasive biomarkers for the diagnosis and prognosis of tumours, GBM included. Exosomes play a role of biological carriers which can perform various tasks through various signalling pathways of carcinogenesis, such as PI3K/AKT, SOX2, PTEN, ERK and STAT3.Materials and methods. Exosomes were isolated from blood plasma taken from patients diagnosed with GBM prior to surgical resection.Results and discussion. Plasma exosomes from patients with GBM had spherical shape and varied in size from 40 to 100 nm matching the exosomes’ morphological characteristics. The combination of ultrafiltration and double ultracentrifugation makes it possible to extract exosome examples from plasma without the presence of contaminating particles over 100 nm in size; the shape and size of these vesicles match the characteristics of exosomes isolated from other biological fluids.Conclusion. The experimental protocol for the extraction of exosomes from GBM patients’ plasma described here proves effective as a method used to ensure the purity of exosomes. Applying this method offers further opportunities for research into the role of exosomes in GBM pathogenesis. Equally this method can be used in research involving other human pathologies.

scholarly journals Determination of felodipine in biological fluids

2019 ◽  
Vol 100 (4) ◽  
pp. 650-656
Author(s):  
L L Kvachakhiya ◽  
V K Shormanov ◽  
N S Kononenko
Keyword(s):  
Blood Plasma ◽  
Biological Object ◽  
Biological Fluid ◽  
Biological Fluids ◽  
Human Blood Plasma ◽  
Gas Liquid Chromatography ◽  
Optimal Conditions ◽  
Mass Ratio ◽  
Layer Chromatography

Aim. Development of methods for the determination of felodipine in blood and plasma. Methods. The study object was felodipine [3-ethyl-5-methyl-4-(2,3-dichlorophenyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate]. The experiments were carried out on model mixtures of felodipine with blood and human blood plasma. Acetone was proposed as an isolating agent for the extraction of felodipine from biological fluids. To identify and quantify felodipine in extracts from blood and plasma, the methods of thin-layer chromatography, spectrophotometry and gas-liquid chromatography in combination with mass spectrometry were proposed. Results. The possibility of using acetone as an isolating agent to extract felodipine from biological fluids is demonstrated. The optimal conditions for the extraction of felodipine with acetone were found to be achieved already at 2-fold infusion of a biological object with an isolating agent, if the mass ratio of isolating liquid and biological material at each infusion stage is at least 2:1, and the infusion time is at least 30 minutes. Optimal felodipine purification conditions were achieved in a macrocolumn (15×1 cm) of Silasorb S-18 sorbent of 30 μm with elution of the substance with the polar eluent acetonitrile-water (7:3). The methods of determining felodipine in the blood and plasma were developed. With the content of felodipine of 25 mg in 25 g of biological fluid, the developed methods allow determining 86.01–87.86% in blood and 95.64–96.18% of the substance in blood plasma. The values of the detection limit of felodipine in the blood and plasma by the developed methods are 200 μg/100 g and 150 μg/100 g, respectively. Conclusion. Methods for the determination of felodipine in biological fluids were developed based on isolating with acetone and purification in the Silasorb S-18 sorbent column; use of these methods allows determining up to 87.86% of the analyte in the blood and up to 96.18% in the blood plasma.

scholarly journals Activated Salivary MMP-2 - A Potential Breast Cancer Marker

2017 ◽  
Vol 8 (1) ◽  
pp. 22-32
Author(s):  
Nabanita Bhattacharyya ◽  
Subhajit Mondal ◽  
Mohammad Nasim Ali ◽  
Ramanuj Mukherjee ◽  
Anjan Adhikari ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Biological Fluid ◽  
Biological Fluids ◽  
Active Form ◽  
Human Saliva ◽  
Breast Cancer Patients ◽  
Non Invasive ◽  
Diagnosis And Prognosis ◽  
Highly Active ◽  
Potential Biomarker

It has been reported that Matrixmetalloproteinase-2 (MMP-2) is involved in the pathogenesis of cancer. The over expression of MMP-2 is associated with the progression of malignancy of several types of carcinoma. Human saliva is a biological fluid with several advantages for non-invasive diagnosis and prognosis of diseases. The aim of this study was to detect MMPs expression and activity in biological fluids (saliva, urine etc.) derived from breast cancer patients. Here, our results showed that the activity of MMP-2 was higher at the time before the surgery than after the saliva collected from the same patients. Therefore, we suggested that the highly active form of MMP-2 presented in saliva could be used as a novel potential biomarker for non-invasive diagnosis of breast cancer.

scholarly journals The core transcriptome of mammalian placentas and the divergence of expression with placental shape

2017 ◽  
Author(s):  
Don L. Armstrong ◽  
Michael R. McGowen ◽  
Amy Weckle ◽  
Priyadarshini Pantham ◽  
Jason Caravas ◽  
...  
Keyword(s):  
Homo Sapiens ◽  
Expression Profiles ◽  
Cell Interactions ◽  
The Other ◽  
Differentially Expressed ◽  
Rna Seq ◽  
The Core ◽  
Multiple Genes ◽  
Evolutionarily Conserved ◽  
Core Genes

AbstractIntroductionThe placenta is arguably the most anatomically variable organ in mammals even though its primary function is conserved.MethodUsing RNA-Seq, we measured the expression profiles of 55 term placentas of 14 species of mammals representing all major eutherian superordinal clades and marsupials, and compared the evolution of expression across clades.ResultsWe identified a set of 115 core genes which is expressed (FPKM ≥ 10) in all eutherian placentas, including genes with immune-modulating properties (ANXA2, ANXA1, S100A11, S100A10, and LGALS1), cell-cell interactions (LAMC1, LUM, and LGALS1), invasion (GRB2 and RALB) and syncytialization (ANXA5 and ANXA1). We also identified multiple pre-eclampsia associated genes which are differentially expressed in Homo sapiens when compared to the other 13 species. Multiple genes are significantly associated with placenta morphology, including EREG and WNT5A which are both associated with placental shape.Discussion115 genes are important for the core functions of the placenta in all eutherian species analyzed. The molecular functions and pathways enriched in the core placenta align with the evolutionarily conserved functionality of the placenta.

scholarly journals Transcriptomal dissection of soybean circadian rhythmicity in two geographically, phenotypically and genetically distinct cultivars

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yanlei Yue ◽  
Ze Jiang ◽  
Enoch Sapey ◽  
Tingting Wu ◽  
Shi Sun ◽  
...  
Keyword(s):  
Gene Expression ◽  
Circadian Clock ◽  
Chromosome Structure ◽  
Clock Genes ◽  
Expression Profiles ◽  
Circadian Rhythmicity ◽  
Rna Seq ◽  
Night Time ◽  
Time Points ◽  
Circadian Clock Genes

Abstract Background In soybean, some circadian clock genes have been identified as loci for maturity traits. However, the effects of these genes on soybean circadian rhythmicity and their impacts on maturity are unclear. Results We used two geographically, phenotypically and genetically distinct cultivars, conventional juvenile Zhonghuang 24 (with functional J/GmELF3a, a homolog of the circadian clock indispensable component EARLY FLOWERING 3) and long juvenile Huaxia 3 (with dysfunctional j/Gmelf3a) to dissect the soybean circadian clock with time-series transcriptomal RNA-Seq analysis of unifoliate leaves on a day scale. The results showed that several known circadian clock components, including RVE1, GI, LUX and TOC1, phase differently in soybean than in Arabidopsis, demonstrating that the soybean circadian clock is obviously different from the canonical model in Arabidopsis. In contrast to the observation that ELF3 dysfunction results in clock arrhythmia in Arabidopsis, the circadian clock is conserved in soybean regardless of the functional status of J/GmELF3a. Soybean exhibits a circadian rhythmicity in both gene expression and alternative splicing. Genes can be grouped into six clusters, C1-C6, with different expression profiles. Many more genes are grouped into the night clusters (C4-C6) than in the day cluster (C2), showing that night is essential for gene expression and regulation. Moreover, soybean chromosomes are activated with a circadian rhythmicity, indicating that high-order chromosome structure might impact circadian rhythmicity. Interestingly, night time points were clustered in one group, while day time points were separated into two groups, morning and afternoon, demonstrating that morning and afternoon are representative of different environments for soybean growth and development. However, no genes were consistently differentially expressed over different time-points, indicating that it is necessary to perform a circadian rhythmicity analysis to more thoroughly dissect the function of a gene. Moreover, the analysis of the circadian rhythmicity of the GmFT family showed that GmELF3a might phase- and amplitude-modulate the GmFT family to regulate the juvenility and maturity traits of soybean. Conclusions These results and the resultant RNA-seq data should be helpful in understanding the soybean circadian clock and elucidating the connection between the circadian clock and soybean maturity.

scholarly journals Identification of the specific long-noncoding RNAs involved in night-break mediated flowering retardation in Chenopodium quinoa

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Qi Wu ◽  
Yiming Luo ◽  
Xiaoyong Wu ◽  
Xue Bai ◽  
Xueling Ye ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Functional Characterization ◽  
Chenopodium Quinoa ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Rna Seq ◽  
Short Day ◽  
Homologous Genes ◽  
The Relationship ◽  
Encoding Genes

Abstract Background Night-break (NB) has been proven to repress flowering of short-day plants (SDPs). Long-noncoding RNAs (lncRNAs) play key roles in plant flowering. However, investigation of the relationship between lncRNAs and NB responses is still limited, especially in Chenopodium quinoa, an important short-day coarse cereal. Results In this study, we performed strand-specific RNA-seq of leaf samples collected from quinoa seedlings treated by SD and NB. A total of 4914 high-confidence lncRNAs were identified, out of which 91 lncRNAs showed specific responses to SD and NB. Based on the expression profiles, we identified 17 positive- and 7 negative-flowering lncRNAs. Co-expression network analysis indicated that 1653 mRNAs were the common targets of both types of flowering lncRNAs. By mapping these targets to the known flowering pathways in model plants, we found some pivotal flowering homologs, including 2 florigen encoding genes (FT (FLOWERING LOCUS T) and TSF (TWIN SISTER of FT) homologs), 3 circadian clock related genes (EARLY FLOWERING 3 (ELF3), LATE ELONGATED HYPOCOTYL (LHY) and ELONGATED HYPOCOTYL 5 (HY5) homologs), 2 photoreceptor genes (PHYTOCHROME A (PHYA) and CRYPTOCHROME1 (CRY1) homologs), 1 B-BOX type CONSTANS (CO) homolog and 1 RELATED TO ABI3/VP1 (RAV1) homolog, were specifically affected by NB and competed by the positive and negative-flowering lncRNAs. We speculated that these potential flowering lncRNAs may mediate quinoa NB responses by modifying the expression of the floral homologous genes. Conclusions Together, the findings in this study will deepen our understanding of the roles of lncRNAs in NB responses, and provide valuable information for functional characterization in future.

scholarly journals Transcriptome profiling of the diaphragm in a controlled mechanical ventilation model reveals key genes involved in ventilator-induced diaphragmatic dysfunction

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ruining Liu ◽  
Gang Li ◽  
Haoli Ma ◽  
Xianlong Zhou ◽  
Pengcheng Wang ◽  
...  
Keyword(s):  
Mechanical Ventilation ◽  
Signaling Pathway ◽  
Wistar Rats ◽  
Cholesterol Metabolism ◽  
Expression Profiles ◽  
Receptor Interaction ◽  
Pathophysiological Mechanism ◽  
Rna Seq ◽  
Diaphragmatic Dysfunction ◽  
Controlled Mechanical Ventilation

Abstract Background Ventilator-induced diaphragmatic dysfunction (VIDD) is associated with weaning difficulties, intensive care unit hospitalization (ICU), infant mortality, and poor long-term clinical outcomes. The expression patterns of long noncoding RNAs (lncRNAs) and mRNAs in the diaphragm in a rat controlled mechanical ventilation (CMV) model, however, remain to be investigated. Results The diaphragms of five male Wistar rats in a CMV group and five control Wistar rats were used to explore lncRNA and mRNA expression profiles by RNA-sequencing (RNA-seq). Muscle force measurements and immunofluorescence (IF) staining were used to verify the successful establishment of the CMV model. A total of 906 differentially expressed (DE) lncRNAs and 2,139 DE mRNAs were found in the CMV group. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to determine the biological functions or pathways of these DE mRNAs. Our results revealed that these DE mRNAs were related mainly related to complement and coagulation cascades, the PPAR signaling pathway, cholesterol metabolism, cytokine-cytokine receptor interaction, and the AMPK signaling pathway. Some DE lncRNAs and DE mRNAs determined by RNA-seq were validated by quantitative real-time polymerase chain reaction (qRT-PCR), which exhibited trends similar to those observed by RNA-sEq. Co-expression network analysis indicated that three selected muscle atrophy-related mRNAs (Myog, Trim63, and Fbxo32) were coexpressed with relatively newly discovered DE lncRNAs. Conclusions This study provides a novel perspective on the molecular mechanism of DE lncRNAs and mRNAs in a CMV model, and indicates that the inflammatory signaling pathway and lipid metabolism may play important roles in the pathophysiological mechanism and progression of VIDD.

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.

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