Observing the Temperature Dependent Transition of the GP2 Peptide Using Terahertz Spectroscopy

The GP2 peptide is derived from the Human Epidermal growth factor Receptor 2 (HER2/nue), a marker protein for breast cancer present in saliva. In this paper we study the temperature dependent behavior of hydrated GP2 at terahertz frequencies and find that the peptide undergoes a dynamic transition between 200 and 220 K. By fitting suitable molecular models to the frequency response we determine the molecular processes involved above and below the transition temperature (T _D). In particular, we show that below T _D the dynamic transition is dominated by a simple harmonic vibration with a slow and temperature dependent relaxation time constant and that above T _D, the dynamic behavior is governed by two oscillators, one of which has a fast and temperature independent relaxation time constant and the other of which is a heavily damped oscillator with a slow and temperature dependent time constant. Furthermore a red shifting of the characteristic frequency of the damped oscillator was observed, confirming the presence of a non-harmonic vibration potential. Our measurements and modeling of GP2 highlight the unique capabilities of THz spectroscopy for protein characterization.     

Malic enzyme: its purification and characterization fromMucor circinelloides and occurrence in other oleaginous fungi

Malic enzyme was purified 43-fold from Mucor circinelloides. The enzyme was dependent on Mg²⁺ or Mn²⁺ for activity, was not active with Dmalate and had a pH optimum at 7.8. The apparent K_m values for malate and NADP⁺ were 488 ΜM and 41 Μm respectively. The M_r of the native enzyme was 160 kDa. Five metabolic analogues of malate: oxaloacetate, tartronic acid, 1-methylenecyclopropane trans-2,3-dicarboxyIic acid, malonic acid and glutaric acid, were found to inhibit malic enzyme activity at 10 mM. Four oleaginous fungi, Mucor circinelloides, Mortierella alpina, Mortierella elongata and Pythium ultimum, were also examined, all possessed a soluble malic enzyme, two also possessed a microsomal malic enzyme.     

Bayesian Insight into a Robust Test for Linear Contrast Based on Asymmetric Censored Samples

A robust test for linear contrast using modified maximum likelihood estimators based on symmetrically censored samples proposed by Tiku (1973, 1982a) is studied in this paper from the Bayesian point of view. The effects of asymmetric censoring on this testing procedure is investigated and a good approximation to its posterior distribution in this case is worked out. We also present an example which illustrates the method of obtaining the highest posterior density interval for the linear combination of the unknown location parameters.     

Population structure and ecology of the African buffalo (Syncerus caffer Sparrman, 1779) in Chebera Churchura National Park,Ethiopia

An investigation of population structure and ecology of the African buffalo (Syncerus caffer Sparrman, 1779) was carried out in the Chebera Churchura National Park, Ethiopia during the wet and dry seasons of 2005–2006. Sample counts of African buffaloes were carried out in an area of 1,215 km². The estimated population of buffalo was 2,617 individuals. Males comprised 35.0%, while females 52.8% of the population. The remaining 12% of the population was young of both sexes and of all ages of unknown sex. It was difficult to categorize the young into male and female in the field, as their primary sexual characteristics were not easily visible. Male to female sex ratio was 1.00 : 1.51. Age structure was dominated by adults, which constituted 72.06% of the total population. Subadults comprised 22.02%, and young accounted for 5.9% of the population. Larger herds of up to 27 individuals were observed during the wet season and smaller herds of eight individuals during the dry season. The mean herd size during wet and dry seasons was 24.81 and 7.77, respectively. The African buffaloes were distributed in four habitat types such as grasslands, woodlands, montane forests and riverine habitat in the study area. They were observed more in the riverine vegetation types during the dry season. Relative abundance of food resources, green vegetation cover and water availability in the area were the major factors governing their distribution in the present study area. They spent a greater proportion of the time in feeding and resting/ruminating activities. On the average, 49.7% of the daytime was spent in feeding, and 38.75% of the day on resting (lying down and standing). Morning and the late afternoon activity peaks were more pronounced during the dry season than the wet season.     

NOD2 gene mutations associate weakly with ulcerative colitis but not with Crohn's disease in Indian patients with inflammatory bowel disease

Background

Three mutations (two missense and one frameshift) in the NOD2 gene are associated with Crohn's disease (CD) in a proportion of patients with Crohn's disease in North America, Europe and Australia. These three mutations are not found in Indian patients with CD. We undertook new studies to identify polymorphisms in the NOD2 gene in the Indian population and to detect whether any of these were associated with inflammatory bowel disease (IBD) in this population.

Methods

Individual exons of the NOD2 gene were amplified by PCR and subjected to denaturing high performance liquid chromatography (DHPLC) to detect heteroduplex formation. All 12 exons of the NOD2 gene were amplified and Sanger-sequenced to detect polymorphisms in the NOD2 gene. 310 patients with CD, 318 patients with ulcerative colitis (UC) and 442 healthy controls (HC) were recruited for association studies. DNA from these participants was evaluated for the identified eight polymorphisms by Sequenom analysis.

Results

Heteroduplex formation was noted by DHPLC in exons 2 and 4 of the NOD2 gene. Sequencing of the entire NOD2 gene data revealed eight polymorphisms – rs2067085, rs2066842, rs2066843, rs1861759, rs2111235, rs5743266, rs2076753, and rs5743291 – of which the latter four were described for the first time in Indians. None of these polymorphisms was associated with CD. The SNPs rs2066842 and rs2066843 were in significant linkage disequilibrium. Both SNPs showed a significant association with UC (P = 0.03 and 0.04 respectively; odds ratio 1.44 and 1.41 respectively).

Conclusion

Four NOD2 polymorphisms were identified for the first time in the Indian population. Of 8 NOD2 polymorphisms, none were associated with CD but two were weakly associated with UC. NOD2 polymorphisms do not play a major role in CD genesis in India.