cDNA Samples Research Articles

Highly sensitive and specific electrochemical biosensor for direct detection of hepatitis C virus RNA in clinical samples using DNA strand displacement

Hepatitis C virus (HCV) is a common blood-borne infection that can lead to long-term illnesses such as hepatocellular cancer and liver cirrhosis. Early diagnosis is crucial for effective management, as no vaccine is available for preventing HCV infection. However, the high cost and complexity of current molecular diagnostic tools hinder efforts to achieve early diagnosis and prevent transmission, particularly in resource-limited settings. We developed a novel electrochemical biosensor for point-of-care testing (POCT) of HCV RNA. The sensor utilizes a strand displacement method, where the target RNA displaces a gold nanoparticle-labeled reporter probe (AuRP) from a pre-hybridized duplex with a magnetic nanoparticle (MNP)-labeled capture probe. The amount of displaced AuRP, detected using differential pulse anodic stripping voltammetry (DPASV), is directly proportional to the target RNA concentration. The biosensor exhibited excellent analytical performance, with a detection limit of 4 fM for synthetic targets and 43 ng/µL for RT-PCR products. Importantly, it successfully detected HCV RNA directly in clinical plasma samples without the need for RNA extraction or amplification. The sensor was used to analyze 30 RNA samples from HCV-positive patients, 20 cDNA samples from viral RNA, 30 HCV-positive plasma samples, and 22 HCV-negative plasma samples. The sensor results show good concordance with the RT-PCR results, demonstrating the sensor’s potential for detecting HCV in clinical samples.

Potential utility of RSAD2 transcript and protein in early detection of pregnancy in buffaloes.

This study investigates a novel early pregnancy marker in water buffaloes, focusing on RSAD2 mRNA expression, known to be upregulated by interferon-tau (IFNT) during pregnancy. While RSAD2 is primarily recognized for its antiviral effect, we hypothesized its role as a conceptus-induced component in regulating pregnancy in buffaloes. Given its differential expression compared to other IFNT-induced genes in cows, RSAD2 may serve as a biomarker for early pregnancy detection in buffaloes. RNA, cDNA, and plasma samples were obtained from archived samples collected before insemination (d0) and at d20, d25 and d40 after insemination. Twelve RNA samples, having optimal optical density and concentration, from six pregnant and six non-pregnant buffaloes were selected. The cDNA was analyzed to measure the abundance of RSAD2 mRNA using real-time quantitative PCR (RT-qPCR) and plasma for protein expression analysis using Western blot. The RT-qPCR analysis showed a transcript of RSAD2 increased significantly by 7-fold and 6-fold on d20 and d25, compared to both d0 and d40 in the pregnant group only. At d20, the sensitivity of RSAD2 was 100% and the specificity was 83.3%, and at d25-d both the sensitivity and specificity was 100%, indicating low incidences of misdiagnosing early pregnancy in buffaloes. In the non-pregnant group, RSAD2 expression remained low and did not change after insemination. Western blot analysis revealed an immunoreactive RSAD2 protein band. Densitometry analysis of the RSAD2-specific protein band, based on gray mean value, showed significantly increased expression of RSAD2 at d25 compared to d0 in the pregnant group. In conclusion, these results indicated that RSAD2 expressions at both the mRNA and protein levels show promising potential for detecting pregnancy at d25 post-insemination.

PLAGL1 overexpression induces cytoplasmic DNA accumulation that triggers cGAS/STING activation.

Pancreatic β-cell damage mediated by apoptosis is believed to be a main trigger of type 1 diabetes mellitus (T1DM), which is proposed as an organ-specific autoimmune disease mediated by T cells. Nonetheless, the fundamental origins of T1DM remain uncertain. Here, we illustrate that an increase in PLAGL1 expression induces β-cell apoptosis, as evidenced by mitochondrial membrane impairment and nucleolar degradation. The gene expression levels from cDNA samples were determined using qRT-PCR method. Western blot and Co-immunoprecipitation were applied for protein expression and interactions, respectively. Flow cytometry and TUNEL assay were used to detect pancreatic β cell apoptosis. Female NOD/LtJ mice with recent-onset T1DM has been used in in vivo studies. Glucose-stimulated insulin secretion (GSIS) and glucose tolerance test (GTT) method is used for islet function assessment. Haematoxylin and Eosin (H&E) and Immunohistochemistry (IHC) were performed to evalute histological improvement of islet beta. Subsequent cytoplasmic DNA accumulation triggers DNA senser, the cyclic guanosine monophosphate-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway. STING activation further stimulates downstream IRF3 and NF-kB pathways, thus boost type-I interferon signalling and NF-kB mediated inflammation. These findings elucidate a molecular mechanism linking PLAGL1 induced cell apoptosis to type-I interferon signalling and suggest a potential benefit for targeting cGAS/STING in T1DM treatment.

Delineating the mechanistic relevance of the TP53 gene and its mutational impact on gene expression and patients’ survival in bladder cancer

Bladder carcinoma (BLCA) is a widespread urological malignancy causing significant global mortality, often hindered by delayed diagnosis and limited treatments. BLCA frequently exhibits TP53 mutations, playing a pivotal role in its pathogenesis and underscoring the potential of targeting TP53 as a therapeutic approach for this prevalent urological malignancy. Tumor tissues from 50 bladder cancer patients were used for mutational analysis in TP53's mutation-rich exons (5, 7, & 8). The gene expression of the TP53 gene, along with a TP53-target gene B‐cell translocation gene 2 (BTG2) was also assessed in the cDNA samples from the same BLCA tissues and 15 urine controls of healthy people. The analysis revealed 22 % of patients with somatic hotspot mutations, 18 % with pathogenic missense mutations, and 12 % with intronic variants. Patients with somatic mutations exhibited the worst prognosis, supported by survival analysis from The Cancer Genome Atlas (TCGA) BLCA data. Interestingly, H296Y missense mutation correlated with higher TP53 expression and improved survival, while intronic SNPs were linked to worse outcomes. Additionally, upregulated BTG2 expression in mutated patients was observed which was correlated with poor prognosis, emphasizing the role of TP53 mutations in bladder cancer progression. The multivariate analysis highlighted the predictive power of TP53 mutations, with a high frequency of high-grade tumors (78.57 %) in mutated patients, underscoring their role in cancer progression. In conclusion, this study emphasizes the crucial role of TP53 mutations in bladder cancer patients from Bangladesh.

Presence of Enteric Viruses in Shellfish Samples from the Persian Gulf.

Shellfishes are a significant economic and nutritious seafood amongst people in different countries. Seafood products, particularly shellfish, are potential reservoirs of enteric viruses. This research investigated the incidence of rotavirus (RoV), norovirus (NoV) GI and GII, hepatitis A virus (HAV), and hepatitis E virus (HEV) in shellfish samples from the Persian Gulf, Iran. One hundred and fifty shellfish samples were collected. RNA extraction and cDNA synthesis were performed using commercial kits. The real-time polymerase chain reaction assessed the presence of enteric viruses in extracted cDNA samples. Thirty-two out of 150 (21.33%) shellfish samples were contaminated with enteric viruses. Prevalence rates of NoV GI, NoV GII, HAV, and RoV amongst shellfish samples were 8.00%, 11.33%, 1.33%, and 0.66%, respectively. There were no contaminated shellfish samples with HEV. Simultaneous prevalence of HAV and NoV GI, and HAV and NoV GII viruses were 0.66% and 0.66%, respectively. Examined viruses had a higher prevalence in shellfish samples collected in the winter season (P<0.05). Prevalence of HAV, RoV, NoV GI, and NoV GII amongst shellfish samples gathered in the winter season was 2.85%, 9.09%, 11.90%, and 20%, respectively. To the best of our knowledge, this was the first report of the incidence of enteric viruses, particularly HAV, NoV GI, NoV GII, and RoV, in shellfish samples from the Persian Gulf, Iran. Shellfish samples may serve as a potential source of enteric viruses for the human population. Therefore, routine viral assessments should be conducted. The consumption of fully cooked shellfish can significantly reduce the risk of HAV, RoV, NoV GI, and NoV GII infections. Furthermore, given the export value and importance of shellfish samples, their microbial quality and safety should be routinely monitored.

Label-Free DNA Hybridization Detection Using a Highly Sensitive Fiber Microcavity Biosensor.

A novel label-free optical fiber biosensor, based on a microcavity fiber Mach-Zehnder interferometer, was developed and practically demonstrated for DNA detection. The biosensor was fabricated using offset splicing standard communication single-mode fibers (SMFs). The light path of the sensor was influenced by the liquid sample in the offset open cavity. In the experiment, a high sensitivity of -17,905 nm/RIU was achieved in the refractive index (RI) measurement. On this basis, the probe DNA (pDNA) was immobilized onto the sensor's surface using APTES, enabling real-time monitoring of captured complementary DNA (cDNA) samples. The experimental results demonstrate that the biosensor exhibited a high sensitivity of 0.32 nm/fM and a limit of detection of 48.9 aM. Meanwhile, the sensor has highly repeatable and specific performance. This work reports an easy-to-manufacture, ultrasensitive, and label-free DNA biosensor, which has significant potential applications in medical diagnostics, bioengineering, gene identification, environmental science, and other biological fields.

Protocol Development for Yielding High Quality DNA and RNA from Archived Formalin-Fixed Paraffin Embedded Tissues

Introduction: While genetic analysis of archived formalin-fixed paraffin embedded (FFPE) tissue specimens would be a significant research resource, extraction of high-quality DNA and RNA from these specimens is a significant challenge. Storage duration, tissue handling and tissue preservation processes as well as their interactions with the nucleic acids could influence the quality and integrity of the DNA or RNA required for genetic analysis.&#x0D; Objectives: The goal of this study was to establish a protocol to extract high quality DNA and RNA from the FFPE tissues for further use in quantitative PCR analysis.&#x0D; Methods: For the purposes of this study, human FFPE biopsy tissues from lung, liver, colon and kidney were obtained from a single center biorepository. GeneJET Genomic DNA Purification Kit (Catalog # K0722) obtained from Thermo Fisher Scientific and RecoverAll Total Nucleic Acid Isolation Kit obtained from Life Technologies were modified and used for extraction of DNA and RNA, respectively. Briefly, modifications involved extending reagent incubation times, increasing sample volumes and wash steps, and increased final nucleic acids recovery and concentration steps. Eight sections around 8-10 ?m thick were microtomed for each tissue sample and used for extraction. The purity of the nucleic acids obtained was verified using Nanodrop Spectrophotometer.&#x0D; Results: The average DNA yield from eight sections for each of the tissues was 270±184 ng/?l and for RNA was 296±188 ng/?l. Nucleic acid quality was assessed by measuring the 260nm/280nm absorbance ratio for protein contamination as well as the 260nm/230nm absorbance ratio for salt contamination. Both were found to be within acceptable ranges. RNA was reverse transcribed to cDNA and qPCR was successfully performed on both DNA and cDNA samples.&#x0D; Conclusions: These results indicate that protocols using the silica-based membrane technology can yield high quality DNA and RNA that can be successfully used for downstream genetic analysis.

Platelet-Restricted Clonal Hematopoiesis

Clonal hematopoiesis (CH) is a common age-related condition in which somatic mutations accumulate in hematopoietic stem cells (HSCs), leading to the clonal expansion of mutated cells. CH has been causatively linked with risk of disease, including atherosclerotic cardiovascular disease (CVD), and reduced overall survival. The current model of hematopoiesis suggests substantial heterogeneity and lineage-priming within the HSC compartment, including the existence of multipotent but platelet (PLT)-biased HSCs. However, all CH studies to date are based on whole blood or granulocyte (GRA) DNA, and therefore they do not assess for PLT-restricted clones, which we reasoned could be particularly important given the association of CH with CVD. We aimed to assess for presence of PLT-biased CH in a cohort of normal individuals, hypothesizing that PLT-biased CH might represent a distinct subgroup of persons with CH. We analysed a cohort of 151 individuals, aged 22.0 to 98.6 years ( x̅ = 74.9; 95% CI, 50.0 to 91.8), with normal blood counts, and no known hematological malignancy. We first established a method for isolation of high-purity cDNA from PLTs alongside isolation of gDNA and cDNA from matched GRAs. Myeloid cell contamination was extremely low in the PLT fraction as assessed by flow cytometry and molecular analysis. We first performed targeted analysis for presence of the JAK2V617F mutation in PLT and GRA fractions due to the known association of JAK2V617F with CVD and myeloid neoplasms, including essential thrombocythemia. We developed a high sensitivity allele specific JAK2V617F droplet digital PCR (ddPCR) assay (variant allele frequency [VAF] limit of detection 0.1%) for parallel assessment of gDNA and cDNA from GRAs and PLTs respectively. When including all cases with a VAF &amp;gt; 0.1%, JAK2V617F CH was detected in 21 (13.9%) individuals, consisting of 2 cases of non-lineage-restricted CH (present in both GRA and PLT fractions), 6 cases of GRA-restricted CH, and 13 cases of PLT-restricted CH. Only 6 cases showed VAF ≥ 2% (consistent with CH of indeterminate potential) and all were PLT restricted. Comparison of median JAK2V617F VAF in PLT cDNA with VAF in GRA gDNA revealed significantly higher VAF in the PLT-derived material (1.00% vs. 0.26%; p = 0.04). We next developed a custom, targeted, hybridisation capture next-generation sequencing (NGS) panel for parallel ultra-deep sequencing of both gDNA and cDNA, covering the major genes and hotspot mutations involved in CH ( DNMT3A, TET2, ASXL1, IDH2, JAK2, CALR, MPL, CBL, KRAS, GNB1, SF3B1, SRSF2, U2AF1, PPM1D and TP53). The panel comprised a total of 250 120-nucleotide-long probes (including 27 cDNA-specific probes) with a combined footprint size 25,083 bp. Performance studies showed acceptable off-target effect and good coverage, alignment rate, uniformity, and complexity. Agreement between the NGS-measured VAF for GRA gDNA and GRA cDNA was high (ρ c = 0.952, alpha = 0.05). In total, we screened GRA gDNA and matched PLT cDNA samples from 42 individuals. At the resolution of VAF ≥ 2%, analysis of PLTs substantially enhanced the number of individuals with detected CH from 12 (28.6%) to 26 (61.9%) (Fig. 1). Amongst the detected variants (n = 44), mutations detected in the GRA fraction (n = 20) accounted for less than half of the detected variants, while the PLT fraction included ~75% of the variants (n = 33), including 55% (n = 24) that were PLT-restricted. Notably, lineage-restriction for the above variants held true when taking into consideration clones with VAF &amp;lt; 2% too. Median VAF for all CH variants was 3.9% (95% CI, 2.2% to 32.3%), with no difference between GRA and PLT CH. The detected variants were distributed across DNMT3A, TET2, ASXL1, JAK2, SF3B1, and PPM1D genes, with evidence of lineage bias towards PLTs for TET2- and JAK2-related CH. PLT-restricted clones included high-VAF (&amp;gt; 5%) variants in DNMT3A (n = 4; x̅VAF = 13.2%), TET2 (n = 2; x̅VAF = 7.7%), JAK2 (n = 2; x̅VAF = 21.6%), and SF3B1 (n = 1), including an individual with DNMT3AQ842R and the SF3B1K666N at VAFs 16.7% and 12.5% respectively. Selected NGS-detected variants were orthogonally validated. We describe PLT-restricted CH as a frequent phenomenon in persons with normal blood parameters. Given the known association between CH and risk of CVD and hematological malignancy, further studies on larger patient cohorts are warranted to determine the importance of PLT vs. GRA CH in relation to clinical endpoints.

Selenium reduces acrylamide-induced testicular toxicity in rats by regulating HSD17B1, StAR, and CYP17A1 expression, oxidative stress, inflammation, apoptosis, autophagy, and DNA damage.

This study investigated the effects of Selenium (Se) on testis toxicity induced by Acrylamide (ACR) in rats. In our study, 50 male adult rats were used, and the rats were divided into five groups; control, ACR, Se0.5 + ACR, Se1 + ACR, and Se1. Se and ACR treatments were applied for 10 days. On the 11th day of the experimental study, intracardiac blood samples from the rats were taken under anesthesia and euthanized. Sperm motility and morphology were evaluated. Dihydrotestosterone, FSH, and LH levels in sera were analyzed with commercial ELISA kits. MDA, GSH, TNF-α, IL-6, and IL-1β levels and SOD, GPx, and CAT, activities were measured to detect the level of oxidative stress and inflammation in rat testis tissues. Expression analysis of HSD17B1, StAR, CYP17A1, MAPk14, and P-53 as target mRNA levels were performed with Real Time-PCR System technology for each cDNA sample synthesized from rat testis RNA. Testicular tissues were evaluated by histopathological, immunohistochemical, and immunofluorescent examinations. Serum dihydrotestosterone and FSH levels decreased significantly in the ACR group compared to the control group, while LH levels increased and a high dose of Se prevented these changes caused by ACR. A high dose of Se prevented these changes caused by ACR. ACR-induced testicular oxidative stress, inflammation, apoptosis, changes in the expression of reproductive enzymes, some changes in sperm motility and morphology, DNA, and tissue damage, and Se administration prevented these pathologies caused by ACR. As a result of this study, it was determined that Se prevents oxidative stress, inflammation, apoptosis, autophagy, and DNA damage in testicular toxicity induced by ACR in rats.

The identification and expression pattern of the sex determination genes and their sex-specific variants in the egg parasitoid Trichogramma dendrolimi Matsumura (Hymenoptera: Trichogrammatidae).

Introduction: Trichogramma wasps are egg parasitoids of agricultural lepidopteran pests. The sex of Trichogramma is determined by its ploidy as well as certain sex ratio distorters, such as the endosymbiotic bacteria Wolbachia spp. and the paternal sex ratio (PSR) chromosome. The sex determination systems of hymenopterans, such as Trichogramma spp., involve cascades of the genes transformer (tra), transformer-2 (tra2), and doublesex (dsx) and are associated with sex-specific tra and dsx splicing. First, these genes and their sex-specific variants must be identified to elucidate the interactions between the sex ratio disorders and the sex determination mechanism of Trichogramma. Methods: Here, we characterized the sex determination genes tra, tra2, and dsx in Trichogramma dendrolimi. Sex-specific tra and dsx variants were detected in cDNA samples obtained from both male and female Trichogramma wasps. They were observed in the early embryos (1-10h), late embryos (12-20h), larvae (32h and 48h), pre-pupae (96h), and pupae (144h, 168h, 192h, and 216h) of both male and female T. dendrolimi offspring. Results: We detected female-specific tra variants throughout the entire early female offspring stage. The male-specific variant began to express at 9-10h as the egg was not fertilized. However, we did not find any maternally derived, female-specific tra variant in the early male embryo. This observation suggests that the female-specific tra variant expressed in the female embryo at 1-9h may not have originated from the maternal female wasp. Discussion: The present study might be the first to identify the sex determination genes and sex-specific gene splicing in Trichogramma wasps. The findings of this study lay the foundation for investigating the sex determination mechanisms of Trichogramma and other wasps. They also facilitate sex identification in immature T. dendrolimi and the application of this important egg parasitoid in biological insect pest control programs.

Flexible genosensors based on polypyrrole and graphene quantum dots for PML/RARα fusion gene detection: A study of acute promyelocytic leukemia in children

Acute promyelocytic leukemia (APL) in children is associated with a favorable initial prognosis. However, minimal residual disease (MRD) follow-up remains poorly defined, and relapse cases are concerning due to their recurrent nature. Thus, we report two electrochemical flexible genosensors based on polypyrrole (PPy) and graphene quantum dots (GQDs) for label-free PML-RARα oncogene detection. Atomic force microscopy (AFM), scanning electron microscope (SEM), cyclic voltammetry (CV), and electrochemical impedance spectroscopy (EIS) were used to characterize the technological biosensor development. M7 and APLB oligonucleotide sequences were used as bioreceptors to detect oncogenic segments on chromosomes 15 and 17, respectively. AFM characterization revealed heterogeneous topographical surfaces with maximum height peaks for sensor layers when tested with positive patient samples. APLB/Genosensor exhibited a percentage change in anode peak current (ΔI) of 423 %. M7/Genosensor exhibited a ΔI of 61.44 % for more concentrated cDNA samples. The described behavior is associated with the biospecific recognition of the proposed biosensors. Limits of detection (LOD) of 0.214 pM and 0.677 pM were obtained for APLB/Genosensor and M7/Genosensor, respectively. The limits of quantification (LOQ) of 0.648 pM and 2.05 pM were estimated for APLB/Genosensor and M7/Genosensor, respectively. The genosensors showed reproducibility with a relative standard deviation of 7.12 % for APLB and 1.18 % for M7 and high repeatability (9.89 % for APLB and 1.51 % for M7). In addition, genetic tools could identify the PML-RARα oncogene in purified samples, plasmids, and clinical specimens from pediatric patients diagnosed with APL with high bioanalytical performance. Therefore, biosensors represent a valuable alternative for the clinical diagnosis of APL and monitoring of MRD with an impact on public health.

G-protein couple receptor (GPER1) plays an important role during ovarian folliculogenesis and early development of the Chinese Alligator

The critical role of the G protein-coupled receptor 1 (GPER1), a member of the seven-transmembrane G protein-coupled receptor family, in the functional regulation of oocytes accumulated abundant theories in the early research on model animals. However, the full-length cDNA encoding GPER1 and its role in the folliculogenesis has not been illustrated in crocodilians. 0.5, 3, and 12 months old Alligator sinensis cDNA samples were used to clone the full-length cDNA encoding GPER1. Immunolocalization and quantitative analysis were performed using Immunofluorescence technique, RT-PCR and Western blot. Simultaneously, studies on GPER1's promoter deletion and cis-acting transcriptional regulation mechanism were conducted. Immunolocalization staining for the germline marker DDX4 and GPER1 demonstrated that DDX4-positive oocytes were clustered tightly together within the nests, whereas scarcely any detectable GPER1 was present in the oocytes nest in Stage I. After that, occasionally GPER1-positive immunosignal was observed in oocytes and somatic cells additional with the primordial follicles, and it was mainly located at the granulosa cells or thecal cells within the early PFs in the Stage III. The single mutation of the putative SP1 motif, double mutating of Ets/SP1 and SP1/CRE binding sites all depressed promoter activities. This result will help to investigate the role of GPER1 in the early folliculogenesis of A. sinensis.

Molecular and Functional Characterisation of a Novel Intragenic 12q24.21 Deletion Resulting in MED13L Haploinsufficiency Syndrome.

Background and Objectives: Heterozygous pathogenic variants in the MED13L gene cause impaired intellectual development and distinctive facial features with or without cardiac defects (MIM #616789). This complex neurodevelopmental disorder is characterised by various phenotypic features, including plagiocephaly, strabismus, clubfoot, poor speech, and developmental delay. The aim of this study was to evaluate the clinical significance and consequences of a novel heterozygous intragenic MED13L deletion in a proband with clinical features of a MED13L-related disorder through extensive clinical, molecular, and functional characterisation. Materials and Methods: Combined comparative genomic hybridisation and single-nucleotide polymorphism array (SNP-CGH) was used to identify the changes in the proband's gDNA sequence (DECIPHER #430183). Intragenic MED13L deletion was specified via quantitative polymerase chain reaction (qPCR) and Sanger sequencing of the proband's cDNA sample. Western blot and bioinformatics analyses were used to investigate the consequences of this copy number variant (CNV) at the protein level. CRISPR-Cas9 technology was used for a MED13L-gene-silencing experiment in a culture of the control individual's skin fibroblasts. After the MED13L-gene-editing experiment, subsequent functional fibroblast culture analyses were performed. Results: The analysis of the proband's cDNA sample allowed for specifying the regions of the breakpoints and identifying the heterozygous deletion that spanned exons 3 to 10 of MED13L, which has not been reported previously. In silico, the deletion was predicted to result in a truncated protein NP_056150.1:p.(Val104Glyfs*5), partly altering the Med13_N domain and losing the MedPIWI and Med13_C domains. After MED13L gene editing was performed, reduced cell viability; an accelerated aging process; and inhibition of the RB1, E2F1, and CCNC gene expression were found to exist. Conclusions: Based on these findings, heterozygous intragenic 12q24.21 deletion in the affected individual resulted in MED13L haploinsufficiency due to the premature termination of protein translation, therefore leading to MED13L haploinsufficiency syndrome.

Rapid, Point-of-Care Host-Based Gene Expression Diagnostics Using Giant Magnetoresistive Biosensors.

Host-based gene expression analysis is a promising tool for a broad range of clinical applications, including rapid infectious disease diagnostics and real-time disease monitoring. However, the complex instrumentation requirements and slow turnaround-times associated with traditional gene expression analysis methods have hampered their widespread adoption at the point-of-care (POC). To overcome these challenges, we have developed an automated and portable platform that utilizes polymerase chain reaction (PCR) and giant magnetoresistive (GMR) biosensors to perform rapid multiplexed, targeted gene expression analysis at the POC. As proof-of-concept, we utilized our platform to amplify and measure the expression of four genes (HERC5, HERC6, IFI27, and IFIH1) that were previously shown to be upregulated in hosts infected with influenza viruses. The compact instrument conducted highly automated PCR amplification and GMR detection to measure the expression of the four genes in multiplex, then utilized Bluetooth communication to relay results to users on a smartphone application. To validate the platform, we tested 20 cDNA samples from symptomatic patients that had been previously diagnosed as either influenza-positive or influenza-negative using a RT-PCR virology panel. A non-parametric Mann-Whitney test revealed that day 0 (day of symptom onset) gene expression was significantly different between the two groups (p < 0.0001, n = 20). Hence, we preliminarily demonstrated that our platform could accurately discriminate between symptomatic influenza and non-influenza populations based on host gene expression in ∼30 min. This study not only establishes the potential clinical utility of our proposed assay and device for influenza diagnostics but it also paves the way for broadscale and decentralized implementation of host-based gene expression diagnostics at the POC.

Linking the shifts in the metabolically active microbiota in a UASB and hybrid anaerobic-aerobic bioreactor for swine wastewater treatment

Due to the high concentration of pollutants, swine wastewater needs to be treated prior to disposal. The combination of anaerobic and aerobic technologies in one hybrid system allows to obtain higher removal efficiencies compared to those achieved via conventional biological treatment, and the performance of a hybrid system depends on the microbial community in the bioreactor. Here, we evaluated the community assembly of an anaerobic-aerobic hybrid reactor for swine wastewater treatment. Sequencing of partial 16S rRNA coding genes was performed using Illumina from DNA and retrotranscribed RNA templates (cDNA) extracted from samples from both sections of the hybrid system and from a UASB bioreactor fed with the same swine wastewater influent. Proteobacteria and Firmicutes were the dominant phyla and play a key role in anaerobic fermentation, followed by Methanosaeta and Methanobacterium. Several differences were found in the relative abundances of some genera between the DNA and cDNA samples, indicating an increase in the diversity of the metabolically active community, highlighting Chlorobaculum, Cladimonas, Turicibacter and Clostridium senso stricto. Nitrifying bacteria were more abundant in the hybrid bioreactor. Beta diversity analysis revealed that the microbial community structure significantly differed among the samples (p < 0.05) and between both anaerobic treatments. The main predicted metabolic pathways were the biosynthesis of amino acids and the formation of antibiotics. Also, the metabolism of C5-branched dibasic acid, Vit B5 and CoA, exhibited an important relationship with the main nitrogen-removing microorganisms. The anaerobic-aerobic hybrid bioreactor showed a higher ammonia removal rate compared to the conventional UASB system. However, further research and adjustments are needed to completely remove nitrogen from wastewater.

The impact of circulating tumor cell HOXB13 RNA detection in men with metastatic castrate-resistant prostate cancer (mCRPC) treated with abiraterone or enzalutamide.

5060 Background: It has been shown that HOXB13 is an important androgen receptor (AR) coregulator. The primary objective of this analysis was to correlate HOXB13 expression with clinical outcomes in men with mCRPC. Methods: We conducted a retrospective analysis of the multicenter prospective PROPHECY trial of mCRPC men (n=118) treated abiraterone (abi) or enzalutamide (enza). CTC detection and specific HOXB13 cDNA detection and expression was measured using a modified Adnatest using appropriate controls. CTC HOXB13 status was categorized into 3 groups: undetectable CTCs (CTC=0 based on CTC PSMA &amp; PSA=0); CTC+ but HOXB13 CTC negative (&lt;4 copies) or positive (≥4 copies) where the HOXB13 cutoff point was determined by the maximally selected rank statistic for prognostic associations. The association between HOXB13 and overall survival (OS) and radiographic progression-free survival (rPFS) were explored using the proportional hazards model. We also explored the association between the two endpoints and multigroup of HOXB13 at cutoff 0 and CellSearch CTC at cutoff 1 and 5. Results: 102 men who had sufficient CTC cDNA sample for HOXB13 detection. Of those men with detectable CTCs, 19% (n=19) had no detectable HOXB13, while the majority of men at 67% (n=58) had both CTC and HOXB13 detection. The proportion of patients with CTC=0, CTC+ HOXB13-, and CTC+ HOXB13+ using the optimal HOXB13 threshold were 25%, 31% and 44%, respectively. Men with HOXB13- CTCs were more likely to have low PSA (median 3 vs 79 copies), low CTC PSMA (0 vs 99 copies), low AR-FL (47 vs. 89 copies) and CTC AR-V7 (5.9 vs. 42 copies), and more likely to have liver/lung metastases (41% vs 25%). Median OS were 25.7, 25 and 12.1 months while the median rPFS of the three groups were 9.0, 7.2 and 4.7 months, respectively. Compared to CTC=0, men with HOXB13- CTCs did not have a worse hazard rate for OS (HR: 0.9, 95% CI: 0.4-1.9), while HOXB13+ CTC patients had a worse hazard for OS (HR: 2.0, 95% CI: 1.0-3.9), adjusting for prior abi/enza treatment and Halabi clinical risk score. The positive HOXB13 had also statistically significant increased hazard for progression/death (HR: 2.31, 95% CI: 1.24-4.30). Compared to the group with both HOXB13=0 and CellSearch CTC=0, men with HOXB13&gt;0 and CellSearch CTC≥5 had increased hazard on both OS and rPFS (OS: HR:2.39, 95% CI: 1.06-5.4; rPFS: HR: 2.78, 95% CI: 1.38-5.59). Conclusions: Higher CTC HOXB13 expression is associated with AR dependent biomarkers in CTCs and is adversely prognostic in the context of potent AR inhibition in men with mCRPC, and this assay could be useful to select for patients appropriate for AR or future HOXB13 targeted therapies. Clinical trial information: NCT02269982 .

Evaluation of the diagnostic efficacy of a reagent kit for &lt;i&gt;in vitro&lt;/i&gt; diagnosis of West Nile fever using reverse transcription polymerase chain reaction with fluorescent probe-based detection

West Nile fever is a vector-borne zoonotic arbovirus infection with natural foci. Its clinical course is similar to that of acute febrile syndrome, and severe cases may result in neuroinvasive disease. Several genetic lineages (1, 2, and 4) of the West Nile virus (WNV) with different pathogenicity for humans are circulating in the Russian Federation. Therefore, it is an urgent task to develop a diagnostic reagent kit for differentiating between WNV genetic lineages and to implement the kit in clinical laboratory practice.The aim of the study was to conduct technical and clinical tests and evaluate the quality, efficacy, and safety of the Ampligen-WNV-genotype-1/2/4 diagnostic reagent kit for detecting WNV RNA and differentiating between WNV genetic lineages 1, 2, and 4 by reverse transcription polymerase chain reaction (RT-PCR) with fluorescent probe-based detection.Materials and methods. The authors determined the diagnostic sensitivity and specificity of the Ampligen-WNV-genotype-1/2/4 reagent kit (Volgograd Research Institute for Plague Control, Russia) by real-time RT-PCR with 216 clinical samples and 204 biological samples. Sanger sequencing was used as a reference method. Statistical analysis of clinical test results was carried out in accordance with the Russian national standard for clinical laboratory tests (GOST R 53022.3-2008).Results. When tested with the Ampligen-WNV-genotype-1/2/4 reagent kit, real-time RT-PCR demonstrated the analytical sensitivity of 1×104 GEq/mL for the detection of WNV cDNA of genetic lineages 1, 2, and 4. The assessment of its analytical specificity showed no positive results for cDNA samples of heterologous viruses at a concentration of 1×106 GEq/mL. The diagnostic sensitivity with the reagent kit was at least 98.5%, and the diagnostic specificity was at least 99%, with 90% confidence levels for both parameters.Conclusions. The Ampligen-WNV-genotype-1/2/4 reagent kit can be recommended for use in clinical laboratory diagnostics to detect WNV RNA and differentiate between WNV genetic lineages 1, 2, and 4.

Determination of sex in cDNA samples from mice.

The need to take sex into account in biomedical research is now recognized and mandated by funding institutions. In laboratory rodents, such as mice, sexing is usually performed anatomically or by genotyping using multiplex or simplex PCR techniques on genomic DNA. Here we present a simple RT-PCR-based method targeting Kdm5c and Kdm5d to determine genetic sex in mouse cDNA samples, allowing for retrospective sex determination.

Detection of pathogenic viruses in the urban wastewater in Kuwait-implications for monitoring viral disease outbreaks.

Effective surveillance for epidemic-prone viral diseases is essential for emergency preparedness to respond to threats and occurrences of pandemics. While it is difficult and expensive to conduct health facility-based surveillance, there is a growing interest in conducting sewage-based epidemiological studies to monitor the health of the urban population because of the relative ease of sample collection and the availability of advanced molecular techniques for the detection of pathogens in the sewage. Sewage samples offer unique means to study the aggregate health of the population as opposed to the monitoring of the health of any individual by traditional methods. We worked together with the Ministry of Public Works in Kuwait and developed a platform for the collection and testing of sewage samples from different regions of Kuwait for studying population health. In this report, we describe the results of a cross-sectional study conducted between 16 and 23 September 2019 in an attempt to detect influenza, Noro, Rota, hepatitis A, and hepatitis E viruses in urban sewage samples collected in Kuwait. All five targeted viruses were detected in the samples collected from urban wastewater in Kuwait using reverse-transcriptase quantitative PCR (RT-qPCR). We recently checked for the presence of SARS-CoV-2 in the stored cDNA samples and confirmed the absence of SARS-CoV-2 in them. This is the first report that demonstrates the preparedness in Kuwait for using sewage samples for the detection and monitoring of many pathogenic viruses which may greatly increase the capacity of the country to deal with a viral disease outbreak in the future.

MUCOSAL EXPRESSION OF GENES PI3, ANXA1, AND VDR DESCRIMINATES CROHNS DISEASE FROM ULCERATIVE COLITIS IN INFLAMMATORY BOWEL DISEASE PATIENTS

Abstract INTRODUCTION Differential diagnosis of Inflammatory Bowel Disease Unclassified (IBDU) patients to Crohn’s Disease (CD) or Ulcerative Colitis (UC) at diagnosis is challenging. Personalized disease-specific strategies are becoming state of art and therefore it is of importance for outcome of the patients and treatment decision to be taken by the clinicians to have a precise diagnosis. METHODS Whole transcriptome RNA sequencing was performed using AmpliSeq human gene expression panel on formalin-fixed paraffin-embedded (FFPE) colonic mucosal biopsies of IBD patients (CD, n=16, UC, n=17) and non-IBD controls (n=10) to study differential gene expression between CD and UC samples. Top 100 of the most significant differentially expressed genes were then tested in two independent external GEO datasets. Functional enrichment analysis of 10 successful candidates were performed and 7 genes were selected for further validation. RT-qPCR analyses were performed on an independent patient cohort of 45 CDs and 53 UCs along with 12 non-IBD controls. The cDNA samples were submitted to quality restriction during the statistical analysis resulting in a cut-off of Ct values below 29 for the endogenous control allowing 46 patient samples to enter the analysis. In situ hybridization (ISH) was performed using RNAscope on 11 selected cases for describing tissue localisation and expression. RESULTS Sequencing results showed 308 genes differentially expressed between CD and UC from a total of 14190 genes. The genes MTCL1, SH3PXD2A-AS1, CLCF1, and CD180 were under the limit of detection with RT-qPCR and were excluded from further analysis. Relative expression levels from RT-qPCR for the genes PI3, ANXA1, and VDR, together with the age and sex, resulted in an area under the receiver-operating characteristic curve (AUC) of 0.84 (P = 0.02) in discriminating CD from UC. Significantly higher expression of VDR alone was observed in CD samples with AUCs of 0.77 (P = 0.01). ISH analyses showed expression of PI3, ANXA1, and VDR mRNAs localized to mucosal epithelial cells. CONCLUSION Using whole transcriptome analysis of FFPE sample-derived RNA, we have identified genes that are differentially expressed in CD and UC, and we have developed an RT-qPCR assay including a panel of 3 genes (PI3, ANXA1, VDR) for the differential diagnosis among IBD unclassified (IBDU) patients. We propose that the RT-qPCR assay could be used in a clinical routine setup for distinguishing UC from CD.