Quantitation of HIV-1 RNA in breast milk by real time PCR

HIV-1 RNA in breast milk is a strong predictor of HIV-1 transmission through breastfeeding. In the present report, breast milk samples from HIV-1 uninfected donors were spiked with dilution of quantified culture supernatant from HIV-1(NDK) infected PBMC. Two RNA extraction techniques based on silica extraction, Nuclisens (BioMerieux) and Triazol (Qiagen), two techniques based on guanidine thiocynanate/chloroforme extraction, TRIzol (Life Technologie) and Amplicor HIV-1 Monitor (Roche Diagnostic Systems), and one technique based on electrostatic adsorption on iron oxide micro beads (Promega) were compared. HIV-1 RNA was quantitated by real time PCR (LTR gene) and Amplicor HIV-1 Monitor. Combining magnetic micro beads extraction and real time PCR quantitation allowed to correctly quantify breast milk HIV-1 RNA, with a difference between the expected and measured HIV-1 RNA levels always lower than 0.3 log copies/ml. The same combination was confirmed on 25 breast milk samples from HIV-1 infected women collected in Kwazulu-Natal, South Africa, by comparing measurements with those obtained by the Amplicor HIV-1 Monitor (r(2)=0.88). Nucleic acid extraction by magnetic micro beads followed by real time PCR is a reliable, sensitive, rapid and simple procedure to quantify HIV-1 RNA in breast milk and allows for PCR inhibitors found frequently in these samples.     

Development of a real time quantitative PCR assay for detection of porcine endogenous retrovirus

Real time PCR technology was applied to the development of assays for detection and quantitation of porcine endogenous retrovirus (PERV) RNA and DNA sequences in tissues and cells of human or animal origin. A plasmid construct encoding the PERV-pol gene or the in vitro transcribed RNA derived from the plasmid (cRNA) serves as a standard template for amplification of a 178 bp fragment. This study showed that the detection of this target sequence was linear over a range from 20 copies to 2 million copies of the plasmid and from 100 copies to 1 million copies of the cRNA. In addition, amplification of the target sequence was not inhibited by the presence of exogenous genomic DNA. These results demonstrate that a real time (TaqMan-based) PCR or RT-PCR assay can provide a sensitive, reproducible, and robust method for detecting and quantifying PERV DNA or RNA sequences in samples of human or guinea pig origin.     

Determination of expression profile of p53 gene in different grades of breast cancer tissues by real time PCR

BackgroundPakistan has a high incidence of breast cancer in Asia, where annually 16,232 deaths are reported. There are many exogenous and endogenous risk factors that affect the tumor suppressor genes and oncogenes. The p53 gene is a tumor suppressor gene and it has a role to protect the whole genome from external and internal stresses, which causes damages to the genome.ObjectiveThe aim of the current study was to investigate the p53 gene expression by using the real-time PCR technique in different grades of breast cancer as compared to the normal tissue.MethodsFresh Modified Radical Mastectomy (MRM) samples (grade1-grade3) were collected from different hospitals of the Lahore. The project was approved by an ethical review committee of Jinnah Hospital, Lahore. And before sampling an informed consent was obtained from patients and clinicians. RNA from fresh biopsies was extracted by Qiagen extraction kit and cDNA was formed. Real time PCR performed by using SYBR green master mix (ABI) and the data was evaluated by using Livak method. Statistical analysis was done by using Microsoft Excel.ResultsThere was an abnormal gene expression of p53 in all grades of the breast tumors. Non-significant (p>0.05) difference of down and up regulation of p53 in different grades of breast tumor was found. However, as a whole up-regulation was more than down-regulation with significant difference (p<0.0011).ConclusionThe abnormal expression of p53 shows that there are some genetic and epigenetic factors which are the primal cause of an abnormal gene expression. It is recommended that perform next generation sequencing (NGS) of the gene to find out the mutations causing the abnormal behavior of p53 gene.     

长链非编码RNA在结肠癌组织与癌旁组织中的表达研究

目的:筛选出结肠癌差异表达的长链非编码RNA(lncRNA),并分析其在结肠癌组织和相应癌旁组织中的差异表达情况。方法:从lncRNAtor数据库下载结肠癌组织中差异表达的lncRNA数据(Colon adenocarcinoma:Person neoplasm cancer status),包含36例结肠癌组织及29例正常结肠组织,以P0.01且差异表达倍数大于2或小于0.5的条件筛选出lncRNA,并用real-time PCR进一步验证其在60对结肠癌组织及癌旁组织中的表达情况。结果:分析结肠癌lncRNA数据发现,与正常组织相比,结肠癌组织共有50个lncRNA差异表达,其中28个高表达,22个低表达(P0.01)。筛选的4个lncRNA在60对结肠癌及癌旁组织标本中的验证结果为:HNF1AAS1和ZDHHC8P1的表达均上调(P0.01),SUZ12P表达下调(P0.05)。临床Ⅰ-Ⅱ期结肠癌组织中HNF1AAS1的表达水平明显低于Ⅲ-Ⅳ期(P0.05),ROC曲线分析显示,HNF1A-AS1、ZDHHC8P1和SUZ12P诊断结肠癌的ROC曲线下面积(AUC)分别为0.729(敏感性为78%,特异性为67%)、0.617(敏感性为68%,特异性为55%)和0.689(敏感性为65%,特异性为55%)。结论:长链非编码HNF1A-AS1和ZDHHC8P1在结直肠癌组织中表达上调,SUZ12P在结直肠癌组织中表达下调,其表达水平可能与结肠癌的发生存在关联。     

Quantitation of HIV-1 RNA levels in plasma and CSF of asymptomatic HIV-1 infected patients from South India using a TaqMan real time PCR assay.

BACKGROUND: Most of the quantitation assays for HIV-1 RNA used currently are designed and optimized for HIV-1 subtype B viruses and hence may not be suitable for India, where the predominant subtype is HIV-1 subtype C. OBJECTIVES: Development and standardization of HIV-1 TaqMan real time PCR assay suitable for measuring plasma and CSF viral RNA levels in HIV subtype C infected individuals. STUDY DESIGN: A TaqMan real time PCR was developed using primers and probes selected in the gag region for detection of Indian HIV-1 subtype C strain. Plasma (n=120) and CSF samples (n=46) obtained from HIV infected subjects were used to evaluate the sensitivity and specificity of the assay. A comparative evaluation was carried out with a commercially available quantitative HIV viral load assay (Roche Amplicor Version 1.5). RESULTS: The TaqMan assay was able to amplify all HIV-1 group M subtypes except subtype E. Viral loads could be estimated in all the plasma (n=120) and 40/46 CSF samples obtained from HIV positive subjects. Sensitivity of this assay was found to be 180 copies/ml. Correlation with the commercially available viral load assay was very good (r=0.885). CONCLUSIONS: A TaqMan real time PCR was standardized for HIV-1 subtype C and it was more sensitive (180 copies/ml) than standard Amplicor monitor assay, Version 1.5 (400 copies/ml).     

Quantitation of mitomycin C in human ocular tissues by high-performance liquid chromatography-photo-diode array detection

A chromatographic method, which can quantitate mitomycin C (MMC) along with two antiglaucoma drugs, is described. The separation of MMC, alphagan and timolol was performed on a reversed-phase C18 column with water-methanol-trifluoroacetic acid (65:35:0.01, v/v) as the mobile phase. By monitoring at 360, 248 and 296 nm, the lower limits of detection for MMC, alphagan and timolol are, respectively, 1.0, 2.0 and 5.0 ng (injection amount) at three-time S/N ratio. The dynamic ranges of quantitation for the three drugs are, respectively, 1.0 ng-10.0 microg, 2.0 ng-10.0 microg and 5.0 ng-10.0 microg with linearity being larger than 0.9960. This method was applied to the determination of MMC levels in Tenon's and trabeculum tissues of 10 glaucoma patients. MMC levels in these tissues, which were obtained from glaucoma filtering surgery, were determined following a multiple extraction with methanol. The recovery of MMC for a two-batch extraction was better than 91.2%. The reproducibility of measurement for the MMC levels in these tissues is 2.5-6.0% RSD for triplicate injections. The intra-day variation of retention times for the MMC peaks was less than 1.6% RSD (n=3). The inter-day variation of retention times for the MMC peaks was less than 4.8% RSD (n=3). MMC was detectable in three trabeculum tissues out of 10 cases (ranging from 0.8 to 25.5 ng/mg specimen), while MMC was detected in nine Tenon's tissues out of 10 cases (ranging from 0.3 to 21.1 ng/mg specimen). The results obtained show that the method is sensitive and selective for the quantitation of MMC.     

Quantitation of defective and ecotropic viruses during LP-BM5 infection by real time PCR and RT-PCR

Murine AIDS (MAIDS) is a pathology induced by the LP-BM5 murine leukaemia virus mixture in susceptible strains of mice such as C57BL/6J resulting in lymphoproliferation and progressive immunodeficiency. The etiologic agent of this pathology is BM5d, a replication defective virus. BM5e is a replication competent virus in the viral mixture that functions as a helper virus. This paper describes real time PCR and RT-PCR assays for quantitation of the proviral DNA and viral RNA of BM5d and BM5e. Data is presented describing the change in BM5d and BM5e proviral DNA levels and viral RNA levels in both blood and spleen in the first 8 weeks of infection. Infected mice have increasing levels of BM5d and BM5e viral DNA and RNA detectable from as early as 2 weeks post infection. Similar levels of proviral DNA was found for BM5d and BM5e in PBMC and spleen, however higher levels of BM5e viral RNA were observed in both tissues throughout infection. The assays described can be used as both a diagnostic tool and to investigate the direct effect of treatments on the BM5d and BM5e viruses and MAIDS development.     

Keratin expression in human tissues and neoplasms

Keratin expression in human tissues and neoplasms Keratin filaments constitute type I and type II intermediate filaments (IFs), with at least 20 subtypes named keratin 1-20. Since certain keratin subtypes are only expressed in some normal human tissues but not others, and vice versa, various tissues have been subclassified according to the pattern of keratin staining. Simple epithelia generally express the simple epithelial keratins 7, 18, 19, and 20, while complex epithelia express complex epithelial keratins 5/6, 10, 14, and 15. When an epithelium undergoes malignant transformation, its keratin profile usually remains constant. The constitution and expression patterns of keratin filaments in human epithelial neoplasms are complex and often distinctive. In this article, we first briefly review the molecular and cell biology of keratin filaments. We then focus on the expression patterns of keratin filaments in various human neoplasms.     

Prostatic acid phosphatase expression in human tissues

Prostate cancer is the most common cancer and the second leading cause of cancer deaths among males in most Western countries. Autologous cellular immunotherapy for the treatment of cancer seeks to induce tumor-specific immunity in the patient and is consequently dependent on a suitable target antigen and effective presentation of that antigen to the patient's immune system. Prostatic acid phosphatase (PAP) has been tested as a target antigen due to its high and apparently specific expression in the prostate. We used a variety of approaches to analyze PAP expression, including immunohistochemistry, in situ hybridization, and quantitative polymerase chain reaction. We complemented these laboratory-based techniques with an in silico analysis of reported PAP expression in human cDNA libraries. Our studies confirmed that, while PAP expression is not restricted to prostate tissues, its expression in other human tissues is approximately 1-2 orders of magnitude less than that observed in the prostate. The relative specificity of PAP expression in the prostate supports its use as a target of autologous cellular immunotherapy. The approach described here, involving the use of multiple correlates of tissue-specific expression, is warranted as a prerequisite in selecting any suitable target for immunotherapy.     

Hepcidin messenger RNA expression in human lymphocytes

Hepcidin regulates intracellular iron levels by interacting with and promoting the degradation of ferroportin, a membrane protein and the only known cellular iron exporter. Studies of hepcidin expression and regulation have focused on its effects in innate immunity and as a regulator of systemic iron metabolism. In the present study we characterized the expression of hepcidin messenger RNA (mRNA) in human peripheral blood mononuclear cells (PBMCs) with a focus on peripheral blood lymphocytes (PBLs). We found that (1) all human PBMCs analyzed express basal hepcidin mRNA levels; (2) hepcidin mRNA expression increases after T‐lymphocyte activation; (3) expression by PBLs increases in response to challenge by holotransferrin (Fe‐TF) and by ferric citrate in vitro; (4) the Fe‐TF‐mediated up‐regulation of hepcidin decreases ferroportin expression at the cytoplasmic membrane of PBLs; and (5) silencing of tumour necrosis factor‐α (TNF‐α) abrogates the effect of Fe‐TF. In summary, we show that hepcidin expression determines intracellular iron levels by regulating the expression of ferroportin, as described in other cells, and that inappropriately low expression of hepcidin impairs normal lymphocyte proliferation. The results establish hepcidin as a new player in lymphocyte biology.     

Hamartin and tuberin expression in human tissues.

Tuberous sclerosis (TSC) is a bigenic autosomal dominant disease caused by mutations in one of two tumor-suppressor genes, TSC1 and TSC2, resulting in benign hamartomas and low grade neoplasms in multiple organs including brain, heart, kidney, and skin. We report the results of an immunohistochemical study of the expression of the TSC gene products, tuberin and hamartin, in multiple tissues obtained at autopsy from 12 non-TSC affected patients ranging in age from 20 weeks gestation to 8 years, and surgical specimens from some organs. Tuberin and hamartin are expressed and are colocalized in most tissues. Contrary to a previous report, immunostaining with our antisera detected hamartin in liver, small and large intestine, prostate, and testes. We did not detect significant developmental differences in tuberin or hamartin expression in comparable tissues from patients of different ages. Although tuberin and hamartin colocalize in most tissues and cell types, we provide data that hamartin is more abundantly expressed than tuberin in cells within some tissues including the distal nephron and a population of cells of the endocrine pancreas. These data support the hypothesis that hamartin and tuberin interact and may function together in many tissues where they are co-expressed, but also suggest that hamartin has a discrete and specialized function in certain cell types.     

Characterization of X-tropic endogenous retrovirus-specific RNA uninfected tissues and lymphosarcoma of BALB/c mice

Analysis of endogenous X-tropic BALB/c retrovirus-specific RNAs in a BALB/c mouse tissue containing mostly non-driving cells (liver), in two normal tissues having significant proportions of dividing cells (20-h regenerating liver and 12-day embryo) and in cells of a lymphosarcoma of BALB/c mice were carried out by determining the extent to which the RNAs from these tissues hybridized to the virus 3H-cDNA probe and by their relative sedimentation values in a sucrose gradient. RNAs from 20-h regenerating liver, 12-day embryo and lymphosarcoma, each containing a significant proportion of proliferating cells, showed 8 to 21 % higher hybridization values than normal liver RNA. Differences in the exact size classes of virus-specific RNAs and, in their relative proportions were found to exist in the four different tissue types examined and no correlation between a specific RNA size-profile and the proliferating activity of a tissue could be detected.