Real-time RT-PCR on SAG1 and BAG1 gene expression during stage conversion in immunosuppressed mice infected with Toxoplasma gondii Tehran strain

Toxoplasmic encephalitis is caused by reactivation of bradyzoites to rapidly dividing tachyzoites of the apicomplexan parasite Toxoplasma gondii in immunocompromised hosts. Diagnosis of this life-threatening disease is problematic, because it is difficult to discriminate between these 2 stages. Toxoplasma PCR assays using gDNA as a template have been unable to discriminate between an increase or decrease in SAG1 and BAG1 expression between the active tachyzoite stage and the latent bradyzoite stage. In the present study, real-time RT-PCR assay was used to detect the expression of bradyzoite (BAG1)- and tachyzoite-specific genes (SAG1) during bradyzoite/tachyzoite stage conversion in mice infected with T. gondii Tehran strain after dexamethasone sodium phosphate (DXM) administration. The conversion reaction was observed in the lungs and brain tissues of experimental mice, indicated by SAG1 expression at day 6 after DXM administration, and continued until day 14. Bradyzoites were also detected in both organs throughout the study; however, it decreased at day 14 significantly. It is suggested that during the reactivation period, bradyzoites not only escape from the cysts and reinvade neighboring cells as tachyzoites, but also converted to new bradyzoites. In summary, the real-time RT-PCR assay provided a reliable, fast, and quantitative way of detecting T. gondii reactivation in an animal model. Thus, this method may be useful for diagnosing stage conversion in clinical specimens of immunocompromised patients (HIV or transplant patients) for early identification of tachyzoite-bradyzoite stage conversion.

Risk-based classification of leukemia by cytogenetic and multiplex molecular methods: results from a multicenter validation study

Modern management of leukemia and selection of optimal treatment approaches entails the analysis of multiple recurrent cytogenetic abnormalities with independent diagnostic or prognostic value. We report the first multicenter validation of a multiplex molecular assay for 12 relevant fusion transcripts relative to cytogenetic methods. Performance was evaluated using a set of 280 adult and pediatric acute or chronic leukemias representative of the variety of presentations and pre-analytical parameters encountered in the clinical setting. The positive, negative and overall agreements were >98.5% with high concordance at each of the four sites. Positive detection of cases with low blast count or at relapse was consistent with a method sensitivity of 1%. There was 98.7% qualitative agreement with independent reference molecular tests. Apparent false negatives corresponded to rare alternative splicing isoforms not included in the panel. We further demonstrate that clinical sensitivity can be increased by adding those rare variants and other relevant transcripts or submicroscopic abnormalities. We conclude that multiplex RT-PCR followed by liquid bead array detection is a rapid and flexible method attuned to the clinical laboratory workflow, complementing standard cytogenetic methods and generating additional information valuable for the accurate diagnosis, prognosis and subsequent molecular monitoring of leukemia.

S1 gene sequence analysis of new variant isolates of avian infectious bronchitis virus in Tunisia

Purpose

Tissue samples were collected from suspected broiler flocks showing respiratory signs to identify infectious bronchitis virus (IBV), characterize emerging field strains, and study their relationships with the Massachusetts H120 strain, the only IB vaccine used in Tunisia.

Samples and methods

Several IBV isolates were identified from field samples collected from flocks located in different regions in the northeast of Tunisia. The IBV isolates were characterized and compared to commonly used vaccine strains (including 793B, D274, and H120 types), other reference IBV strains from Europe, and the recently characterized Tunisian field variants TN20/00, TN200/01, and TN335/01. Reverse transcription-polymerase chain reaction and nucleotide sequencing analyses of the hypervariable regions of the S1 gene were carried out.

Results

Four new IBV variants were isolated during the period 2007-10 and were designated TN295/07, TN296/07, TN556/07, and TN557/07. The amino acid sequence data showed 100% similarity between TN295/07 and TN296/07, suggesting that these two isolates are identical and belong to the same genotype. Similar results were demonstrated for TN556/07 and TN557/07. Sequence identity values indicated that TN296/07 and TN556/07 share 55% amino acid homologies between each other, but are very different from the reference IBV serotypes, in particular the H120 strain. It was also shown that they have 50%-77% similarities with the Tunisian virus isolated between 2000 and 2001. Phylogenetic clustering allowed classification of these Tunisian isolates as new genotypes that are closer to TN200/01, TN335/01 Tunisian field variants, and Italy02 variant than MassH120 vaccine strain.

Conclusion

S1 sequence analyses confirmed the cocirculation of H120 vaccine strain with novel IBV variants isolated from Tunisian field.

Expression of Sox2 and Oct4 and their clinical significance in human non-small-cell lung cancer

Sox2 and Oct4 are transcription factors with the characteristics of regulating self-renewal and differentiation of embryonic stem cell. The aim of this study was to detect the expression of Sox2 and Oct4 and analyze their clinical significance in human non-small-cell lung cancer (NSCLC). Expression of Sox2 and Oct4 were assayed in cancer tissues and their corresponding paracancerous tissues from 44 patients with NSCLC and 21 patients with benign tumors using immunohistochemistry, Western blot, reverse transcription polymerase chain reaction (RT-PCR). The correlation between the expression of Sox2 and Oct4 and tumor type, grade and prognosis and the utility of the two genes in discriminating between benign and malignant tumors were analyzed as well. The results showed that Sox2 and Oct4 positive staining was only seen in the nuclei of cancer cells but not in either the precancerous tissues or benign tumor tissues by immunohistochemistry (p < 0.01). Furthermore, in the lung cancer tissue, the positive rate for Sox2 and Oct4 was 70.5% and 54.5%, respectively. Meanwhile, clinicopathological correlations showed that the Oct4 expression level was significantly associated with poorer differentiation and higher TNM stage of the cancer (p < 0.05). Western blot and RT-PCR analysis showed similar results to immunohistochemistry. Follow-up analysis revealed that expression of Oct4 was significantly associated with poor prognosis of lung cancer. The conclusion is that Sox2 and Oct4 may act as the promising unit markers in directing NSCLC diagnosis and therapy. Also, Oct4 can be regarded as a novel predictor of poor prognosis for NSCLC patients undergoing resection.

Molecular Characterization of Phylogenetically Distinct Isolates of Grapevine fanleaf virus from Iran Based on 2A(HP) Gene

Movement and coat protein genes from Grapevine fanleaf virus (GFLV) isolates have been characterized previously from Iran. In this study, an optimized reverse transcription polymerase chain reaction protocol was established to amplify RNA2 genomic segment corresponding to the hypothetical protein (2A(HP)). The sequence of 2A(HP) was compared with that of previously reported GFLV strains/isolates from other countries which showed 82-86% sequence identities. The 2A(HP) gene from Iran appeared to be standing distinct from other isolates of GFLV when genetic distance- or parsimony-based phylogeneitc analyses were carried out. The present study for the first time reports characterization of Iranian isolate of GFLV based on 2A(HP) gene.

Prevalence and molecular genotyping of group a rotaviruses in Iranian children

Rotavirus is the leading cause of acute gastroenteritis in worldwide young children. Effective vaccines to prevent rotavirus infection are currently available, although their clinical use is still limited, and rotavirus still causes many episodes of infantile gastroenteritis, mainly during the winter season. The aim of this study was to evaluate the prevalence of rotavirus infection in children aged <5-years-old who were hospitalised for gastroenteritis. One hundred and sixty-three stool samples from hospitalised children (<5-years-old) complicated with severe diarrhoea, in two hospitals in Jahrom City, Iran were collected from 2009 to 2010. Antigenic prevalence of rotavirus group A was distinguished by enzyme immunoassay. The antigen of group A rotavirus was diagnosed by EIA in 75 of 163 collected samples. The genotype of EIA-positive samples was determined by nested RT-PCR. The frequency of rotavirus genotypes G1, G2, G3, G4 and G9 was 17.33, 13.34, 2.67, 30.66 and 2.67 %, respectively. Also, the frequency of mixed and non-typable genotypes was detected in 2.67 and 30.66 %, respectively. G1/G8 mixed infection was the first of these rotavirus genotypes to be reported in Iran. Detection of high prevalence of group A rotavirus infection in hospitalised children with diarrhoea, and determination of circulating rotavirus genotypes in this region of Iran, provide useful data for formulating effective vaccines; especially for infants less than 5-years-old.

Seroprevalence and Molecular Characterisation of Human Hepatitis A virus in Serum Samples of Tunisian Patients with Clinical Symptoms of Viral Hepatitis

The aim of the present study was to investigate the seroprevalence of Hepatitis A virus antibodies in patients with clinical symptoms of viral hepatitis and molecular characterization of the detected isolates. The present study deals with the seroprevalence and the genetic diversity of HAV in 400 Tunisian patients presenting in dispensaries (160 patients) and in University Hospitals (240 patients) with hepatitis symptoms between 2006 and 2008. The patients with acute hepatitis were mainly from rural regions. However, the total number of patients was decreased over time. The collected samples were from patients with hepatitis symptoms occurring mainly during January-March (36.7, 26, and 35.5%) and September-December (39.4, 43.4, and 35.5%) during the three years of study, respectively. However, HAV infection was established for only 110 among 400 patients. The detected isolates were clustered within sub-genotype IA. The present study constituted another report of the continued surveillance of HAV infection in the region of Monastir and the molecular characterisation of the detected strains.

A Screening Method for the ALK Fusion Gene in NSCLC

Lung cancer research has recently made significant progress in understanding the molecular pathogenesis of lung cancer and in developing treatments for it. Such achievements are directly utilized in clinical practice. Indeed, the echinoderm microtubule-associated protein-like 4–anaplastic lymphoma kinase (ALK) fusion gene was first described in non-small cell lung cancer in 2007, and a molecularly targeted drug against the fusion was approved in 2011. However, lung cancer with the ALK fusion constitutes only a small fraction of lung cancers; therefore, efficient patient selection is crucial for successful treatment using the ALK inhibitor. Currently, RT-PCR, fluorescent in situ hybridization (FISH), and immunohistochemistry are commonly used to detect the ALK fusion. Although FISH is currently the gold standard technique, there are no perfect methods for detecting these genetic alterations. In this article, we discuss the advantages and disadvantages of each method and the possible criteria for selecting patients who are more likely to have the ALK fusion. If we can successfully screen patients, then ALK inhibitor treatment will be the best example of personalized therapy in terms of selecting patients with an uncommon genotype from a larger group with the same tumor phenotype. In other words, the personalized therapy may offer a new challenge for current clinical oncology.

Gene expression profiles in genetically different mice infected with Toxoplasma gondii: ALDH1A2, BEX2, EGR2, CCL3 and PLAU

Toxoplasma gondii can modulate host cell gene expression; however, determining gene expression levels in intermediate hosts after T. gondii infection is not known much. We selected 5 genes (ALDH1A2, BEX2, CCL3, EGR2 and PLAU) and compared the mRNA expression levels in the spleen, liver, lung and small intestine of genetically different mice infected with T. gondii. ALDH1A2 mRNA expressions of both mouse strains were markedly increased at day 1-4 postinfection (PI) and then decreased, and its expressions in the spleen and lung were significantly higher in C57BL/6 mice than those of BALB/c mice. BEX2 and CCR3 mRNA expressions of both mouse strains were significantly increased from day 7 PI and peaked at day 15-30 PI (P<0.05), especially high in the spleen liver or small intestine of C57BL/6 mice. EGR2 and PLAU mRNA expressions of both mouse strains were significantly increased after infection, especially high in the spleen and liver. However, their expression patterns were varied depending on the tissue and mouse strain. Taken together, T. gondii-susceptible C57BL/6 mice expressed higher levels of these 5 genes than did T. gondii-resistant BALB/c mice, particularly in the spleen and liver. And ALDH1A2 and PLAU expressions were increased acutely, whereas BEX2, CCL3 and EGR2 expressions were increased lately. Thus, these demonstrate that host genetic factors exert a strong impact on the expression of these 5 genes and their expression patterns were varied depending on the gene or tissue.

Expression of adaptor protein containing PH domain, PTB domain and leucine zipper motif 1 in colorectal carcinogenesis

AIM: To investigate the relationship between expression of adaptor protein containing PH domain, PTB domain and leucine zipper motif 1(APPL1) and clinicopathological parameters of colorectal cancer.

METHODS: Expression of APPL1 protein and mRNA in 35 surgical specimens of colorectal carcinoma (CRC) and 27 normal colorectal tissue specimens was detected by immunohistochemistry and reverse transcription-polymerase chain reaction (RT-PCR), respectively.

RESULTS: The expression of APPL1 in CRC was significantly higher than that in normal mucosa. APPL1 expression was correlated with histological differentiation, lymph node metastasis and TNM stage (all P < 0.05), but not with sex, age, or tumor size (all P > 0.05) in patients with CRC.

CONCLUSION: The expression of APPL1 protein is increased in CRC. APPL1 protein expression is closely related with tumor differentiation, lymph node metastasis and TNM stage in patients with colorectal cancer. APPL1 may be a novel therapeutic target for CRC.

Functional expression of potassium channels in cardiomyocytes derived from embryonic stem cells

Royan B(1) stem cell can be differentiated to specialized cell types including cardiomyocytes. This developmental change is accompanied with expression of various K(+) channel types. The aim of this study was to detect functional expression of K(+) currents from stem cell stage and one week and two weeks after differentiation into cardiomyocyte. Mouse stem cell derived cardiomyocytes (ES-cardiomyocytes) were isolated to single cell suspension for K(+) current recording using whole cell patch-clamp technique. The predominant depolarizing current in ES-cardiomyocytes was a tetraethylammonium (TEA) (10 mM) sensitive current which was partially blocked by nifedipine (1 μM) and attenuated by increasing concentration of EGTA (10 mM) in the pipette solution. Pharmacology and electrophysiological properties of this oscillatory sustained current very well matched with characteristics of Ca(2+) activated K(+) current. In addition there was another kind of sustained outward K(+) current which was resistance to TEA but was inhibited by 3,4-diaminopyridine. The characteristic features of this current indicate that this current was due to activation of delayed rectifier K(+) channels. RT-PCR study also confirmed expression of these two types of K(+) channels in ES-cardiomyocytes. Therefore, present study shows functional expression of two types of K(+) ionic current in ES-cardiomyocytes.

Anti-influenza Activity of a Novel Polyoxometalate Derivative (POM-4960)

There are many effective chemotherapeutic agents used in influenza disease which some of them inhibit virus replication by interfering with FluV (influenza virus) viral binding or its penetration into cell membrane. A series of polyoxometalates compounds such as POM-523 and PM-504 have been synthesized and have showed inhibitory effects on viruses. In this study we examined anti influenza activity of a novel polyoxometalate derivative (POM-4960) synthesized in the Faculty of Chemistry of Damghan University of Basic Sciences. To evaluate the anti-influenza activity of POM, following the treatment of FluV with POM at different temperatures and incubation periods, viral titer reduction was assessed by haemaglutination assay (HA). The 3-(4,5- dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay was used to determine TCID50 (tissue culture infective dose) of virus, CC50 (median cytotoxic concentration) of POM, protection percentage and antiviral activity of POM in cell culture. RT-PCR and direct Immunofluorescent assays were performed to evaluate the effect of POM on viral infection and viral RNA load, respectively. POM reduced HA titer near to zero in all cell culture specimens and showed high protection against viral infection of the cells. Reduction in viral infection was confirmed by RT-PCR and Immunofluorescent staining methods. Moreover, this POM derivative has a dual (cumulative) effect on attachment and penetration inhibition compared to other POM's with just one inhibitory effect. POM-4960 could be considered as a powerful anti-influenza agent with low toxicity and high antiviral potency.

Biological and Molecular Characterization of Two Distinct Tomato Strains of Cucumber mosaic virus Based on Complete RNA-3 Genome and Subgroup Specific Diagnosis

Cucumber mosaic virus (CMV) is one of the most important viral pathogen infecting several plant species in India. Five isolates of CMV obtained from cucumber, muskmelon, tobacco and tomato from distinct geographical locations in India were analysed based on host-reactions and genome sequence. The majority of the isolates were very similar and only two isolates, Tfr-In and Tss-In showed distinct symptoms in tomato and high sequence diversity (77.8%) in coat protein (CP) gene. Tfr-In was isolated from tomato fruit showing grey patches in Aurangabad and Tss-In from tomato plant showing shoe-string symptoms in New Delhi. The RNA-3 genomes of Tfr-In (2,214 nt; JF279606), shared only 70.3% nucleotide sequence identity with Tss-In (2,178 nt; JF279605. The complete RNA-3 genome of Tss-In and Tfr-In were compared with that of 65 CMV isolates reported from various plants of the world, which formed four distinct subclades-IA, -IB, -IC and -II. The Tfr-In isolate clustered with the CMV subgroup-IB and Tss-In with the subgroup-II. The comparison of the RNA-3 sequence of both the isolates revealed maximum heterogeneity in the intergenic region (IR). Reverse transcriptase polymerase chain reaction (RT-PCR) based detection of CMV subgroup-I and -II was developed designing primers from flanking IR region. The specificity of the RT-PCR detection was confirmed using Tfr-In and Tss-In representing subgroup-I and -II and validated with field samples of tomato, cucurbits and chilli. This is the first report of complete RNA-3 of subgroup-IB CMV causing grey patches in tomato fruit and subgroup-II CMV causing shoe-string symptoms in tomato in India. The present and previous studies together showed that tomato in India was affected by multiple strains of CMV.

The influence of tumour necrosis factor- α (TNF-α) on amyloid-β (Aβ)-degrading enzymes in vitro

Pro-inflammatory cytokines, such as tumour necrosis factor-α (TNF-α), are increased in serum and CSF in Alzheimer's disease (AD). We investigated the effect of TNF-α on gene and protein expression levels of Aβ degrading enzymes (ACE, ECE-1, ECE- 2, IDE and NEP) in vitro. Differentiated (DC) and non-differentiated (NDC) neuroblastoma cells (SH-SY5Y) were exposed to TNF-α for 15 minutes and 3 hours and protein and gene expression levels measured using western blotting or sandwich ELISA (ECE-2), and real time-PCR (RT-PCR). Only ECE-2 protein levels decreased significantly in NDCs in a dose-dependent manner after 15 minutes of TNF-α exposure but reverted to basal levels after 3 hours. Basal NEP gene expression levels were higher in control DCs compared to NDCs but TNF-α treatment did not significantly alter the levels of expression of any of the Aβ degrading enzymes. In conclusion, apart from a transient reduction in ECE-2 protein levels, TNF-α had no impact in our in vitro experimental system on transcription or translation of any of our selected mediators of Aβ degradation.

The role of Nrf2 in migration and invasion of human glioma cell U251

OBJECTIVE

NF-E2-related factor 2 (Nrf2) is a transcription factor that is related to tumor cell multidrug resistance and proliferation. Here we studied the involvement of Nrf2 in the migration and invasion of human U251 glioma cells.

METHODS

Two kinds of plasmid, that is, pEGFP-Nrf2 and Si-Nrf2, were constructed and transfected to upregulate or downregulate the expression of Nrf2 in U251 glioma cell line. Blank vectors or random siRNA plasmid were used as negative control. Cells treated with lipofectamine only were set up as blank control. Protein and mRNA level of Nrf2 and matrix metalloproteinase 9 (MMP9) were investigated by reverse transcriptase-polymerase chain reaction and western blot after transfection. Wound healing assay and transwell assay were used to study migration and invasion of U251 after transfection. Gelatin zymography was performed to reveal the change of MMP9 activity after transfection.

RESULTS

The mRNA and protein level of Nrf2 was upregulated in U251-pEGFP-Nrf2 while downregulated in U251-Si-Nrf2 48 hours after transfection. In the wound healing assay, there were more cells in group pEGFP-Nrf2 crossing the scratch line than in group Si-Nrf2. Furthermore, in transwell migration and invasion assay, there were more cells in group pEGFP-Nrf2 penetrating the membranes than in group Si-Nrf2. Then we investigated the change of MMP9 activity, mRNA, and protein levels after transfection. The results suggested that upregulation of Nrf2 led to an increase in MMP9 expression and activity whereas downregulation of Nrf2 led to a decrease in MMP9 expression and activity.

CONCLUSION

Nrf2 is involved in migration and invasion of U251 cells, which may be related to MMP9.

Co-expression of metalloproteinases 11 and 12 in cervical scrapes cells from cervical precursor lesions

The metalloproteinases (MMP) 11 and 12 have been shown to be expressed in cervical cancer (CC). In order to extend our previous results, these MMPs were evaluated in cervical precursor lesions. One hundred seventeen cervical scrapes: thirty-six normal, thirty-six low grade squamous lesions (LSIL), thirty-six high grade (HSIL), nine CC; and, also ninety-nine paraffin-embedded cervical lesions: fifteen normal cervices, thirty eight LSIL, sixteen HSIL, and five CC were collected. The samples were analyzed for relative expression by real time RT-PCR or immunohistochemistry assay. We were able to identify a relative increased expression of MMP11 in 75% and 78% from LSIL and HSIL samples, respectively. While MMP12 expression was 64% and 75% in LSIL and HSIL, respectively. Positive samples for MMP11 expression were also positive for MMP12 expression and also increased according to illness progression. In the tissues, MMP11 or MMP12 expression was observed in the cytoplasm of the neoplastic cells, while in the normal epithelium was absent. The reaction was always stronger for MMP12 than MMP11. MMP11 expression was present in 77% and 66% of LSIL and HSIL, while MMP12 expression was 73% and 68%. There was a relationship between MMP11 or MMP12 expression and HPV infection. Our data are showing a relationship between diagnostic of precursor lesions and the MMP11 and 12 expressions, suggesting that their expression could be an early event in the neoplastic lesions of the cervix and could have clinical significance.

Differential Expression of Large-Conductance Ca-Activated K Channels in the Carotid Body between DBA/2J and A/J Strains of Mice

The carotid body (CB) is a primary chemosensory organ for arterial hypoxia. Inhibition of K channels in chemosensory glomus cells (GCs) are considered to be responsible for hypoxic chemoreception and/or chemotransduction of the CB. Hypoxic sensitivity of large-conductance calcium-activated K (BK) channels has been established in the rat CB. Our previous work has shown the BK channel β2 subunits are more expressed in the CB of the DBA/2J mouse than that of the A/J mouse. Because the DBA/2J mouse is more sensitive to hypoxia than the A/J mouse, our general hypothesis is that BK channels play a role in the sensitivity of the mouse CB to mild hypoxia. We performed vigorous analysis of the gene expression of α, β2, and β4 subunits of BK channels in the CB. We found that α and β2 subunits were expressed more in the CB of the DBA/2J mice than that of the A/J mice. No differences were found in the β4 subunit expression. These differences were not seen in the neighboring tissues, the superior cervical ganglion and the carotid artery, suggesting that the differences are CB specific. Further, the sensitivity of BK channels in GCs to mild hypoxia was examined in patch clamp experiments using undissociated CBs. Iberiotoxin significantly inhibited K current of GCs in the DBA/2J mice, but not in the A/J mice. When reducing PO₂ to ∼70 mmHg, K current reversibly decreased in GCs of the DBA/2J, but not of the A/J mice. In the presence of iberiotoxin, mild hypoxia did not inhibit K current in either strains. Thus, the data suggest that BK channels in GCs of the DBA/2J mice are sensitive to mild hypoxia. Differential expression of BK channel β subunits in the CBs may, at least in part, explain the different hypoxic sensitivity in these mouse strains.

Clinicopathological significance of Rb and E2F1 expression in esophageal squamous cell carcinoma

AIM: To investigate the expression of Rb and E2F1 in esophageal squamous cell carcinoma (ESCC) and to analyze their clinicopathological significance.

METHODS: Forty-eight ESCC specimens were taken from Xinjiang Kazaks patients and used in the study. Matched normal esophageal mucosal tissues were used as controls. The expression of Rb and E2F1 was detected by RT-PCR. The correlation of Rb and E2F1 expression with the development and progression of ESCC was then analyzed.

RESULTS: The positive rate of Rb expression was higher in ESCC than in normal esophageal mucosal tissue (64.6% vs 43.8%, P < 0.05). E2F1 expression in ESCC showed no significant difference with that in normal esophageal mucosal tissue (70.8% vs 75%, P > 0.05). Rb and E2F1 expression showed no significant correlation with tumor differentiation and stage (both P > 0.05). Rb expression was positively correlated with that of E2F1 in ESCC (r = 0.867, P < 0.05).

CONCLUSION: High expression of Rb may be involved in the development and progression of ESCC.

Starch accumulation, activities of key enzyme and gene expression in starch synthesis of wheat endosperm with different starch contents

In order to investigate starch accumulation, and the enzymes activity changes and the expression levels of genes and their relationships among them at different developmental stages of wheat grain. We choose Annong9912 and E28 were used in the study. During starch accumulating rate and grain filling rate, and there were obvious genotype difference between Annong9912 and E28. Whether low or high starch content of starch content, the accumulation courses of amylopectin, amylose and total starch were well fitted to the logistic equation by relating starch contents against DAP. The simulation parameters revealed that the higher contents of amylopectin and amylose resulted from earlier initiating accumulation time and greater accumulation rate. And amylose, amylopectin and total starch accumulation rate of two wheat cultures were significantly and positively correlated with activities of SBE, SSS and GBSS, but amylose accumulation rate of E28 had no correlation with the activities of SBE. In addition, there were significant correlations among activities of SBE, SSS and GBSS in two wheat cultivars. We speculated that these enzymes proteins may have a coordinating action in starch biosynthesis within the amyloplast, operating as functional multiprotein complexes. And expression levels of enzyme genes demonstrated a single-peak curve, and 12-18 DAP reached their peaks and then began to drop, and all had high expression level in earlier stage of endosperm development, but in E28 were higher than in Annong9912. The GBSS-I transcripts on average were expressed over 60 times more than GBSS-II transcript in E28. SBE, SSS, DBE may control starch synthesis at the transcriptional level, and GBSS-I may control starch synthesis at the post transcriptional level. The expression level of DBE on average was lower than SS-1 and SBE-IIa genes, and similar to SS-III and SBE-IIb genes, but higher than GBSS-I and GBSS-II genes.

Use of genomic data in risk assessment case study: II. Evaluation of the dibutyl phthalate toxicogenomic data set

An evaluation of the toxicogenomic data set for dibutyl phthalate (DBP) and male reproductive developmental effects was performed as part of a larger case study to test an approach for incorporating genomic data in risk assessment. The DBP toxicogenomic data set is composed of nine in vivo studies from the published literature that exposed rats to DBP during gestation and evaluated gene expression changes in testes or Wolffian ducts of male fetuses. The exercise focused on qualitative evaluation, based on a lack of available dose-response data, of the DBP toxicogenomic data set to postulate modes and mechanisms of action for the male reproductive developmental outcomes, which occur in the lower dose range. A weight-of-evidence evaluation was performed on the eight DBP toxicogenomic studies of the rat testis at the gene and pathway levels. The results showed relatively strong evidence of DBP-induced downregulation of genes in the steroidogenesis pathway and lipid/sterol/cholesterol transport pathway as well as effects on immediate early gene/growth/differentiation, transcription, peroxisome proliferator-activated receptor signaling and apoptosis pathways in the testis. Since two established modes of action (MOAs), reduced fetal testicular testosterone production and Insl3 gene expression, explain some but not all of the testis effects observed in rats after in utero DBP exposure, other MOAs are likely to be operative. A reanalysis of one DBP microarray study identified additional pathways within cell signaling, metabolism, hormone, disease, and cell adhesion biological processes. These putative new pathways may be associated with DBP effects on the testes that are currently unexplained. This case study on DBP identified data gaps and research needs for the use of toxicogenomic data in risk assessment. Furthermore, this study demonstrated an approach for evaluating toxicogenomic data in human health risk assessment that could be applied to future chemicals.

[Apport de l'immunocapture-Elisa au diagnostic de l'infection à virus grippal A(H1N1)pdm09 : une alternative à la RT-PCR ?]

AIM OF THE STUDY

To evaluate immunocapture-Elisa (ICE) sensitivity versus RT-PCR in diagnosis of influenza A(H1N1)pdm09 virus infection.

METHODS

Sixty-seven RT-PCR-negative and 282 RT-PCR-positive nasopharyngeal swabs collected during winter 2009-2010 have been analyzed using ICE.

RESULTS

Among all the samples tested, a sensitivity of 31.3% was found for ICE. The sensitivity of ICE was directly correlated to the virus load determined through the number of cycling reactions necessary to reach detection by RT-PCR.

CONCLUSION

ICE can be a suitable method compared to RT-PCR when RT-PCR cannot be used for economical or epidemiological reasons. Its sensitivity is largely dependent of the nasopharyngeal sampling quality.

A comparative analysis of routine techniques: Reverse transcriptase polymerase chain reaction (RT-PCR) and five cell lines for detection of enteroviruses in stool specimens

BACKGROUND AND OBJECTIVES

Each year, Enteroviruses infect millions of people and cause different diseases. The agents are usually detected using cell culture. RD (Rhabdomyosarcoma) and L20B (L cells) are among the recommended cells by the World Health Organisation (WHO) for this purpose. Even though cell culture is the most common method used in diagnosing Enteroviruses in stool specimens, this particular method poses some problems, which include false positive or negative results, lack of a unique cell line for diagnosing all Enterovirus types in addition to being time consuming. For these reasons, an attempt was made to find better techniques of Enterovirus detection. RT-PCR (Reverse Transcriptase Polymerase Chain Reaction) is a technique used in place of the cell culture method. In this study, the cell culture method was compared with RT-PCR for detection of Enteroviruses in stool specimens.

MATERIAL AND METHOD

First, the chloroform treated stool samples were inoculated onto five cell lines, including RD, L20B, Hep-2 (Human Epidermoid carcinoma cell line), Vero (Verde Reno) and GMK (Green Monkey Kidney). The results were then compared with data from Enterovirus detection using the RT-PCR technique.

RESULTS AND CONCLUSION

The difference between RT-PCR and cell culture results was significant. Enteroviruses were detected in 24% of specimens using RT-PCR while cell lines could isolate Enteroviruses in just 14.4% of the samples.

Diversity of Apple mosaic virus Isolates in India Based on Coat Protein and Movement Protein Genes

Apple mosaic virus (ApMV), an Ilarvirus is one of the most common pathogens of apple worldwide. During field surveys in commercial plantations of Himachal Pradesh and Jammu & Kashmir, observations of bright chlorotic mosaic like symptoms on apple trees indicated probable infection by the virus, which was later detected by double antibody sandwich-enzyme linked immunosorbent assay (DAS-ELISA). An incidence of 24 and 28% (based on ELISA) was obtained as 6/25 and 15/53 samples from HP and J&K were positive, respectively. An amplification of approximately 700 and 850 bp was obtained for coat and movement protein genes (CP and MP), respectively. The CP was 223 amino acids in length and showed 87-99% identity when compared to 21 ApMV isolates. Whereas, MP (286 amino acids) showed 91-95% identity with other isolates. However, the gene sequences were quite conserved among Indian isolates and grouped together phylogenetically. CP of the Indian isolates showed maximum identity of 95% with Korean isolate (AY 125977) in apple and in other host these showed a maximum identity of 98% to Czech Republic pear isolate. MP showed maximum identity with Chinese isolate i.e., 95%. The diversity study will also help in analyzing variability among the isolates and also to formulate diagnostic and resistance strategies.

Biomarkers of transplantation tolerance: more hopeful than helpful?

A major limitation to the translation of tolerogenic therapies to clinical transplantation is a lack of biomarkers that can be used as surrogate measures for predicting the successful induction of immune tolerance which would allow for the safe withdrawal of immunosuppression. We have used three different mouse models of donor specific tolerance to skin grafts together with quantitative RT-PCR to search for potential biomarkers of tolerance using criteria based on the presence or activity of regulatory T cells and antigen presenting cells (APCs) within grafts or lymphoid organs. We find that significant differences in gene expression between tolerated and rejecting grafts are observed primarily within the grafted skin and not systemically or in the draining lymph node. The pattern of gene expression within long-term surviving tolerated grafts appear very similar to syngeneic grafts, with both having low levels of T cell and APC infiltration and a bias toward relative over-expression of “regulatory-associated” genes, while allografts destined for rejection show an overall increase in both “regulatory” and “effector” cell associated transcripts. We also, however, find an increase in a large number of regulatory genes, of both innate and T cell origin, even after grafting syngeneic skin. Taken together, these findings suggest that there may be no tissue biomarkers uniquely able to predict donor antigen specific tolerance per se, but that patterns of gene expression within tolerated grafts may be similar to those found in self tissues recovering from an inflammatory insult.

Anoxia- and hypoxia-induced expression of LDH-A* in the Amazon Oscar, Astronotus crassipinis

Adaptation or acclimation to hypoxia occurs via the modulation of physiologically relevant genes, such as erythropoietin, transferrin, vascular endothelial growth factor, phosphofructokinase and lactate dehydrogenase A. In the present study, we have cloned, sequenced and examined the modulation of the LDH-A gene after an Amazonian fish species, Astronotus crassipinis (the Oscar), was exposed to hypoxia and anoxia. In earlier studies, we have discovered that adults of this species are extremely tolerant to hypoxia and anoxia, while the juveniles are less tolerant. Exposure of juveniles to acute hypoxia and anoxia resulted in increased LDH-A gene expression in skeletal and cardiac muscles. When exposed to graded hypoxia juveniles show decreased LDH-A expression. In adults, the levels of LDH-A mRNA did not increase in hypoxic or anoxic conditions. Our results demonstrate that, when given time for acclimation, fish at different life-stages are able to respond differently to survive hypoxic episodes.

Survey and RT-PCR Based Detection of Cardamom mosaic virus Affecting Small Cardamom in India

Mosaic or marble or katte disease caused by Cardamom mosaic virus (CdMV) is an important production constraint in all cardamom growing regions of the world. In the present study, 84 cardamom plantations in 44 locations of Karnataka and Kerala were surveyed. The incidence of the disease ranged from 0 to 85%. The incidence was highest in Madikeri (Karnataka) while no incidence was recorded in Peermade (Kerala). In general, incidence and severity of the disease was higher in cardamom plantations of Karnataka. A procedure for total RNA isolation from cardamom and detection of CdMV through reverse transcription-polymerase chain reaction (RT-PCR) using primers targeting the conserved region of coat protein was standardized and subsequently validated by testing more than 50 field cardamom samples originating from Karnataka and Kerala states. The method can be used for indexing the planting material and identifying resistant lines/cultivars before either they are further multiplied in large scale or incorporated in breeding.

Detection of Rotavirus Infection in Bovine Calves by RNA-PAGE and RT-PCR

A total of 128 diarrhoeic faecal samples were collected from cattle and buffalo calves from Pantnagar and Dehradun during winter months. Of the 110 cattle calves screened by RNA-PAGE, rotavirus was detected in 13 samples (11.81%) while no sample from buffalo calves was found positive. All samples were found to have long electropherotype and two distinct electropherotypes having segment variation were observed. The overall prevalence of rotavirus was 10.15% (13/128). RT-PCR targeting group specific VP6 gene confirmed Group A rotavirus in 10 out of 13 samples, while three samples remained un-groupable.

Significance of expression of vascular endothelial growth factor B and its splice isoforms in different types of liver lesions

AIM: To detect the mRNA expression of vascular endothelial cell growth factor B (VEGF-B) and its splice isoforms VEGF-B167 and VEGF-B186 in different types of liver lesions and to assess their clinical significance.

METHODS: The mRNA expression of VEGF-B, VEGF-B167 and VEGF-B186 in liver cancer, cancer-adjacent tissue, liver cirrhosis, chronic hepatitis B, and normal liver tissue was detected by quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR). The correlation of VEGF-B, VEGF-B167, and VEGF-B186 expression with the clinical pathological data of patients was analyzed, and survival analysis was performed using follow-up data.

RESULTS: There were no statistical differences in the expression levels of total VEGF-B and VEGF-B186 among each group, while the expression level of VEGF-B167 mRNA was significantly different among each group, highest in the normal group but lowest in liver cirrhosis group (252.59 vs 168.00, P = 0.005). The expression level of VEGF-B167 mRNA was significantly higher in the liver cancer group than in the chronic hepatitis B group (234.13 vs 170.72, 168.00, both P < 0.05). The overall survival rate and tumor-free survival rate of patients with low VEGF-B167 expression tended to be higher than those of patients with high VEGF-B167 expression (P = 0.097, 0.023). The expression levels of total VEGF-B, VEGF-B167 and VEGF-B186 had no significant correlation with sex, age, virus infection, liver cirrhosis, Child-Pugh score, AFP score, tumor number or size, vascular invasion, TNM stage, or tumor differentiation.

CONCLUSION: VEGF-B is involved in hepatocarcinogenesis and VEGF-B167 plays a more important role than VEGF-B186 in this process. Patients with low VEGF-B167 expression have good prognosis since their postoperative overall survival rate and tumor-free survival rate are higher than those with high VEGF-B167 expression.

Comparative expression profile of orphan receptor tyrosine kinase ROR1 in Iranian patients with lymphoid and myeloid leukemias

It has recently been shown that ROR1, a member of the receptor tyrosine kinase family, is overexpressed in leukemic B cells of Chronic Lymphocytic Leukemia (CLL) and a subset of Acute Lymphoblastic Leukemia (ALL). In this comparative study the expression profile of ROR1 mRNA was investigated in Iranian patients with CLL and Acute Myelogenous Leukemia (AML) and the results were compared with those previously reported in our Iranian ALL patients. RT-PCR was performed on bone marrow and/or peripheral blood samples of 84 CLL and 12 AML patients. CLL samples were classified into immunoglobulin heavy chain variable region (IGHV) gene mutated (n = 55) and unmutated (n = 29) and also indolent (n = 42) and progressive (n = 39) subtypes. ROR1 expression was identified in 94% of our CLL patients, but none of the AML patients expressed ROR1. No significant differences were observed between different CLL subtypes for ROR1 expression. Taken together the present data and our previous results on ROR1 expression in ALL, our findings propose ROR1 as a tumor-associated antigen overexpressed in a large proportion of lymphoid (CLL and ALL), but not myeloid (AML) leukemias. Expression of ROR1 seems to be associated to lineage and differentiation stages of leukemic cells with a potential implication for immunotherapy.

In silicio expression analysis of PKS genes isolated from Cannabis sativa L

Cannabinoids, flavonoids, and stilbenoids have been identified in the annual dioecious plant Cannabis sativa L. Of these, the cannabinoids are the best known group of this plant's natural products. Polyketide synthases (PKSs) are responsible for the biosynthesis of diverse secondary metabolites, including flavonoids and stilbenoids. Biosynthetically, the cannabinoids are polyketide substituted with terpenoid moiety. Using an RT-PCR homology search, PKS cDNAs were isolated from cannabis plants. The deduced amino acid sequences showed 51%-73% identity to other CHS/STS type sequences of the PKS family. Further, phylogenetic analysis revealed that these PKS cDNAs grouped with other non-chalcone-producing PKSs. Homology modeling analysis of these cannabis PKSs predicts a 3D overall fold, similar to alfalfa CHS2, with small steric differences on the residues that shape the active site of the cannabis PKSs.

Molecular Characterization of Classical swine fever virus Involved in the Outbreak in Mizoram

Classical swine fever is the most insidious and devastating disease of pigs and wild boars. The virus is closely related to the other members of the genus Pestivirus. The outbreak recorded in Mizoram, India was strategically important as the state shares porous international boundary with East Asian countries. Both immunodiagnostic and molecular techniques were used to confirm the involvement of Classical swine fever virus (CSFV) in this outbreak. Sandwich ELISA and direct FAT could detect CSFV in the tissue samples. RT-nPCR specifically amplified E2 and 5'NTR product of 271 bp. Phylogenetic analysis showed, that the Mizoram isolate (MZ4/69) was very close to the Chinese strain Shimen-HVRI (93.0%) rather than other Indian isolate (CSF-30-03). Present study provides a valuable sequence based molecular data on Indian isolate of CSFV and will be useful in investigation on transmission of such disease from neighbour countries.

Use of genomic data in risk assessment case study: I. Evaluation of the dibutyl phthalate male reproductive development toxicity data set

A case study was conducted, using dibutyl phthalate (DBP), to explore an approach to using toxicogenomic data in risk assessment. The toxicity and toxicogenomic data sets relative to DBP-related male reproductive developmental outcomes were considered conjointly to derive information about mode and mechanism of action. In this manuscript, we describe the case study evaluation of the toxicological database for DBP, focusing on identifying the full spectrum of male reproductive developmental effects. The data were assessed to 1) evaluate low dose and low incidence findings and 2) identify male reproductive toxicity endpoints without well-established modes of action (MOAs). These efforts led to the characterization of data gaps and research needs for the toxicity and toxicogenomic studies in a risk assessment context. Further, the identification of endpoints with unexplained MOAs in the toxicity data set was useful in the subsequent evaluation of the mechanistic information that the toxicogenomic data set evaluation could provide. The extensive analysis of the toxicology data set within the MOA context provided a resource of information for DBP in attempts to hypothesize MOAs (for endpoints without a well-established MOA) and to phenotypically anchor toxicogenomic and other mechanistic data both to toxicity endpoints and to available toxicogenomic data. This case study serves as an example of the steps that can be taken to develop a toxicological data source for a risk assessment, both in general and especially for risk assessments that include toxicogenomic data.

Reemergence of Chikungunya virus in Indian Subcontinent

Chikungunya virus (CHIKV), a reemerging arboviral disease of public health concern is characterized by a triad of fever, rash and arthralgia. It was responsible for a number of epidemics in Asia and Africa. The severity of the current epidemic can be judged by the fact that an estimated 1.38 million people in India and one-third of the La Reunion population (by April 2006) were affected by CHIKV. Aedes aegypti and Aedes albopictus are the major mosquitoes transmitting CHIKV in Asia. Various neurological complications and CHIKV associated deaths were encountered during the current outbreak (2005-2010). The aggressive nature of the recent CHIKV epidemic was attributed to the mutations in the viral genome in addition to their adaptation and spread to vectors like Aedes albopictus. Proper diet, adequate rest and symptomatic treatment using non-salicylate analgesics and Non-steroidal anti inflammatory drugs (NSAIDS) helped the patients in recovering from CHIKV infections. In the absence of an effective vaccine, rapid implementation of mosquito control measures and establishment of a system for continuous surveillance of the disease seems to be the only possible solution to prevent any such outbreak in the near future.

Significance of HDGF expression in hepatocellular carcinoma tissue and HepG2 cells

AIM: To investigate the expression of hepatoma-derived growth factor (HDGF) in hepatocellular carcinoma (HCC) tissue and HepG2 cells and to analyze its significance.

METHODS: Ten HCC tissue samples and matched noncancerous tissue samples were collected. The mRNA expression of HDGF in these HCC samples, noncancerous tissue samples and HepG2 cells was detected by real-time RT-PCR. The protein expression of HDGF in 137 HCC tissue samples and 49 normal liver tissue samples was examined by immunohistochemistry. The relationship between HDGF expression and clinicopathological parameters in HCC was then analyzed.

RESULTS: The expression levels of HDGF mRNA were 21.11 and 11.39 times higher in HCC tissue and HepG2 cells than in noncancerous tissue, respectively. The positive rate of HDGF expression in HCC tissue was significantly higher than that in normal liver tissue (77.4% vs 51.5%, P = 0.011). High expression of HDGF protein was positively correlated with T classification, N classification and clinical stage (all P < 0.05) in HCC patients. Univariate Cox analysis showed that HDGF expression, N classification and clinical stage had significant correlation with survival prognosis of HCC patients (P = 0.028, 0.041 and 0.000; HR = 1.557, 1.526 and 2.316, respectively). Multivariate analysis showed that HDGF expression might be an independent prognostic indicator (P = 0.000, HR = 0.358) for the development and progression of HCC. Patients with higher HDGF expression showed a significantly shorter overall survival time than those with low HDGF expression.

CONCLUSION: HDGF is highly expressed in HCC tissue and HepG2 cells. High HDGF expression is an independent prognostic factor in HCC patients. High HDGF expression is associated with poor overall survival in patients with HCC.

Fluidized-bed bioartificial liver assist devices (BLADs) based on microencapsulated primary porcine hepatocytes have risk of porcine endogenous retroviruses transmission

PURPOSE

Bioartificial liver assist devices (BLADs) are expected to bridge liver failure patients to liver transplantation, but porcine endogenous retroviruses (PERVs) still pose a potential risk in pig-to-human xenotransplantation and thereby limit the use of bioartificial liver therapy. In our lab, fluidized-bed BLADs based on microencapsulated primary porcine hepatocytes have been successfully used to treat liver failure pigs. We detected the risk of PERVs transmission of microencapsulated primary porcine hepatocytes-the key component of fluidized-bed BLADs, to evaluate the biosafety of this device for further clinical applications.

METHODS

Microencapsulated primary porcine hepatocytes (cell diameter = 300 μm) were cultured in Dulbecco's modified Eagles medium (DMEM). Microencapsulated cell culture supernatants were collected at 6, 12, 24 and 72 h. HEK-293 were cocultured with these supernatants, and the cocultured cells were harvested every 7 days. RT-PCR was used to detect PERVs transmission. RT-qPCR was used to get the number of virus copies. PK-15 was used as the positive control whereas HepG2 was used as the negative control.

RESULTS

PERV was detected in all supernatants, and the viral load of the supernatants increased with time. Moreover, cocultured 293 cells were positive for PERV-specific sequences.

CONCLUSION

The kind of fluidized-bed BLADs based on microencapsulated primary porcine hepatocytes have risk of PERVs transmission. Further extensive pre-clinical study focused on biosafety is warranted.

Frequencies of BCR-ABL1 fusion transcripts among Sudanese chronic myeloid leukaemia patients

The incidence of one or other rearrangement in chronic myeloid leukemia (CML) patients varies in different reported series. In this study we report the frequencies of BCR-ABL1 fusion transcript variants studied in 43 CML patients from Sudan. The study includes 46 Sudanese patients, three of which negative for the BCR-ABL1 fusion transcript. More than half of 43 positive patients showed b2a2 fusion transcript (53.5%), while (41.9%) showed b3a2 transcript and the remaining (4.6%) coexpression of b3a2/ b2a2 and b3a2/b2a2/e19a2. We detected neither coexpression of p210/p190 nor e1a2 alone. Male patients showed a tendency to express b2a2, while female tende to express b3a2 (p = 0.017). Moreover, a single nucleotide polymorphism was detected in BCR exon 13 in one out of four patients and this patient showed only b2a2 expression. In conclusion, we observed a significant correlation between sex and type of BCR-ABL1 transcript, an observation that deserves further investigation.

Effects of simulated weightlessness on liver Hsp70 and Hsp70mRNA expression in rats

Space flight is known to induce a number of hepatic physiological alterations. In this study, we investigated Hsp70 expressing features of rat liver under simulated weightlessness. Tail-suspension was used to simulate the weightlessness animal model. Forty-eight male Wistar rats were randomly assigned to 6 experimental groups and Hsp70 protein and mRNA expressions in the liver were detected by Western blot and RT-PCR respectively. The tail-suspension significantly increased Hsp70mRNA expression levels in rat liver (P<0.05). The semi-quantitative PCR showed that Hsp70mRNA was upregulated as early as 6 hours of suspension. Western blot analysis indicated that Hsp70 protein was significantly upregulated in the early stage of suspension as compared with controls (P<0.05). The results suggest that simulated weightlessness acts as a kind of stress to elevate liver Hsp70 expression both at protein and mRNA levels. This may be meaningful in astronaut's trainings by preadaptation to non-damaging stress exposures or other environmental factors to foster the astronaut's ability of weightless tolerance.

Molecular analysis of MEN1 expression in MCF7, T47D and MDA-MB 468 breast cancer cell lines treated with adriamycin using RT-PCR and immunocytochemistry

BACKGROUND AND THE PURPOSE OF THE STUDY

MEN1 is an important tumor suppressor gene that encodes a nuclear protein called menin. Recent data suggest that interactions between menin and other proteins have important roles in control of the cell cycle and apoptosis. In addition, estrogen receptor (ER), an important prognostic factor is differentially expressed in breast cancer cells. In this study the MEN1 gene and protein expression in MCF7, T47D and MDA-MB-468 breast cancer cell lines with different ER status following exposure to adriamycin (ADR) was investigated.

MATERIALS AND METHODS

Cytotoxicity of ADR on these cell lines was determined using MTT assay. The mRNA and protein levels were analyzed in tested cell lines using RT-PCR and immunocytochemistry (ICC) assays, respectively.

RESULTS

ADR cytotoxicity was highest on MDA-MB-468 and lowest on MCF7 cells. MEN1 mRNA showed significant decrease after ADR exposure only in the MDA-MB-468 cell line. Menin protein expression was higher in MDA-MB-468 and lower in MCF7 cells.

CONCLUSION

Differential molecular responses to adriamycin were observed in cancer cell lines. Molecular data also suggest that MEN1 as a new biomarker can be used in combination with current biomarkers for prediction of response to chemotherapy.

Upregulation of the ERG11 gene in Candida krusei by azoles

BACKGROUND AND THE PURPOSE OF THE STUDY

Candida species are the agents of local and systemic opportunistic infections and have become a major cause of morbidity and mortality in the last few decades. Azole resistance in Candida krusei (C. krusei) species appears to be the result of gene alterations in relation to the ergosterol biosynthesis pathway, as well as efflux pumps. The main objective of this study was to examine the RNA expression of ERG11 in C. krusei which had been identified to be resistance to azoles.

METHODS

The ERG11 mRNA expression was investigated in four Iranian clinical isolates of C. krusei, which were resistant to fluconazole and itraconazole by a semiquantitative RT-PCR.

RESULTS

The mRNA expression levels were observed in all four isolates by this technique. Furthermore, it was found that ERG11 expression levels vary among four representative isolates of C. krusei. Although DNA sequencing revealed no significant genetic alteration in the ERG11 gene, one heterozygous polymorphism was observed in two isolates, but not in others. This polymorphism was found in the third base of codon 313 for Thr (ACT>ACC).

MAJOR CONCLUSION

Even though such a polymorphism creates a new Ear1 restriction site, no significant effect was found on the resistance of C. krusei to azoles. RESULTS of this investigation are consistent with previous studies and may provide further evidence for the genetic heterogeneity and complexity of the ergosterol biosynthetic pathway or efflux pumps.

Type II and III Taste Bud Cells Preferentially Expressed Kainate Glutamate Receptors in Rats

Glutamate-induced cobalt uptake reveals that non-NMDA glutamate receptors (GluRs) are present in rat taste bud cells. Previous studies involving glutamate induced cobalt staining suggest this uptake mainly occurs via kainate type GluRs. It is not known which of the 4 types of taste bud cells express subunits of kainate GluR. Circumvallate and foliate papillae of Sprague-Dawley rats (45~60 days old) were used to search for the mRNAs of subunits of non-NMDA GluRs using RT-PCR with specific primers for GluR1-7, KA1 and KA2. We also performed RT-PCR for GluR5, KA1, PLCbeta2, and NCAM/SNAP 25 in isolated single cells from taste buds. Taste epithelium, including circumvallate or foliate papilla, express mRNAs of GluR5 and KA1. However, non-taste tongue epithelium expresses no subunits of non-NMDA GluRs. Isolated single cell RT-PCR reveals that the mRNAs of GluR5 and KA1 are preferentially expressed in Type II and Type III cells over Type I cells.

Identification and detection of a novel human endogenous retrovirus-related gene, and structural characterization of its related elements

Up-regulation of human endogenous retroviruses (HERVs) is associated with many diseases, including cancer. In this study, an H family HERV (HERV-H)-related gene was identified and characterized. Its spliced transcript lacks protein-coding capacity and may belong to the emerging class of noncoding RNAs (ncRNAs). The 1.3-kb RNA consisting of four exons is transcribed from an Alu element upstream of a 5.0-kb structurally incomplete HERV-H element. RT-PCR and quantitative RT-PCR results indicated that expression of this HERV-related transcript was negatively associated with colon, stomach, and kidney cancers. Its expression was induced upon treatment with DNA methylation and histone deacetylation inhibitors. A BLAT search using long terminal repeats (LTRs) identified 50 other LTR homogenous HERV-H elements. Further analysis of these elements revealed that all are structurally incomplete and only five exert transcriptional activity. The results presented here recommend further investigation into a potentially functional HERV-H-related ncRNA.

P38 mitogen activated protein kinase expression and regulation by interleukin-4 in human B cell non-Hodgkin lymphomas

The prevalence and regulation of p38 mitogen activated protein kinase (MAPK) expression in human lymphomas have not been extensively studied. In order to elucidate the role of p38 MAPK in lymphomagenesis, we examined the expression of native and phosphorylated p38 (p-p38) MAPK in cell lines derived from human hematopoietic neoplasms including B cell lymphoma-derived cell lines using Western blot analysis. The p-p38 MAPK protein was also analyzed in 30 B cell non-Hodgkin lymphoma (NHL) tissue biopsies by immunohistochemistry. Our results show that the expression of p38 MAPK was up-regulated in most of the cell lines as compared with peripheral blood lymphocytes, while the expression of p-p38 MAPK was more variable. A subset of B cell NHL biopsies showed increased expression of p-p38 MAPK relative to reactive germinal center cells. Interleukin-4 (IL-4) induced a dose-dependent increase in the expression of p-p38 MAPK (1.6- to 2.8-fold) in cell lines derived from activated B cell-like diffuse large B cell lymphoma (DLBCL) but not those from germinal center-like DLBCL. No change was seen in native p38 MAPK. The in vitro kinase activity of p38 MAPK, however, was induced (1.6- to 3.2-fold) in all five cell lines by IL-4. Quantitative fluorescent RT-PCR demonstrated that all four isoforms of p38 MAPK gene were expressed in the lymphoma cell lines, with p38γ and p38β isoforms being predominant. IL-4 stimulation increased the expression of β, γ, and δ isoforms but not α isoform in two cell lines. In conclusion, there is constitutive expression and activation of p38 MAPK in a large number of B-lymphoma-derived cell lines and primary lymphoma tissues, supportive of its role in lymphomagenesis. The differential IL-4 regulation of p38 MAPK expression in cell lines derived from DLBCL may relate to the cellular origin of these neoplasms.

Kv4 Channels Underlie the Subthreshold-Operating A-type K-current in Nociceptive Dorsal Root Ganglion Neurons

The dorsal root ganglion (DRG) contains heterogeneous populations of sensory neurons including primary nociceptive neurons and C-fibers implicated in pain signaling. Recent studies have demonstrated DRG hyperexcitability associated with downregulation of A-type K⁺ channels; however, the molecular correlate of the corresponding A-type K⁺ current (I_A) has remained hypothetical. Kv4 channels may underlie the I_A in DRG neurons. We combined electrophysiology, molecular biology (Whole-Tissue and Single-Cell RT-PCR) and immunohistochemistry to investigate the molecular basis of the I_A in acutely dissociated DRG neurons from 7- to 8-day-old rats. Whole-cell recordings demonstrate a robust tetraethylammonium-resistant (20 mM) and 4-aminopyridine-sensitive (5 mM) I_A. Matching Kv4 channel properties, activation and inactivation of this I_A occur in the subthreshold range of membrane potentials and the rate of recovery from inactivation is rapid and voltage-dependent. Among Kv4 transcripts, the DRG expresses significant levels of Kv4.1 and Kv4.3 mRNAs. Also, single small-medium diameter DRG neurons (∼30 μm) exhibit correlated frequent expression of mRNAs encoding Kv4.1 and Nav1.8, a known nociceptor marker. In contrast, the expressions of Kv1.4 and Kv4.2 mRNAs at the whole-tissue and single-cell levels are relatively low and infrequent. Kv4 protein expression in nociceptive DRG neurons was confirmed by immunohistochemistry, which demonstrates colocalization of Kv4.3 and Nav1.8, and negligible expression of Kv4.2. Furthermore, specific dominant-negative suppression and overexpression strategies confirmed the contribution of Kv4 channels to I_A in DRG neurons. Contrasting the expression patterns of Kv4 channels in the central and peripheral nervous systems, we discuss possible functional roles of these channels in primary sensory neurons.

Sequencing and phylogenetic analysis of the infectious bursal disease virus isolates from outbreak in layer flocks in the state of Minas Gerais

Sequencing and phylogenetic analysis based on the nucleotide sequence of the gene encoding VP2 protein was carried out in order to characterize the agent of two outbreaks of infectious bursal disease in layer flocks in the state of Minas Gerais in 2004. The results indicate the outbreaks could be related to the vaccinal virus.

Identifications of SUMO-1 cDNA and its expression patterns in Pacific white shrimp Litopeanaeus vannamei

Small ubiquitin-like modifiers (SUMO) work in a similar way as ubiquitin to alter the biological properties of a target protein by conjugation. A shrimp SUMO cDNA named LvSUMO-1 was identified in Litopenaeus vannamei. LvSUMO-1 cDNA contains a coding sequence of 282 nucleotides with untranslated regions of 37 bp at 5'-end and 347 bp at 3'-end, respectively. The deduced 93 amino acids exhibit 83% identity with the Western Honeybee SUMO-1, and more than 65% homologies with human and mouse SUMO-1. LvSUMO-1 mRNA is expressed in most L. vannamei tissues with the highest level in hepatopancrease. The mRNA expression of LvSUMO-1 over development stages in L. Vammamei is distinguished by a low level in nauplius stage and relatively high level in postlarva stage with continuous expression until juvenile stage. The LvSUMO-1 protein and its conjugated proteins are detected in both cytoplasm and nucleus in several tissues. Interestingly, LvSUMO-1 mRNA levels are high in abdominal muscle during the premolt stage, wherein it has significant activities of protein degradation, suggesting its possible role in the regulation of shrimp muscle protein degradation.

Functional genomics of allergen gene families in fruits

Fruit consumption is encouraged for health reasons; however, fruits may harbour a series of allergenic proteins that may cause discomfort or even represent serious threats to certain individuals. Thus, the identification and characterization of allergens in fruits requires novel approaches involving genomic and proteomic tools. Since avoidance of fruits also negatively affects the quality of patients' lives, biotechnological interventions are ongoing to produce low allergenic fruits by down regulating specific genes. In this respect, the control of proteins associated with allergenicity could be achieved by fine tuning the spatial and temporal expression of the relevant genes.

Incidence of Viruses Infecting Tomato and Their Natural Hosts in the Southeast and Central Regions of Iran

A survey was conducted to determine the incidence of Cucumber mosaic virus (CMV), Beet curly top virus (BCTV), Tomato yellow leaf curl virus (TYLCV), Tomato chlorotic spot virus (TcSV), Potato virus Y (PVY), Potato virus S (PVS), Tomato spotted wilt virus (TSWV), Tomato ringspot virus (TRSV), Tomato aspermy virus (TAV), Arabis mosaic virus (ArMV), Tobacco streak virus (TSV), Tomato bushy stunt virus (TBSV), Tobacco mosaic virus (TMV), and Tomato mosaic virus (ToMV) on tomato (Solanum lycopersicum) in the major horticultural crop growing areas in the southeast and central regions of Iran. A total of 1,307 symptomatic leaf samples from fields and 603 samples from greenhouses were collected from January 2003 to July 2005 in five southeastern and central provinces of Iran. Samples of symptomatic plants were analyzed for virus infection by enzyme-linked immunosorbent assay (ELISA) using specific polyclonal antibodies. ArMV and CMV were the most frequently found viruses, accounting for 25.6 and 23.4%, respectively, of the collected samples. BCTV, TSWV, TMV, PVY, ToMV, and TYLCV were detected in 6.1, 5.8, 5.6, 5, 4.8, and 1.6% of the samples, respectively. TBSV, TAV, TSV, PVS, and TRSV were not detected in any of the samples tested. Double and triple infections involving different combination of viruses were found in 13.9 and 1.7% of samples, respectively. This is the first report of PVY and ArMV as viruses naturally infecting tomato in Iran. Infection of tomato plants with PVY and ArMV was confirmed. Six out of 20 plant species belonging to six genera, growing in tomato fields or in the nearby areas, were found infected with TSWV, TMV, PVY, and CMV.

Laboratory diagnosis of mumps in a partially immunized population: The Nova Scotia experience

BACKGROUND

In 2007, Atlantic Canada experienced a large outbreak of mumps predominately in university students who had received a single dose of measles, mumps and rubella vaccine. The present study describes the performance characteristics of reverse transcriptase polymerase chain reaction (RT-PCR) on buccal and urine specimens and immunoglobulin M (IgM) serology in this partially immune population.

METHODS

Patients presenting with symptoms suspicious for mumps had a serum, urine and a buccal swab collected for diagnostic testing. Persons were classified as a 'confirmed' case according to the Public Health Agency of Canada's definition. Sera were tested using an enzyme-linked immunoassay. Detection of mumps virus in buccal swabs and urine samples was performed by RT-PCR.

RESULTS

A subset of 155 cases and 376 non-cases that had all three specimens submitted was used for calculating the performance characteristics. The sensitivity of RT-PCR on buccal swabs, urine specimens and IgM serology were 79%, 43% and 25%, respectively. The specificity of RT-PCR on buccal swabs, urine specimens and IgM serology was 99.5%, 100% and 99.7%, respectively. Only 12 of 134 (9%) patients had positive urine specimens in the presence of negative oral swabs.

CONCLUSION

RT-PCR on buccal swabs is the ideal specimen for diagnosis. Testing an additional urine sample in an outbreak setting did not increase the diagnostic yield significantly, but doubled testing volume and cost. In addition, the data suggest that, in this partially immune group, IgM serology has little value in the diagnosis of acute infection.

Detection of MAGE and SSX gene expressions by RT-nested PCR using common primers in head and neck cancer. Clin Exp Otorhinolaryngol. 2008;1:97-102. [PMID: 19434280 PMCID: PMC2671794 DOI: 10.3342/ceo.2008.1.2.97]

Objectives

The melanoma antigen gene (MAGE) and synovial sarcoma on X chromosome (SSX) gene families are silent in most normal adult tissues, but are expressed in a variety of malignant lesions. Therefore, detection of MAGE and SSX transcription may be useful for the diagnosis of head and neck cancers. The aim of this study is to detect MAGE and SSX gene transcripts of head and neck cancers using the MAGE 1-6 assay and the SSX 1-9 assay.

Methods

The transcripts of MAGE 1-6 and SSX 1-9 genes were detected by the MAGE 1-6 assay and the SSX 1-9 assay respectively, in cancer cell lines, cancer tissue, and induced sputum specimens from head and neck cancer patients.

Results

The transcripts of MAGE 1-6 and SSX 1-9 genes were detected in 82.8% and 75.9% of head and neck cancer tissues (N=29) respectively, and 96.6% of cancer tissues expressed at least one of MAGE 1-6 or SSX 1-9 genes. In the induced sputum of head and neck cancer patients (N=18), the transcripts of MAGE 1-6 and SSX 1-9 genes were detected in 72.2% and 77.8%, respectively, and 94.4% of the sputum specimens were positive for either the MAGE 1-6 or the SSX 1-9 assay.

Conclusion

These results suggest that the combination of MAGE 1-6 and SSX 1-9 assays may be useful in the diagnosis of head and neck cancer.

Serial changes in expression of functionally clustered genes in progression of liver fibrosis in hepatitis C patients

AIM: To investigate the relationship of changes in expression of marker genes in functional categories or molecular networks comprising one functional category or multiple categories in progression of hepatic fibrosis in hepatitis C (HCV) patients.

METHODS: Marker genes were initially identified using DNA microarray data from a rat liver fibrosis model. The expression level of each fibrosis associated marker gene was analyzed using reverse transcription-polymerase chain reaction (RT-PCR) in clinical biopsy specimens from HCV-positive patients (n = 61). Analysis of changes in expression patterns and interactions of marker genes in functional categories was used to assess the biological mechanism of fibrosis.

RESULTS: The profile data showed several biological changes associated with progression of hepatic fibrosis. Clustered genes in functional categories showed sequential changes in expression. Several sets of clustered genes, including those related to the extracellular matrix (ECM), inflammation, lipid metabolism, steroid metabolism, and some transcription factors important for hepatic biology showed expression changes in the immediate early phase (F1/F2) of fibrosis. Genes associated with aromatic amino acid (AA) metabolism, sulfur-containing AA metabolism and insulin/Wnt signaling showed expression changes in the middle phase (F2/F3), and some genes related to glucose metabolism showed altered expression in the late phase of fibrosis (F3/F4). Therefore, molecular networks showing serial changes in gene expression are present in liver fibrosis progression in hepatitis C patients.

CONCLUSION: Analysis of gene expression profiles from a perspective of functional categories or molecular networks provides an understanding of disease and suggests new diagnostic methods. Selected marker genes have potential utility for biological identification of advanced fibrosis.