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PubMed2025

Expression regulation network in papillae of sea cucumbers: Whole-transcriptome and DNA methylation datasets.

To elucidate the expression regulation network of papilla size of sea cucumbers (Apostichopus japonicus), the whole-transcriptome and DNA methylome datasets of different sizes of papillae in sea cucumbers were generated. Average clean bases of whole-transcriptome (16.35 G) and DNA methylome (28.92 G) were obtained using RNA sequencing and whole-genome bisulfite sequencing techniques. A total of 3,188 ceRNA networks were also identified including 3,081 long non-coding RNAs (lncRNA)/microRNAs (miRNA)/mRNA networks and 107 circular RNA (circRNA)/miRNA/mRNA networks. Methylome data indicate that there were 3,307 and 3,776 differentially methylated regions (DMRs) with high-level methylation as well as 3,125 and 3,016 DMRs with low-level methylation in big papillae compared to small papillae. The identified DMRs were mainly distributed in introns, promotors, or exons. The whole-transcriptome and DNA methylome datasets generated from this study not only established a robust theoretical foundation (especially from the epigenetic aspect) for elucidating expression regulation network determining papilla size in sea cucumbers but also can be a valuable resource of biomarker mining for papilla appearance-based selective breeding in sea cucumbers.

DNA Methylation↗
PubMed2025

Experimental study on the role and biomarker potential of CX3CR1 in osteoarthritis.

BACKGROUND: Osteoarthritis (OA) is a chronic joint disorder marked by progressive degeneration of articular cartilage and the formation of secondary osteophytes. Despite extensive research, the underlying molecular mechanisms remain poorly understood. This study aimed to identify OA-associated genes and elucidate the molecular pathways implicated, with the goal of discovering reliable diagnostic biomarkers. METHODS: The microarray dataset was retrieved from the Gene Expression Omnibus (GEO) and analyzed using R software to identify the signature gene, CX3CR1. Differentially expressed genes (DEGs) correlated with CX3CR1 were subsequently subjected to Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and immune infiltration analyses. A ceRNA regulatory network was also constructed. Vali-dation of CX3CR1 expression was conducted through qRT-PCR, Western blotting, and immunohistochemistry. RESULTS: CX3CR1 emerged as a candidate gene significantly associated with OA, exhibiting regulatory roles primarily in lipid metabolism-related and extra-cellular matrix-related biological processes and signaling cascades. The infiltration levels of immune cells, particularly activated mast cells, appeared to modulate OA progression. Both in vitro and in vivo experiments demonstrated elevated CX3CR1 expression in OA tissues relative to controls, with a robust positive correlation observed between CX3CR1 and MMP13 levels. CONCLUSION: CX3CR1 represents a potential biomarker for OA diagnosis and therapeutic targeting, exerting its effects by modulating lipid metabolism, extracellular matrix dynamics, and immune cell infiltration.

CX3C Chemokine Receptor 1↗
PubMed2026

A Novel Long Noncoding RNA-LNC000133 Associated With Steroid-Induced Osteonecrosis of the Femoral Head Promotes Osteoblast Differentiation Through Bone Marrow Mesenchymal Stem Cells-Derived Exosomes Pathway: A Bioinformatics Validation and Detailed Mechanistic Study.

Steroid-induced osteonecrosis of the femoral head (SONFH) is a debilitating disease caused by glucocorticoid abuse, characterized by complex pathogenesis and unclear molecular mechanisms. Dysfunction of bone marrow mesenchymal stem cells (BMSCs) and their exosome-mediated signalling is a key contributor to SONFH, although the precise mechanisms remain to be elucidated. In this study, the differential expression profiles of long noncoding RNAs (lncRNAs), microRNAs (miRNAs) and messenger RNAs (mRNAs) in exosomes derived from human BMSCs (hBMSCs) obtained from patients with SONFH compared to controls with femoral neck fractures were identified. Through next-generation sequencing, a novel lncRNA, LNC000133, associated with SONFH was discovered. Using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and competing endogenous RNA (ceRNA) network construction, the LNC000133/miR-362-5p/TGF-β3/SMAD3/BMP2 signalling axis was established. The definitive expression, localization and full-length sequence of LNC000133 in BMSCs were subsequently validated by Northern blot, quantitative real-time polymerase chain reaction (qRT-PCR), fluorescence in situ hybridization (FISH) and rapid amplification of cDNA ends (RACE). Most notably, mechanistic studies demonstrated that LNC000133-modified BMSCs-derived exosomes were efficiently taken up by osteoblasts, which promoted proliferation and osteogenic differentiation by targeting the miR-362-5p/TGF-β3/SMAD3/BMP2 signalling pathway.

Humans↗
PubMed2000

Molecular and evolutionary characterization of the cp32/18 family of supercoiled plasmids in Borrelia burgdorferi 297.

In this study, we characterized seven members of the cp32/18 family of supercoiled plasmids in Borrelia burgdorferi 297. Complete sequence analysis of a 21-kb plasmid (cp18-2) confirmed that the strain 297 plasmids are similar in overall content and organization to their B31 counterparts. Of the 31 open reading frames (ORFs) in cp18-2, only three showed sequence relatedness to proteins with known functions, and only one, a ParA/SopA ortholog, was related to nonborrelial polypeptides. Besides the lipoproteins, none of the ORFs appeared likely to encode a surface-exposed protein. Comparison with the B31 genomic sequence indicated that paralogs for most of the ORFs in cp18-2 can be identified on other genetic elements. cp18-2 was found to lack a 9- to 10-kb fragment present in the 32-kb homologs which, by extrapolation from the B31 cp32 sequences, contains at least 15 genes presumed to be unnecessary for plasmid maintenance. Sequence analysis of the lipoprotein-encoding variable loci provided evidence that recombinatorial processes within these regions may result in the acquisition of exogenous DNA. Pairwise analysis with random shuffling revealed that the multiple lipoproteins (Mlp; formerly designated 2.9 LPs) fall into two distinct homology groups which appear to have arisen by gene fusion events similar to those recently proposed to have generated the three OspE, OspF, and Elp lipoprotein families (D. R. Akins, M. J. Caimano, X. Yang, F. Cerna, M. V. Norgard, and J. D. Radolf, Infect. Immun. 67:1526-1532, 1999). Comparative analysis of the variable regions also indicated that recombination within the loci of each plasmid may occur independently. Last, comparison of variable loci revealed that the cp32/18 plasmid complements of the B31 and 297 isolates differ substantially, indicating that the two strains have been subject to divergent adaptive pressures. In addition to providing evidence for two different types of recombinatorial events involving cp32/18 plasmids, these findings underscore the need for genetic analysis of diverse borrelial isolates in order to elucidate the Lyme disease spirochete's complex parasitic strategies.

Amino Acid Sequence↗
PubMed2024

RNA-seq reveals differentially expressed lncRNAs and circRNAs and their associated functional network in HTR-8/Svneo cells under hypoxic conditions.

Placental hypoxia is hazardous to maternal health as well as fetal growth and development. Preeclampsia and intrauterine growth restriction are common pregnancy problems, and one of the causes is placental hypoxia. Placental hypoxia is linked to a number of pregnancy illnessesv. To investigate their potential function in anoxic circumstances, we mimicked the anoxic environment of HTR-8/Svneo cells and performed lncRNA and circRNA studies on anoxic HTR-8/Svneo cells using high-throughput RNA sequencing. The miRNA target genes were predicted by integrating the aberrant expression of miRNAs in the placenta of preeclampsia and intrauterine growth restriction, and a ceRNA network map was developed to conduct a complete transcriptomic and bioinformatics investigation of circRNAs and lncRNAs. The signaling pathways in which the genes were primarily engaged were predicted using GO and KEGG analyses. To propose a novel explanation for trophoblastic organism failure caused by lncRNAs and circRNAs in an anoxic environment.

Humans↗
PubMed2024

Whole transcriptome sequencing analyses of islets reveal ncRNA regulatory networks underlying impaired insulin secretion and increased β-cell mass in high fat diet-induced diabetes mellitus.

AIM: Our study aims to identify novel non-coding RNA-mRNA regulatory networks associated with β-cell dysfunction and compensatory responses in obesity-related diabetes. METHODS: Glucose metabolism, islet architecture and secretion, and insulin sensitivity were characterized in C57BL/6J mice fed on a 60% high-fat diet (HFD) or control for 24 weeks. Islets were isolated for whole transcriptome sequencing to identify differentially expressed (DE) mRNAs, miRNAs, IncRNAs, and circRNAs. Regulatory networks involving miRNA-mRNA, lncRNA-mRNA, and lncRNA-miRNA-mRNA were constructed and functions were assessed through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. RESULTS: Despite compensatory hyperinsulinemia and a significant increase in β-cell mass with a slow rate of proliferation, HFD mice exhibited impaired glucose tolerance. In isolated islets, insulin secretion in response to glucose and palmitic acid deteriorated after 24 weeks of HFD. Whole transcriptomic sequencing identified a total of 1324 DE mRNAs, 14 DE miRNAs, 179 DE lncRNAs, and 680 DE circRNAs. Our transcriptomic dataset unveiled several core regulatory axes involved in the impaired insulin secretion in HFD mice, such as miR-6948-5p/Cacna1c, miR-6964-3p/Cacna1b, miR-3572-5p/Hk2, miR-3572-5p/Cckar and miR-677-5p/Camk2d. Additionally, proliferative and apoptotic targets, including miR-216a-3p/FKBP5, miR-670-3p/Foxo3, miR-677-5p/RIPK1, miR-802-3p/Smad2 and ENSMUST00000176781/Caspase9 possibly contribute to the increased β-cell mass in HFD islets. Furthermore, competing endogenous RNAs (ceRNA) regulatory network involving 7 DE miRNAs, 15 DE lncRNAs and 38 DE mRNAs might also participate in the development of HFD-induced diabetes. CONCLUSIONS: The comprehensive whole transcriptomic sequencing revealed novel non-coding RNA-mRNA regulatory networks associated with impaired insulin secretion and increased β-cell mass in obesity-related diabetes.

Mice↗
PubMed1978

Contribution to the serological diagnosis of sarcocystosis.

The importance of the IFA-test (Indirect Fluorescent Antibody Test) in the diagnosis of sarcocystosis in the intermediate host has been confirmed in the present paper. We assessed the time of the first appearance of serum antibodies in the intermediate host in mice inoculated experimentally with the species Sarcocystis dispersa. By means of the IFA-test, the first antibodies were found on day 20 p.i. Cross-reactions among antisera of S. dispersa and a heterologous antigen of S. cernae disclosed that the reaction was not species-specific, but genus-specific. In addition, we confirmed serologically that the antigenic structure of the genus Frenkelia was identical to that of the genus Sarcocystis, because the results of cross reactions obtained with the IFA-test were identical.

Animals↗
PubMed1986

Histopathological changes in the liver tissue of house mouse and common vole during sarcocytosis.

The asexual reproduction of Sarcocystis dispersa was studied in the liver of the house mouse. Histopathological examinations revealed infection of parenchymal cells with the parasite and diffuse cellular infiltrations with the presence of polymorphonuclear cells, monocytes and eosinophilic leukocytes. The volume and number of cellular infiltrates increased gradually from day 3 till day 10 p.i. Then appeared necrotic foci and both phenomena reached the maximum on days 10-12 p.i. On days 21-34 p.i., no changes occurred in the tissue and the liver healed without scars. The infection of common vole with Sarcocystis cernae sporocysts caused cellular infiltrations in the liver around the portobiliary veins. The parasite was present from day 3 till day 7 p.i. The histopathological picture of liver changes was similar to that in the house mouse.

Animals↗
PubMed2005

Enhancement of in vitro and in vivo tumor cell radiosensitivity by valproic acid.

Valproic acid (VA) is a well-tolerated drug used to treat seizure disorders and has recently been shown to inhibit histone deacetylase (HDAC). Because HDAC modulates chromatin structure and gene expression, parameters considered to influence radioresponse, we investigated the effects of VA on the radiosensitivity of human brain tumor cells grown in vitro and in vivo. The human brain tumor cell lines SF539 and U251 were used in our study. Histone hyperacetylation served as an indicator of HDAC inhibition. The effects of VA on tumor cell radiosensitivity in vitro were assessed using a clonogenic survival assay and gammaH2AX expression was determined as a measure of radiation-induced DNA double strand breaks. The effect of VA on the in vivo radioresponse of brain tumor cells was evaluated according to tumor growth delay analysis carried out on U251 xenografts. Irradiation at the time of maximum VA-induced histone hyperacetylation resulted in significant increases in the radiosensitivity of both SF539 and U251 cells. The radiosensitization was accompanied by a prolonged expression of gammaH2AX. VA administration to mice resulted in a clearly detectable level of histone hyperacetylation in U251 xenografts. Irradiation of U251 tumors in mice treated with VA resulted in an increase in radiation-induced tumor growth delay. Valproic acid enhanced the radiosensitivity of both SF539 and U251 cell lines in vitro and U251 xenografts in vivo, which correlated with the induction of histone hyperacetylation. Moreover, the VA-mediated increase in radiation-induced cell killing seemed to involve the inhibition of DNA DSB repair.

Acetylation↗
PubMed1981

Effect of concurrent calcium leucovorin infusion on 5-fluorouracil cytotoxicity against murine L1210 leukemia.

We examined the effect of concurrent SC infusion of calcium leucovorin (LV) on the action of 5-fluorouracil (FUra) against mouse L1210 leukemia implanted either SC or IP. Mice bearing the SC tumor treated with FUra (100 mg/kg, IP, day 1) plus infusion with either LV (11.5 mg . kg-1 . day-1, days 1-4), or 0.9% NaCl (days 1-4) resulted in an identical increase in median lifespan (ILS) of 28%. Similar experiments with FUra (100 mg/kg) plus LV infusion (115 mg . kg-1 . day-1) or FUra (200 mg/kg) plus LV infusion (115 mg . kg-1 . day-1) resulted in 50% and 59% ILS, respectively, which were not different from that obtained with the same doses of FUra plus 0.9% NaCl infusion. Mice bearing the IP tumor treated with FUra (100 mg/kg, IP, day 1) plus infusion with either LV (11.5 mg . kg-1 . day-1, days 1-4) or 0.9% NaCl (days 1-4) had an identical 56% ILS. Similar experiments with FUra (100 mg/kg) plus LV infusion (115 mg . kg-1 . day-1) or FUra (200 mg/kg) plus LV infusion (115 mg . kg-1 . day-1) resulted in 67% and 94% ILS, respectively, which were not different from those obtained with the same doses of FUra plus 0.9% NaCl infusion. Treatment of normal mice with FUra (200 mg/kg, IP, day 0) plus LV infusion (115 mg . kg-1 . day-1, days 0-3) was no more toxic than FUra plus 0.9% NaCl infusion, judging by similar transient decreases in body weight and no mortality. The data indicate that concurrent infusion with the LV failed to enhance the action of FUra against the mouse L1210 leukemia.

Animals↗
PubMed1982

Uridine rescue from the lethal toxicity of 5-fluorouracil in mice.

To determine the relationship between 5-fluorouracil (FUra) toxicity and its RNA- and DNA-directed actions we examined the ability of continuous SC infusions with uridine (Urd), thymidine (dThd), or deoxyuridine (dUrd) to rescue mice from the lethal toxicity of FUra. Male B6D2F1 mice were treated with a single IP injection of FUra (800 mg/kg) followed in 24 h by a 5-day infusion with either 0.9% NaCl or Urd (0.1, 1, 5, or 10 g/kg/day). Survivors were then followed up for 30 days after FUra treatment. Urd (1, 5, or 10 g/kg/day) rescued mice from the lethal toxicity of FUra, whereas Urd (0.1 g/kg/day) was as ineffective as 0.9% NaCl as a rescue agent. With variable doses of FUra followed in 24 h by a Urd infusion (5 g/kg/day) for 5 days. Urd rescued mice treated with FUra (400, 600, or 800 mg/kg) but was ineffective against higher doses of FUra (1,000 or 1,200 mg/kg). Mice treated with FUra (800 mg/kg) followed in 24 h by a 5-day infusion with either dThd (1, 5, or 10 g/kg/day) or a dUrd (1 or 5 g/kg/day) could not be rescued from the lethal toxicity of FUra. In all experiments deaths occurred between 6 and 12 days after FUra. These results, which demonstrate a specificity for Urd, but not for either dThd or dUrd, for rescuing mice from the lethal toxicity of FUra, suggest the importance of the RNA- rather than the DNA-directed actions of FUra as a determinant of its toxicity in mice.

Animals↗
PubMed1994

Perianal actinomycosis--a complication of a fistula-in-ano. Report of a case.

Perianal actinomycosis is a rare complication of fistula-in-ano. We report a case of an 82-year-old male with an atypical fistula that had an internal opening at a posterior crypt and, over an extense perianal and gluteal area, induration with multiple suppurative draining sinus tracts. He underwent fistulotomy and an ample excision of the diseased areas. The pathology report was actinomycosis. Further treatment with antibiotics was continued until the patient was clinically cured. The diagnosis of perianal actinomycosis requires a high degree of suspicion, and should be kept in mind when a fistula presents the aforementioned characteristics or in case of a recurrence after adequate surgical therapy.

Actinomycosis↗
PubMed1989

Protein heterogeneity of Francisella tularensis: detection of proteins with antigenic determinants.

The autolyzates of three different strains of Francisella tularensis 15L, 130 and SCHU were tested for their immunogenic potential and protein heterogeneity. The autolyzates induce the production of specific antibodies, the delayed type of hypersensitivity, and some degree of protection against European virulent strain 130. This material (as antigen) was especially suitable for ELISA. When the autolyzates were subjected to SDS gradient PAGE, a variety of polypeptides were distinguished. The composition of polypeptides from all three strains on SDS-PAGE was almost identical. After the detection of antigenic determinants by Western blotting more than twenty bands appeared. The visualization with polyclonal antisera against live laboratory strain 15L and against autolyzates 15L, 130 and SCHU revealed differences in the composition of the antigenic determinants of these strains.

Animals↗