Using established biorepositories for emerging research questions: a feasibility study

Active-site rich nanostructure with dual-enhanced electron transfer for ultra-sensitive electrochemiluminescence detection of DNA methylation in colon cancer.

The core promoter of hepatitis B virus (HBV) is crucial in viral replication. Our previous investigation in clinical serum samples indicated that deletions in the viral core promoter (from nucleotide 1758 to 1777 and 1749 to 1768 respectively) may lead to increase in viral replication. We propose to characterize these deletion mutants in a cell-based system that supports HBV replication. Replicative HBV genome developed in our laboratory was used as template to generate deletions in viral core promoter corresponding to those found in clinical samples. These deletion constructs were used to transfect HepG2 cells, which then support the subsequent infection of cells from these deleted but replicative genomes. The effect of deletion on the viral replication was measured by comparing the amount of hepatitis B virus surface antigen (HBsAg) secreted in the culture medium with that from cells transfected with the wild type HBV genome. The amount of secreted HBsAg in cells transfected with deletion mutants was significantly lower than those transfected with the wild type genome. Our results provide a new system for molecular characterization of mechanism of HBV replication. Contrary to the increased replication observed in clinical samples, the reduced viral replication in genomes carrying deletions in the core promoter suggests a complex regulatory mechanism of viral replication which may involve other elements in the viral core promoter.

Two sequence dimorphisms of DPB1 define the immunodominant serologic epitopes of HLA-DP

Label-free microfluidic paper-based electrochemical aptasensor for ultrasensitive and simultaneous multiplexed detection of cancer biomarkers

Diagnosis of Epstein–Barr virus infection in clinical serum samples by an SPR biosensor assay

Calibration of Cystatin C in the National Health and Nutrition Examination Surveys (NHANES)

In this study, approximately 40 endogenous metabolites were identified and quantified by (1)H NMR in urine samples from male rats dosed with two proximal tubule toxicants, cisplatin and gentamicin. The excreted amount of a majority of those metabolites in urine was found to be dose-dependent and exhibited a strong correlation with histopathology scores of overall proximal tubule damage. MetaCore pathway analysis software (GeneGo Inc.) was employed to identify nephrotoxicant-associated biochemical changes via an integrated quantitative analysis of both urine metabolomic and kidney transcriptomic profiles. Correlation analysis was applied to establish quantitative linkages between pairs of individual metabolite and gene transcript profiles in both cisplatin and gentamicin studies. This analysis revealed that cisplatin and gentamicin treatments were strongly linked to declines in mRNA transcripts for several luminal membrane transporters that handle each of the respective elevated urinary metabolites, such as glucose, amino acids, and monocarboxylic acids. The integrated pathway analysis performed on these studies indicates that cisplatin- or gentamicin-induced renal Fanconi-like syndromes manifested by glucosuria, hyperaminoaciduria, lactic aciduria, and ketonuria might be better explained by the reduction of functional proximal tubule transporters rather than by the perturbation of metabolic pathways inside kidney cells. Furthermore, this analysis suggests that renal transcription factors HNF1alpha, HNF1beta, and HIF-1 might be the central mediators of drug-induced kidney injury and adaptive response pathways.

Introduction: Hepatic steatosis is the histological observation of numerous lipid inclusions due to an excess accumulation of triacylglycerols. They are a concern with new therapeutic candidates because they signify altered lipid metabolism that can progress to more serious liver toxicity.Areas covered: This article is based on an article search using the PubMed database from 1987 to 2011 and confirms associations for several previously marketed drugs with four basic hepatocellular mechanisms. The article also describes how these mechanisms are controlled by master regulators of lipid metabolism, which include gene transcription factors, nuclear receptors, hormonal signaling, energy sensing proteins, endoplasmic reticulum stress signaling and certain key metabolic intermediates.Expert opinion: Drug-induced hepatic steatosis is typically not detectable by conventional means other than invasive histological examinations. By understanding the basic mechanisms, key regulators and energy signaling systems of the liver, the investigator is better equipped to avoid xenobiotics with steatogenic potential in the drug discovery or early development process. There are now a number of methods for detecting this potential, specifically gene expression or metabolomic profiling and pathway analysis or mechanism-based in vitro systems.

PCV3 capsid protein (Cap) is an important antigen for diagnosis and vaccine development. To achieve high-level expression of recombinant PCV3 Cap in Escherichia coli (E. coli), the gene of wild-type entire Cap (wt-eCap) was amplified from clinical samples, and three optimized entire Cap (opti-eCap) and one optimized Cap deleted nuclear location signal (NLS) (opti-dCap) gene fragments encoding the same amino acid sequence with wt-eCap were synthesized based on the codon bias of E. coli. Those gene fragments were inserted into the pET30a expression vector. One recombinant strain with the highest expressed soluble eCap from four entire Cap (one wt-eCap and three opti-eCap) and one recombinant strain expressed opti-dCap were selected for further purification. The purified eCap and dCap were identified by transmission electron microscopy (TEM), a large number of round hollow particles with a diameter of 10 nm virus-like particles (VLPs) were observed in eCap, whereas irregular aggregation of proteins observed in dCap. After formation the VLPs were applied as a coating antigen to establish an indirect ELISA (I-ELISA) for detection of PCV3-specific antibody in swine serum. 373 clinical swine serum samples from China collected in 2019 were tested utilizing the VLP-based I-ELISA method under optimized conditions. To the best of our knowledge, this is the first report of self-assembly into VLPs of PCV3 recombinant Cap. Our results demonstrated that the VLP-based I-ELISA will be a valuable tool for detecting the presence of PCV3 antibodies in serum samples and will facilitate screening of large numbers of swine serum for clinical purposes.

Background The onset and progression of type 1 diabetes mellitus (T1DM) is closely related to autoimmunity. Effective monitoring of the immune system and developing targeted therapies are frontier fields in T1DM treatment. Currently, the most available tissue that reflects the immune system is peripheral blood mononuclear cells (PBMCs). Thus, the aim of this study was to identify key PBMC biomarkers of T1DM.Methods Common differentially expressed genes (DEGs) were screened from the Gene Expression Omnibus (GEO) datasets GSE9006, GSE72377, and GSE55098, and PBMC mRNA expression in T1DM patients was compared with that in healthy participants by GEO2R. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and protein-protein interaction (PPI) network analyses of DEGs were performed using the Cytoscape, DAVID, and STRING databases. The vital hub genes were validated by reverse transcription-polymerase chain reaction using clinical samples. The disease-gene-drug interaction network was built using the Comparative Toxicogenomics Database (CTD) and Drug Gene Interaction Database (DGIdb).Results We found that various biological functions or pathways related to the immune system and glucose metabolism changed in PBMCs from T1DM patients. In the PPI network, the DEGs of module 1 were significantly enriched in processes including inflammatory and immune responses and in pathways of proteoglycans in cancer. Moreover, we focused on four vital hub genes, namely, chitinase-3-like protein 1 (CHI3L1), C-X-C motif chemokine ligand 1 (CXCL1), matrix metallopeptidase 9 (MMP9), and granzyme B (GZMB), and confirmed them in clinical PBMC samples. Furthermore, the disease-gene-drug interaction network revealed the potential of key genes as reference markers in T1DM.Conclusion These results provide new insight into T1DM pathogenesis and novel biomarkers that could be widely representative reference indicators or potential therapeutic targets for clinical applications.

BackgroundAge-related macular degeneration (AMD) is the leading cause of vision loss in the developed world and the detection of its onset and progression are based on retinal morphological assessments. MicroRNA (miRNA) have been explored extensively as biomarkers for a range of neurological diseases including AMD, however differences in experimental design and the complexity of human biology have resulted in little overlap between studies. Using preclinical animal models and clinical samples, this study employs a novel approach to determine a serum signature of AMD progression.MethodsSerum miRNAs were extracted from mice exposed to photo-oxidative damage (PD; 0, 1, 3 and 5 days), and clinical samples from patients diagnosed with reticular pseudodrusen or atrophic AMD. The expression of ~800 miRNAs was measured using OpenArray™, and differential abundance from controls was determined using the HTqPCR R package followed by pathway analysis with DAVID. MiRNA expression changes were compared against quantifiable retinal histological indicators. Finally, the overlap of miRNA changes observed in the mouse model and human patient samples was investigated.ResultsDifferential miRNA abundance was identified at all PD time-points and in clinical samples. Importantly, these were associated with inflammatory pathways and histological changes in the retina. Further, we were able to align findings in the mouse serum to those of clinical patients.ConclusionIn conclusion, serum miRNAs are a valid tool as diagnostics for the early detection of retinal degeneration, as they reflect key changes in retinal health. The combination of pre-clinical animal models and human patient samples led to the identification of a preliminary serum miRNA signature for AMD. This study is an important platform for the future development of a diagnostic serum miRNA panel for the early detection of retinal degeneration.

Transplantomics and Biomarkers in Organ Transplantation: A Report From the First International Conference

Surface-enhanced Raman scattering holography chip for rapid, sensitive and multiplexed detection of human breast cancer-associated MicroRNAs in clinical samples

Molecular recognition triggered aptazyme cascade for ultrasensitive detection of exosomes in clinical serum samples

A novel self-powered DNA biosensor was successfully developed based on a dual-chambered microbial fuel cell (MFC) apparatus as a power supply and ketamine (KET) as a hybridization indicator. A graphite electrode coated with gold nanoparticles (GNP/graphite electrode), which provided larger surface area for immobilization of thiolated single-stranded (ssDNA) probe, was used as biocathode in the MFC system. When KET was used as the hybridization indicator for detection of ssDNA probe, the indicator exhibited excellent selectivity in detecting and discriminating the complementary, single-base mismatched, and noncomplementary target sequences. Furthermore, this self-powered biosensor based on MFC apparatus served as the biosensing platform for determination of KET in clinical serum samples. Under the steady-state operation condition, the difference between power densities of the ssDNA probe-modified GNP/graphite cathode in the absence and presence of accumulated KET (ΔP) served as the detection signal with a detection limit of 0.54 nM. The proposed MFC-based self-powered biosensor, as a low-cost portable device, showed a high sensitivity, stability, and reproducibility. Therefore, it can become a promising platform for determination of KET in clinical researches.