Longitudinal peripheral tissue RNA‐Seq transcriptomic profiling, hyperalgesia, and wound healing in the rat plantar surgical incision model

Pepper (Capsicum annuum L.) fruits are one of the most consumed vegetables worldwide. This produce has a great agro-economical relevance, since it is extensively cultivated. These fruits are characterized by their high content of vitamins C and A [1]. Capsicum annuum has many varieties, whose fruits differ in size, shape, color, and pungency, this last characteristic being due to the presence, in different degrees, of capsaicinoids and alkaloids, which are exclusive to the genus Capsicum [2]. The present study focuses on the transcriptomic profiling of an autochthonous Spanish variety called “Padrón” (mild hot) [3]. Pepper “Padrón” plants were grown in farms under the local conditions (42°44′05″ N 8°37′42″ W), and fruits at both green and red ripe ripening stages were collected. The transcriptome profiling was carried out in both types of fruits by RNA sequencing (RNA-seq) using the NextSeq550 system (Illumina®) [4,5]. RNA-seq analysis revealed that the expression of more than half of the 17,499 identified transcripts was modulated during ripening. Comparing to green fruits, 5626 and 5241 genes were up- and down-regulated, respectively, in red fruits. These differentially expressed genes (DEGs) have been analyzed to determine the functional categories that orchestrate the ripening process at the genetic level of this non-climacteric fruit.

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A Comparative Histological Study of Wound Healing following Nd:YAG Laser with Different Energy Parameters and Conventional Surgical Incision in Rat Skin

Journal of Clinical Laser Medicine & Surgery ◽

10.1089/clm.1995.13.11 ◽

1995 ◽

Vol 13 (1) ◽

pp. 11-16 ◽

Cited By ~ 13

Author(s):

GEORGE E. ROMANOS ◽

STAVROS PELEKANOS ◽

JÖRG-RUDOLF STRUB

Keyword(s):

Wound Healing ◽

Nd:Yag Laser ◽

Histological Study ◽

Rat Skin ◽

Surgical Incision ◽

Energy Parameters

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Transcriptomic Profiling of Adipose Derived Stem Cells Undergoing Osteogenesis by RNA-Seq

Scientific Reports ◽

10.1038/s41598-019-48089-1 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 8

Author(s):

Shahensha Shaik ◽

Elizabeth C. Martin ◽

Daniel J. Hayes ◽

Jeffrey M. Gimble ◽

Ram V. Devireddy

Keyword(s):

Stem Cells ◽

Adipose Derived Stem Cells ◽

Rna Seq ◽

Transcriptomic Profiling

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Evaluation of the effect of Teucrium polium ointment on the episiotomy wound healing in primiparous women

Immunopathologia Persa ◽

10.34172/ipp.2021.33 ◽

2021 ◽

Vol 7 (2) ◽

pp. e33-e33

Author(s):

Atena Mohammady Rouzbahani ◽

Mahrokh Dolatian ◽

Tayebeh Jahedbozorgan ◽

Faraz Mojab ◽

Majid Tajik

Keyword(s):

Clinical Trial ◽

Wound Healing ◽

Surgical Incision ◽

Second Stage Of Labor ◽

Second Stage ◽

Significant Difference ◽

Teucrium Polium ◽

The Mean ◽

First Time ◽

Primiparous Women

Introduction: Episiotomy is a surgical incision at the vaginal opening performed in the second stage of labor during childbirth. The purpose of performing an episiotomy is to increase the size of the soft tissue of the pelvis floor and prevent damage to the perineum, facilitate delivery, and reduce the time during childbirth. Objectives: This study aimed to determine the effect of Teucriumpolium ointment on wound healing in primiparous women. Patients and Methods: This triple-blinded clinical trial was conducted on 84 primiparous women referred to Mahdieh hospital in Tehran. Participants randomly received 2% T. polium ointment and placebo. The first time the ointment was started 24 hours after delivery and continued twice a day for 10 days. Wound healing rate was measured by redness, edema, ecchymosis, discharge, and approximation (REEDA) scale on days 1, 5, and 10 postpartum. The data were analyzed using SPSS version 23. Results: The results were performed on 84 women, 43 people using T. polium ointment and 41 people using placebo ointment. There was no significant difference between the two groups regarding obstetrics and demographic characteristics at the beginning of the study. The mean scores of REEDA in the T. polium group in the first 12 hours, days 5 and 10 were significantly different from the placebo group (P<0.001). Conclusion: Wound healing following episiotomy can be accelerated due to antibacterial, anti-inflammatory, and antiseptic properties of T. polium ointment. Trial Registration: The trial protocol was approved by the Iranian registry of clinical trial (#IRCT20100130003226N18; https://en.irct.ir/trial/40004, ethical code# IR.SBMU.RETECH.1398.055).

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Integrative Analysis of Axolotl Gene Expression Data From Regenerative and Wound Healing Limb Tissues

10.1101/693523 ◽

2019 ◽

Author(s):

Mustafa Sibai ◽

Cüneyd Parlayan ◽

Pelin Tuğlu ◽

Gürkan Öztürk ◽

Turan Demircan

Keyword(s):

Gene Expression ◽

Wound Healing ◽

Differential Expression Analysis ◽

Limb Regeneration ◽

Ambystoma Mexicanum ◽

Integrative Analysis ◽

Control Group ◽

Rna Seq ◽

Amputation Injury ◽

Study Designs

ABSTRACTAxolotl (Ambystoma mexicanum) is a urodele amphibian endowed with remarkable regenerative capacities manifested in scarless wound healing and full restoration of amputated limbs. Several regenerative cues of the axolotl limb were successfully unraveled due to the advent of high-throughput technologies and their employment in tackling research questions on several OMICS levels. The field of regenerative biology and medicine has therefore utilized the axolotl as a major and powerful experimental model. Studies which have previously unraveled differentially expressed (DE) genes en masse in different phases of the axolotl limb regeneration have primarily used microarrays and RNA-Seq technologies. However, as different labs are conducting such experiments, sufficient consistency may be lacking due to statistical limitations arising from limited number of sample replicates as well as possible differences in study designs. This study, therefore, aims to bridge such gaps by performing an integrative analysis of publicly available microarray and RNA-Seq data from axolotl limb samples having comparable study designs. Three biological groups were conceived for the analysis; homeostatic tissues (control group), from amputation/injury timepoint up to around 50 hours post amputation (wound healing group), and from 50 hours to 28 days post amputation/injury (regenerative group). Integrative analysis was separately carried out on the selected microarray and RNA-Seq data from axolotl limb samples using the “merging” method. Differential expression analysis was separately implemented on the processed data from both technologies using the R/Bioconductor “limma” package. A total of 1254 genes (adjusted P < 0.01) were found DE in regenerative samples compared to the control, out of which 351 showed magnitudes of Log Fold Changes (LogFC) > 1 and were identified as the top DE genes from data of both technologies. Downstream analyses illustrated consistent correlations of the logFCs of DE genes distributed among the biological comparisons, within and between both technologies. Gene ontology annotations demonstrated concordance with the literature on the biological process involved in the axolotl limb regeneration. qPCR analysis validated the observed gene expression level differences between regenerative and control samples for a set of five genes. Future studies may benefit from the utilized concept and approach for enhanced statistical power and robust discovery of biomarkers of regeneration.

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Interaction between envelope protein of Jaagsiekte Sheep Retrovirus and Hippo signaling pathway is inferred from transcriptome analysis of naturally infected Ovine Pulmonary Adenomatosis

10.21203/rs.3.rs-1103218/v1 ◽

2021 ◽

Author(s):

XuJie Duan ◽

Hui Yang ◽

Liang Zhang ◽

Huiping Li ◽

Zhiwei Zhi Sun ◽

...

Keyword(s):

Wound Healing ◽

Cell Viability ◽

Signaling Pathway ◽

Colony Formation ◽

Hippo Signaling ◽

Rna Seq ◽

Healthy Individuals ◽

Hippo Signaling Pathway ◽

Qrt Pcr ◽

Pulmonary Adenomatosis

Abstract Background Ovine pulmonary adenomatosis (OPA) is a contagious lung epithelial tumor of sheep caused by jaagsiekte sheep retrovirus (JSRV), which causes severe economic losses for the sheep industry in the world. The specific oncogenic mechanism of JSRV is not yet clarified. Methods In this study, RNA was extracted from lung tissues of 3 naturally infected OPA cases and 3 healthy individuals for transcriptome sequencing (RNA-Seq). Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was used to confirm the sequencing data. Immunohistochemistry (IHC) and western blot (WB) were performed to confirm the signaling pathway enriched by DEGs that was activated in naturally infected OPA cases. Cell viability, wound-healing, transwell and colony formation assays were performed to assess the cell malignant transformation of sheep trophoblast cells (STCs) transformed with JSRV- env lentivirus in vitro, and then WB was performed to confirm the signaling pathway that had been validated in the lung tissues. Results A total of 366 DEGs (154 up-regulated and 212 down-regulated) were identified by RNA-Seq of lung tissues of naturally infected OPA cases and healthy individuals. GO analysis showed that 366 DEGs were significantly enriched in 178 GO terms, including 114 biological processes, 19 cellular components and 45 molecular functions. KEGG analysis showed that the DEGs mainly enriched in cell proliferation, differentiation, apoptosis and migration, such as PI3K/Akt/mTOR, MAPK and Hippo signaling pathway, and Hippo signaling pathway has never been reported in naturally infected OPA cases. qRT-PCR results of 10 DEGs which were selected randomly were consistent with RNA-Seq results. The protein expression of Hippo signaling pathway were up-regulated in naturally infected OPA lung tissues. Cell viability, wound-healing, transwell and colony formation assays confirmed that JSRV- env lentivirus caused malignant transformation of STCs and JSRV Env increased the protein expression of Hippo signaling pathway. Conclusions This research first identified the changes in the transcriptome level of naturally infected OPA lung tissues. These data confirm that the Hippo signaling pathway is involved in the mechanism of OPA, clarify the interaction between Hippo signaling pathway and JSRV Env, provide further evidence for the tumorigenic mechanism of JSRV.

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Cross-platform ultradeep transcriptomic profiling of human reference RNA samples by RNA-Seq

Scientific Data ◽

10.1038/sdata.2014.20 ◽

2014 ◽

Vol 1 (1) ◽

Cited By ~ 11

Author(s):

Joshua Xu ◽

Zhenqiang Su ◽

Huixiao Hong ◽

Jean Thierry-Mieg ◽

Danielle Thierry-Mieg ◽

...

Keyword(s):

Rna Seq ◽

Transcriptomic Profiling ◽

Cross Platform

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RNA-Seq-Derived Whole Genome Transcriptomic Profiling Following Challenge to Mt. Cedar in a Pollen Challenge Chamber Uncover Novel Insights Into Allergic Rhinoconjunctivitis Pathogenesis

Journal of Allergy and Clinical Immunology ◽

10.1016/j.jaci.2012.12.825 ◽

2013 ◽

Vol 131 (2) ◽

pp. AB40

Author(s):

Nathan Harper ◽

John Castiblanco ◽

Cynthia Rather ◽

Charles Andrews ◽

Daniel Ramirez ◽

...

Keyword(s):

Allergic Rhinoconjunctivitis ◽

Whole Genome ◽

Rna Seq ◽

Transcriptomic Profiling

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Analysis on Risk Factors of Nosocomial Infection in Orthopedic Patients and Research on Nursing Strategies

Infection International ◽

10.1515/ii-2017-0125 ◽

2016 ◽

Vol 5 (1) ◽

pp. 27-30 ◽

Cited By ~ 1

Author(s):

Zhitao Guo

Keyword(s):

Risk Factors ◽

Wound Healing ◽

Nosocomial Infection ◽

Bone Tissue ◽

Blood Supply ◽

Emergency Surgery ◽

Operation Time ◽

Delayed Wound Healing ◽

Surgical Incision ◽

Orthopedic Patients

Abstract Orthopedic patients mostly comprise traumatic patients and elderly or sick individuals. More patients with emergency surgery suffer from open wounds and serious pollution, and operation time is relatively long. Thus, orthopedic patients with surgical incision infection account for a large proportion of incidence of hospital infection. Orthopedic patients are also bedridden for long periods, and they receive poor bone tissue blood supply. In surgical incision infections, mild cases suffer from delayed wound healing, whereas severe cases can form osteomyelitis. This study reviews progress of research on risk factors of nosocomial infection among orthopedic patients in recent years.

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