High resolution crystal structure of dengue‐3 envelope protein domain III suggests possible molecular mechanisms for serospecific antibody recognition

Dengue viruses are classified into four serotypes. Here, we report a 1.7 Å crystal structure of a recombinant dengue‐3 envelope protein domain III (ED3), which contains most of the putative epitopes. Although the fold was well conserved, we found that a local backbone deformation in the first β‐strand, which contains the putative epitope‐1, occurred upon domain isolation. Furthermore, a comparison with dengue‐2 ED3 indicated a large structural change by as much as 4.0 Å at Asp⁶⁶², located in epitope‐2. These minute structural and surface properties changes observed in the high resolution ED3 structure represent potential determinants for serospecificity and epitope recognition by antibodies. © 2012 Wiley Periodicals, Inc.     

Docosahexaenoic acid suppresses migration of triple-negative breast cancer cell through targeting metastasis-related genes and microRNA under normoxic and hypoxic conditions

There is insufficient evidence with respect to the effect of the standard anticancer therapeutic agents as well as common dietary supplements on the expression of such genes and microRNAs (miRNAs). Therefore, this study was aimed to study the effect of applying linoleic acid (LA) and docosahexaenoic acid (DHA) fatty acids alone or combined with Taxol on the expression of the matrix metalloproteinase (MMP)-9, MMP-2, vimentin, and talin2 genes, tumor-suppressor miR-194 and, onco-miR-106b in triple-negative breast cancer cell line, known as MDA-MB-231. MDA-MB-231 as metastatic breast cancer cell line was cultured and treated using 0.3 μM Taxol, 100 μM DHA, and 50 μM LA for 24 hours, alone or combined with Taxol under the normoxic and hypoxic conditions. Cells were harvested, after RNA extraction and complementary DNA synthesis, analysis of the expression levels of the studied genes and miRNAs was done through the use of the quantitative real-time polymerase chain reaction (qRT-PCR). Wound healing assay and Western blot analysis were also performed for confirmation. The results of qRT-PCR showed that treating the MDA-MB-231 cells with DHA caused an increase in the miR-194 expression and a decrease in the miR-106b expression, leading to the downregulation of the MMP-2 and MMP-9, and vimentin, and upregulation of the talin2 under the normoxic and hypoxic conditions. The results of the wound healing scratch assay revealed that the administration of the DHA and the DHA-Taxol combination caused the repression of cell migration in comparison with the control groups under the normoxic and hypoxic conditions. The results of the Western blot analysis demonstrated that DHA and the DHA-Taxol combination caused an increase in the expression of the talin2 protein rather than the control cells under both normoxic and hypoxic conditions. This study showed that DHA has significant antimetastatic effects against the triple-negative breast cancer cells. DHA could serve as a promising supplementation for suppressing the breast cancer cell migration, especially under the hypoxic condition.     

MicroRNA-330 inhibits growth and migration of melanoma A375 cells: In vitro study

Melanoma skin cancer is one of the main causes of male cancer-related deaths worldwide. It has been suggested that miR-330-5p can act as a tumor suppressor in various types of cancers. So, in this study, we replaced miR-330 in melanoma cancer cells by vector-based miR-330 to evaluate the effects of this microRNA on the growth and migration inhibition of melanoma cancer cells, and to determine the molecular mechanisms underlying its action. By using the MTT assay, the IC₅₀ of Geneticin antibiotic was obtained as 460 µg/mL. The results of the qRT-PCR showed the increased expression level of miR-330 and decreased expression levels of MMP-9, CXCR4, Vimentin, melanoma cell adhesion molecule, AKT1, and E2F1 messenger RNA in A375 transfected cells. The cytotoxicity assay results demonstrated the inhibition of cancer cells proliferation. Furthermore, the wound healing test results showed a migration reduction of transfected cells with miR-330 compared with nontransfected ones. In addition, 4′,6-diamidino-2-phenylindoleLB: Luria-Bertani (DAPI) staining revealed the significant nucleus fragmentation in miR-330 replaced cells, which correspond to apoptosis induction in replaced cells. The results showed that increase in miR-330 expression level could significantly inhibit the tumor cell growth and the migration of melanoma cancer cells.     

Ubiquitination is involved in glucose-mediated downregulation of GIP receptors in islets

Glucose-dependent insulinotropic polypeptide (GIP) is a gastrointestinal hormone that has a potent stimulatory effect on insulin release under conditions of normal glucose tolerance. However, its insulinotropic effect is reduced or even absent entirely in type 2 diabetic patients. In this study, we addressed the role of glucose concentration in the diabetic range of >or=11 mM, i.e., hyperglycemia per se, as a cause of the lack of response to GIP. Culturing rat and human pancreatic islets in >or=11 mM glucose for up to 24 h resulted in prevention of GIP-mediated intracellular cAMP increase compared with culturing in 5 mM glucose. Western blot analysis revealed a selective 67 +/- 2% (rat) and 60 +/- 8% (human) decrease of GIP-R expression in islets exposed to >or=11 mM glucose compared with 5 mM glucose (P < 0.001). We further immunoprecipitated GIP-R from islets and found that GIP-R was targeted for ubiquitination in a glucose- and time-dependent manner. Downregulation of GIP-R was rescued by treating isolated islets with proteasomal inhibitors lactacystin and MG-132, and the islets were once again capable of increasing intracellular cAMP levels in response to GIP. These results suggest that the GIP-R is ubiquitated, resulting in downregulation of the actions of GIP.     

The benefits of using diverse animal models for studying pertussis

Pertussis, a respiratory disease caused by infection with Bordetella pertussis, represents one of the most devastating diseases in infants and young children worldwide. Significant research efforts over the last five decades have led to the introduction of two types of vaccines, which are now available worldwide and which have significantly reduced the global incidence of pertussis. The use of animal models and, in particular, the mouse model has benefited in the development of these vaccines tremendously. However, open questions regarding the duration of immunity, the type of immune response needed for protection and the role of mucosal and innate immunity in disease protection still remain. Here, we review the various animal models available currently and their benefits for studying this important disease.     

Biodegradation of Aliphatic and Aromatic Fractions of Heavy Crude Oil-Contaminated Soil: A Pilot Study

Crude oil is one of the major contaminants of soil and water. Biodegradation is a good option for reducing oil contamination in soil. Soil fertilizers can help the microorganisms biodegrade oil with higher efficiency. In this study, the effect of chemical fertilizers and animal manure on crude oil reduction was compared and the reduction of the aliphatic and aromatic fractions was studied during 8 months. The higher reduction of crude oil (54%) was observed in tests containing chemical fertilizers and wood chips, followed by those containing animal manure (46%). The reduction of aliphatic and aromatic fractions was also higher in fertilized tests. Our results showed that in the experiments with mixed chemical fertilizers and wood chips, the reduction of crude oil and its aliphatic and aromatic fractions was higher than the experiments with only chemical fertilizers and those with animal manure. The reductions in the experiments with animal manure, however, were higher than those with only chemical fertilizers.     

Alpha7 nicotinic acetylcholine receptors in lung inflammation and carcinogenesis: Friends or foes?

The lung tissue expresses the cholinergic system including nicotinic acetylcholine receptors (nAChRs) which included in many physiologic and pathologic processes. Mounting evidence revealed that these receptors have important roles in lung carcinogenesis via modulating either stimulatory or inhibitory signaling pathways. Among different members of nicotinic receptors family, alpha7-subtype of nAChR (α7nAChR) is a critical mediator involved in both inflammatory responses and cancers. Several studies have shown that this receptor is the most powerful regulator of responses that stimulate lung cancer processes such as proliferation, angiogenesis, metastasis, and inhibition of apoptosis. Moreover, aside from its roles in the regulation of cancer pathways, there is growing evidence indicating that α7nAChR has profound impacts on lung inflammation through the cholinergic anti-inflammatory pathway. Regarding such diverse effects as well as the critical roles of nicotine as an activator of α7nAChR on lung cancer pathogenesis, its modulation has emerged as a promising target for drug developments. In this review, we aim to highlight the detrimental as well as the possible beneficial influences of α7nAChR downstream signaling cascades in the control of lung inflammation and cancer-associated properties. Consequently, by considering the significant global burden of lung cancer, delineating the complex influences of α7 receptors would be of great interest in designing novel anticancer and anti-inflammatory strategies for the patients suffering from lung cancer.     

Stimulation of Native Microorganisms for Improving Loose Salty Sand

Prolonged droughts and excessive water harvesting in western Asia has accelerated desertification and caused longer dry seasons of salt lakes. The Aral Sea experience has proven that dust from saline soil is a serious health issue. Various stabilization techniques to reduce wind erosion have been used in the past. However, in recent years, a potentially viable method has been developed; microbial induced calcite precipitation (MICP) has been introduced as a method of soil stabilization, though its effectiveness in saline soils remains to be examined. The effect of salt content in loose sandy soil on calcite precipitation of calcite through stimulation of native bacteria is investigated in this article. Samples with salinity up to 30% salt content were prepared and treated with different culture medium compounds. A number of tests were used to evaluate the effect of the mentioned parameters. The results show that improvement increases with increasing salinity up to 5% salt, and further increase in salinity reduces the effectiveness of improvement. It is also shown that the addition of urea in the culture medium has a significant effect on the urea hydrolysis which resulted in a five-fold increase in compressive strength. Four native strains of halotolerant urease-positive bacteria were also identified.     

Cardiolipin Interactions with Proteins

Cardiolipins (CL) represent unique phospholipids of bacteria and eukaryotic mitochondria with four acyl chains and two phosphate groups that have been implicated in numerous functions from energy metabolism to apoptosis. Many proteins are known to interact with CL, and several cocrystal structures of protein-CL complexes exist. In this work, we describe the collection of the first systematic and, to the best of our knowledge, the comprehensive gold standard data set of all known CL-binding proteins. There are 62 proteins in this data set, 21 of which have nonredundant crystal structures with bound CL molecules available. Using binding patch analysis of amino acid frequencies, secondary structures and loop supersecondary structures considering phosphate and acyl chain binding regions together and separately, we gained a detailed understanding of the general structural and dynamic features involved in CL binding to proteins. Exhaustive docking of CL to all known structures of proteins experimentally shown to interact with CL demonstrated the validity of the docking approach, and provides a rich source of information for experimentalists who may wish to validate predictions.     

A Combined Pulmonary Function and Emphysema Score Prognostic Index for Staging in Chronic Obstructive Pulmonary Disease

Introduction

Chronic Obstructive Pulmonary Disease (COPD) is characterized by high morbidity and mortality. Lung computed tomography parameters, individually or as part of a composite index, may provide more prognostic information than pulmonary function tests alone.

Aim

To investigate the prognostic value of emphysema score and pulmonary artery measurements compared with lung function parameters in COPD and construct a prognostic index using a contingent staging approach.

Material-Methods

Predictors of mortality were assessed in COPD outpatients whose lung computed tomography, spirometry, lung volumes and gas transfer data were collected prospectively in a clinical database. Univariate and multivariate Cox proportional hazard analysis models with bootstrap techniques were used.

Results

169 patients were included (59.8% male, 61.1 years old; Forced Expiratory Volume in 1 second % predicted: 40.5±19.2). 20.1% died; mean survival was 115.4 months. Age (HR = 1.098, 95% Cl = 1.04–1.252) and emphysema score (HR = 1.034, 95% CI = 1.007–1.07) were the only independent predictors of mortality. Pulmonary artery dimensions were not associated with survival. An emphysema score of 55% was chosen as the optimal threshold and 30% and 65% as suboptimals. Where emphysema score was between 30% and 65% (intermediate risk) the optimal lung volume threshold, a functional residual capacity of 210% predicted, was applied. This contingent staging approach separated patients with an intermediate risk based on emphysema score alone into high risk (Functional Residual Capacity ≥210% predicted) or low risk (Functional Residual Capacity <210% predicted). This approach was more discriminatory for survival (HR = 3.123; 95% CI = 1.094–10.412) than either individual component alone.

Conclusion

Although to an extent limited by the small sample size, this preliminary study indicates that the composite Emphysema score-Functional Residual Capacity index might provide a better separation of high and low risk patients with COPD, than other individual predictors alone.