Comparative analysis of protein expression in differentiated thyroid tumours: a multicentre study

This study compared clinical features and protein expression profiles in differentiated thyroid tumours to identify protein markers with the potential for indicating malignancy status. Tissue microarrays were constructed using 119 thyroid tumour samples (45 papillary carcinomas, 26 follicular carcinomas, 48 adenomas). Generally, there was overexpression of proliferating cell nuclear antigen (PCNA), p53, matrix metalloproteinase (MMP)-7, Hector Battifora mesothelial-1 (HBME-1), MMP-2, pituitary tumour-transforming gene (PTTG) and human telomerase reverse transcriptase (hTERT) in malignant thyroid carcinomas, and overexpression of fragile histidine triad (FHIT), p16 and E-cadherin in thyroid adenomas. Multiple factor binary logistic regression analysis indicated that MMP-2, HBME-1, p16 and FHIT were independently related to differentiated thyroid tumours. Receiver-operating characteristics for these four factors showed HBME-1 as best for diagnostic accuracy. Sensitivity and specificity were enhanced using an HBME-1 and p16 cluster. HBME-1 expression was not significantly different for papillary and follicular carcinomas, whereas p16 expression was significantly specific.

Neurochemical phenotypes of the afferent and efferent projections of the mouse medial habenula

The medial habenula (MHb) is a key bridge between limbic forebrain and midbrain monoaminergic centers. Although its exact behavioral function remains enigmatic, it is implicated in regulating many behaviors such as stress responses and circadian rhythm. Fundamental information such as the neurotransmitters in the afferent and efferent projections of the MHb remains unclear. By combining retrograde tract tracing and genetic labeling of GABAergic neurons in mice, we find that the medial septum (MS) and nucleus of diagonal band (NDB) provide GABA-ergic input to the MHb. By anterograde tracing and immunostaining against a marker of glutamatergic synapses, we find that the projection from the triangular septal nucleus (TS) to the MHb has the capacity to release glutamate. This suggests that in addition to ATP, glutamate is another neurotransmitter for the TS-->MHb projection. Finally, by combining anterograde tracing and immunostaining, we find that the MHb neurons projecting to the interpeduncular nucleus (IPN) have the capacity to release glutamate. This suggests that, in addition to acetylcholine and substance P, glutamate is another neurotransmitter used by MHb projection neurons. Our findings reveal the organization of two key neurotransmitters for the MHb afferent and efferent projections, and lay framework for future functional studies of this pathway in the brain.

Performance of microbiological control by a point-of-use filter system for drinking water purification

Purification capacity of a faucet mounted type water filter for home use was evaluated, particularly with regard to microbiological performance under different running conditions. Biofilms were formed inside the filter, affecting the bacterial quality of the effluent water. Low flow rate, long stagnation period and high filter temperature were found favorable for bacterial growth inside. By commercial analytical profile index (API) kits, ten different bacterial species were identified in drinking water, four of which were probably contributed to the biofilm formation since they were also present in the biofilm. Fluorescence in situ hybridization (FISH) was used to confirm the API identification results, and direct viable count (DVC) method was employed to improve the sensitivity of FISH for the isolated Acinetobacter spp. and Pseudomonas putida as models. Relationship between the filter operating condition and the bacterial community alteration was partly revealed, which could provide the basic knowledge for the filter design and its practical use.

Evolution of the redox function in mammalian apurinic/apyrimidinic endonuclease

Human apurinic/apyrimidinic endonuclease (hApe1) encodes two important functional activities: an essential base excision repair (BER) activity and a redox activity that regulates expression of a number of genes through reduction of their transcription factors, AP-1, NFkappaB, HIF-1alpha, CREB, p53 and others. The BER function is highly conserved from prokaryotes (E. coli exonuclease III) to humans (hApe1). Here, we provide evidence supporting a redox function unique to mammalian Apes. An evolutionary analysis of Ape sequences reveals that, of the 7 Cys residues, Cys 93, 99, 208, 296, and 310 are conserved in both mammalian and non-mammalian vertebrate Apes, while Cys 65 is unique to mammalian Apes. In the zebrafish Ape (zApe), selected as the vertebrate sequence most distant from human, the residue equivalent to Cys 65 is Thr 58. The wild-type zApe enzyme was tested for redox activity in both in vitro EMSA and transactivation assays and found to be inactive, similar to C65A hApe1. Substitution of Thr 58 with Cys in zApe, however, resulted in a redox active enzyme, suggesting that a Cys residue in this position is indeed critical for redox function. In order to further probe differences between redox active and inactive enzymes, we have determined the crystal structures of vertebrate redox inactive enzymes, the C65A human Ape1 enzyme and the zApe enzyme at 1.9 and 2.3A, respectively. Our results provide new insights on the redox function and highlight a dramatic gain-of-function activity for Ape1 in mammals not found in non-mammalian vertebrates or lower organisms.

Comparative biology of rAAV transduction in ferret, pig and human airway epithelia

Differences between rodent and human airway cell biology have made it difficult to translate recombinant adeno-associated virus (rAAV)-mediated gene therapies to the lung for cystic fibrosis (CF). As new ferret and pig models for CF become available, knowledge about host cell/vector interactions in these species will become increasingly important for testing potential gene therapies. To this end, we have compared the transduction biology of three rAAV serotypes (AAV1, 2 and 5) in human, ferret, pig and mouse-polarized airway epithelia. Our results indicate that apical transduction of ferret and pig airway epithelia with these rAAV serotypes closely mirrors that observed in human epithelia (rAAV1>rAAV2 congruent withrAAV5), while transduction of mouse epithelia was significantly different (rAAV1>rAAV5>>rAAV2). Similarly, ferret, pig and human epithelia also shared serotype-specific differences in the polarity (apical vs basolateral) and proteasome dependence of rAAV transduction. Despite these parallels, N-linked sialic acid receptors were required for rAAV1 and rAAV5 transduction of human and mouse airway epithelia, but not ferret or pig airway epithelia. Hence, although the airway tropisms of rAAV serotypes 1, 2 and 5 are conserved better among ferret, pig and human as compared to mouse, viral receptors/co-receptors appear to maintain considerable species diversity.

Effect of Co doping on the structural, optical and magnetic properties of ZnO nanoparticles

We report the results of a detailed investigation of sol-gel-synthesized nanoscale Zn(1-x)Co(x)O powders processed at 350 °C with 0≤x≤0.12 to understand how the structural, morphological, optical and magnetic properties of ZnO are modified by Co doping, in addition to searching for the theoretically predicted ferromagnetism. With x increasing to 0.03, both lattice parameters a and c of the hexagonal ZnO decreased, suggesting substitutional doping of Co at the tetrahedral Zn(2+) sites. For x>0.03, these trends reversed and the lattice showed a gradual expansion as x approached 0.12, probably due to additional interstitial incorporation of Co. Raman spectroscopy measurements showed a rapid change in the ZnO peak positions for x>0.03, suggesting significant disorder and changes in the ZnO structure, in support of additional interstitial Co doping possibility. Combined x-ray photoelectron spectroscopy (XPS), electron paramagnetic resonance spectroscopy, photoluminescence spectroscopy and diffuse reflectance spectroscopy showed clear evidence for tetrahedrally coordinated high-spin Co(2+) ions occupying the lattice sites of ZnO host system, which became saturated for x>0.03. Magnetic measurements showed a paramagnetic behaviour in Zn(1-x)Co(x)O with increasing antiferromagnetic interactions as x increased to 0.10. Surprisingly, a weak ferromagnetic behaviour was observed for the sample with x = 0.12 with a characteristic hysteresis loop showing a coercivity H(c)∼350 Oe, 25% remanence M(r), a low saturation magnetization M(s)∼0.04 emu g(-1) and with a Curie temperature T(c)∼540 K. The XPS data collected from Zn(1-x)Co(x)O samples showed a gradual increase in the oxygen concentration, changing the oxygen-deficient undoped ZnO to an excess oxygen state for x = 0.12. This indicates that such high Co concentrations and appropriate oxygen stoichiometry may be needed to achieve adequate ferromagnetic exchange coupling between the incorporated Co(2+) ions.

VEGF-Targeted RNA Interference Suppresses Angiogenesis and Tumor Growth of Retinoblastoma

Vascular endothelial growth factor (VEGF) is one of the most important angiogenic growth factors for tumor angiogenesis which has been verified to be involved in neovascularization of retinoblastoma. Here, we sought to explore whether RNA interference (RNAi) targeting VEGF could inhibit retinoblastoma angiogenesis and tumor growth. Stable transfection of the two human retinoblastoma cell lines SO-RB50 and HXO-RB44 with VEGF-targeted small interfering RNA (siRNA) expression plasmid significantly inhibited VEGF expression determined by real-time polymerase chain reaction (PCR), enzyme-linked immunosorbent assay and Western blot, whereas the control transfection showed no effects. The chemically synthesized VEGF siRNA dramatically suppressed tumor angiogenesis (CD34 immunohistochemistry) and tumor growth in the SO-RB50 subcutaneous xenograft model. Significant downregulation of VEGF expression both on messenger RNA and protein levels in VEGF-siRNA-treated SO-RB50 subcutaneous xenograft was confirmed by real-time PCR and Western blot compared to control. Our data demonstrate the suppression function on angiogenesis and tumor growth of retinoblastoma by VEGF-targeted RNAi. This novel therapeutic strategy promises to play a part in the clinical management of retinoblastoma.

Characterization of HLA-B*5516, -B*1313, -B*9512, and -DRB1*1457 alleles identified in a southwest Chinese population

The human leukocyte antigen (HLA)-B*5516 allele differs from the B*5502 by a single 97 T --> C substitution (His to Tyr at position 33) in exon 2. The B*1313 allele results from 419 T --> A and 420 A --> C substitutions, encoding a Leu to Tyr substitution at 140 in exon 2 of the B*1301 allele. The B*9512 allele differs from B*1502 by a single 360 G --> C substitution (Gln to His at 120) in exon 3. The DRB1*1457 allele appears to be a hybrid molecule generated by recombination between the DRB1*13 and DRB1*14 alleles. The serological equivalents of these new alleles are HLA-B22, -B13, -B15, and DR13, respectively. Family studies detected two rare haplotypes: A*11, B*9512, DRB1*14 and A*24, B*52, Cw*07, DRB1*1457, DRB3*020201, DQB1*050301. The gene frequencies of these alleles in the Chinese population are less than 0.0001.

Storage protein profiles in Spanish and runner market type peanuts and potential markers

BACKGROUND

Proteomic analysis has proven to be the most powerful method for describing plant species and lines, and for identification of proteins in complex mixtures. The strength of this method resides in high resolving power of two-dimensional electrophoresis (2-DE), coupled with highly sensitive mass spectrometry (MS), and sequence homology search. By using this method, we might find polymorphic markers to differentiate peanut subspecies.

RESULTS

Total proteins extracted from seeds of 12 different genotypes of cultivated peanut (Arachis hypogaea L.), comprised of runner market (A. hypogaea ssp. hypogaea) and Spanish-bunch market type (A. hypogaea ssp. fastigiata), were separated by electrophoresis on both one- and two-dimensional SDS-PAGE gels. The protein profiles were similar on one-dimensional gels for all tested peanut genotypes. However, peanut genotype A13 lacked one major band with a molecular weight of about 35 kDa. There was one minor band with a molecular weight of 27 kDa that was present in all runner peanut genotypes and the Spanish-derivatives (GT-YY7, GT-YY20, and GT-YY79). The Spanish-derivatives have a runner-type peanut in their pedigrees. The 35 kDa protein in A13 and the 27 kDa protein in runner-type peanut genotypes were confirmed on the 2-D SDS-PAGE gels. Among more than 150 main protein spots on the 2-D gels, four protein spots that were individually marked as spots 1-4 showed polymorphic patterns between runner-type and Spanish-bunch peanuts. Spot 1 (ca. 22.5 kDa, pI 3.9) and spot 2 (ca. 23.5 kDa, pI 5.7) were observed in all Spanish-bunch genotypes, but were not found in runner types. In contrast, spot 3 (ca. 23 kDa, pI 6.6) and spot 4 (ca. 22 kDa, pI 6.8) were present in all runner peanut genotypes but not in Spanish-bunch genotypes. These four protein spots were sequenced. Based on the internal and N-terminal amino acid sequences, these proteins are isoforms (iso-Ara h3) of each other, are iso-allergens and may be modified by post-translational cleavage.

CONCLUSION

These results suggest that there may be an association between these polymorphic storage protein isoforms and peanut subspecies fastigiata (Spanish type) and hypogaea (runner type). The polymorphic protein peptides distinguished by 2-D PAGE could be used as markers for identification of runner and Spanish peanuts.

Functional expression of the particulate methane mono-oxygenase gene in recombinantRhodococcus erythropolis

In order to construct an expression system for the particulate methane mono-oxygenase (pMMO) gene (pmo), the structural gene cluster pmoCAB amplified from Methylosinus trichosporium OB3b was inserted into a shuttle vector pBS305 under the control of a dsz promoter and transformed into Rhodococcus erythropolis LSSE8-1. A stable transformant was successfully obtained using ethane as the sole carbon source. Fluorescence in situ hybridization results showed that the dsz promoter allowed the pmo genes to be transcribed in the recombinant strain. The effects of Cu2+ and Zn2+ concentrations on cell growth and pMMO activity in ethane-containing medium were examined. It was discovered that 7.5 microM Cu2+ and 1.8 microM Zn2+ were suitable to achieve high cell concentration and pMMO activity, but the amount of methanol accumulated during methane oxidation by the recombinant strain was still low.

The visfatin gene is associated with glucose and lipid metabolism in a Chinese population

AIMS

Visfatin is a newly discovered adipokine found in abundance in visceral fat. It lowers plasma glucose in humans and mice. In this study, we explored the relationships between the plasma level of visfatin and genetic single nucleotide polymorphisms (SNPs) and Type 2 diabetes mellitus (T2DM) and anthropometric and metabolic parameters in Chinese subjects.

METHODS

Oral glucose tolerance tests (OGTT) and biochemical assays for plasma insulin, lipid profiles and serum visfatin were performed in 241 newly diagnosed T2DM patients, subjects with impaired glucose regulation (IGR), and normal glucose tolerant subjects more than 40 years of age. Genotyping for three SNP loci: -1535C/T, rs2058539 and rs10953502 were performed using the allele-specific real-time PCR method.

RESULTS

Visfatin levels were similar in T2DM patients, IGR and normal glucose tolerant subjects. However, visfatin levels were significantly lower in obese than normal-weight subjects (13.66 +/- 0.87 vs. 15.46 +/- 0.47 ng/ml, P = 0.03). There was suggestively significant correlation between visfatin level and body mass index (r = -0.17 P = 0.07) and waist-hip ratio (r = 0.16 P = 0.08) in male subjects, but not in female subjects. Allele and common haplotype frequencies of the three SNP loci were similar in T2DM patients, IGR and normal glucose tolerant subjects. However, significant associations were found between these three SNP loci and plasma glucose concentration at 0 and 120 min during OGTT, the area under the response curve for plasma glucose, and triglyceride and total cholesterol levels.

CONCLUSIONS

Serum visfatin levels may be related to visceral obesity in men, and the visfatin gene may account for variation of glucose and lipid parameters in Chinese subjects.

Identification of Transcripts Involved in Resistance Responses to Leaf Spot Disease Caused by Cercosporidium personatum in Peanut (Arachis hypogaea)

ABSTRACT Late leaf spot disease caused by Cercosporidium personatum is one of the most destructive foliar diseases of peanut (Arachis hypogaea) worldwide. The objective of this research was to identify resistance genes in response to leaf spot disease using microarray and real-time polymerase chain reaction (PCR). To identify transcripts involved in disease resistance, we studied the gene expression profiles in two peanut genotypes, resistant or susceptible to leaf spot disease, using cDNA microarray containing 384 unigenes selected from two expressed sequenced tag (EST) cDNA libraries challenged by abiotic and biotic stresses. A total of 112 spots representing 56 genes in several functional categories were detected as up-regulated genes (log(2) ratio > 1). Seventeen of the top 20 genes, each matching gene with known function in GenBank, were selected for validation of their expression levels using real-time PCR. The two peanut genotypes were also used to study the functional analysis of these genes and the possible link of these genes to the disease resistance trait. Microarray technology and real-time PCR were used for comparison of gene expression. The selected genes identified by microarray analysis were validated by real-time PCR. These genes were more greatly expressed in the resistant genotype as a result of response to the challenge of C. personatum than in the susceptible genotype. Further investigations are needed to characterize each of these genes in disease resistance. Gene probes could then be developed for application in breeding programs for marker-assisted selection.

Proliferation-dependent pattern of expression of a dihydrofolate reductase-thymidylate synthase gene from Daucus carota

The pattern of expression of a carrot dhfr-ts gene was evaluated in different plant organs, in somatic embryos, and in hypocotyl explants induced to dedifferentiate in vitro by the addition of the synthetic auxin 2,4 dichorophenoxyacetic acid. The promoter of this gene was also placed upstream of a uidA (GUS) reporter gene and, using biolistic and protoplasts transient expression assays, was shown to drive a particularly high level of expression in actively growing suspension cells. The results from these expression analyses combined with the presence of putative cell cycle-related cis-acting elements in the dhfr-ts promoter, strongly point to a cell division-dependent expression of this gene.

Development of a pyrosequencing approach for rapid screening of rifampin, isoniazid and ethambutol-resistant Mycobacterium tuberculosis

SETTING

The need to minimize the transmission of drug-resistant Mycobacterium tuberculosis requires rapid identification procedures.

OBJECTIVE

To develop a pyrosequencing approach for rapid screening of rifampin, isoniazid and ethambutol-resistant M. tuberculosis based on characterization of resistance-associated hot mutations.

DESIGN

Three pairs of PCR primers and three pyrosequencing sequencing primers for detecting mutations at codon 526 and 531 of the rpoB gene, codon 315 of the katG gene, and codon 306 of the embB gene were chosen. The sensitivity of the pyrosequencing approach was determined by assaying PCR products generated from 10-fold serial dilutions of the DNA from the H37Rv strain. The efficacy of the pyrosequencing approach was evaluated by analyzing clinical isolates with a known antibiotic phenotype.

RESULTS

Resistance-associated hot mutations could be determined within 2 h after PCR amplification using pyrosequencing. About 45 fg DNA per reaction was required to obtain sufficient PCR products to produce a clear, accurate pyrosequencing pattern. No mutations were found in all 20 drug-susceptible clinical isolates, while all isolates with mutations showed corresponding drug resistances.

CONCLUSION

This pyrosequencing approach can be used for rapid screening of rifampin-, isoniazid- and ethambutol-resistant M. tuberculosis prior to standard drug susceptibility testing.