The influence of HER2 genotypes as molecular markers on breast cancer outcome

Alterations of the human epidermal growth factor receptor 2 (HER2) protooncogene have been implicated in the carcinogenesis and prognosis of breast cancer. A polymorphism has been identified at codon 655 (ATC/isoleucine to GTC/valine [I655V]) in the transmembrane domain-coding region of this gene, which may be associated with the risk of breast cancer. In this study we aimed to determine whether the risk of breast cancer is associated with the I655V polymorphism of HER2 transmembrane domain-coding region at codon 655. The genomic DNA from breast cancer patients and control subjects underwent analysis by the polymerase chain reaction-fragment length polymorphism. We observed no overall association between HER2 genotype and breast cancer (p = 0.53). However, an elevated positive association was observed for Ile/Val+Val/Val versus Ile/Ile genotypes in women >age 60 years (p = 0.02). Further, other risk factors--namely, the body mass index and family history--were found to be risk factors for developing breast cancer (p = 0.006 and p = 0.00, respectively). In conclusion, results of this study suggest that polymorphisms of the HER2 gene may be important susceptibility biomarkers for breast cancer risk among older women.     

Detection of conjugative plasmids and antibiotic resistance genes in anthropogenic soils from Germany and India

PCR typing methods were used to assess the presence of plasmids of the incompatibility (Inc) groups IncP, IncN, IncW, IncQ and rolling circle plasmids of the pMV158 type in total DNA extracts from anthropogenic soils from India and Germany. Ten different soils from two different locations in Germany, the urban park Berlin Tiergarten and the abandoned sewage field Berlin-Buch, and from four different locations in India were analysed. PCR amplification of the total DNA extracts revealed the prevalence of IncP-specific sequences in Berlin Buch and Indian soil samples. The detected IncP plasmids contained at least one transfer function, the origin of transfer, oriT. In contrast to IncP-specific sequences, IncQ, IncN, IncW and pMV158-specific sequences were never detected. The presence of ampC, tet (O), ermB, SHV-5, mecA, and vanA antibiotic resistance genes was also tested. Three Indian soil samples irrigated with wastewater contained the ampC gene, whereas the other resistance genes were not found in any of the samples. Detection of IncP trfA2 and oriT sequences by PCR amplification and hybridization is a clear indication that IncP plasmids are prevalent in these habitats. Exogenous plasmid isolation revealed conjugative plasmids belonging to the IncPbeta group encoding resistance to ampicillin.     

Gene module level analysis: identification to networks and dynamics

Nature exhibits modular design in biological systems. Gene module level analysis is based on this module concept, aiming to understand biological network design and systems behavior in disease and development by emphasizing on modules of genes rather than individual genes. Module level analysis has been extensively applied in genome wide level analysis, exploring the organization of biological systems from identifying modules to reconstructing module networks and analyzing module dynamics. Such module level perspective provides a high level representation of the regulatory scenario and design of biological systems, promising to revolutionize our view of systems biology, genetic engineering as well as disease mechanisms and molecular medicine.     

Caffeic acid phenethyl ester (CAPE) protects brain against oxidative stress and inflammation induced by diabetes in rats

Diabetic patients reveal significant disorders, such as nephropathy, cardiomyopathy, and neuropathy. As oxidative stress and inflammation seem to be implicated in the pathogenesis of diabetic brain, we aimed to investigate the effects of caffeic acid phenethyl ester (CAPE) on oxidative stress and inflammation in diabetic rat brain. Diabetes was induced by a single dose of streptozotocin (45 mg kg⁻¹, i.p.) injection into rats. Two days after streptozotocin treatment 10 μM kg⁻¹ day⁻¹ CAPE was administrated and continued for 60 days. Here, we demonstrate that CAPE significantly decreased the levels of nitric oxide and malondialdehyde induced by diabetes, and the activities of catalase, glutathione peroxidase, and xanthine oxidase in the brain. However, glutathione levels were increased by CAPE. The mRNA expressions of tumor necrosis factor (TNF)-α and interferon (IFN)-γ, and inducible nitric oxide synthase (iNOS) were remarkably enhanced in brain by diabetes. CAPE treatments significantly suppressed these inflammatory cytokines (about 70% for TNF-α, 26% for IFN-γ) and NOS (completely). Anti-inflammatory cytokine IL-10 mRNA expression was not affected by either diabetes or CAPE treatments. In conclusion, diabetes induces oxidative stress and inflammation in the brain, and these may be contributory mechanisms involved in this disorder. CAPE treatment may reverse the diabetic-induced oxidative stress in rat brains. Moreover, CAPE reduces the mRNA expressions of TNF-α and IFN-γ in diabetic brain; suggesting CAPE suppresses inflammation as well as oxidative stress occurred in the brain of diabetic patients.     

Engineering the active site of ascorbate peroxidase.

The oxidation of a number of thioethers, namely methyl phenyl sulphide (1), ethyl phenyl sulphide (2), isopropyl phenyl sulphide (3), n-propyl phenyl sulphide (4), p-chlorophenyl methyl sulphide (5), p-nitrophenyl methyl sulphide (6) and methyl naphthalene sulphide (7), by recombinant pea cytosolic ascorbate peroxidase (rAPX) and a site-directed variant of rAPX in which the distal tryptophan 41 residue has been replaced with an alanine (W41A) has been examined. The electronic spectrum (pH 7.0, mu = 0.10 M, 25.0 degrees C) for the ferric derivative of W41A (lambda(max)/nm = 411, 534, 560, 632) is indicative of an increased quantity of 6-coordinate, high-spin and/or 6-coordinate, low-spin haem compared to rAPX. Steady state oxidation of sulphides 1-4 and 7, gave values for kcat that are approximately 10-fold and 100-fold, respectively, higher for W41A than for rAPX. For rAPX, essentially racemic mixtures of R- and S-sulphoxides were obtained for all sulphides. With the exception of sulphide 7, the W41A variant shows substantial enhancements in enantioselectivity, with R : S ratios varying between R : S = 63 : 37 (sulphides 1 and 4) and R : S = 85 : 15 (sulphide 6). Incubation of sulphide 2 with rAPX or W41A and [(18)O] H(2)O(2) shows 95% (rAPX) and 96% (W41A) transfer of labelled oxygen to the substrate. Structure-based modelling techniques have provided a fully quantitative rationalization of all the experimentally determined R : S ratios and have indicated that reorientation of the sidechain of Arg38, such that access to the haem is much less restricted, is influential in controlling the stereoselectivity for both rAPX and W41A.     

Sharing is caring? Measurement error and the issues arising from combining 3D morphometric datasets

Geometric morphometrics is routinely used in ecology and evolution and morphometric datasets are increasingly shared among researchers, allowing for more comprehensive studies and higher statistical power (as a consequence of increased sample size). However, sharing of morphometric data opens up the question of how much nonbiologically relevant variation (i.e., measurement error) is introduced in the resulting datasets and how this variation affects analyses. We perform a set of analyses based on an empirical 3D geometric morphometric dataset. In particular, we quantify the amount of error associated with combining data from multiple devices and digitized by multiple operators and test for the presence of bias. We also extend these analyses to a dataset obtained with a recently developed automated method, which does not require human‐digitized landmarks. Further, we analyze how measurement error affects estimates of phylogenetic signal and how its effect compares with the effect of phylogenetic uncertainty. We show that measurement error can be substantial when combining surface models produced by different devices and even more among landmarks digitized by different operators. We also document the presence of small, but significant, amounts of nonrandom error (i.e., bias). Measurement error is heavily reduced by excluding landmarks that are difficult to digitize. The automated method we tested had low levels of error, if used in combination with a procedure for dimensionality reduction. Estimates of phylogenetic signal can be more affected by measurement error than by phylogenetic uncertainty. Our results generally highlight the importance of landmark choice and the usefulness of estimating measurement error. Further, measurement error may limit comparisons of estimates of phylogenetic signal across studies if these have been performed using different devices or by different operators. Finally, we also show how widely held assumptions do not always hold true, particularly that measurement error affects inference more at a shallower phylogenetic scale and that automated methods perform worse than human digitization.     

Effects of ascorbic acid on cadmium-induced oxidative stress and performance of broilers

The effects of cadmium on performance, antioxidant defense system, liver and kidney functions, and cadmium accumulation in selected tissues of broiler chickens were studied. Whether the possible adverse effects of cadmium would reverse with the antioxidant ascorbic acid was also investigated. Hence, 4 treatment groups (3 replicates of 10 chicks each) were designed in the study: control, ascorbic acid, cadmium, and cadmium plus ascorbic acid. Cadmium was given via the drinking water at a concentration of 25 mg/L for 6 wk. Ascorbic acid was added to the basal diet at 200 mg/kg either alone or with cadmium. Cadmium decreased the body weight (BW), body weight gain (BWG), and feed efficiency (FE) significantly at the end of the experiment, wheras its effect on feed consumption (FC) was not significant. Cadmium increased the plasma malondialdehyde (MDA) level as an indicator of lipid peroxidation and lowered the activity of blood superoxide dismutase (SOD). Liver function enzymes, aspartate amino transferase (AST), alanine aminotransferase (ALT), lactate dehydrogenase (LDH), and gamma glutamyl transferase (GGT) activities were not changed by cadmium. Cadmium ingestion did not alter serum creatinine levels. Although the serum cadmium level was not elevated, cadmium mainly accumulated in the kidneys, liver, pancreas, and muscle. Ascorbic acid supplementation resulted in a reduction of MDA level previously increased by cadmium and a restoration in SOD activity. However, ascorbic acid did not ameliorate the growth inhibitory effect of cadmium nor did it prevent accumulation of cadmium in analyzed tissues. These data indicate that oxidative stress, induced by cadmium, plays a role in decreasing the performance of broilers and that dietary supplementation by ascorbic acid might be useful in reversing the lipid peroxidation induced by cadmium and partly alleviating the adverse effect of cadmium on performance of broilers.     

A self-sufficient cytochrome p450 with a primary structural organization that includes a flavin domain and a [2Fe-2S] redox center

p450 RhF from Rhodococcus sp. NCIMB 9784 is the first example of a new class of cytochrome p450 in which electrons are supplied by a novel, FMN- and Fe/S-containing, reductase partner in a fused arrangement. We have previously cloned the gene encoding the enzyme and shown it to comprise an N-terminal p450 domain fused to a reductase domain that displays similarity to the phthalate family of oxygenase reductase proteins. A reductase of this type had never previously been reported to interact with a cytochrome p450. In this report we describe the purification and partial characterization of p450 RhF. We show that the enzyme is self-sufficient in catalyzing the O-dealkylation of 7-ethoxycoumarin. The p450 RhF catalyzed O-dealkylation of 7-ethoxycoumarin is inhibited by several compounds that are known inhibitors of cytochrome p450. Presteady state kinetic analysis indicates that p450 RhF shows a 500-fold preference for NAPDH over NADH in terms of Kd value (6.6 microm versus 3.7 mm, respectively). Potentiometric studies show reduction potentials of -243 mV for the two-electron reduction of the FMN and -423 mV for the heme (in the absence of substrate).     

Squamous cell carcinoma of the oral mucosa after release of submucous fibrosis and bilateral small radial forearm flap reconstruction

Oral submucous fibrosis is a collagen disorder that affects the submucosal layer of the upper digestive tract. The major cause is the habit of betel quid chewing, which is common in central, southern, and southeast Asia. The progressive and irreversible course of disease results with trismus, dysphagia, xerostomia, and rhinolalia. The most serious complication of this disorder is the development of oral carcinoma, and the incidence in different series varies from 1.9 to 10 percent. A sufficient mouth opening can be achieved by complete release of fibrotic tissue, and coronoidectomy and temporal muscle myotomy when needed, and reconstruction of the resultant defect can be best achieved by microsurgical free-tissue transfer because of the discouraging results with skin grafting or local flaps. From April of 1997 to May of 2001, a total of 26 patients received reconstructive surgery with small radial forearm flaps after release of submucous fibrosis with or without temporalis muscle myotomy and coronoidectomy. All patients were men, with a mean age of 40.1 years (range, 18 to 62 years) and all had a history of betel nut chewing ranging from 8 to 40 years. The interincisal distance ranged from 5 to 29 mm, with a mean of 15 mm, before operation. After the release procedure, the interincisal distance increased to 40 mm (range, 35 to 50 mm). At a follow-up period of 3 to 48 months, the interincisal distance was a mean of 35 mm (range, 18 to 57 mm), with an average increase of 20 mm compared with the preoperative distance. During follow-up, three patients developed squamous cell carcinoma of the oral cavity 24 to 36 months after submucous fibrosis release. Two of them occurred in the release site and the other one occurred at the soft palate. Oral cancer occurred in three of 13 patients who had received release of submucous fibrosis and who were followed for longer than 2 years (range, 24 to 48 months), which means that 23 percent of these patients developed squamous cell carcinoma of the intraoral mucosa. High risk of cancer occurrence strongly indicates the importance of an earlier and more aggressive surgical approach toward submucous fibrosis, and long-term follow-up on a regular basis. The purpose of an early and aggressive approach to submucous fibrosis is to provide a good quality of life to the patient by improving oral hygiene and oral intake quality and at the same time to obtain a sufficient mouth opening, which is mandatory for the inspection of the excision site and the remaining oral mucosa during follow-up.