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Background: Human epidermal growth factor receptor 2 (HER2) is as a target gene for trastuzumab in patients with breast cancer. Accurate determination of HER2 status and strict quality control are necessary to ensure reproducibility and accuracy of the techniques used for the determination of HER2 status. Methods: We used three different types of samples: formalin-fixed and paraffin-embedded (FFPE) samples prepared from cell lines, agarose gel samples using cell lines, and xenograft tumor samples. One cell line for FFPE or xenografts did not overexpress HER2, while the others showed different levels of HER2 overexpression. We compared the morphology, HER2 gene amplification status, and HER2 protein expression status of these samples with those of clinical specimens. Results: We successfully produced three kinds of samples for quality control. Cells from the cell line-sample sections were dispersed while those from the agarose gel-sample sections and xenograft tumor sample sections (prepared from the both cell lines) were concentrated in one area. The FISH results for all three kinds of samples were as expected. The IHC results of the cell line samples and xenograft tumor samples were as expected, but the staining level of the agarose gel samples, using HER2-overexpressed cell lines was weak which might be regarded as a false negative result. Conclusions: Xenograft tumor samples might be used as an additional option for quality control in FISH and IHC. However, it might not replace the clinical specimen quality controls directly. [ABSTRACT FROM AUTHOR]

Background: Aspergillus westerdijkiae produces ochratoxin A (OTA) in Aspergillus section Circumdati. It is responsible for the contamination of agricultural crops, fruits, and food commodities, as its secondary metabolite OTA poses a potential threat to animals and humans. As a member of the filamentous fungi family, its capacity for enzymatic catalysis and secondary metabolite production is valuable in industrial production and medicine. To understand the genetic factors underlying its pathogenicity, enzymatic degradation, and secondary metabolism, we analysed the whole genome of A. westerdijkiae and compared it with eight other sequenced Aspergillus species. Results: We sequenced the complete genome of A. westerdijkiae and assembled approximately 36Mb of its genomic DNA, in which we identified 10,861 putative protein-coding genes. We constructed a phylogenetic tree of A. westerdijkiae and eight other sequenced Aspergillus species and found that the sister group of A. westerdijkiae was the A. oryzae - A. flavus clade. By searching the associated databases, we identified 716 cytochrome P450 enzymes, 633 carbohydrate-active enzymes, and 377 proteases. By combining comparative analysis with Kyoto Encyclopaedia of Genes and Genomes (KEGG), Conserved Domains Database (CDD), and Pfam annotations, we predicted 228 potential carbohydrate-active enzymes related to plant polysaccharide degradation (PPD). We found a large number of secondary biosynthetic gene clusters, which suggested that A. westerdijkiae had a remarkable capacity to produce secondary metabolites. Furthermore, we obtained two more reliable and integrated gene sequences containing the reported portions of OTA biosynthesis and identified their respective secondary metabolite clusters. We also systematically annotated these two hybrid t1pksnrps gene clusters involved in OTA biosynthesis. These two clusters were separate in the genome, and one of them encoded a couple of GH3 and AA3 enzyme genes involved in sucrose and glucose metabolism. Conclusions: The genomic information obtained in this study is valuable for understanding the life cycle and pathogenicity of A. westerdijkiae. We identified numerous enzyme genes that are potentially involved in host invasion and pathogenicity, and we provided a preliminary prediction for each putative secondary metabolite (SM) gene cluster. In particular, for the OTA-related SM gene clusters, we delivered their components with domain and pathway annotations. This study sets the stage for experimental verification of the biosynthetic and regulatory mechanisms of OTA and for the discovery of new secondary metabolites. [ABSTRACT FROM AUTHOR]

Bispecific antibodies (BsAbs) recognize two different epitopes. This dual specificity opens up a wide range of applications, including redirecting T cells to tumor cells, blocking two different signaling pathways simultaneously, dual targeting of different disease mediators, and delivering payloads to targeted sites. The approval of catumaxomab (anti-EpCAM and anti-CD3) and blinatumomab (anti-CD19 and anti-CD3) has become a major milestone in the development of bsAbs. Currently, more than 60 different bsAb formats exist, some of them making their way into the clinical pipeline. This review summarizes diverse formats of bsAbs and their clinical applications and sheds light on strategies to optimize the design of bsAbs. [ABSTRACT FROM AUTHOR]

Background: Food allergy has been reported increasingly around the world during the past several decades. Epstein-Barr virus (EBV), a common herpesvirus with high infection rate, is now suspected to be a risk or protective factor in food allergy. The aim of the study was to investigate the possible role of EBV infection in IgE-mediated food allergy. Methods: 34 patients with an egg allergy and 34 healthy controls participated in this study. Egg allergy was confirmed by open-food challenge. Serum anti-viral capsid antigen (VCA), anti-Epstein-Barr nuclear antigen 1 (EBNA-1) IgG and egg specific (yolk and white)-IgE levels were evaluated by enzyme linked immunosorbent assay (ELISA). At the same time, EBV DNA as well as viral miRNAs in these samples was quantified by real-time PCR. Results: The results showed that serum anti EBNA-1 IgG and two viral miRNAs (miR-BART1-5p and miR-BART7) were highly expressed in patients with egg allergy compared with healthy controls (p < 0.05, < 0.001 and < 0.01, respectively). Moreover, the expressions of anti EBNA-1 specific IgG, miR-BART1-5p and miR-BART7 positively correlated with the level of egg-specific IgE (p < 0.05, < 0.01 and < 0.01, respectively). The differences in anti VCA IgG concentration and EBV DNA copy number between the allergy patients and control individuals were not statistically significant. Conclusions: The high expression of EBV-specific antibody and miRNAs indicated that EBV infection might play a promoting role in IgE-mediated egg food allergy, and viral miRNAs-related immunomodulatory pathway was likely involved in this allergy process. [ABSTRACT FROM AUTHOR]

Background: Numerous studies have demonstrated that autophagy plays a vital role in maintaining cellular homeostasis. Interestingly, several anticancer agents were found to exert their anticancer effects by triggering autophagy. Emerging data suggest that autophagy represents a novel mechanism that can be exploited for therapeutic benefit. Pharmacologically active natural compounds such as those from marine, terrestrial plants and animals represent a promising resource for novel anticancer drugs. There are several prominent examples from the past proving the success of natural products and derivatives exhibiting anticancer activity. Helenalin, a sesquiterpene lactone has been demonstrated to have potent anti-inflammatory and antitumor activity. Albeit previous studies demonstrating helenalin's multi modal action on cellular proliferative and apoptosis, the mechanisms underlying its action are largely unexplained. Methods: To deduce the mechanistic action of helenalin, cancer cells were treated with the drug at various concentrations and time intervals. Using western blot, FACS analysis, overexpression and knockdown studies, cellular signaling pathways were interrogated focusing on apoptosis and autophagy markers. Results: We show here that helenalin induces sub-G1 arrest, apoptosis, caspase cleavage and increases the levels of the autophagic markers. Suppression of caspase cleavage by the pan caspase inhibitor, Z-VAD-fmk, suppressed induction of LC3-B and Atg12 and reduced autophagic cell death, indicating caspase activity was essential for autophagic cell death induced by helenalin. Additionally, helenalin suppressed NF-κB p65 expression in a dose and time dependent manner. Exogenous overexpression of p65 was accompanied by reduced levels of cell death whereas siRNA mediated suppression led to augmented levels of caspase cleavage, autophagic cell death markers and increased cell death. Conclusions: Taken together, these results show that helenalin mediated autophagic cell death entails inhibition of NF-κB p65, thus providing a promising approach for the treatment of cancers with aberrant activation of the NF-κB pathway. [ABSTRACT FROM AUTHOR]

Background: Simultaneous and sequential allantoic cavity inoculations of Specific-pathogen-free (SPF) chicken eggs with Influenza virus (AIV) and Newcastle disease virus (NDV) demonstrated that the interaction of AIV and NDV during co-infection was variable. Our research revisited the replication interference potential of AIV and NDV using real-time reverse transcription-polymerase chain reaction (real-time RT-PCR) for AIV and NDV to specifically detect the viral genomes in mixed infections. Results: Data from this survey showed that when different doses of NDV (Lasota or F48E8) and AIV (F98 or H5N1) were simultaneously inoculated into embryonating chicken eggs (ECE), interference with the growth of NDV occurred, while interference with the growth of AIV did not occur. When equal amount of the two viruses were sequentially employed, the degree of interference was dependent upon the time of superinfection and the virulence of virus. Conclusion: AIV have a negative impact on NDV growth if they are inoculated simultaneously or sequentially and that the degree of interference depended upon the quantity and relative virulence of the virus strains used; however, interference with AIV was not observed. Only if NDV were inoculated at an earlier time will NDV able to interfere with the growth of AIV. [ABSTRACT FROM AUTHOR]

Background: Quantification of hepatitis B virus (HBV) DNA can be used for diagnosing HBV infection and monitoring the effect of antiviral therapy. However, probably because of mismatches between the template and primer/probe, HBV DNA in some HBV infections could not be detected using currently available commercial assays with single primer/probe. By aligning the HBV sequences, we developed a duplex real-time polymerase chain reaction (PCR) assay using two sets of primers/probes and a specific armored DNA as internal control (IC). Results: The limit of the duplex real-time PCR assay was 29.5 IU/ml, whereas the specificity was 100%. The within-run precision coefficient of variation (CV) ranged from 1.02% to 2.73%, while the between-run CV ranged from 0.83% to 1.25%. The optimal concentration of armored DNA IC in the HBV DNA duplex real-time PCR assay was 1 000 copies/ml. Data from 69 serum samples with HBV infection showed that the performance of the duplex real-time PCR assay was comparable to that of the COBAS Ampliprep/Cobas Taqman (CAP/CTM) HBV assay and was superior to those of the domestic commercial HBV assays. Conclusions: The duplex real-time PCR assay is sufficiently sensitive, specific, accurate, reproducible and costeffective for the detection of HBV DNA. It is suitable for high throughput screening and frequent HBV DNA level monitoring. [ABSTRACT FROM AUTHOR]

Background: For decades, scientists have tried to understand the environmental factors involved in the development of systemic lupus erythematosus (SLE), in which viral infections was included. Previous studies have identified Epstein-Barr virus (EBV) to incite SLE. Human herpesvirus 8 (HHV-8), another member of the gammaherpesvirus family, shares a lot in common with EBV. The characteristics of HHV-8 make it a well-suited candidate to trigger SLE. Results: In the present study, serum samples from patients (n = 108) with diagnosed SLE and matched controls (n = 122) were collected, and the prevalence of HHV-8 was compared by a virus-specific nested PCR and a whole virus enzyme-linked immunoassay (EIA). There was significant difference in the prevalence of HHV-8 DNA between SLE patients and healthy controls (11 of 107 vs 1 of 122, p = 0.001); significant difference was also found in the detection of HHV-8 antibodies (19 of 107 vs 2 of 122, p < 0.001). We also detected the antibodies to Epstein-Barr virus viral capsid antigen (EBV-VCA) and Epstein-Barr nuclear antigen-1 (EBNA-1). Both patients and controls showed high seroprevalence with no significant difference (106 of 107 vs 119 of 122, p = 0.625). Conclusion: Our finding indicated that there might be an association between HHV-8 and the development of SLE. [ABSTRACT FROM AUTHOR]

Background: Recent controversy has surrounded the question of whether xenotropic murine leukaemia virusrelated virus (XMRV) contributes to the pathogenesis of chronic fatigue syndrome (CFS). To investigate the question in a Chinese population, 65 CFS patients and 85 blood donor controls were enrolled and multiplex realtime PCR or reverse transcriptase PCR (RT-PCR) was developed to analyze the XMRV infection status of the study participants. The assay was standardized by constructing plasmid DNAs and armored RNAs as XMRV standards and competitive internal controls (CICs), respectively. Results: The sensitivities of the multiplex real-time PCR and RT-PCR assays were 20 copies/reaction and 10 IU/ml, respectively, with 100% specificity. The within-run precision coefficient of variation (CV) ranged from 1.76% to 2.80% and 1.70% to 2.59%, while the between-run CV ranged from 1.07% to 2.56% and 1.06% to 2.74%. XMRV was not detected in the 65 CFS patients and 65 normal individuals out of 85 controls. Conclusions: This study failed to show XMRV in peripheral blood mononuclear cells (PBMCs) and plasma of Chinese patients with CFS. The absence of XMRV nucleic acids does not support an association between XMRV infection and the development of CFS in Chinese. [ABSTRACT FROM AUTHOR]

Background: The hepatitis C virus (HCV) genome is extremely heterogeneous. Several HCV infections can not be detected using currently available commercial assays, probably because of mismatches between the template and primers/probes. By aligning the HCV sequences, we developed a duplex real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay using 2 sets of primers/probes and a specific armored RNA as internal control. The 2 detection probes were labelled with the same fluorophore, namely, 6-carboxyfluorescein (FAM), at the 5' end; these probes could mutually combine, improving the power of the test. Results: The limit of detection of the duplex primer/probe assay was 38.99 IU/ml. The sensitivity of the assay improved significantly, while the specificity was not affected. All HCV genotypes in the HCV RNA Genotype Panel for Nucleic Acid Amplification Techniques could be detected. In the testing of 109 serum samples, the performance of the duplex real-time RT-PCR assay was identical to that of the COBAS AmpliPrep (CAP)/COBAS TaqMan (CTM) assay and superior to 2 commercial HCV assay kits. Conclusions: The duplex real-time RT-PCR assay is an efficient and effective viral assay. It is comparable with the CAP/CTM assay with regard to the power of the test and is appropriate for blood-donor screening and laboratory diagnosis of HCV infection. [ABSTRACT FROM AUTHOR]

Background: In assays for anti-hepatitis E virus (HEV) immunoglobulin M (IgM), large volumes of the patient's sera cannot be easily obtained for use as a positive control. In this study, we investigated an alternative chemical method in which rabbit anti-HEV IgG was conjugated with human IgM and was used as a positive control in the anti-HEV IgM assay. Rabbit anti-HEV IgG was isolated from immune sera by chromatography on protein A-Sepharose and was conjugated with human IgM by using 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) as a crosslinker. Results: The specific anti-HEV IgG antibody titer was 100,000 times that of the negative control, i.e., prebleed rabbit serum. The results of anti-HEV IgM enzyme-linked immunosobent assay showed that the antibody conjugate was similar to anti-HEV IgM antibodies produced in humans. The results of a stability experiment showed that the antibody conjugate was stable for use in external quality assessment or internal quality control trials. Conclusions: We concluded that the chemically conjugated rabbit-human antibody could be used instead of the traditional serum control as a positive control in the anti-HEV IgM assay. [ABSTRACT FROM AUTHOR]

Background: While progresses have been made in mapping transcriptional regulatory networks, posttranscriptional regulatory roles just begin to be uncovered, which has arrested much attention due to the discovery of miRNAs. Here we demonstrated a combinatorial approach to incorporate transcriptional and posttranscriptional regulatory sequences with gene expression profiles to determine their probabilistic dependencies. Results: We applied the proposed method to microarray time course gene expression profiles and could correctly predict expression patterns for more than 50% of 1,132 genes, based on the sequence motifs adopted in the network models, which was statistically significant. Our study suggested that the contribution of miRNA regulation towards gene expression in plants may be more restricted than that of transcription factors; however, miRNAs might confer additional layers of robustness on gene regulation networks. The programs written in C++ and PERL implementing methods in this work are available for download from our supplemental data web page. Conclusion: In this study we demonstrated a combinatorial approach to incorporate miRNA target motifs (miRNA-mediated posttranscriptional regulatory sites) and TFBSs (transcription factor binding sites) with gene expression profiles to reconstruct the regulatory networks. The proposed approach may facilitate the incorporation of diverse sources with limited prior knowledge. [ABSTRACT FROM AUTHOR]

Background: The retina is a well-defined portion of the central nervous system (CNS) that has been used as a model for CNS development and function studies. The full specification of transcripts in an individual tissue or cell type, like retina, can greatly aid the understanding of the control of cell differentiation and cell function. In this study, we have integrated computational bioinformatics and microarray experimental approaches to classify the tissue specificity and developmental distribution of mouse retina transcripts. Results: We have classified a set of retina-specific genes using sequence-based screening integrated with computational and retina tissue-specific microarray approaches. 33,737 non-redundant sequences were identified as retina transcript clusters (RTCs) from more than 81,000 mouse retina ESTs. We estimate that about 19,000 to 20,000 genes might express in mouse retina from embryonic to adult stages. 39.1% of the RTCs are not covered by 60,770 RIKEN full-length cDNAs. Through comparison with 2 million mouse ESTs, spectra of neural, retinal, late-generated retinal, and photoreceptor -enriched RTCs have been generated. More than 70% of these RTCs have data from biological experiments confirming their tissue-specific expression pattern. The highest-grade retina-enriched pool covered almost all the known genes encoding proteins involved in photo-transduction. Conclusion: This study provides a comprehensive mouse retina transcript profile for further gene discovery in retina and suggests that tissue-specific transcripts contribute substantially to the whole transcriptome. [ABSTRACT FROM AUTHOR]

Background: In clinical practice, the common strategy for immunotherapy of nasopharyngeal carcinoma (NPC) is to infuse cytotoxic T-lymphocyte (CTL) lines several times by intravenous injection, but it is difficult by laboratory research to investigate the relationship between treatment time-point, the amount of CTL added and the therapeutic effect. The objective of this study is to establish a mathematical model to study the therapeutic effect of different treatment time-points and amounts of CTL, and to predict the change in therapeutic effect when the percentage of EBV LMP2-specific CTL is increased from 10% to 20%., Results: The concentration of epidermal growth factor receptor (EGFR) in the tumor cell cytomembranes increases after CTL is added. Concurrently, there is a marked downward trend of the phosphorylated transforming growth factor-α (TGFα)-EGFR complex in the tumor cell cytomembranes, which indicates restriction of tumor growth after CTL immunotherapy. The relationships among the time of addition of CTL, the amount of CTL added, different CTL specificities for LMP2 and the increment rate k of the total number of tumor cells were evaluated., Conclusions: The simulation results quantify the relationships among treatment time-points, amount of CTL added, and the corresponding therapeutic effect of immunotherapy for NPC.