Protein-protein interaction analysis of Alzheimer`s disease and NAFLD based on systems biology methods unhide common ancestor pathways

Aim: Analysis reconstruction networks from two diseases, NAFLD and Alzheimer`s diseases and their relationship based on systems biology methods

Background: NAFLD and Alzheimer`s diseases are two complex diseases, with progressive prevalence and high cost for countries. There are some reports on relation and same spreading pathways of these two diseases. In addition, they have some similar risk factors, exclusively lifestyle such as feeding, exercises and so on. Therefore, systems biology approach can help to discover their relationship

Methods: DisGeNET and STRING databases were sources of disease genes and constructing networks. Three plugins of Cytoscape software, including ClusterONE, ClueGO and CluePedia, were used to analyze and cluster networks and enrichment of pathways. An R package used to define best centrality method. Finally, based on degree and Betweenness, hubs and bottleneck nodes were defined

Results: Common genes between NAFLD and Alzheimer`s disease were 190 genes that used construct a network with STRING database. The resulting network contained 182 nodes and 2591 edges and comprises from four clusters. Enrichment of these clusters separately lead to carbohydrate metabolism, long chain fatty acid and regulation of JAK-STAT and IL-17 signaling pathways, respectively. Also seven genes selected as hub-bottleneck include: IL6, AKT1, TP53, TNF, JUN, VEGFA and PPARG. Enrichment of these proteins and their first neighbors in network by OMIM database lead to diabetes and obesity as ancestors of NAFLD and AD

Conclusion: Systems biology methods, specifically PPI networks, can be useful for analyzing complicated related diseases. Finding Hub and bottleneck proteins should be the goal of drug designing and introducing disease markers

rapid and sensitive assay to identify HLA-DQ2/8 risk alleles for celiac disease using real-time PCR method

Aim: To perform a simple, rapid and sensitive Real-time PCR based SYBR Green method to determine the human leukocyte antigen [HLA]-DQ 2/8 alleles in celiac disease [CD] patients

Background: Many molecular techniques are available to determine the HLA-DQ2 and DQ8 alleles, but they are too expensive and have many steps that make them difficult to use

Methods: To determine the HLA-DQ 2/8 alleles we have developed a new real-time PCR assay, using SYBR Green technique with melting curve analysis on genomic DNA isolated from 75 CD patients and 94 healthy controls. The specific primers to examine HLADQA1* 05, HLA-DQB1*02 and HLA-DQB1*0302 alleles were used and results were compared with commercially available kits

Results: Using this method, the presence of HLA-DQ2 and HLA-DQ8 alleles were determined with sensitivity and specificity 80% and 100% respectively and compared to low resolution commercially available kits, the results of this method were more efficient. The frequency of DQ2 and DQ8 in patients was 76% and 29%, respectively and overall 96% of patients were carries DQ2 and/or DQ8 alleles

Conclusion: The result of this study showed that Real-time PCR using SYBR Green method with melting curve analysis has good efficiency to identify the HLA-DQ2/8 risk alleles

Comparative study of gastric cancer and chronic gastritis via network analysis

Aim: In this study the significant differentially expressed genes [DEGs] related to gastric cancer [GC] and chronic gastritis were screened to introduce common and distinctive genes between the two diseases

Background: Diagnosis of gastric cancer as a mortal disease and chronic gastritis the stomach disorder which can be considered as risk factor of GCs required safe and effective molecular biomarkers

Methods: Microarray profiles were downloaded from Gene Expression Omnibus [GEO] and analyzed via GEO2R. The candidate DEGs plus relevant genes from STRING database were interacted by Cytoscape software version 3.6.0 the central nodes were determined and analyzed

Results: JUN, GAPDH, FOS, TP53, PRDM10, VEGFA, and CREB1 as central nodes and TFF1 and ERG1 as the top changed expressed genes were determined as critical nodes related to gastric cancer. GAPDH, PRDM10, TP53, JUN, AKT1, EGFR, MAPK1, EGF, DECR1, and MYC were identified as common remarkable genes between GC and chronic gastritis

Conclusion: Identification of distinctive and common genes between GC and chronic gastritis can be useful in the early stage detection of disease and reducing risk of GCs

Introducing crucial protein panel of gastric adenocarcinoma disease

Aim: Since interactome analysis of diseases can provide candidate biomarker panel related to the diseases, in this research, proteinprotein interaction [PPI] network analysis is used to introduce the involved crucial proteins in Gastric adenocarcinoma [GA]

Background: Gastric adenocarcinoma [GA] is the most common type of stomach cancer. There is no efficient diagnostic molecular method for GA

Methods: Applying Cytoscape software 3.4.0 and String Database, the PPI network was constructed for 200 genes. Based on centrality parameters, the critical nodes were screened. Gene ontology of the key proteins for pathway analysis and molecular function processing were done and the highlighted pathways and activities were discussed

Results: Among 200 initial genes, 141 genes were included in a main connected network. Seven crucial proteins, including tumor protein p53, epidermal growth factor receptor, albumin, v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog [avian], v-akt murine thymoma viral oncogene homolog 1, v-src sarcoma [Schmidt-Ruppin A-2] viral oncogene homolog [avian] and catenin [cadherin-associated protein], beta 1, 88kDa, and Myogenic differentiation 1, were introduced as key nodes of the network. These identified proteins are mostly involved in pathways and activities related to cancer

Conclusion: In conclusion, the finding is corresponding to the significant roles of these introduced proteins in GA disease. This protein panel may be a useful probe in the management of GA

Oral squamous cell cancer protein-protein interaction network interpretation in comparison to esophageal adenocarcinoma

Aim: The aim of this study is to present the oral Squamous Cell Cancer protein-protein interaction network interpretation in comparison to esophageal adenocarcinoma

Background: Oral squamous cell cancer [OSCC] is a common disease worldwide, with poor prognosis and limited treatment. Thus, introducing molecular markers through network analysis can be helpful

Methods: STRING database [DB] was applied for network construction through Cytoscape 3.4.0. Clue GO handled the gene annotation for the retrieved clusters. Eight proteins were indicated to be differential in the network constitution

Results: The centrality and clustering analysis indicate that TP53 plays an over-significant role in network integrity among eight most central proteins including TP53, AKT1, EGFR, MYC, JUN, CDH1, CCND1, and CTNNB1. The suggested biomarker set is very similar to the related biomarker panel of esophageal adenocarcinoma

Conclusion: The ontology analysis implies that the prominent proteins are involved in regulation of smooth muscle cell proliferation, regulation of fibroblast proliferation, and response to UV-A processes. In conclusion, these proteins and their associated biological processes may be more critical compared to other reported biomarkers for OSCC. Nevertheless, validation studies are required for confirming the pivotal role of potential candidates. Similar biomarker panel of this disease and esophagus adenocarcinoma is corresponded to the origin of the two malignancies

Network analysis of common genes related to esophageal, gastric, and colon cancers

Aim: The aim of this study was to provide a biomarker panel for esophageal, gastric and colorectal cancers. It can help introducing some diagnostic biomarkers for these diseases

Background: Gastrointestinal cancers [GICs] including esophageal, gastric and colorectal cancers are the most common cancers in the world which are usually diagnosed in the final stages and due to heterogeneity of these diseases, the treatments usually are not successful. For this reason, many studies have been conducted to discover predictive biomarkers

Methods: In the present study, 507 genes related to esophageal, gastric and colon cancers were extracted. The network was constructed by Cytoscape software [version 3.4.0]. Then a main component of the network was analyzed considering centrality parameters including degree, betweenness, closeness and stress. Three clusters of the protein network accompanied with their seed nodes were determined by MCODE application in Cytoscape software. Furthermore, Gene Ontology [GO] analysis of the key genes in combination to the seed nodes was performed

Results: The network of 17 common differential expressed genes in three esophageal, gastric and colon adenocarcinomas including 1730 nodes and 9188 edges were constructed. Eight crucial genes were determined. Three Clusters of the network were analyzed by GO analysis

Conclusion: The analyses of common genes of the three cancers showed that there are some common crucial genes including TP53, EGFR, MYC, AKT1, CDKN2A, CCND1 and HSP90AA1 which are tightly related to gastrointestinal cancers and can be predictive biomarkers for these cancers

systems biology analysis protein-protein interaction of NASH and IBD based on comprehensive gene information

Aim: Analysis reconstruction networks from two diseases, IBD and NASH and their relationship, based on systems biology methods

Background: IBD and NASH are two complex diseases, with progressive prevalence and high cost for countries. There are some reports on co-existence of these two diseases. In addition, they have some similar risk factors such as age, obesity, and insulin resistance. Therefore, systems biology approach can help to discover their relationship

Methods: DisGeNET and STRING databases were sources of disease genes and constructing networks. Three plugins of Cytoscape software, including ClusterONE, ClueGO and CluePedia, were used to analyze and cluster networks and enrichment of pathways. Based on degree and Betweenness, hubs and bottleneck nodes were defined

Results: Common genes between IBD and NASH construct a network with 99 nodes. Common genes between IBD and NASH were extracted and imported to STRING database to construct PPI network. The resulting network contained 99 nodes and 333 edges. Five genes were selected as hubs: JAK2, TLR2, TP53, TLR4 and STAT3 and five genes were selected as bottleneck including: JAK2, TP53, AGT, CYP3A4 and TLR4. These genes were hubs in analysis network that was constructed from hubs of NASH and IBD networks

Conclusion: Systems biology methods, specifically PPI networks, can be useful for analyzing complicated related diseases. Finding Hub and bottleneck proteins should be the goal of drug designing and introducing disease markers

Protein-protein interaction network analysis of cirrhosis liver disease

Aim: Evaluation of biological characteristics of 13 identified proteins of patients with cirrhotic liver disease is the main aim of this research

Background: In clinical usage, liver biopsy remains the gold standard for diagnosis of hepatic fibrosis. Evaluation and confirmation of liver fibrosis stages and severity of chronic diseases require a precise and noninvasive biomarkers. Since the early detection of cirrhosis is a clinical problem, achieving a sensitive, specific and predictive novel method based on biomarkers is an important task

Methods: Essential analysis, such as gene ontology [GO] enrichment and protein-protein interactions [PPI] was undergone EXPASy, STRING Database and DAVID Bioinformatics Resources query

Results: Based on GO analysis, most of proteins are located in the endoplasmic reticulum lumen, intracellular organelle lumen, membrane-enclosed lumen, and extracellular region. The relevant molecular functions are actin binding, metal ion binding, cation binding and ion binding. Cell adhesion, biological adhesion, cellular amino acid derivative, metabolic process and homeostatic process are the related processes. Protein-protein interaction network analysis introduced five proteins [fibroblast growth factor receptor 4, tropomyosin 4, tropomyosin 2 [beta], lectin, Lectin galactoside-binding soluble 3 binding protein and apolipoprotein A-I] as hub and bottleneck proteins

Conclusion: Our result indicates that regulation of lipid metabolism and cell survival are important biological processes involved in cirrhosis disease. More investigation of above mentioned proteins will provide a better understanding of cirrhosis disease

Metabolomic analysis of human cirrhosis, hepatocellular carcinoma, non-alcoholic fatty liver disease and non-alcoholic steatohepatitis diseases

Metabolome analysis is used to evaluate the characteristics and interactions of low molecular weight metabolites under a specific set of conditions. In cirrhosis, hepatocellular carcinoma, non-alcoholic fatty liver disease [NAFLD] and non-alcoholic steatotic hepatitis [NASH] the liver does not function thoroughly due to long-term damage. Unfortunately the early detection of cirrhosis, HCC, NAFLD and NASH is a clinical problem and determining a sensitive, specific and predictive novel method based on biomarker discovery is an important task. On the other hand, metabolomics has been reported as a new and powerful technology in biomarker discovery and dynamic field that cause global comprehension of system biology. In this review, it has been collected a heterogeneous set of metabolomics published studies to discovery of biomarkers in researches to introduce diagnostic biomarkers for early detection and the choice of patient-specific therapies

Effects of saffron [Crocus sativus L.] stigma extract and its active constituent crocin on neuropathic pain responses in a rat model of chronic constriction injury

This study was designed to investigate the therapeutic effects of saffron [Crocus Sativus L] and its main constituent crocin on neuropathic pain behavioral responses induced by chronic constriction injury [CCI] in rats. Adult male Wistar rats [200 to 250 g] were randomly assigned into 5 groups: Sham + saline, CCI + saline, CCI+ saffron [30 mg/kg], CCI +crocin [15 mg/kg] and CCI + crocin [30 mg/kg]. CCI was induced by applying 4 loose ligatures around the sciatic nerve. Two weeks after nerve lesion, injections of saline, saffron or crocin were started and continued until 26th day post-surgery. Pain behavioral responses including mechanical allodynia [von Frey filament testing] and thermal hyperalgesia were measured in 14, 17, 20, 23, 26, and 40th days after CCI. CCI significantly increased pain behavioral responses. Saffron and crocin [30 mg/kg] decreased thermal hyperalgesia and mechanical allodynia on day 26, and this effect continued until the day 40. Crocin at lower dose [15 mg/kg] was ineffective. These findings indicate that treatment of saffron and crocin after CCI may have a therapeutic effect against neuropathic pain, suggesting that these substances may offer new strategies for the treatment of this highly debilitating condition

Evaluation of organs at risk's dose in external radiotherapy of brain tumors

Radiotherapy plays an important role in the management of most malignant and many benign primary central nervous system [CNS] tumors. Radiotherapy affects both tumor cells and uninvolved normal cells; so, it is important to estimate absorbed dose to organs at risk in this kind of treatment. The aim of this study was to determine the absorbed dose to chiasma, lens, optic nerve, retina, parotid, thyroid and submandibular gland in frontal lobe brain tumors radiotherapy based on treatment planning system [TPS] calculation and direct measurement on the phantom. A head and neck phantom was constructed using natural human bone and combination of paraffin wax and Sodium Chloride [NaCl] as tissue-equivalent material. Six cylinders were made of phantom material which had cavities to insert Thermoluminescent Dosimeters [TLDs] at several depths in order to measure absorbed dose to chiasma, lens, optic nerve, retina, parotid, thyroid and submandibular gland. Three routine conventional plans associated with tumors of this region and a new purposed technique were performed on the phantom and dose distribution and absorbed dose to critical organs were compared using treatment planning system [TPS] calculation and direct measurement on the phantom. Absorbed doses were measured with calibrated TLDs and are expressed in centigray [cGy]. In all techniques absorbed dose to all organs except the lenses were at their tolerance dose levels and in the new purposed technique, absorbed dose to chiasma was significantly reduced. Our findings showed differences in the range of 1-5% in all techniques between TPS calculation and direct measurements for all organs except submandibular glands and thyroid. Because submandibular glands and thyroid are far from primary radiation field, TLD reading in these regions although small but differs from TPS calculation which shows very smaller doses. This might be due to scattered radiation which is not well considered in the TPS. In the new technique, because the chiasma is out of the radiation field, absorbed dose was reduced significantly

Protein-Protein Interaction Network could reveal the relationship between the breast and colon cancer

This study is aimed to elicit the possible correlation between breast and colon cancer from molecular prospective by analyzing and comparing pathway-based biomarkers. Breast and colon cancer are known to be frequent causes of morbidity and mortality in men and women around the world. There is some evidence that while the incident of breast cancer in young women is high, it is reported lower in the aged women. In fact, aged women are more prone to colorectal cancer than older men. . In addition, many studies showed that several biomarkers are common among these malignancies. The genes were retrieved and compared from KEGG database and WikiPathway, and subsequently, protein-protein interaction [PPI] network was constructed and analyzed using Cytoscape v:3.2.1 software and related algorithms. More than forty common genes were identified among these malignancies; however, by pathways comparison, twenty genes are related to both breast and colon cancer. Centrality and cluster screening identified hub genes, including SMAD2, SMAD3, [SMAD4, MYC], JUN, BAD, TP53. These seven genes are enriched in regulation of transforming growth factor beta receptor signaling pathway, positive regulation of Rac protein signal transduction, positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway, and positive regulation of mitotic metaphase/anaphase transition respectively. As there are numerous genes frequent between colorectal cancer and breast cancer, there may be a common molecular origin for these malignancies occurrences. It seems that breast cancer in females interferes with the rate of colorectal cancer incidence

High-dose-rate 192Ir brachytherapy dose verification: a phantom study

The high-dose-rate [HDR] brachytherapy might be an effective tool for palliation of dysphagia. Because of some concerns about adverse effects due to absorbed radiation dose, it is important to estimate absorbed dose in risky organs during this treatment. This study aimed to measure the absorbed dose in the parotid, thyroid, and submandibular gland, eye, trachea, spinal cord, and manubrium of sternum in brachytherapy in an anthropomorphic phantom. To measure radiation dose, eye, parotid, thyroid, and submandibular gland, spine, and sternum, an anthropomorphic phantom was considered with applicators to set thermoluminescence dosimeters [TLDs]. A specific target volume of about 23 cm3 in the upper thoracic esophagus was considered as target, and phantom planned computed tomography [CT] for HDR brachytherapy, then with a micro-Selectron HDR [192Ir] remote after-loading unit. Absorbed doses were measured with calibrated TLDs and were expressed in centi-Gray [cGy]. In regions far from target [>/= 16 cm] such as submandibular, parotid and thyroid glands, mean measured dose ranged from 1.65 to 5.5 cGy. In closer regions [

Introducing biomarker panel in esophageal, gastric, and colon cancers; a proteomic approach

Cancer research is an attractive field in molecular biology and medicine. By applying large-scale tools such as advanced genomics and proteomics, cancer diagnosis and treatment have been improved greatly. Cancers of esophagus, gastric, and colon accounted for major health problem globally. Biomarker panel could bring out the accuracy for cancer evaluation tests as it can suggest a group of candidate molecules specified to particular malignancy in a way that distinguishing malignant tumors from benign, differentiating from other diseases, and identifying each stages with high specificity and sensitivity. In this review, a systematic search of unique protein markers reported by several proteomic literatures are classified in their specific cancer type group as novel panels for feasible accurate malignancy diagnosis and treatment. About thousands of introduced proteins were studied; however, a small number of them belonged to a specific kind of malignancy. In conclusion, despite the fact that combinatorial biomarkers appear to be hopeful, more evaluation of them is crucial to achieve the suitable biomarker panel for clinical application. This effort needs more investigations and researches for finding a specific and sensitive panel

Protein drug targets of Lavandula angustifolia on treatment of rat Alzheimer's disease

Different treatment strategies of Alzheimer›s disease [AD] are being studied for treating or slowing the progression of AD. Many pharmaceutically important regulation systems operate through proteins as drug targets. Here, we investigate the drug target proteins in beta-amyloid [A beta] injected rat hippocampus treated with Lavandula angustifolia [LA] by proteomics techniques. The reported study showed that lavender extract [LE] improves the spatial performance in AD animal model by diminishing A beta production in histopathology of hippocampus, so in this study neuroprotective proteins expressed in A beta injected rats treated with LE were scrutinized. Rats were divided into three groups including normal, A beta injected, and A beta injected that was treated with LE. Protein expression profiles of hippocampus tissue were determined by two-dimensional electrophoresis [2DE] method and dysregulated proteins such as Snca, NF-L, Hspa5, Prdx2, Apoa1, and Atp5a1were identified by MALDI-TOF/TOF. KEGG pathway and gene ontology [GO] categories were used by searching DAVID Bioinformatics Resources. All detected protein spots were used to determine predicted interactions with other proteins in STRING online database. Different isoforms of important protein, Snca that exhibited neuroprotective effects by anti-apoptotic properties were expressed. NF-L involved in the maintenance of neuronal caliber. Hspa5 likewise Prdx2 displays as anti-apoptotic protein that Prdx2 also involved in the neurotrophic effects. Apoa1 has anti-inflammatory activity and Atp5a1, produces ATP from ADP. To sum up, these proteins as potential drug targets were expressed in hippocampus in response to effective components in LA may have therapeutic properties for the treatment of AD and other neurodegenerative diseases

Apoptosis/necrosis induction by ultraviolet, in ER positive and ER negative breast cancer cell lines

Background: Ultraviolet [UV] light exposure has been one of the major inducers of apoptosis. UV exposure has caused pyrimidine dimers and DNA fragmentation which might lead to cell cycle arrest and apoptosis signals activation. UV induced apoptosis has investigated in MDA-MB 468 as an ER negative breast adenocarcinoma and MCF-7 as an ER positive breast cancer cell line. Apoptosis induction rate by UV might be different in these two types of cells due to different biological characteristics of the cell

Objectives: In this paper we have evaluated serial dose of UV-B exposure on ER positive and ER negative breast cancer cell lines and its effect on apoptosis or necrosis induction in these cells

Materials and Methods: MDA-MB468 and MCF-7 cell lines have cultured for 24 hours and UV exposure has carried out at 290 nm at dose of 154 J/m[2] to 18 KJ/m[2] using UV lamp. UV exposed cells have incubated in cell culture condition for 24 or 48 hours following UV exposure and the cells have stained and analyzed by flow cytometry for apoptosis evaluation by Annexin V/PI method

Results: Apoptosis rate [PI and Annexin V double positive cells] after 24 hours incubation was higher in 24 hours in comparison with 48 hours incubation in both cell lines. The frequency of PI positive MDA-MB 468 cells was higher than PI and Annexin V double positive cells after 48 hours. PI positive MDA-MB 468 cells were significantly higher than MCF-7 cells in 24 hours incubation time

Conclusions: The results have shown that MDA-MB 468 cells were more sensitive to UV exposure and DNA fragmentation and necrosis pathway was dominant in these cells

Vitamin D Binding Protein as screening biomarker candidate for late-onset preeclampsia without intrauterine growth restriction during 16 week of gestation

The aim of this investigation was conducted to proteomic analysis of plasma obtained from pregnant women who destined to develop late-onset preeclampsia without intrauterine growth restriction [IUGR] during 16[th] week of gestation. Plasma was obtained from primiparous women during 16[th] week of gestation. 2-DE proteomic analysis was done for plasma from 11 healthy pregnant women and 11 women who developed preeclampsia later. Using bioinformatic analysis with Progenesis SameSpots ver4.0 software and ANOVA test, expression of 2 spots were statistically different between two groups. In preeclamptic state, expression of both were decreased, one of these spots was vitamin D binding protein [p-value: 0.047], the other one will be discussed in another paper. According to results, we concluded that during 16[th] week of gestation, occurance of late-onset preeclampsia without IUGR is predictable. During this week, pathology of disease is present and may be the process of placental degeneration and impaired placentation are include in disease pathology

Stabilizing and dispersing methods of TiO[2] nanoparticles in biological studies

TiO[2] nanoparticles [NPs] might be considered as the most important photosensitizer due to high photocatalytic and sonocatalytic efficiency, low toxicity, excellent biocompatibility, low cost and high chemical stability. TiO[2]-NPs normally tend to aggregate in physiological medium and which results to decreased cell viability and inducing expression of stress-related genes. Thus dispersion and stability of TiO[2] NPs should be considered in biological application. This paper deals on various dispersing methods such as ultrasonication, electrostatic, steric electrosteric stabilization that suppress agglomeration and stabilizes the dispersed NPs in aqueous medium

Sonication breaks up agglomerated NPs in a solvent. The results showed that probe sonication performs better than bath sonication in dispersing TiO[2] agglomerates, but sonication couldn't prevent long term aggregation of nanoparticles and in order to form stable dispersions, it is not enough to break nanoparticles apart. Agglomerated NPs can be separated by overcoming the weaker attractive forces by electrostatic, steric or electrosteric interactions. Electrostatic stabilization takes place when charges accumulate at the surface of particles. At values of potential more than 30 mV or less than -30 mV no agglomeration occurs. Ionic strength and pH influence on electrostatic stabilization; when pH is far from the isoelectric point, agglomeration is suppressed. In a sterically stabilized dispersion large molecules such as polymers, surfactants and biomolecules, adsorbed on to the surface of particles suppress re-agglomeration. PEG is a hydrophilic polymer, non-toxic and non-immunogenic, and has favorable pharmacokinetics and tissue distribution. PEGylation of NPs not only prevents agglomeration, but also enhances their biocompatibility and increases the in vivo circulation time

study of "dihydropyrimidinase related proteins [DRPs]" expression changes influence in malignant astrocytoma brain tumor

Dihydropyrimidinase Related Proteins [DRPs] have known homologous to the Collapsing Response Mediator Proteins [CRMPs]. The DRP gene family has comprised four members, DRP 1, 2, 3, and 4, all out of which have considered to be involved in axonal outgrowth and path-finding. The protein has extracted from tumor, normal brain tissues, and then the protein purity has evaluated by Bradford test and spectrophotometric methods. In this study, proteins has separated by Two-Dimensional Gel [2DG] electrophoresis method and then spots have analyzed and compared using statistical data and specific software [Progenesis Same Spots].Spots have identified by pH isoelectric, molecular weights and data banks. The 2D gel has shown 800 spots totally. Two spots have reported for DRP2, and one spot has reported for DRP3 in the human brain proteome, that have differed in pH isoelectric, and Molecular Weights values. This protein family has involved in neuronal differentiation and axonal guidance, and abundantly influenced in the developing brain, but their expression persisted into adulthood. DRP2 has regulated by phosphorylation, Glycogen synthase kinase 3, regulate phosphorylation of DRP2 an inactive from, and induced neuronal polarity

Cluster and principal component analysis of human glioblastoma multiforme [GBM] tumor proteome

Glioblastoma Multiforme [GBM] or grade IV astrocytoma is the most common and lethal adult malignant brain tumor. Several of the molecular alterations detected in gliomas may have diagnostic and/or prognostic implications. Proteomics has been widely applied in various areas of science, ranging from the deciphering of molecular pathogen nests of discuses. In this study proteins were extracted from the tumor and normal brain tissues and then the protein purity was evaluated by Bradford test and spectrophotometry. In this study, proteins were separated by 2-Dimensional Gel [2DG] electrophoresis method and the spots were then analyzed and compared using statistical data and specific software. Protein clustering analysis was performed on the list of proteins deemed significantly altered in glioblastoma tumors [t-test and one-way ANOVA; P< 0.05]. The 2D gel showed totally 876 spots. We reported, 172 spots were exhibited differently in expression level [fold > 2] for glioblastoma. On each analytical 2D gel, an average of 876 spots was observed. In this study, 188 spots exhibited up regulation of expression level, whereas the remaining 232 spots were decreased in glioblastoma tumor relative to normal tissue. Results demonstrate that functional clustering [up and down regulated] and Principal Component Analysis [PCA] has considerable merits in aiding the interpretation of proteomic data. 2D gel electrophoresis is the core of proteomics which permitted the separation of thousands of proteins. High resolution 2DE can resolve up to 5,000 proteins simultaneously. Using cluster analysis, we can also form groups of related variables, similar to what is practiced in factor analysis