Research progress in SARS-CoV-2 nucleic acid detection based on microfluidic platforms / 医疗卫生装备

The detection principle of microfluidic microfluidic technology was introduced.The current research status of microfluidic platform-based SARS-CoV-2 nucleic acid detection technologies were reviewed such as reverse transcription quantitative real-time polymerase chain reaction(RT-qPCR),digital PCR,isothermal amplification and clustered regularly interspaced palindromic repeats/CRISPR-associated protein.The deficiencies of microfluidic platform-based SARS-CoV-2 nucleic acid detection were analyzed.It's pointed out microfluidic platform-based SARS-CoV-2 nucleic acid detection had to be optimized and validated clinically in specialty,sensitivity,detection limit,reproducibility,informatization,quality control and reagent cost.[Chinese Medical Equipment Journal,2024,45(1):101-107]

Assessment and preliminary clinical application of a domestic nucleic acid detection reagent for hepatitis D virus / 中华检验医学杂志

Objective:This study aims to evaluate the quality and explore the preliminary clinical applications of a domestically developed hepatitis D virus nucleic acid quantification reagent (abbreviated as"domestic HDV RNA reagent").Methods:The sensitivity and accuracy of the reagent were evaluated in accordance with the WHO HDV RNA international standard, employing the Bio-Rad CFX Opus 96 real-time fluorescence quantitative PCR analysis system. Serial dilutions of pseudo-viruses or cell culture-derived virus were used to determine the linear range of the domestic HDV RNA reagent. Specificity was assessed using positive samples of HAV, HBV, HCV infection, and HEV national reference materials. Precision was evaluated with samples at both high and low concentrations. In a comparative analysis, 30 HDV IgG positive samples were tested using both the domestic HDV RNA reagent and the RoboGene HDV RNA kit based on the ABI 7500 FAST DX system. The Pearson correlation coefficient (r) was used to examine the correlation between the two reagents.Results:The domestic HDV RNA reagent demonstrated a high sensitivity of up to 6 IU/ml, consistent with that of the comparator reagent. The calibration curve for WHO HDV RNA standards had a slope of -3.286, with an amplification efficiency of 101.6%. The linear detection range spanned from 10 to 10 8 IU/ml for eight HDV genotypes. The domestic HDV RNA reagent exhibited exceptional specificity, without cross-reactivity observed with HAV, HBV, HCV, or HEV. Accuracy assessments at five concentration levels met the required standards, with intra-assay precision coefficient of variation ( CV) ranging from 1.20% to 4.20%, and inter-assay precision CV from 1.20% to 7.90%. The detection results for HDV IgG positive samples were highly correlated with the comparator reagent ( r=0.984, P<0.001), achieving a diagnostic accuracy of 100% compared to sequencing results. Conclusion:In this study, the domestic HDV RNA reagent possesses excellent specificity, accuracy, precision, and a broad linear range, attaining a sensitivity level on par with international reagents of the same type.

Development and optimization of an exosomal miRNA extraction method / 中国生物制品学杂志

@#Objective To develop and optimize the extraction method of exosomal miRNA and compare it with traditional methods. Methods The exosomal miRNA of MSC,NK and CIK cells was used as the research subject. The removal efficiency of genomic DNA from exosomal miRNA by gDNA removal column was detected by UV spectrophotometer and agarose gel electrophoresis. The lysates(exosome G2 lysate and exosome miRNA lysate)and aggregation reagents(absolute ethanol and isopropanol)were optimized by using concentration,purity and gene expression level(Ct value)as evaluation indexes.Exosomal miRNA of MSC,NK,CIK cells and healthy human serum was extracted by the developed method,Trizol method and Trizol magnetic beads method,and detected by RT-qPCR. Results The gDNA removal column effectively removed genomic DNA from exosomal miRNA. The concentrations of exosomal miRNA extracted from MSC,NK and CIK cells by using exosome miRNA lysate were significantly higher than those by using exosome G2 lysate(t = 6. 358,P = 0. 020). The purity of miRNA samples extracted by exosome G2 lysate was low,and there was foreign protein pollution,but exosome miRNA lysate effectively removed the pollution. The Ct values of miR-Let-7i,miR-16-1 and miR-150 genes in exosomal miRNA of CIK cells extracted by exosome miRNA lysate were significantly lower than those by exosome G2 lysate(t = 30. 120,P =0. 008). The concentration of exosomal miRNA extracted from MSC,NK and CIK cells by isopropanol was significantly higher than that by absolute ethanol(t = 8. 567,P = 0. 010),and the purity was significantly lower than that by absolute ethanol(t = 6. 214,P = 0. 020). The Ct values of miR-Let-7i,miR-16-1 and miR-150 genes in exosomal miRNA extracted from CIK cells by two aggregation reagents had no significant difference(t = 2. 297,P = 0. 120). Compared with Trizol method and Trizol magnetic beads method,the expression of miR-Let-7i,miR-16-1,miR-Let-7a and miR-150 genes in exosomal miRNA extracted from CIK,NK,MSC cells and healthy human serum by the developed method was more abundant,and the overall Ct value was lower. The dissolution peak was prominent and sharp,exhibiting a single main peak. Conclusion The exosomal miRNA extracted by the developed method has high concentration and purity with stable Ct value,and the method has high sensitivity and good specificity. This study lays a foundation for further research on exosomal miRNA.

Detection of arboviruses in Aedes aegypti through transovarian analysis: A study in Goiânia, Goiás

Abstract Background: Arboviral diseases are a group of infectious diseases caused by viruses transmitted by arthropods, mainly mosquitoes. These diseases, such as those caused by the dengue (DENV), Zika (ZIKV), chikungunya (CHIKV), and yellow fever (YFV) viruses, have a significant impact worldwide. In this context, entomological surveillance plays a crucial role in the control and prevention of arboviruses by providing essential information on the presence, distribution, and activity of vector mosquitoes. Based on entomological surveillance, transovarian transmission provides information regarding the maintenance and dissemination of arboviruses. The objective of this study was to detect these arboviruses in Goiânia, Goiás, and analyze the occurrence of transovarian transmission. Methods: Aedes aegypti eggs were collected from different regions of Goiânia and cultivated under controlled laboratory conditions until the emergence of adult mosquitoes. Adult females were grouped into pools containing their heads and thoraxes. These pools were subsequently evaluated using reverse-transcription quantitative polymerase chain reaction (RT-qPCR) assay. Results: A total of 157 pools (N=1570) were analyzed, with two pools testing positive for CHIKV and one pool testing positive for ZIKV, indicating that the offspring resulting from transovarian transmission are potentially infectious. Conclusions: In summary, the demonstration of the vertical transmission mechanisms of CHIKV and ZIKV in A. aegypti serves as an alert to health authorities, as these diseases are still underreported, and their primary urban vector has likely acquired this capacity, contributing to the dissemination of these infections.

Cuantificación de la expresión del gen amo-A en poblaciones bacterianas y archaeales presentes en muestras de suelos de un lote arrocero caracterizado por ambientes

El ciclo del nitrógeno representa uno de los procesos biogeoquímicos más importantes para los ecosistemas terrestres y acuáticos. Las comunidades microbianas desempeñan un papel crucial en los procesos de transformación del nitrógeno en el suelo, ya que participan en diversas etapas como la nitrificación, de gran importancia para la producción agrícola. Dentro de los marcadores moleculares más utilizados para evaluar la actividad de poblaciones microbianas oxidantes de amonio se han considerado ampliamente los genes que codifican enzimas claves como la subunidad A de la actividad amonio monooxigenasa (AMO). Sin embargo, no se comprende completamente si la expresión de esta enzima tiene relación directa con el rendimiento de los cultivos. En este contexto, se evaluó la expresión del gen amo-A de comunidades bacterianas y archaeales presentes en un lote arrocero previamente caracterizado por ambientes. Para cuantificar la abundancia de arqueas y bacterias oxidantes de amonio, (AOA y AOB, respectivamente) se emplearon las técnicas de PCR en tiempo real (RT-qPCR) y PCR digital (RT-dPCR). En este trabajo se encontró a través del análisis de datos metagenómicos que hubo una mayor presencia de AOB en las muestras de suelo rizosférico mientras que las AOA fueron predominantes en las muestras de suelo de soporte "bulk", sin embargo, no se detectó la expresión del gen amo-A asociada a la comunidad de bacterias en las muestras de suelo analizadas. Por otra parte, no se presentaron diferencias entre los transcritos del gen amo-A asociados a la comunidad de AOA de los ambientes caracterizados. Además, la expresión de transcritos no estuvo relacionada con alguna de las propiedades químicas evaluadas. Finalmente, las estrategias de cuantificación para RT-qPCR (plásmido y templete) resultaron ser homólogas y funcionales para identificar la expresión del gen amo-A de AOA, mientras que la técnica de RT-dPCR fue más precisa para el análisis de la comunidad de AOB y AOA.

The nitrogen cycle represents one the most important biogeochemical process for terrestrial and aquatic ecosystems. Microbial communities play a crucial role in the processes of transformation of soil nitrogen in the, since they participate in various stages such as nitrification, which is of great importance for agricultural production. Among the most used molecular markers to assess ammonium oxidizing microbial populations activity have been considered widely the genes encoding key enzymes such as ammonium monooxygenase (AMO) subunit A. However, it is not fully understood whether the expression of this enzyme is directly related to the crop yield. In this context, this research work evaluated the expression of the amo-A gene of bacterial and archaeal communities present in a rice field previously characterized by environments. Real-time PCR (RT-qPCR) and digital PCR (RT-dPCR) techniques were used to quantify the abundance of archaea and ammonium-oxidizing bacteria (AOA and AOB, respectively). In this work it was found that in the analysis of metagenomic data there was a greater presence of AOB in rhizospheric soil samples while AOA were predominant in bulk soil samples, however, the expression of the amo-A gene was not detected. associated with the community of bacteria in the soil samples analyzed. On the other hand, it was found that the transcripts of the amo-A gene of the AOA community did not present differences between the characterized environments. Furthermore, the expression of transcripts is not related to any of the chemical properties evaluated. Finally, the quantification strategies for RT-qPCR (plasmid and quenching) turned out to be homologous and functional to identify the expression of the AOA amo-A gene, while the RT-dPCR technique was more precise for the analysis of the community of AOB and AOA.

Improvement of bovine pestiviral diagnosis by the development of a cost-effective method for detecting viral RNA in fresh specimens and samples spotted in filter papers / Optimización del diagnóstico de Pestivirus bovinos mediante el desarrollo de una metodología económica para detectar ARN viral en muestras frescas y fijadas en papeles de filtro

Abstract Bovine pestiviruses are the causative agents of bovine viral diarrhea, a disease thatcauses severe economic losses in cattle. The aim of this study was to improve their diagnosisby developing a RT-qPCR to detect bovine pestiviruses A, B and H; and to set up a protocolfor collecting, shipping and preserving bovine pestiviral RNA on filter papers. The developedRT-qPCR showed high sensitivity in detecting these viruses in different matrices: viral stocks,semen and serum samples. With regard to the possibility of using the technique to test serumpools, it was possible to identify a positive serum sample within a pool containing 30 sera.In addition to evaluating the qPCR from fresh samples, the use of filter papers to sow bovinesamples was analyzed. The sampling method on two different filter papers using bovine blooddrops was a useful alternative for diagnostic purposes and allowed to preserve pestiviral RNAfor up to 12 months under refrigeration.

Resumen Los Pestivirus bovinos son los agentes causales de la diarrea viral bovina, una enfermedad que genera importantes pérdidas económicas en el ganado vacuno. El objetivo de este trabajo fue mejorar su diagnóstico mediante el desarrollo de una RT-qPCR para detectar los Pestivirus bovinos A, B y H y disenar un protocolo de recolección, envío y conservación de ARN viral en papeles de filtro. La RT-qPCR desarrollada demostró alta sensibilidad en la detección de estos virus en diferentes matrices: stock viral, suero y semen. Respecto de la posibilidad de usar la técnica para testear pools de suero, fue posible identificar un suero positivo dentro de un pool compuesto por 30 sueros. Además de evaluar la qPCR en muestras frescas, se analizó el uso de papeles de filtro para sembrar muestras de bovinos. La metodología de toma de muestras en dos tipos de papeles de filtro usando gotas de sangre fue una alternativa útil para el diagnóstico y permitió conservar ARN viral por hasta 12 meses a temperaturas de refrigeración.

Lactic Acid Inhibits the Cytotoxicity of NK-92 Cells via Activating the Lactate Receptor GPR81

Aims: Lactate acid functions as not only an energy source but a signaling molecule through the lactate receptor GPR81 under physiological conditions. However, the pathological role of lactic acid in the tumor microenvironment remains unclear, particularly for immune cells. Methodology: NK-92 cells were treated with L-lactic acid solutions at final concentrations of 10, 20, 30, and 40 mM, and its cell viability and cytotoxicity on A549 cells and A375 cells were evaluated by CCK8 assay and crystal violet assay, respectively. Furthermore, qPCR was used to assess the expression of GPR81 and cytotoxicity-related genes in NK-92 cells treated with antagonist and agonist. And their relationship between lactate/GPR81 pathway and cytotoxicity-related genes were analyzed by Pearson’s correlation. Results: The viability of NK-92 cells was inhibited by L-lactic acid with increasing concentration. Additionally, the cytotoxic activity against tumor cells of NK-92 cells treated with L-lactic acid decreased with increasing concentration. Moreover, qPCR results demonstrated that GPR81 can be activated by lactic acid or agonist (3,5-DHBA) and downregulate the expression cytotoxicity-related genes which included FASLG gene(Fas Ligand),TNF-? gene(Tumor necrosis factor-?), INFG gene (Interferon-?), RPF1 gene (Perforin 1), GZMA gene (Granzyme A), GZMB gene (Granzyme B), GZMH gene (Granzyme H), GAMK gene (Granzyme K) and GZMM gene (Granzyme M). And the expression of GPR81 returned to near-control level when treated with L-lactic acid in the presence of antagonist (3-OBA), the expression of cytotoxicity-related genes did as well. Pearson’s correlation analysis of cytotoxicity-related genes with GPR81 revealed that their correlation coefficient seems negative. Conclusion: Lactic acid can activate the GPR81 to downregulate the expression of cytotoxicity-related genes, subsequently lower the cytotoxicity of NK-92 cells.

Expression of CD24 gene in human malignant pleural mesothelioma and its relationship with prognosis / 中华劳动卫生职业病杂志

Objective: To investigate the expression of CD24 gene in human malignant pleural mesothelioma (MPM) cells and tissues, and evaluate its relationship with clinicopathological characteristics and clinical prognosis of MPM patients. Methods: In February 2021, UALCAN database was used to analyze the correlation between CD24 gene expression and clinicopathological characteristics in 87 cases of MPM patients. The TIMER 2.0 platform was used to explore the relationship between the expression of CD24 in MPM and tumor immune infiltrating cells. cBioportal online tool was used to analyze the correlation between CD24 and MPM tumor marker gene expression. RT-qPCR was used to analyze the expressions of CD24 gene in human normal pleural mesothelial cell lines LP9 and MPM cell lines NCI-H28 (epithelial type), NCI-H2052 (sarcoma type), and NCI-H2452 (biphasic mixed type). RT-qPCR was performed to detect the expressions of CD24 gene in 18 cases of MPM tissues and matched normal pleural tissues. The expression difference of CD24 protein in normal mesothelial tissue and MPM tissue was analyzed by immunohistochemistry. A Kaplan-Meier model was constructed to explore the influence of CD24 gene expression on the prognosis of MPM patients, and Cox regression analysis of prognostic factors in MPM patients was performed. Results: The CD24 gene expression without TP53 mutation MPM patients was significantly higher than that of patients in TP53 mutation (P<0.05). The expression of CD24 gene in MPM was positively correlated with B cells (r(s)=0.37, P<0.001). The expression of CD24 gene had a positive correlation with the expressions of thrombospondin 2 (THBS2) (r(s)=0.26, P<0.05), and had a negative correlation with the expression of epidermal growth factor containing fibulin like extracellular matrix protein 1 (EFEMP1), mesothelin (MSLN) and calbindin 2 (CALB2) (r(s)=-0.31, -0.52, -0.43, P<0.05). RT-qPCR showed that the expression level of CD24 gene in MPM cells (NCI-H28, NCI-H2052 and NCI-H2452) was significantly higher than that in normal pleural mesothelial LP9 cells. The expression level of CD24 gene in MPM tissues was significantly higher than that in matched normal pleural tissues (P<0.05). Immunohistochemistry showed that the expressions of CD24 protein in epithelial and sarcoma MPM tissues were higher than those of matched normal pleural tissues. Compared with low expression of CD24 gene, MPM patients with high expression of CD24 gene had lower overall survival (HR=2.100, 95%CI: 1.336-3.424, P<0.05) and disease-free survival (HR=1.800, 95%CI: 1.026-2.625, P<0.05). Cox multivariate analysis showed that compared with the biphasic mixed type, the epithelial type was a protective factor for the prognosis of MPM patients (HR=0.321, 95%CI: 0.172-0.623, P<0.001). Compared with low expression of CD24 gene, high expression of CD24 gene was an independent risk factor for the prognosis of MPM patients (HR=2.412, 95%CI: 1.291-4.492, P=0.006) . Conclusion: CD24 gene and protein are highly expressed in MPM tissues, and the high expression of CD24 gene suggests poor prognosis in MPM patients.

Establishment and evaluation of a quantitative TaqMan RT-PCR for the detection of SARS-CoV-2 Omicron variants / 中华微生物学和免疫学杂志

Objective:To develop a rapid, simple and cost-effective quantitative TaqMan RT-PCR (RT-qPCR) that could be used as an alternative to sequencing for the detection of Omicron variants and to evaluate its performance.Methods:Primers and TaqMan probes targeting the conserved domains of SARS-CoV-2 ORF1ab and the high-frequency mutation sites in the S gene of Omicron variants were designed. Then a RT-qPCR for the detection of Omicron variants was established. The consistency of the method was verified using samples identified by whole-genome sequencing. The specificity and sensitivity of the method were also evaluated.Results:The established RT-qPCR could distinguish Omicron variants from early epidemic A strains and Alpha and Delta variants of SARS-CoV-2, and the results were consistent with those of whole-genome sequencing with a coincidence rate of 100% (28/28). There was no cross-reactivity with other six respiratory viruses or coxsackievirus group A16. For RNA standards, this method showed good linearity in the range of 10 9-10 3 copies/μl with a correlation coefficient ( R2) greater than 0.99 and detection sensitivity of 10 3 copies/μl. Conclusions:The RT-qPCR designed in this study for Omicron variant detection had good sensitivity and specificity and could be easily performed in laboratories, which would greatly facilitate the monitoring of Omicron variants.

Comparative analysis of Respiratory Syncytial Virus frequency rates and viral load in different patient cohorts in a University Hospital in São Paulo, Brazil, over an eight-year period (2005-2013)

Abstract Respiratory Syncytial Virus (RSV) poses a global health concern, particularly affecting young children, the elderly, and immunosuppressed individuals. RSV viral load is essential for understanding transmission, disease severity, prevention, and treatment. This retrospective study aimed to analyze the frequency rates and viral loads of RSV infections in different patient cohorts and age groups over an eight-year period in a university hospital in São Paulo, Brazil. This study analyzed 1380 Immunocompetent (IC) and Immunosuppressed (IS) patients with acute respiratory tract infections. IC included patients with chronic Heart Disease (HD), Primary Care service recipients (PC), and a subgroup suspected of having Severe Acute Respiratory Syndrome caused by Influenza A (H1N1)pdm09 virus (SARS H1N1). IS comprised transplant patients and those with HIV infection. Respiratory samples were collected between February 2005 and October 2013, with RSV detection and viral load quantification (Log10 copies of RNA/mL) using RT-qPCR. Overall RSV infection rate was 17.3 %, with higher rates in children (23.9 %) than in adults (12.9 %), particularly in children under two years of age (28.2 %). Children in the SARS H1N1 and PC subgroups had higher infection rates (16.4 % and 34.9 %, respectively), with the highest rate in PC children aged 1 to < 2 years (45.45 %). Adults with HD had a significantly higher frequency rate (27.83 %) than those in the SARS H1N1 (2.65 %) and IS (15.16 %) subgroups and higher hospitalization rate among adults under 65 years. RSV viral load ranged from 2.43 to 10.15 Log10 RNA copies/mL (mean ± SD 5.82 ± 2.19), with hospitalized patients exhibiting significantly higher viral loads (7.34 ± 1.9) than outpatients (4.38 ± 1.89). Elderly bone marrow transplant patients also had significantly higher viral loads (7.57 ± 2.41) than younger adults (5.12 ± 1.87). This study provides insights into the RSV infection patterns in different patient cohorts in Brazil. Further investigations are needed to understand susceptibility and risk factors associated with RSV infection. In conclusion, high RSV viral load among hospitalized patients could serve as a surrogate marker of disease severity. Additionally, patients with chronic heart disease deserve greater attention regarding complications associated with RSV infection.

Prevalencia de virus de ARN en tubérculos-semilla certificados de Solanum tuberosum cv. Diacol Capiro de la sabana Cundiboyacense

La papa (Solanum tuberosum) Diacol Capiro es uno de los cultivares con mayor producción y consumo interno en Colombia, siendo los departamentos de Cundinamarca y Boyacá, los principales productores. Este cultivo, se ve afectado por un complejo de virus, que disminuye la calidad de los tubérculos y los rendimientos. En este trabajo, se evaluó la prevalencia de los virus de ARN: PLRV, PVY, PVX, PVS, PVV, PYVV, PMTV y PVB, en brotes de tubérculos-semilla certificados, provenientes de la sabana Cundiboyacense, mediante RT-qPCR. Los resultados revelan la ocurrencia de siete de los ochos virus en las muestras, con niveles de infección de 100 % (PVS, PVX y PYVV), 75 % (PLRV), 50 % (PVY), 37,5 % (PMTV) y 12,5 % (PVB). Adicionalmente, con el fin de obtener información de los genomas de los virus detectados, se utilizó secuenciación de alto rendimiento (HTS), de una muestra compuesta (bulk) de brotes, siendo posible obtener el genoma completo del PLRV y el genoma parcial del PVY. Los análisis filogenéticos realizados con dichas secuencias ubicaron a los virus PLRV y PVY en clados, conformados por aislamientos colombianos, con niveles de identidad superiores al 97 %. Estos hallazgos evidencian la necesidad de fortalecer los programas de certificación de tubérculos-semilla de papa en el país, mediante la utilización de pruebas moleculares de detección viral.

Diacol-Capiro is one of the most important potato (Solanum tuberosum) cultivars in Colombia with most production concentrated in the provinces of Cundinamarca and Boyacá. Unfortunately, this crop is seriously affected by several viruses that compromise the quality of tubers and yields. In this work, it was evaluated the prevalence of the RNA viruses: PLRV, PVY, PVX, PVS, PVV, PYVV, PMTV, and PVB in certified tuber-seed sprouts produced in the highlands of Cundinamarca and Boyacá by RT-qPCR. Results revealed a prevalence of 100 % for PVS, PVX, and PYVV; 75 % for PLRV, 50 % for PVY, 37.5 % for PMTV, and 12.5 % for PVB. Additionally, high-throughput sequencing from a sprout´s bulk sample was used to gather genomic information of infecting viruses, which resulted in a partial PVY sequence, and a complete PLRV genome. Phylogenetic analysis revealed that both assemblies cluster within clades comprising other Colombian isolates with more than 97 % nucleotide sequence identity. These findings highlight the need to update potato seed-tuber certification programs in Colombia with the implementation of more sensitive molecular tests.

A validated triplex RT-qPCR protocol to simultaneously detect chikungunya, dengue and Zika viruses in mosquitoes

Background & objectives: Recently, the incidences of chikungunya, dengue and Zika infections have increased due to globalization and urbanization. It is vital that reliable detection tools become available to assess the viral prevalence within mosquito populations. Methods: Based on the previous publications on clinical diagnosis in human infections, for the first time, we described a customized triplex RT-qPCR protocol for simultaneous detection of chikungunya virus (CHIKV), dengue virus serotypes 1-4 (DENV1-4) and Zika virus (ZIKV) in mosquitoes. Results: In preliminary assessment to determine the specificity and sensitivity of primers and probes, all six targets were detected individually with the following thresholds as indicated by calculated pfu equivalents: 3.96x100 for CHIKV, 3.80x101 for DENV1, 3.20x101 for DENV2, 8.00x10-1 for DENV3, 1.58x100 for DENV4, and 6.20x100 for ZIKV. When tested in a full combination of six targets (CDZ mix), CHIKV, DENV1-4 mix or ZIKV were all detected with the thresholds of 1.32x100 for CHIKV, 3.79x100 for DENV1-4 and 2.06x100 for ZIKV. All targets, individually or in full combination were detected in the mixtures of Aedes aegypti (L.) homogenate and viral lysates. A robust evaluation with three replicates in each of three plates for CHIKV, DENV1-4 and ZIKV individually or in full combination was conducted. In individual assays, CHIKV was detected to 3.96x10-1, DENV1-4 to 1.14x100 and ZIKV to 3.20x100 . In full combination assays, CHIKV was detected to 1.32x10-1, DENV1-4 to 3.79x101 and ZIKV to 1.07x100 . Interpretation & conclusion: This triplex RT-qPCR assay appears to consistently detect all six targets and does not cross react with Ae. aegypti homogenate, making it a feasible, practical, and immediately adoptable protocol for use among vector control and other entities, particularly in the endemic areas of CHIKV, DENVs and ZIKV.

Accurate quantification of 3'-terminal 2'-O-methylated small RNAs by utilizing oxidative deep sequencing and stem-loop RT-qPCR / 医学前沿

The continuing discoveries of novel classes of RNA modifications in various organisms have raised the need for improving sensitive, convenient, and reliable methods for quantifying RNA modifications. In particular, a subset of small RNAs, including microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), are modified at their 3'-terminal nucleotides via 2'-O-methylation. However, quantifying the levels of these small RNAs is difficult because 2'-O-methylation at the RNA 3'-terminus inhibits the activity of polyadenylate polymerase and T4 RNA ligase. These two enzymes are indispensable for RNA labeling or ligation in conventional miRNA quantification assays. In this study, we profiled 3'-terminal 2'-O-methyl plant miRNAs in the livers of rice-fed mice by oxidative deep sequencing and detected increasing amounts of plant miRNAs with prolonged oxidation treatment. We further compared the efficiency of stem-loop and poly(A)-tailed RT-qPCR in quantifying plant miRNAs in animal tissues and identified stem-loop RT-qPCR as the only suitable approach. Likewise, stem-loop RT-qPCR was superior to poly(A)-tailed RT-qPCR in quantifying 3'-terminal 2'-O-methyl piRNAs in human seminal plasma. In summary, this study established a standard procedure for quantifying the levels of 3'-terminal 2'-O-methyl miRNAs in plants and piRNAs. Accurate measurement of the 3'-terminal 2'-O-methylation of small RNAs has profound implications for understanding their pathophysiologic roles in biological systems.

Research Progress of DNA-Based Technologies for Postmortem Interval Estimation / 法医学杂志

In criminal investigations, postmortem interval (PMI) is important information to be inferred in homicide investigations, as well as the focus and the difficulty in forensic pathology research. Because the DNA content in different tissues is relatively constant and shows changes regularly with the extension of PMI, it has become a research hotspot of PMI estimation. This paper reviews the recent progress of PMI estimation technologies including DNA-based single cell gel electrophoresis, image analysis, flow cytometry, real-time fluorescence quantitative PCR and high-throughput sequencing, hoping to provide references for forensic medicine practice and scientific research.

Application and Prospect of RNA Profiling Analysis in Forensic Body Fluid Identification / 法医学杂志

In forensic physical evidence identification, the accurate identification of the individual origin and their body fluid composition of the biological samples obtained from the crime scene play a critical role in determining the nature of a crime. In recent years, RNA profiling has become one of the fastest developing methods for body fluids identification. Due to the characteristics of tissue or body fluid specific expression, various types of RNA markers have been proven to be promising candidate markers for body fluids identification in previous studies. This review summarizes the research progress of RNA markers in body fluids identification, including the RNA markers that have been effectively verified in current research and their advantages and disadvantages. Meanwhile, this review prospects the application of RNA markers in forensic medicine.

Epidemiologia molecular del SARS CoV-2, VSR y FLU en niños hospitalizados con infección respiratoria aguda grave

La Covid-19 en niños puede ocasionar cuadros graves al igual que en adultos, en nuestro medio no se conoce la caracterización de virus respiratorios de relevancia causantes de infección respiratoria aguda grave (IRAG) desde el inicio de la pandemia por Covid-19. Objetivo: evaluar el comportamiento epidemiológico de SARS CoV-2, VSR y FLU como responsables de IRAG en población internada en el Hospital del Niño Manuel Ascencio Villarroel en Cochabamba. Métodos: se incluyó a 41 pacientes de hasta 5 años de edad, internados durante junio 2021 a junio 2022. Se empleó la reacción en cadena de la polimerasa (RT-qPCR) para la detección de SARS-CoV-2, VSR y FLU tipo A y B. Resultados: en el 47,6 % de los pacientes se detectó VSR, en el 42,9 % SARS-CoV-2 y en 9,5 % se detectó coinfección entre SARS CoV-2 y VSR, no se presentó casos de infección por FLU. Se reportó principalmente con el 76,2% fiebre y 61,9 % tos. El 14,3% de los pacientes ingresó a terapia intensiva, 2 pacientes fallecieron, uno presentó coinfección viral SARS CoV-2/ VSR y el otro infección viral simple por SARS CoV-2. Conclusiones: tras el desconfinamiento después del inicio de la pandemia por Covid-19 se encontró como agentes causantes de IRAG a VSR y SARS CoV-2 con una frecuencia de circulación similar. Las manifestaciones respiratorias son más frecuentes, mostrando en la mayoría estados estables y recuperación favorable. Es necesario una constante vigilancia epidemiológica ante la experiencia vivida por la pandemia por Covid-19.

Covid-19 in children can cause serious cases just like in adults. In our environment, the characterization of respiratory viruses that cause severe acute respiratory infection (SARI) is not known since the beginning of the Covid-19 pandemic. Objective: to evaluate the epidemiological behavior of SARS CoV-2, RSV and FLU as the cause of SARI in patients admitted to the Manuel Ascencio Villarroel Children's Hospital in Cochabamba. Methods: 41 patients up to 5 years of age admitted from June 2021 to June 2022 were included. Polymerase chain reaction (RT-qPCR) was used to detect SARS-CoV-2, RSV and FLU type A and B. Results: RSV was detected in 47.6% of patients, SARS-CoV-2 in 42.9%, and coinfection between SARS CoV-2 and RSV in 9.5%. There were no cases of FLU infection. Fever and cough were reported mainly in 76.2% and 61.9% respectively. 14.3% of patients were admitted to intensive care, two patients died, one with a viral coinfection SARS CoV-2/RSV and the other with simple viral infection by SARS CoV-2. Conclusions: after the easing of restrictions following the start of the Covid-19 pandemic, RSV and SARS CoV-2 were found to be the agents causing SARI with a similar frequency of circulation. Respiratory manifestations are more frequent, showing mostly stable states and favorable recovery in most cases. Constant epidemiological surveillance is necessary given the experience of the Covid-19 pandemic.

Effect of boric acid application on antioxidant enzymes activity and gene expression in Safflower (Carthamus tinctorius L) cultivars

Abstract: Boron is one of the most important micronutrients for plants. Plants may suffer from deficiency or with boron toxicity. Boron plays a role in significant physiological and biochemical events in plants such as synthesis of the cell wall, membrane integrity, antioxidation, transport of photosynthesis products to other organs of the plant. The enzyme activities of ascorbate peroxidase (APX), catalase (CAT), glutathione reductase (GR) and superoxide dismutase (SOD) in three different safflower cultivars (Balcı, Dinçer and Remzibey) subjected to different boric acid concentrations (0, 5, 10, 15 mM) were measured spectrophotometrically, and the changes in the expression levels of the genes that encode these enzymes were obtained by quantitative RT-qPCR. When both the spectrophotometric measurements and the mRNA values were evaluated together, both the activity and mRNA values of APX and GR enzymes were found to be the highest in the Dinçer cultivar among the varieties treated with 15 mM boric acid, while the lowest values of these enzymes were determined in the Remzibey cultivar. According to the RT-qPCR results, the lowest SOD and CAT values were determined in Remzibey. The Dinçer cultivar was found to have the highest antioxidant capacity (APX, GR) to cope with oxidative stress caused by boric acid application at high concentrations. The sensitive Remzibey cultivar was found to have the lowest antioxidant capacity to cope with such oxidative stress. Balcı was found to be closer to Dinçer than to Remzibey in terms of boron tolerance. As a result, the boron-sensitive cultivar had low antioxidant activity.

Enzymatic activity and gene expression related to drought stress tolerance in maize seeds and seedlings

Drought stress is a major limiting factor for the development of maize, and the identification of the expression of genes related to this stress in seeds and seedlings can be an important tool to accelerate the selection process. The expression of genes related to tolerance to water deficit in seeds and in different tissues of maize seedlings were evaluated. Four tolerant genotypes (91-T, 32-T, 91x75-T, 32x75-T) and four non-tolerant genotypes (37-NT, 57-NT, 37x57-NT and 31x37-NT) were seeded in a substrate with 10% (stress) and 70% (control) water retention capacity. The expression of 4 enzymes were evaluated: catalase (CAT), peroxidase (PO), esterase (EST), and heat-resistant protein (HRP), as well as the relative expression of 6 genes: ZmLEA3, ZmPP2C, ZmCPK11, ZmDREB2A/2.1s, ZmDBP3 and ZmAN13 were evaluated in seed, shoots and roots of seedlings submitted or not to stress. There was variation in the expression of CAT, PO, SOD, EST and HRP enzymes among the evaluated genotypes and also in the different tissues evaluated. Higher expression of the CAT and PO was observed in the shoots. There was a greater expression of the EST in the genotypes non-tolerant to water deficit. HRP was expressed only in seeds. In the aerial part of maize seedlings, classified as tolerant, higher expression of genes ZmLEA3 and ZmCPK11 was observed. There was a higher expression of the ZmAN13 and ZmDREB2A/2.1S genes in roots developed under stress conditions and a higher expression of the ZmPP2C gene in seeds of line 91-T, which is classified as tolerant to drought stress.

Screening and validation of RT-qPCR reference genes of Viola yedoensis under different light intensities / 中国中药杂志

Screening the reference genes that were stably expressed under different light intensities for Viola yedoensis could provide reference for the related molecular research. In this study, 11 candidate reference genes were detected by RT-qPCR for tissues of V. yedoensis treated with different light intensities. Ge Norm, Norm Finder, Best Keeper, and Ref Finder website were used to comprehensively evaluate the reference genes, and verify the stability of the reference gene based on CAT1. Finally, the ideal reference gene was determined. The results showed that CYP, Actin, and SAMDC had small Ct value ranges and stable expression. Ge Norm demonstrated that CYP, SAMDC, and Actin were suitable reference genes. Norm Finder showed that the expression of α-TUB was the most stable. Best Keeper recommended CYP, Actin, and SAMDC as reference genes. Ref Finder assessed that SAMDC, CYP, α-TUB, and Actin had better stability, while GAPDH had the worst stability. The expression trend of CAT1 gene was consistent when calibrated with SAMDC, CYP, and Actin, while it was quite different from that calibrated with GAPDH. In summary, SAMDC, CYP, and Actin can be used as ideal reference genes for the gene expression profiling of V. yedoensis under different light intensities.

Correlation between gut microbiota and FGF21 in mice with insulin resistance / 中国药理学通报

Aim To study the effect of normal glucose tolerance fecal microbiota transplantation ( FMT) on the gut microbiota in mice with insulin resistance(IR) and its correlation with FGF21 , and to explore the possible mechanisms of gut microbiota affecting IR.Methods After the establishment of IR model with high-fat diet feeding, 30 successful IR model mice were randomly divided into three groups; insulin resistance ( IR ) group, IR + metformin( Met) group, and IR + glucose tolerance normal fecal microbiota transplantation (FMT)group, and blank control(Control) group, with 10 mice in each group.After eight weeks of administration, the body mass and fasting blood glucose of mice at 8th week were recorded, then the number of target bacteria in fecal samples and the mRNA expression levels of FGF21 and its receptors in liver, colon and ileum tissues were detected by Real-time quantitative PCR( RT-qPCR).Results ® Compared with control group, the body mass and fasting blood glucose increased in IR group mice, while the mRNA expression levels of FGF21/p-Klolho/FGFRl/FGFR4 in liver, colon and ileum tissues were down-regulated.The levels of Bacteroules and R.sarlorii were reduced in fecal samples, and the levels of P.distasonis, M.schaedleri and R.gnavus increased.These indices were reverted by Met and FMT treatment.(2) The expression of FGF21 was negatively correlated with FBG, P.distasonis , M.schaedleri and R.gnavus, and positively correlated with Bacteroides and B.sartorii.Conclusions FMT can increase the expression level of FGF21 and regulate gut microbiota, and the two are closely related , which may be one of the important mechanisms of FMT in improving insulin resistance.