Elucidation of the role of the methylene-tetrahydromethanopterin dehydrogenase MtdA in the tetrahydromethanopterin-dependent oxidation pathway in Methylobacterium extorquens AM1.

The methylotroph Methylobacterium extorquens AM1 oxidizes methanol and methylamine to formaldehyde and subsequently to formate, an intermediate that serves as the branch point between assimilation (formation of biomass) and dissimilation (oxidation to CO2). The oxidation of formaldehyde to formate is dephosphotetrahydromethanopterin (dH4MPT) dependent, while the assimilation of carbon into biomass is tetrahydrofolate (H4F) dependent. This bacterium contains two different enzymes, MtdA and MtdB, both of which are dehydrogenases able to use methylene-dH4MPT, an intermediate in the oxidation of formaldehyde to formate. Unique to MtdA is a second enzymatic activity with methylene-H4F. Since methylene-H4F is the entry point into the biomass pathways, MtdA plays a key role in assimilatory metabolism. However, its role in oxidative metabolism via the dH4MPT-dependent pathway and its apparent inability to replace MtdB in vivo on methanol growth are not understood. Here, we have shown that an mtdB mutant is able to grow on methylamine, providing a system to study the role of MtdA. We demonstrate that the absence of MtdB results in the accumulation of methenyl-dH4MPT. Methenyl-dH4MPT is shown to be a competitive inhibitor of the reduction of methenyl-H4F to methylene-H4F catalyzed by MtdA, with an estimated Ki of 10 µM. Thus, methenyl-dH4MPT accumulation inhibits H4F-dependent assimilation. Overexpression of mch in the mtdB mutant strain, predicted to reduce methenyl-dH4MPT accumulation, enhances growth on methylamine. Our model proposes that MtdA regulates carbon flux due to differences in its kinetic properties for methylene-dH4MPT and for methenyl-H4F during growth on single-carbon compounds.

Lattice-matched transition metal disulfide intergrowths: the metallic conductors Ag2Te(MS2)3 (M = V, Nb).

We present new chalcogenide compounds, Ag2Te(MS2)3 (M = V, Nb), built up of alternating planes of [MS2] and [Ag2Te]. The Ag and Te atoms are linearly coordinated by S atoms in the [MS2] layers and held in place by covalent interactions. Structural polymorphism was found by single crystal X-ray diffraction studies, where long-range ordering or disorder of the Ag and Te atoms within the hexagonal planar [Ag2Te] layer yielded two distinct crystal forms. When the Ag and Te atoms are ordered, the two isostructural compounds crystallize in the non-centrosymmetric P62m space group, with a = 5.5347(8) Å, c = 8.0248(16) Å, and V = 212.89(6) Å(3) for α-Ag2Te(VS2)3 and a = 5.7195(8) Å, c = 8.2230(16) Å, and V = 232.96(6) Å(3) for α-Ag2Te(NbS2)3. For the occupationally disordered Ag/Te arrangement, a subcell of the ordered phase that crystallizes in the non-centrosymmetric P6m2 space group, with a = 3.2956(6) Å (=a(a)/(3)(1/2)), c = 8.220(2) Å, and V = 77.31(3) Å(3) for ß-Ag2Te(VS2)3, was identified. Furthermore, pair distribution function analysis revealed local distortions in the [Ag2Te] layer. Band structure calculations at the density functional theory level were carried out to investigate the electronic structure of Ag2Te(MS2)3. Electronic transport measurements on Ag2Te(MS2)3 show that they exhibit p-type metallic behavior. Thermal analyses and temperature-dependent powder X-ray diffraction studies were focused on the stability and transformation/decomposition of the Ag2Te(MS2)3 phases. Magnetic susceptibility data are also reported. The new intercalated Ag2Te(MS2)3 system features a unique hypervalent Te with a three-center, four-electron bonding environment isoelectronic to that found in I3(-).

The expression of calcitonin receptor detected in malignant cells of the brain tumour glioblastoma multiforme and functional properties in the cell line A172.

AIM: Previous studies have indicated that expression of calcitonin receptor (CTR) could be induced in a proinflammatory environment. In the present study, CTR-immunoreactivity (CTR-ir) was investigated in brain tissue from patients with glioblastoma multiforme (GBM). METHODS AND RESULTS: In immunohistochemical analysis of GBM samples, tissues with complex glomeruloid structures surrounded by malignant cells were analysed for CTR-ir using anti-human CTR antibodies generated against two separate epitopes of CTR. CTR-ir was associated predominantly with glial cells. Regions with CTR-ir cells were found in 12 of 14 GBM tumours (P < 0.05). Using confocal microscopy, CTR-ir cells were identified that were also positive for glial fibrillary acidic protein, nestin and CD133. Antibodies were verified using immunoblots and confocal microscopy of the Cercopithecus aethiops(COS)-7 transfectants. Immunoblots of membrane preparations from the CTR-positive cell lines demonstrated a major band (≈ 67 kDa) and minor band (≈ 52 kDa), but the intensity was reversed for the GBM cell line A172. In cultured A172 cells, functional studies demonstrated calcitonin stimulation of adenylyl cyclase and inhibition of extracellular-regulated kinase (ERK)1/2 phosphorylation. CONCLUSIONS: The findings that (i) CTR was expressed by glioma cells in a majority of GBM tumours tested, (ii) CTR(+) /CD133(+) cells were identified and (iii) second messenger systems were functionally modified by calcitonin in A172 cells suggest that CTR might be a useful therapeutic target in GBM.

Thallium chalcohalides for X-ray and γ-ray detection.

We report that the chalcohalide compound Tl(6)SeI(4) is a promising material for efficient X-ray and γ-ray detection. This material has a higher figure of merit than the current state-of-the-art material for room-temperature operation, Cd(0.9)Zn(0.1)Te (CZT). We have synthesized high-quality single-crystalline wafers of Tl(6)SeI(4) with detector-grade resistivities and good carrier transport of both electrons and holes. We demonstrate that pulse height spectra recorded using Co-57 radiation show an energy resolution matching that of a commercial CZT detector material.

(Ag2TeS3)2·A2S6 (A = Rb, Cs): layers of silver thiotellurite intergrown with alkali-metal polysulfides.

The layered compounds RbAg(2)TeS(6) and CsAg(2)TeS(6) crystallize in the noncentrosymmetric space group P6(3)cm, with a = 19.15 Å, c = 14.64 Å, and V = 4648 Å(3) and a = 19.41 Å, c = 14.84 Å, and V = 4839 Å(3), respectively. The structures are composed of neutral [Ag(2)TeS(3)] layers alternating with charge-balanced salt layers containing polysulfide chains of [S(6)](2-) and alkali-metal ions. RbAg(2)TeS(6) and CsAg(2)TeS(6) are air- and water-stable, wide-band-gap semiconductors (E(g) ∼ 2.0 eV) exhibiting nonlinear-optical second-harmonic generation.

Analysis of methylated circulating DNA in cancer patients' blood.

Circulating extracellular nucleic acids derived from body fluids such as blood are commonly analyzed to assess malignant diseases. Efficient isolation, extraction, quantification, modification, and analysis methods remain important for utilizing circulating nucleic acids as potential molecular biomarkers. Our refined techniques of DNA isolation from serum, sodium bisulfite modification of extracted DNA, and methylation analysis provide a robust approach for quantitative analysis of circulating tumor-related DNA. The approach allows direct comparison of methylated and nonmethylated genomic sequences in a specimen.

Human high molecular weight-melanoma-associated antigen: utility for detection of metastatic melanoma in sentinel lymph nodes.

PURPOSE: Detection of micrometastasis in melanoma-draining lymph nodes is important for staging and prognosis. Immunohistochemical staining (IHC) using S-100p-HMB-45-, and MART-1-specific antibodies is used for detecting metastases in sentinel lymph nodes (SLN). However, improvement in IHC is needed for melanoma micrometastasis detection. EXPERIMENTAL DESIGN: Paraffin-embedded archival tissue (PEAT) specimens were obtained from 42 non-SLN macrometastases, 42 SLN metastases, and 16 tumor-negative SLNs of 100 melanoma patients who underwent SLN biopsy. PEAT specimens were assessed by IHC with high molecular weight-melanoma-associated antigen (HMW-MAA)-specific monoclonal antibodies (mAb) and with S-100p-, HMB-45-, and MART-1-specific antibodies. Quantitative real-time reverse-transcriptase PCR assay was used for HMW-MAA and MART-1 mRNA detection. RESULTS: Expression frequency and immunostaining intensity were higher for HMW-MAA than MART-1 in nodal macrometastases (P < 0.0001 and P < 0.0001, respectively) and micrometastases (P < 0.0001 and P = 0.004, respectively). All 52 (100%) macrometastases were positive with HMW-MAA-specific mAbs, whereas 43 (83%) were positive with MART-1-specific mAbs. In a comparison analysis, 23 of 23 (100%) micrometastases were HMW-MAA-positive, whereas 21 (91%) and 18 (78%) specimens were S-100p- and HMB-45-positive, respectively. Quantitative real-time reverse-transcriptase PCR analysis of 48 nodal metastases showed HMW-MAA mRNA detection in SLNs with metastases. CONCLUSIONS: HMW-MAA is more sensitive and specific than MART-1, S-100p, and HMB-45 for IHC-based detection of SLN micrometastases. SLN PEAT-based detection specificity of melanoma micrometastases can be improved by IHC with HMW-MAA-specific mAbs.

Activation of Toll-like receptors 2, 3, and 4 on human melanoma cells induces inflammatory factors.

Toll-like receptors (TLR) have been shown to be expressed on various types of cancers; however, their functional activity is not known. We examined TLR profiles of human melanoma cells and showed that TLR2, TLR3, and TLR4 were found to be highly expressed. By PCR array analysis, specific stimulation of TLR2, TLR3, and TLR4 on melanoma cells showed significant activation of the adaptor protein MyD88, as well as downstream signal transduction factors nuclear factor-kappaB and inflammatory response-related factors. Specific ligand activation of TLR2, TLR3, and TLR4 was shown to induce cell migration. Peripheral blood lymphocytes and melanoma purified RNA was shown to activate TLR3 on melanoma cells. These studies show expression and functional activity of specific TLRs on melanoma cells and as potential therapeutic targets to control tumor progression.

Bacteriologic analysis of bone biopsy from diabetic foot infections within a VA patient population.

Diabetic patients with foot infections were evaluated over a 5-year period from April 2005 to March 2010. Cultures were obtained from 92 patients after surgical debridement. All of the patients were classified as "severe" diabetic foot infections (DFIs) and PEDIS grade 4. Wound specimens were collected by bone biopsy and sent to San Francisco VA Medical Center Microbiology Department for aerobic and anaerobic cultures. Among the 92 cases, the study resulted in a total of 410 pathogens, which 203 pathogens were from bone cultures and 207 pathogens were from soft tissue cultures. 74% of cases were polymicrobial and 26% had growth of a single organism. Staphylococcus aureus presented in 49.35% of bone cultures and 55.38% of soft tissue cultures, Streptococcus species presented in 44.16% and 36.92% respectably and roughly 33% of both bone and soft tissue had staphylococcus coagulase negative present. Gram-negative organisms occurred in 25% of all cultures taken. Pseudomonas accounted for 15% of soft tissue infections but only 1.3% bone cultures. MRSA was found in 17.39% of cultures and VRE was seen in 4.34% of all culture results. Staphylococcus aureus was the most prevalent organisms seen. This study presents a comprehensive microbiological survey of diabetic patients with DFIs within the San Francisco VA Medical Center and this study will help guide physicians to improve clinical outcomes of DFIs by using proper antibiotics.

Preparation and properties of metallic, superhard rhenium diboride crystals.

Single crystals of ReB(2) have been prepared from an aluminum flux under inert gas flow. The crystals are typically 1-3 mm in diameter and 500 microm thick, growing along the [002] direction with a distinct hexagonal morphology. Vickers microhardness and nanoindentation testing indicate that the (002) plane possesses the highest hardness with measured values of 40.5 and 36.4 GPa, respectively. The elastic anisotropy was examined and the indentation moduli of the basal plane and an (hk0) plane of unknown indices are 675 and 510 GPa, respectively. Four-probe electrical resistivity measurements demonstrate that ReB(2) is the hardest material known to exhibit metallic behavior. Thermogravimetric analysis indicates that the crystals are stable in air up to 1000 degrees C due to the formation of a protective boron oxide coating.

Estrogen receptor and HER2/neu status affect epigenetic differences of tumor-related genes in primary breast tumors.

INTRODUCTION: Estrogen receptor (ER)-positive breast cancers are considered prognostically more favorable than ER-negative tumors, whereas human epidermal growth factor receptor (HER)2/neu-positive breast cancers are associated with worse prognosis. The objective of the present study was to determine whether ER-positive and ER-negative status relates to epigenetic changes in breast cancer-related genes. To evaluate epigenetic differences in tumor-related genes relating to ER and HER2/neu status of primary tumors, we examined the promoter methylation status of the promoter region CpG islands of eight major breast tumor-related genes (RASSF1A, CCND2, GSPT1, TWIST, APC, NES1, RARbeta2, and CDH1). METHODS: Paired ER-positive (n = 65) and ER-negative (n = 65) primary breast tumors (n = 130) matched for prognostic factors were assessed. DNA was extracted from paraffin-embedded tumor tissue after microdissection, and methylation-specific PCR and capillary-array electrophoresis analysis were performed. RESULTS: In early stages of tumor progression (T1 and N0), RASSF1A and CCND2 were significantly (P < 0.05) more methylated in ER-positive than in ER-negative tumors. GSTP1 hypermethylation was more frequent in the lymph node metastasis positive group than in the negative group. Double negative (ER-negative, HER2/neu-negative) breast cancers had significantly lesser frequencies of RASSF1A, GSTP1, and APC methylation (P < 0.0001, P < 0.0001, and P = 0.0035, respectively). Both ER and HER2/neu status correlated independently with these epigenetic alterations. CONCLUSION: We demonstrated significant differences in tumor-related gene methylation patterns relevant to ER and HER2/neu status of breast tumors. This may be of significance in the assessment of targeted therapy resistance related to ER and HER2/neu status in breast cancer patients.

Estrogen receptor-alpha methylation predicts melanoma progression.

The role of estrogen receptor alpha (ER-alpha) in melanoma is unknown. ER-alpha expression may be regulated in melanoma via hypermethylation of promoter CpG islands. We assessed ER-alpha hypermethylation in primary and metastatic melanomas and sera as a potential tumor progression marker. ER-alpha methylation status in tumor (n = 107) and sera (n = 109) from American Joint Committee on Cancer (AJCC) stage I to IV melanoma patients was examined by methylation-specific PCR. The clinical significance of serum methylated ER-alpha was assessed among AJCC stage IV melanoma patients receiving biochemotherapy with tamoxifen. Rates of ER-alpha methylation in AJCC stage I, II, and III primary melanomas were 36% (4 of 11), 26% (5 of 19), and 35% (8 of 23), respectively. Methylated ER-alpha was detected in 42% (8 of 19) of stage III and 86% (30 of 35) of stage IV metastatic melanomas. ER-alpha was methylated more frequently in metastatic than primary melanomas (P = 0.0003). Of 109 melanoma patients' sera in AJCC stage I, II, III, and IV, methylated ER-alpha was detected in 10% (2 of 20), 15% (3 of 20), 26% (5 of 19), and 32% (16 of 50), respectively. Serum methylated ER-alpha was detected more frequently in advanced than localized melanomas (P = 0.03) and was the only factor predicting progression-free [risk ratio (RR), 2.64; 95% confidence interval (95% CI), 1.36-5.13; P = 0.004] and overall survival (RR, 2.31; 95% CI, 1.41-5.58; P = 0.003) in biochemotherapy patients. Hypermethylated ER-alpha is a significant factor in melanoma progression. Serum methylated ER-alpha is an unfavorable prognostic factor.

Predictive utility of circulating methylated DNA in serum of melanoma patients receiving biochemotherapy.

PURPOSE: Currently, no validated blood-based assays accurately predict treatment response or outcome in melanoma patients. We hypothesized that methylation of tumor-related genes detected in serum DNA could predict disease outcome and therapeutic response in patients receiving concurrent biochemotherapy (BC) for metastatic melanoma. PATIENTS AND METHODS: American Joint Committee on Cancer stage IV melanoma patients (N = 50) had blood drawn before administration of BC. Patients (n = 47) were classified as BC responders or nonresponders. Responders (n = 23) demonstrated a complete or partial response following BC; nonresponders (n = 24) demonstrated progressive disease. Hypermethylation of Ras association domain family 1 (RASSF1A), retinoic acid receptor-beta2 (RAR-beta2), and O6-methylguanine DNA methyltransferase (MGMT) genes were assessed by methylation-specific polymerase chain reaction. RESULTS: Circulating methylated RASSF1A was significantly less frequent for responders (three of 23 patients; 13%) than nonresponders (10 of 24 patients; 42%; P = .028). Patients with RASSF1A, RAR-beta2, or at least one serum methylated gene had significantly worse overall survival than patients with no methylated genes (log-rank, P = .013, .021, and .01, respectively). Methylated RASSF1A was the only factor that significantly correlated with overall survival and BC response (risk ratio, 2.38; 95% CI, 1.16 to 4.86; P = .018; odds ratio = 0.21; 95% CI, 0.05 to 0.90; P = .036). CONCLUSION: Detection of circulating methylated DNA in serum can predict response to BC and disease outcome.

Quantification of LINE1 in circulating DNA as a molecular biomarker of breast cancer.

Developing a noninvasive test for detecting and monitoring breast cancer progression would help in providing better procedures for the treatment of breast cancer. Increases in the absolute quantity of circulating DNA and DNA integrity have been previously reported in breast cancer patients. LINE1 is one of the most abundant sequences in the human genome, with about 520,000 copies per genome. To assess the combination of circulating DNA quantity and DNA integrity, we developed a long LINE1 (about 300-bp amplicon size) quantitative method. A quantitative real-time PCR (qPCR) technique was used to detect long LINE1. Breast cancer patients' sera was assessed preoperatively before primary tumor surgery. LINE1 could be detected in high levels of breast cancer patients' sera and in limited levels in normal females. We demonstrated that long LINE1 quantification of circulating DNA was useful for detecting early-stage breast cancer, and that copy number correlated with tumor size. This preliminary study demonstrates the potential clinical utility of LINE1 copy numbers in breast cancer patients.