scholarly journals Multiomics study of a heterotardigrade, Echinisicus testudo, suggests the possibility of convergent evolution of abundant heat-soluble proteins in Tardigrada

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yumi Murai ◽  
Maho Yagi-Utsumi ◽  
Masayuki Fujiwara ◽  
Sae Tanaka ◽  
Masaru Tomita ◽  
...  
Keyword(s):  
Convergent Evolution ◽  
Structural Changes ◽  
Molecular Mechanisms ◽  
Extreme Environments ◽  
Soluble Proteins ◽  
Random Coil ◽  
Rna Seq ◽  
Stress Response Genes ◽  
Molecular Components

Abstract Background Many limno-terrestrial tardigrades can enter an ametabolic state, known as anhydrobiosis, upon desiccation, in which the animals can withstand extreme environments. Through genomics studies, molecular components of anhydrobiosis are beginning to be elucidated, such as the expansion of oxidative stress response genes, loss of stress signaling pathways, and gain of tardigrade-specific heat-soluble protein families designated CAHS and SAHS. However, to date, studies have predominantly investigated the class Eutardigrada, and molecular mechanisms in the remaining class, Heterotardigrada, still remains elusive. To address this gap in the research, we report a multiomics study of the heterotardigrade Echiniscus testudo, one of the most desiccation-tolerant species which is not yet culturable in laboratory conditions. Results In order to elucidate the molecular basis of anhydrobiosis in E. testudo, we employed a multi-omics strategy encompassing genome sequencing, differential transcriptomics, and proteomics. Using ultra-low input library sequencing protocol from a single specimen, we sequenced and assembled the 153.7 Mbp genome annotated using RNA-Seq data. None of the previously identified tardigrade-specific abundant heat-soluble genes was conserved, while the loss and expansion of existing pathways were partly shared. Furthermore, we identified two families novel abundant heat-soluble proteins, which we named E. testudo Abundant Heat Soluble (EtAHS), that are predicted to contain large stretches of disordered regions. Likewise the AHS families in eutardigrada, EtAHS shows structural changes from random coil to alphahelix as the water content was decreased in vitro. These characteristics of EtAHS proteins are analogous to those of CAHS in eutardigrades, while there is no conservation at the sequence level. Conclusions Our results suggest that Heterotardigrada have partly shared but distinct anhydrobiosis machinery compared with Eutardigrada, possibly due to convergent evolution within Tardigrada. (276/350).

scholarly journals Multiomics study of a heterotardigrade, Echinisicus testudo, suggests convergent evolution of anhydrobiosis-related proteins in Tardigrada

2020 ◽  
Author(s):  
Yumi Murai ◽  
Maho Yagi-Utsumi ◽  
Masayuki Fujiwara ◽  
Masaru Tomita ◽  
Koichi Kato ◽  
...  
Keyword(s):  
Water Content ◽  
Molecular Mechanism ◽  
Convergent Evolution ◽  
Structural Changes ◽  
Extreme Environments ◽  
Random Coil ◽  
Related Protein ◽  
Α Helix ◽  
Related Proteins

AbstractMany limno-terrestrial tardigrades can enter an ametabolic state upon desiccation, in which the animals can withstand extreme environments. To date, studies of the molecular mechanism have predominantly investigated the class Eutardigrada, and that in the Heterotardigrada, remains elusive. To this end, we report a multiomics study of the heterotardigrade Echiniscus testudo, which is one of the most desiccation-tolerant species. None of the previously identified tardigrade-specific anhydrobiosis-related genes was conserved, while the loss and expansion of existing pathways were partly shared. Furthermore, we identified two families of novel abundant heat-soluble proteins and the proteins exhibited structural changes from random coil to α-helix as the water content decreased in vitro. These characteristics are analogous to those of anhydrobiosis-related protein in eutardigrades, while there is no conservation at the sequence level. Our results suggest that Heterotardigrada have partly shared but distinct anhydrobiosis machinery compared with Eutardigrada, possibly due to convergent evolution within Tardigrada.

Effects of in-Office and at-Home Bleaching on Human Enamel and Dentin: An in vitro Application of Fourier Transform Infrared Study

2008 ◽  
Vol 62 (11) ◽  
pp. 1274-1279 ◽  
Author(s):  
Feride Severcan ◽  
Kurtulus Gokduman ◽  
Ayca Dogan ◽  
Sukran Bolay ◽  
Saadet Gokalp
Keyword(s):  
Fourier Transform ◽  
Structural Changes ◽  
Protein Denaturation ◽  
Random Coil ◽  
Protein Ratio ◽  
Band Frequency ◽  
Human Enamel ◽  
Ft Ir ◽  
At Home

In-office and at-home bleaching techniques are widely used methods for the whitening of teeth. However, the safety of these techniques has not been clarified yet. The aim of the current study is to investigate the in-office- and at-home-bleaching-induced structural and quantitative changes in human enamel and dentin at the molecular level, under in vitro conditions. The Fourier transform mid-infrared (mid-FT-IR) spectroscopic technique was used to monitor bleaching-induced structural changes. Band frequency and intensity values of major absorptions such as amide A, amide I, phosphate (PO4), and carbonate (CO3−2) bands, for treatment groups and control, were measured and compared. The results revealed that both procedures have negligible effects on dentin constituents. In office-bleached enamel, in addition to demineralization, a decrease in protein and polysaccharide concentrations, mineral-to-protein ratio, and the strength of hydrogen bonds around NH groups, as well as a change in protein secondary structure were observed. The protein structure changed from β-sheet to random coil, which is an indication of protein denaturation. However, no significant variations were observed for at-home bleached enamel. The control, at-home, and in-office bleached enamel samples were differentiated with a high accuracy using cluster analysis based on FT-IR data. This study revealed that office bleaching caused deleterious alterations in the composition and structure of enamel that significantly affected the crystallinity and mineralization of the tissue. Therefore, at-home bleaching seems to be much safer than in-office bleaching in terms of molecular variations.

scholarly journals Dual RNA-Seq Analysis of Trichophyton rubrum and HaCat Keratinocyte Co-Culture Highlights Important Genes for Fungal-Host Interaction

Genes ◽  
2018 ◽  
Vol 9 (7) ◽  
pp. 362 ◽  
Author(s):  
Monise Petrucelli ◽  
Kamila Peronni ◽  
Pablo Sanches ◽  
Tatiana Komoto ◽  
Josie Matsuda ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Trichophyton Rubrum ◽  
Glyoxylate Cycle ◽  
Human Keratinocytes ◽  
Rna Seq ◽  
Fungal Host ◽  
Host Interaction ◽  
Genes Encoding ◽  
Hacat Keratinocyte

The dermatophyte Trichophyton rubrum is the major fungal pathogen of skin, hair, and nails that uses keratinized substrates as the primary nutrients during infection. Few strategies are available that permit a better understanding of the molecular mechanisms involved in the interaction of T. rubrum with the host because of the limitations of models mimicking this interaction. Dual RNA-seq is a powerful tool to unravel this complex interaction since it enables simultaneous evaluation of the transcriptome of two organisms. Using this technology in an in vitro model of co-culture, this study evaluated the transcriptional profile of genes involved in fungus-host interactions in 24 h. Our data demonstrated the induction of glyoxylate cycle genes, ERG6 and TERG_00916, which encodes a carboxylic acid transporter that may improve the assimilation of nutrients and fungal survival in the host. Furthermore, genes encoding keratinolytic proteases were also induced. In human keratinocytes (HaCat) cells, the SLC11A1, RNASE7, and CSF2 genes were induced and the products of these genes are known to have antimicrobial activity. In addition, the FLG and KRT1 genes involved in the epithelial barrier integrity were inhibited. This analysis showed the modulation of important genes involved in T. rubrum–host interaction, which could represent potential antifungal targets for the treatment of dermatophytoses.

scholarly journals Transcriptomic Analysis of mRNA-lncRNA-miRNA Interactions in Hepatocellular Carcinoma

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Xia Tang ◽  
Delong Feng ◽  
Min Li ◽  
Jinxue Zhou ◽  
Xiaoyuan Li ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Rna Seq ◽  
Pairwise Interactions ◽  
Micro Rnas ◽  
Non Coding Rnas ◽  
First Time

Abstract Fully elucidating the molecular mechanisms of non-coding RNAs (ncRNAs), including micro RNAs (miRNAs) and long non-coding RNAs (lncRNAs), underlying hepatocarcinogenesis is challenging. We characterized the expression profiles of ncRNAs and constructed a regulatory mRNA-lncRNA-miRNA (MLMI) network based on transcriptome sequencing (RNA-seq) of hepatocellular carcinoma (HCC, n = 9) patients. Of the identified miRNAs (n = 203) and lncRNAs (n = 1,090), we found 16 significantly differentially expressed (DE) miRNAs and three DE lncRNAs. The DE RNAs were highly enriched in 21 functional pathways implicated in HCC (p < 0.05), including p53, MAPK, and NAFLD signaling. Potential pairwise interactions between DE ncRNAs and mRNAs were fully characterized using in silico prediction and experimentally-validated evidence. We for the first time constructed a MLMI network of reciprocal interactions for 16 miRNAs, three lncRNAs, and 253 mRNAs in HCC. The predominant role of MEG3 in the MLMI network was validated by its overexpression in vitro that the expression levels of a proportion of MEG3-targeted miRNAs and mRNAs was changed significantly. Our results suggested that the comprehensive MLMI network synergistically modulated carcinogenesis, and the crosstalk of the network provides a new avenue to accurately describe the molecular mechanisms of hepatocarcinogenesis.

scholarly journals Pituitary Transcriptomic Study Reveals the Differential Regulation of lncRNAs and mRNAs Related to Prolificacy in Different FecB Genotyping Sheep

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 157 ◽  
Author(s):  
Jian Zheng ◽  
Zhibo Wang ◽  
Hua Yang ◽  
Xiaolei Yao ◽  
Pengcheng Yang ◽  
...  
Keyword(s):  
Litter Size ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Expression Profiles ◽  
Pituitary Cells ◽  
Rna Seq ◽  
Non Coding Rna ◽  
Long Non Coding Rna ◽  
Hu Sheep

Long non-coding RNA (LncRNA) have been identified as important regulators in the hypothalamic-pituitary-ovarian axis associated with sheep prolificacy. However, their expression pattern and potential roles in the pituitary are yet unclear. To explore the potential mRNAs and lncRNAs that regulate the expression of the genes involved in sheep prolificacy, we used stranded specific RNA-seq to profile the pituitary transcriptome (lncRNA and mRNA) in high prolificacy (genotype FecB BB, litter size = 3; H) and low prolificacy sheep (genotype FecB B+; litter size = 1; L). Our results showed that 57 differentially expressed (DE) lncRNAs and 298 DE mRNAs were found in the pituitary between the two groups. The qRT-PCR results correlated well with the RNA-seq results. Moreover, functional annotation analysis showed that the target genes of the DE lncRNAs were significantly enriched in pituitary function, hormone-related pathways as well as response to stimulus and some other terms related to reproduction. Furthermore, a co-expression network of lncRNAs and target genes was constructed and reproduction related genes such as SMAD2, NMB and EFNB3 were included. Lastly, the interaction of candidate lncRNA MSTRG.259847.2 and its target gene SMAD2 were validated in vitro of sheep pituitary cells. These differential mRNA and lncRNA expression profiles provide a valuable resource for understanding the molecular mechanisms underlying Hu sheep prolificacy.

scholarly journals Impact of Sickle Cell Trait Hemoglobin on the Intraerythrocytic Transcriptional Program of Plasmodium falciparum

mSphere ◽  
2021 ◽  
Author(s):  
Joseph W. Saelens ◽  
Jens E. V. Petersen ◽  
Elizabeth Freedman ◽  
Robert C. Moseley ◽  
Drissa Konaté ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Molecular Mechanisms ◽  
Sickle Cell Trait ◽  
Rna Seq ◽  
Transcriptional Program ◽  
Content Type ◽  
Life Threatening ◽  
The Impact

Sickle-trait hemoglobin (HbAS) confers nearly complete protection from severe, life-threatening malaria, yet the molecular mechanisms that underlie HbAS protection from severe malaria remain incompletely understood. Here, we used transcriptome sequencing (RNA-seq) to measure the impact of HbAS on the blood-stage transcriptome of Plasmodium falciparum in in vitro time series experiments and in vivo samples from natural infections.

scholarly journals Investigations into the effects and related upstream/downstream regulatory mechanisms of long non-coding RNA WT1-AS in the maintenance and development of gastric cancer stem cells in vitro and in vivo

2021 ◽  
Author(s):  
Xiaobei Zhang ◽  
Meng Jin ◽  
Shiqi Liu ◽  
Mingde Zang ◽  
Lei Hu ◽  
...  
Keyword(s):  
Stem Cells ◽  
Cancer Stem Cells ◽  
Molecular Mechanisms ◽  
Rna Seq ◽  
Non Coding Rna ◽  
Gastric Cancer Stem Cells ◽  
Long Non Coding Rna ◽  
Development Of Gastric Cancer

Abstract Background Cancer stem cells (CSCs) are proposed to be responsible for almost all malignant phenotypes (e.g. heterogeneity, uncontrolled growth, metastasis, recurrence, chemoresistance) of tumors. Long non-coding RNA WT1 antisense RNA (WT1-AS) has been found to be involved in the regulation of lung cancer cell stemness. However, the roles and molecular mechanisms of WT1-AS in the maintenance and development of gastric cancer stem cells (GSCs) have not been investigated. Methods mRNA and protein expression was measured by RT-qPCR and western blot. CCK8 and Soft agar colony formation assays were performed to assess cell viability and colony clone formation ability. Cell cycle and apoptosis were determined by flow cytometry analysis. Cell transwell and wound healing analyses were carried out to assess cell migration ability. In vitro angiogenesis and 3D spheroid cultures assays were also performed. Moreover, in vitro experiments were carried out to explore the function of WT1-AS on tumor growth, metastasis and cell stemness. The upstream transcription factors or downstream genes of WT1-AS were screened through Bioinformatics, dual-luciferase assays and RNA-sequencing (RNA-seq) technology. Results Our present study demonstrated that WT1-AS knockdown or wilms tumor 1 (WT1) overexpression improved GSC proliferative and migratory capacities, promoted GSC EMT, enhanced GSC stemness, inhibited GSC apoptosis, potentiated the resistance of GSCs to 5-FU and induced HUVEC angiogenesis in vitro. WT1-AS loss or WT1 increase facilitated the formation of in-vitro 3D GSC aggregates. WT1-AS ameliorated the malignant phenotypes of GSCs by down-regulating WT in vitro. Additionally, WT1-AS inhibited tumor growth and metastasis, and reduced tumor stemness in GSCs-derived xenografts (s.c., i.p., and i.v.) in vivo. Furthermore, XBP1 was identified as an upstream regulator of WT1-AS in GSCs. RNA-seq and RT-qPCR data suggested that PSPH, GSTO2, FYN, and PHGDH might be the downstream targets of WT1-AS in GSCs. Conclusions Our data demonstrated that WT1-AS weakened the stem-cell like behaviors and characteristics of GSCs in vitro and in vivo by down-regulating WT1. Also, some upstream regulators and downstream targets of WT1-AS were identified in GSCs. Investigations on the molecular mechanisms underlying the complex phenotypes of GSCs might contribute to the better management of headaches in cancers.

scholarly journals LncRNA AC245100.4 affects the tumorigenesis of prostate cancer via regulating the STAT3/NR4A3 axis

2020 ◽  
Author(s):  
Chi Liu ◽  
Ping Lin ◽  
Jiabin Zhao ◽  
Hui Xie ◽  
Tianhu Zheng ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Cancer Progression ◽  
Molecular Mechanisms ◽  
Rna Seq ◽  
Rna Immunoprecipitation ◽  
Cancer Tissues ◽  
Promising Avenue

Abstract Background Prostate cancer (PCa) is the second most common cancer and the fifth leading cause of cancer deaths among men globally. However, the molecular mechanisms leading to the progression have not been fully elucidated. Methods The expression and location of AC245100.4 were examined by RT-qPCR and nuclear-cytoplasmic separation assay. RNA-seq analysis was performed to identify the downstream of AC245100.4. RNA immunoprecipitation was performed to identify the proteins those bind to AC245100.4. Western blotting was performed to quantify the expression of proteins. Finally, a series of gain- or loss-functional assays were done to prove the precise role of AC245100.4 and NR4A3 in PCa. Results We identify a critical lncRNA AC245100.4, which is significantly up-regulated in prostate cancer tissues and cells. Knockdown of AC21500.4 can significantly inhibit prostate cancer progression in vitro and in vivo. Further RNA-seq analysis shows that NR4A3 may be the potential target of AC245100.4. Mechanistically, AC245100.4 de-regulates NR4A3 transcriptionally via increasing p-STAT3, which is a transcriptional repressor of NR4A3. Conclusion Our results demonstrated that AC245100.4 was a critically oncogenic lncRNA in PCa via inhibiting NR4A3 and paved a promising avenue to combat PCa progression by targeting AC245100.4 or NR4A3.

scholarly journals ZRANB1 Drives Hepatocellular Carcinoma Progression through SP1-LOXL2 Axis

2021 ◽  
Author(s):  
Peiyi Xie ◽  
Qing Li ◽  
Qing Chao ◽  
Jiayu Fang ◽  
Jing Xie ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Molecular Mechanisms ◽  
Lysyl Oxidase ◽  
Expression Patterns ◽  
Rna Seq ◽  
Loss Of Function ◽  
Close Relationship ◽  
Hcc Cells

Abstract BackgroundDeubiquitinase (DUB) zinc finger RANBP2-type containing 1 (ZRANB1/TRABID) has been reported to have a close relationship with cancers. However, its underlying role and molecular mechanisms in hepatocellular carcinoma (HCC) remain elusive. MethodsGene and protein expression of ZRANB1 in HCC tissues were determined by qRT-PCR, western blot and immunohistochemistry. A series of gain- and loss-of-function assays were used to investigated the role of ZRANB1 in HCC cells progression. Moreover, RNA-seq were used to identify the downstream targets of ZRANB1 in HCC cells. The interaction between ZRANB1 and SP1 was examined through co-IP experiment and in vitro ubiquitination assay.ResultsZRANB1 was highly expressed in HCC tissues and ZRANB1 can regulate HCC cell growth and metastasis in vitro and in vivo. Through RNA-seq, we identified that Lysyl oxidase-like 2 (LOXL2) was the most significantly downregulated gene after ZRANB1 knockdown. Furthermore, the scatter plots indicated a significant positive correlation between ZRANB1 and LOXL2 expression in clinical HCC specimens. Additionally, LOXL2 was essential for ZRANB1-mediated HCC growth and metastasis. More importantly, specificity protein 1 (SP1) was critical in ZRANB1-mediated regulation of LOXL2 expression. Mechanistically, ZRANB1 bound with SP1 directly and stabilized the SP1 protein by deubiquitinating it. The expression patterns of ZRANB1, SP1 and LOXL2 were evaluated in HCC patients. ConclusionZRANB1 overexpression facilitates the carcinogenesis of HCC through stabilizing and upregulating SP1 to promote LOXL2 expression, suggesting ZRANB1 can be novel prognostic biomarker for HCC treatment.

scholarly journals Decidual cell differentiation is evolutionarily derived from fibroblast activation

2020 ◽  
Author(s):  
Longjun Wu ◽  
Daniel J. Stadtmauer ◽  
Jamie Maziarz ◽  
Günter P. Wagner
Keyword(s):  
Molecular Mechanisms ◽  
Embryo Implantation ◽  
Cell Types ◽  
Developmental Model ◽  
Decidual Cell ◽  
Rna Seq ◽  
Cell Type ◽  
Fibroblast Activation ◽  
Decidual Cells

AbstractWhat the molecular mechanisms underlying the evolutionary origin of novel cell types are is a major unresolved question in biology. The uterine decidual cell is a novel cell type of placental mammals which serves as the interface between maternal and fetal tissues during pregnancy. In this paper, we investigate two models for the nature of the differentiation of decidual cells: first, that it represents a mesenchymal-epithelial transition (MET), and second, that it evolved from wound-induced fibroblast activation (WIFA). Immunocytochemistry and RNA-seq analysis of decidualizing human endometrial fibroblasts cast doubt on the MET hypothesis and instead demonstrate a similarity between decidualization and fibroblast activation, including a central role for TGFB1. Through single-cell RNA-seq, we found a transient myofibroblast-like cell population in the in vitro differentiation trajectory of human decidual cells and found that these cells represent a pre-decidual state approaching the inferred transcriptomic transition to decidual cells. We propose an evolutionary developmental model wherein the decidual cell is a novel cell type not equivalent to the myofibroblast, but the process of decidual differentiation itself evolved as an endometrial-specific modification to fibroblast activation in response to the wound caused by embryo implantation.

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