Two sequential phosphates 3' adjacent to the 8-oxoguanosine are crucial for lesion excision by E. coli Fpg protein and human 8-oxoguanine-DNA glycosylase

Escherichia coli formamidopyrimidine-DNA glycosylase (Fpg) and human 8-oxoguanine-DNA glycosylase (hOGG1) are base excision repair enzymes involved in the 8-oxoguanine (oxoG) repair pathway. Specific contacts between these enzymes and DNA phosphate groups play a significant role in DNA-protein interactions. To reveal the phosphates crucial for lesion excision by Fpg and hOGG1, modified DNA duplexes containing pyrophosphate and OEt-substituted pyrophosphate internucleotide (SPI) groups near the oxoG were tested as substrate analogues for both proteins. We have shown that Fpg and hOGG1 recognize and specifically bind the DNA duplexes tested. We have found that both enzymes were not able to excise the oxoG residue from DNA containing modified phosphates immediately 3' to the 8-oxoguanosine (oxodG) and one nucleotide 3' away from it. In contrast, they efficiently incised DNA duplexes bearing the same phosphate modifications 5' to the oxodG and two nucleotides 3' away from the lesion. The effect of these phosphate modifications on the substrate properties of oxoG-containing DNA duplexes is discussed. Non-cleavable oxoG-containing DNA duplexes bearing pyrophosphate or SPI groups immediately 3' to the oxodG or one nucleotide 3' away from it are specific inhibitors for both 8-oxoguanine-DNA glycosylases and can be used for structural studies of complexes comprising a wild-type enzymes bound to oxoG-containing DNA.     

Prediction of MHC class I binding peptides with a new feature encoding technique

The recognition of specific peptides, bound to major histocompatibility complex (MHC) class I molecules, is of particular importance to the robust identification of T-cell epitopes and thus the successful design of protein-based vaccines. Here, we present a new feature amino acid encoding technique termed OEDICHO to predict MHC class I/peptide complexes. In the proposed method, we have combined orthonormal encoding (OE) and the binary representation of selected 10 best physicochemical properties of amino acids derived from Amino Acid Index Database (AAindex). We also have compared our method to current feature encoding techniques. The tests have been carried out on comparatively large Human Leukocyte Antigen (HLA)-A and HLA-B allele peptide binding datasets. Empirical results show that our amino acid encoding scheme leads to better classification performance on a standalone classifier.     

Rat Brain Type II 5'-Iodothyronine Deiodinase Activity Is Extremely Sensitive to Stress

Abstract: The effects of different kinds of acute stressor on thyroid hormone concentrations and deiodinase activities were investigated in four brain regions (frontal cortex, amygdala, hypothalamus, and cerebellum) and in the pituitaries and livers of adult male rats. Five groups of rats were killed after each of the following stressors: (a) an intraperitoneal injection of saline, (b) intragastric intubation, (c) and (d) two different forms of handling, being grasped as for intraperitoneal injection and being moved from one cage to another, and (e) a 2-h period spent in a slowly rotating drum. Two other groups were placed in the rotating drums for 10 and 19 h (sleep deprivation experiment), respectively. All stressors induced significant (in some cases up to 200%) increases in the activity of type II 5′-iodothyronine deiodinase, which catalyzes the deiodination of the prohormone l -thyroxine (T₄) to the active metabolite 3,3′,5-triiodo-l -thyronine (T₃). As a consequence, the tissue concentrations of T₄ fell, and those of T₃ rose (sometimes by up to 300%). However, these changes were limited to selected areas of the brain that were specific for each stressor and were not seen in all brain regions investigated in any group. No clear-cut effects of stress were seen on the activities of the type III 5-iodothyronine deiodinase isoenzyme, which catalyzes the inactivation of T₃, on liver or serum thyroid hormone concentrations or on liver of brain type I 5′-iodothyronine deiodinase activities. In summary, our results show that even mild and very brief stress can induce marked increases in T₃ concentrations specifically in brain but not in liver or blood. Thus, contrary to common opinion, thyroid hormones may play an important physiological role in stress reactions, at least in tissues that contain type II 5′-iodothyronine deiodinase, such as brain and pituitary.     

Voltage dependence of the Ca<Superscript>2+</Superscript> transient in endocardial and epicardial myocytes from the left ventricle of Goto–Kakizaki type 2 diabetic rats

There is much evidence that a combination of ibuprofen (IBU) and Aspirin (ASA) can antagonize the irreversible inhibition of platelet function. This study was designed to investigate the degree of gastric damage, bleeding time (BT) and fluctuations in the serum levels of prostaglandin E₂ (PGE₂) and thromboxane A₂ (TXA₂) after oral administration of ASA (200 mg/kg) and IBU (50 mg/kg) either alone or in combination in rats in vivo. The stomach was assessed for any damage either after 6 h, 18 h or 6 days and carboxymethylcellulose (1% CMC) served as a vehicle and control. ELISA was used to measure TXA₂ and PGE₂ in serum. Bleeding time was assessed using tail blood. The results show that ASA and IBU either alone or in combination can cause gastric ulceration in 25–100% of the rats at 6 and 18 h. In contrast, gastric ulceration was seen in 50% of rats with a combination of ASA given before IBU only after 6 days of oral administration. BT was unaffected either by ASA or IBU when administered alone except after 18 h for IBU. In contrast, BT was significantly reduced when IBU was administered before ASA after 18 h and 6 days (P < 0.001). Serum PGE₂ levels decreased significantly after ASA administered either alone or in combination with IBU for 6 h, 18 h and 6 days (P < 0.05). Serum TXA₂ levels were significantly reduced after 6 h, 18 h and 6 days following ASA and IBU administration except for IBU alone which caused a significant increase in serum TXA₂ 6 days after its administration (P < 0.01). It can be concluded that ASA and IBU administered either alone or in combination can cause gastric ulcers in the rat stomach after 6 h and 18 h, but less severe after 6 days. IBU either alone or in combination with ASA reduced BT only after 18 h and 6 days of administration. Together, the results show that gastric ulceration correlated well with the inhibition of serum PGE₂ and TXA₂ levels.     

Function changing mutations in glucocorticoid receptor evolution correlate with their relevance to mode coupling

Nonlinear effects in protein dynamics are expected to play role in function, particularly of allosteric nature, by facilitating energy transfer between vibrational modes. A recently proposed method focusing on the non‐Gaussian shape of the configurational population near equilibrium projects this information onto real space in order to identify the aminoacids relevant to function. We here apply this method to three ancestral proteins in glucocorticoid receptor (GR) family and show that the mutations that restrict functional activity during GR evolution correlate significantly with locations that are highlighted by the nonlinear contribution to the near‐native configurational distribution. Our findings demonstrate that the analysis of nonlinear effects in protein dynamics can be harnessed into a predictive tool for functional site determination. Proteins 2016; 84:655–665. © 2016 Wiley Periodicals, Inc.     

Integration of system dynamics approach toward deepening and broadening the life cycle sustainability assessment framework: a case for electric vehicles

Purpose

Quantitative life cycle sustainable assessment requires a complex and multidimensional understanding, which cannot be fully covered by the current portfolio of reductionist-oriented tools. Therefore, there is a dire need on a new generation of modeling tools and approaches that can quantitatively assess the economic, social, and environmental dimensions of sustainability in an integrated way. To this end, this research aims to present a practical and novel approach for (1) broadening the existing life cycle sustainability assessment (LCSA) framework by considering macrolevel environmental, economic, and social impacts (termed as the triple bottom line), simultaneously, (2) deepening the existing LCSA framework by capturing the complex dynamic relationships between social, environmental, and economic indicators through causal loop modeling, (3) understanding the dynamic complexity of transportation sustainability for the triple bottom line impacts of alternative vehicles, and finally (4) investigating the impacts of various vehicle-specific scenarios as a novel approach for selection of a macrolevel functional unit considering all of the complex interactions in the environmental, social, and economic aspects.

Methods

To alleviate these research objectives, we presented a novel methodology to quantify macrolevel social, economic, and environmental impacts of passenger vehicles from an integrated system analysis perspective. An integrated dynamic LCSA model is utilized to analyze the environmental, economic, and social life cycle impact as well as life cycle cost of alternative vehicles in the USA. System dynamics modeling is developed to simulate the US passenger transportation system and its interactions with economy, the environment, and society. Analysis covers manufacturing and operation phase impacts of internal combustion vehicles (ICVs), hybrid electric vehicles (HEVs), plug-in hybrid electric vehicles (PHEVs), and battery electric vehicles (BEVs). In total, seven macrolevel indicators are selected; global warming potential, particulate matter formation, photochemical oxidant formation, vehicle ownership cost, contribution to gross domestic product, employment generation, and human health impacts. Additionally, contribution of vehicle choices to global atmospheric temperature rise and public welfare is investigated.

Results and discussion

BEVs are found to be a better alternative for most of sustainability impact categories. While some of the benefits such as contribution to employment and GDP, CO₂ emission reduction potential of BEVs become greater toward 2050, other sustainability indicators including vehicle ownership cost and human health impacts of BEVs are higher than the other vehicle types on 2010s and 2020s. While the impact shares of manufacturing and operation phases are similar in the early years of 2010s, the contribution of manufacturing phase becomes higher as the vehicle performances increase toward 2050. Analysis results revealed that the US transportation sector, alone, cannot reduce the rapidly increasing atmospheric temperature and the negative impacts of the global climate change, even though the entire fleet is replaced with BEVs. Reducing the atmospheric climate change requires much more ambitious targets and international collaborative efforts. The use of different vehicle types has a small impact on public welfare, which is a function of income, education, and life expectancy indexes.

Conclusions

The authors strongly recommend that the dynamic complex and mutual interactions between sustainability indicators should be considered for the future LCSA framework. This approach will be critical to deepen the existing LCSA framework and to go beyond the current LCSA understanding, which provide a snapshot analysis with an isolated view of all pillars of sustainability. Overall, this research is a first empirical study and an important attempt toward developing integrated and dynamic LCSA framework for sustainable transportation research.

     

Low serum insulin-like growth factor-1 in patients with erectile dysfunction

Objective

Endothelial dysfunction and microvascular damage play a crurical role in the pathogenesis of erectile dysfunction (ED). Insulin-like growth factor-1 (IGF-1) is one of the growth factors that have a wide range of biologic effects. IGF-1 is an important mediator of cell growth, differentiation and transformation in various tissues. The purpose of the current study was to determine the association between IGF-1 levels and ED.

Materials and methods

All men were evaluated for ED and divided into two groups: 80 patients suffering from ED for >?1 year and 80 subjects without ED were enrolled as a control group in this study. Diagnosis of ED was based on the International Index of Erectile Function Score-5. IGF-1 levels were measured in serum by an automated chemiluminescence immunoassay. The relationship between IGF-1 levels and ED scores in patients was statistically evaluated.

Results

The mean age of patients in ED group was 60.4?±?11.3 years and 55.4?±?9.6 in control group. The plasma IGF-1 levels were significantly lower in ED than in control group (96.5?±?38.3 and 132.5?±?53.3 ng/ mL, respectively, P?<?0.001). The IGF-1 levels were positively correlated with ED score (r?=?0.623, P?<?0.01).

Conclusion

In this study serum IGF-1 levels were found to be associated with endothelial dysfunction that predicts ED. Serum IGF-1 level appears to be a specific predictor of ED, and it might be used in early prediction of ED in male population.