Gene and protein interaction network analysis in the epithelial-mesenchymal transition of Hertwig's Epithelial Root Sheath reveals periodontal regenerative drug targets – An in silico study

Background and aimHertwig’s Εpithelial Root Sheath (HΕRS) has a major function in the developing tooth roots. Earlier research revealed that it undergoes epithelial–mesenchymal transition, a vital process for the morphogenesis and complete development of the tooth and its surrounding periodontium. Few studies have demonstrated the role of HERS in cementogenesis through ΕMΤ. The background of this in-silico system biology approach is to find a hub protein and gene involved in the EMT of HERS that may uncover novel insights in periodontal regenerative drug targets.Materials and methodsThe protein and gene list involved in epithelial–mesenchymal transition were obtained from literature sources. The protein interaction was constructed using STRING software and the protein interaction network was analyzed. Molecular docking simulation checks the binding energy and stability of protein-ligand complex.ResultsResults revealed the hub gene to be DYRK1A(Hepcidin), and the ligand was identified as isoetharine. SΤRIΝG results showed a confidence cutoff of 0.9 in sensitivity analysis with a condensed protein interaction network. Overall, 98 nodes from 163 nodes of expected edges were found with an average node degree of 11.9. Docking results show binding energy of −4.70, and simulation results show an RMSD value of 5.6 Å at 50 ns.ConclusionIsoetharine could be a potential drug for periodontal regeneration.     

Oncogenic ras-induced down-regulation of pro-apoptotic protease caspase-2 is required for malignant transformation of intestinal epithelial cells

Resistance of carcinoma cells to anoikis, apoptosis that is normally induced by loss of cell-to-extracellular matrix adhesion, is thought to be essential for the ability of these cells to form primary tumors, invade adjacent tissues, and metastasize to distant organs. Current knowledge about the mechanisms by which cancer cells evade anoikis is far from complete. In an effort to understand these mechanisms, we found that ras, a major oncogene, down-regulates protease caspase-2 (which initiates certain steps of the cellular apoptotic program) in malignant human and rat intestinal epithelial cells. This down-regulation could be reversed by inhibition of a protein kinase Mek, a mediator of Ras signaling. We also found that enforced down-regulation of caspase-2 in nonmalignant intestinal epithelial cells by RNA interference protected them from anoikis. Furthermore, the reversal of the effect of Ras on caspase-2 achieved by the expression of exogenous caspase-2 in detached ras-transformed intestinal epithelial cells promoted well established apoptotic events, such as the release of the pro-apoptotic mitochondrial factors cytochrome c and HtrA2/Omi into the cytoplasm of these cells, significantly enhanced their anoikis susceptibility, and blocked their long term growth in the absence of adhesion to the extracellular matrix. Finally, the blockade of the effect of Ras on caspase-2 substantially suppressed growth of tumors formed by the ras-transformed cells in mice. We conclude that ras-induced down-regulation of caspase-2 represents a novel mechanism by which oncogenic Ras protects malignant intestinal epithelial cells from anoikis, promotes their anchorage-independent growth, and allows them to form tumors in vivo.     

DaiCee: A database for anti-cancer compounds with targets and side effect profiles

Identification of the toxicity of compounds is more crucial before entering clinical trials. Awareness of physiochemical properties, possible targets and side effects has become a major public health issue to reduce risks. Experimental determination of analyzing the physiochemical properties of a drug, their interaction with specific receptors and identifying their side-effects remain challenging is time consuming and costly. We describe a manually compiled database named DaiCee database, which contains 2100 anticancer drugs with information on their physiochemical properties, targets of action and side effects. It includes both synthetic and herbal anti-cancer compounds. It allows the search for SMILES notation, Lipinski''s and ADME/T properties, targets and side effect profiles of the drugs. This helps to identify drugs with effective anticancer properties, their toxic nature, drug-likeness for in-vitro and in-vivo experiments. It also used for comparative analysis and screening of effective anticancer drugs using available data for compounds in the database. The database will be updated regularly to provide the users with latest information. The database is available at the URL http://www.hccbif.org/usersearch.php     

Behavioral studies and veterinary management of orangutans at Bukit Merah Orang Utan Island,Perak, Malaysia

The Bukit Merah Orang Utan Island (OUI) Foundation has been conducting behavioral and veterinary research on orangutans as an attempt at ex situ conservation. Since 2010, the Primate Research Institute, Kyoto University has been collaborating with OUI to promote environmental enrichment and infant rearing by biological mothers in addition to the continuous efforts of refining the veterinary management of the endangered species. In 2011, three Bornean orangutans (Pongo pygmaeus pygmaeus) were released on an island, called BJ Island, adjacent to OUI. This island is approximately 5.6 ha in size, and 635 trees belonging to 102 plant species were identified prior to their release. Behavioral monitoring of the released individuals has been conducted to evaluate their behavioral adaptation to the new environment. Two of the three released orangutans were born in the wild, whereas the youngest individual was born on OUI and expected to learn forest survival strategies from the two older individuals. One of the orangutans was pregnant at the time of release and subsequently gave birth to two male infants on BJ Island. The behavioral monitoring indicated that these orangutans traveled more and spent more time on trees following their release onto BJ Island. However, resting was longer for two females both on OUI and BJ Island when compared to other populations. The orangutans consumed some natural food resources on BJ Island. The release into a more naturalistic environment may help the orangutans to develop more naturalistic behavioral patterns that resemble their wild counterparts.     

A glucose-selective fluorescence sensor based on boronic acid-diol recognition

A glucose selective diphenylboronic acid fluorescent sensor (10a) with a K(a) of 1472M(-1) has been synthesized and evaluated. This sensor shows a 43- and 49-fold selectivity for glucose over fructose and galactose, respectively. The binding affinity improvement is about 300-fold and the selectivity improvement for glucose over fructose is about 1400-fold compared with the monoboronic acid compound, phenylboronic acid. 1H NMR studies indicate that sensor 10a binds with alpha-D-glucofuranose in a bidentate manner (1:1 ratio).     

Acute Free-Iron Exposure Does Not Explain the Impaired Haemorheology Associated with Haemochromatosis

Introduction

Given the severity of the current imbalance between blood donor supply and recipient demand, discarded blood drawn from the routine venesections of haemochromatosis (HFE-HH) patients may serve as a valuable alternative source for blood banks and transfusion. We investigated whether functional or biochemical differences existed between HFE-HH and control blood samples, with particular focus upon the haemorheological properties, to investigate the viability of venesected blood being subsequently harvested for blood products.

Methods

Blood samples were collected from HFE-HH patients undergoing venesection treatment (n = 19) and healthy volunteers (n = 8). Moreover, a second experiment investigated the effects of a dose-response of iron (0, 40, 80, 320 mM FeCl₃) on haemorheology in healthy blood samples (n = 7). Dependent variables included basic haematology, iron status, haematocrit, red blood cell (RBC) aggregation (native and standardised haematocrit) and “aggregability” (RBC tendency to aggregate in a standard aggregating medium; 0.4 L/L haematocrit in a Dx70), and RBC deformability.

Results

Indices of RBC deformability were significantly decreased for HFE-HH when compared with healthy controls: RBC deformability was significantly decreased at 1–7 Pa (p < 0.05), and the shear stress required for half maximal deformability was significantly increased (p < 0.05) for HFE-HH. RBC aggregation in plasma was significantly increased (p < 0.001) for HFE-HH, although when RBC were suspended in plasma-free Dx70 no differences were detected. No differences in RBC deformability or RBC aggregation/aggregability were detected when healthy RBC were incubated with varying dose of FeCl₃.

Conclusion

HFE-HH impairs the haemorheological properties of blood; however, RBC aggregability was similar between HFE-HH and controls when cells were suspended in a plasma-free medium, indicating that plasma factor(s) may explain the altered haemorheology in HFE-HH patients. Acute exposure to elevated iron levels does not appear (in isolation) to account for these differences. Further consideration is required prior to utilising routine venesection blood for harvesting RBC concentrates due to the potential risk of microvascular disorders arising from impaired haemorheology.     

Defective MHC class I antigen surface expression promotes cellular survival through elevated ER stress and modulation of p53 function

Defects in Major Histocompatibility class I cell surface expression is thought to allow escape of tumor cells from immune surveillance. Hitherto, it is unclear whether this deficiency confers immune-independent survival advantage. We show here that class I cell surface expression deficiency due to defects in beta2 microglobulin or the transporter-associated with antigen processing (TAP) results in resistance to apoptosis in response to various cytotoxic signals. Reduced apoptosis correlated with altered p53 activation, which was due to compromised nuclear translocation of p53. Binding of p53 to glycogen synthase kinase-3beta (GSK3beta), which is known to phosphorylate and lead to cytoplasmic sequestration of p53, was enhanced in these cells. Consistently, endoplasmic reticulum (ER) stress, which promotes binding of p53 to GSK3beta was constitutively elevated in the absence of class I cell surface expression. Taken together, the results suggest a non-immunological causal role for defective class I cell surface expression in regulating cellular survival in a p53-dependent manner, through the upregulation of ER stress, which could be another mechanism leading to carcinogenesis.     

Characterization of chemically treated bacterial (Acetobacter xylinum) biopolymer: some thermo-mechanical properties

Bacterial cellulose prepared from pellicles of Acetobacter xylinum (Gluconacetobacter xylinus) is a unique biopolymer in terms of its molecular structure, mechanical strength and chemical stability. The biochemical analysis revealed that various alkali treatment methods were effective in removing proteins and nucleic acids from native membrane resulting in pure cellulose membrane. The effect of various treatment regimens on thermo-mechanical properties of the material was investigated. The cellulose in the form of purified cellulose membranes was characterized by differential scanning calorimetry (DSC), thermo-gravimetric analysis (TGA) and dynamic mechanical thermal analysis (DMTA). The glass transition temperature (T(g)) of the native cellulose (untreated, compressed and dried pellicle) was found to be 13.94 degrees C, in contrast, the chemically treated cellulose membranes has higher T(g) values, ranging from 41.41 degrees C to 48.82 degrees C. Investigations on isothermal crystallization were carried out to study the bulk crystallization kinetics. Thermal decomposition pattern of the native as well as alkali treated cellulose was determined by obtaining thermo-gravimetric curves. At higher temperatures (>300 degrees C), the biopolymer was found to degrade. Nevertheless, the alkaline treated cellulose membrane was more stable (between 343.27 degrees C and 370.05 degrees C) in comparison to the native cellulose (298.07 degrees C). Further, the percentage weight loss in case of native cellulose was found to be 26.57%, in comparison to 6.45% for the treated material, at 300 degrees C. The DMTA revealed complex dynamic modulus of the material, at different temperatures and fixed shear stress, applied at a frequency of 5 Hz. The study delineated the effect of alkali treatment regimens, on the thermo-mechanical properties of bacterial cellulose for its application over a wide range of temperatures.     

An apoptotic signaling pathway in the interferon antiviral response mediated by RNase L and c-Jun NH2-terminal kinase

Cellular stress responses induced during viral infections are critical to the health and survival of organisms. In higher vertebrates, interferons (IFNs) mediate the innate antiviral response in part through the action of RNase L, a uniquely regulated enzyme. RNase L is activated by 5'-phosphorylated, 2'-5' oligoadenylates (2-5A) produced from IFN-inducible and double stranded RNA-dependent synthetases. We show that viral activation of the c-Jun NH2-terminal kinases (JNK) family of MAP kinases and viral induction of apoptosis are both deficient in mouse cells lacking RNase L. Also, JNK phosphorylation in response to 2-5A was greatly reduced in RNase L-/- mouse cells. In addition, 2-5A treatment of the human ovarian carcinoma cell line, Hey1b, resulted in specific ribosomal RNA cleavage products coinciding with JNK activation. Furthermore, suppression of JNK activity with the chemical inhibitor, SP600125, prevented apoptosis induced by 2-5A. In contrast, inhibition of alternative MAP kinases, p38 and ERK, failed to prevent 2-5A-mediated apoptosis. Short interfering RNA to JNK1/JNK2 mRNAs resulted in JNK ablation while also suppressing 2-5A-mediated apoptosis. Moreover, Jnk1-/- Jnk2-/- cells were highly resistant to the apoptotic effects of IFN and 2-5A. These findings suggest that JNK and RNase L function in an integrated signaling pathway during the IFN response that leads to elimination of virus-infected cells through apoptosis.