9^th International Conference on Bioinformatics November 13-14, 2017 Paris, France

Guasti P N has a DVM from Federal Rural University of Rio de Janeiro. She obtained her Master’s Degree and PhD in Animal Reproduction from Sao Paulo State University (UNESP/Botucatu). She is currently Postdoctoral Researcher at the Sao Paulo State University. Her research interest focuses on the proteomics of equine seminal plasma, sperm membrane and epididymal fluid and its relations with the fertility.

Seminal plasma (SP) consists of secretions produced by testes, epididymides and accessory sex glands (AG); and contains several compounds that play important roles in sperm maturation and fertilization. The aim of this study was to investigate the expression of SP proteins after orchiectomy in stallions. Fourteen stallions were submitted to semen collection and orchiectomy. Fifteen and 30 days after the procedure, semen collection was performed again. SP samples were centrifuged and determination of total protein was performed by BCA-assay. SP proteins before (SP) and after castration (D15; D30) were analyzed by 2D-LC-MS/MS. Different proteins were identified among groups; 15 proteins in SP, 13 in D15 and 15 in D30. Castration resulted in a decrease in proteins related to reproductive process. Four proteins (KLK1E2, ALB, CLU, Equ-c1) were common to all groups and were involved in binding and catalytic activity. Catalase was identified only in castrated animals; nine proteins were identified only in D30, which were involved in immune system and metabolic process, angiogenesis and biological adhesion. In general, AG conforms to the general pattern of steroid-regulated systems as they are under androgenic control, in which hormone withdrawal may lead to differential decreases in protein expression. SP protein expression is not immediately terminated after castration, possibly due to residual levels of testosterone (under analysis). In conclusion, removal of testes influenced the expression of SP proteins and revealed exclusively expressed proteins related to the inflammatory response and tissue reconstruction; the proteins involved in reproductive process were underexpressed possibly due to decreased testosterone.

Nahed Adam Abdalla Jebrel, Alwatania University, college of medical lab. Khartoum, Sudan.

The aim of this study was to detect the presence of mcr-1 gene in clinical isolates of Enterobacteriaceae in Khartoum State, Sudan, at the period between February and July 2016 using 50 consecutive clinical Enterobacteriaceae isolates. Species was identified using standard biochemical tests. Antimicrobial susceptibility was done by using the following antibiotics; ciprofloxacin, gentamicin, co-trimoxazole, cefotaxime, cefuroxime and cefixime. DNA was extracted by using bacterial genomic extraction Kits. For the entire isolated organism, PCR was done to detect mcr-1 by using specific primer. The most commonly isolated organism was E. coli 38 (76%), followed by Proteus spp. 8 (16%), and K. pneumoniae 4 (8%). Males (60%) are more infected than females (40%), and elderly patients 61-90 years (42%) are found to be more susceptible to infection. We also reported highly resistant rate to ciprofloxacin (66%), gentamicin (68%) and cefuroxime (96%). mcr-1 gene was detected in 7 (14%) isolates, mostly in E. coli. We reported for the first time in Sudan the presence of mcr-1 gene in clinical isolates, and the prevalence of this gene is higher when compared to other countries.

Maryam Bahmanzadeh has completed her PhD from Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran. She is an Assistant Professor in Anatomical Sciences Hamadan University of Medical Sciences, Iran and a Clinical Embryologist. She has published more than 10 papers in reputed journals.

Follicular fluid (FF) results from the transfer of blood plasma components and the secretory activity of the oocyte, granulosa and thecal cells. Certain components of FF might be used as indicators for the maturation and the quantity of the oocytes. Proteins can be used as biomarkers for reproductive diseases using both FF and plasma. Age-related infertility is usually considered as a problem that can be solved by assisted reproduction technology. Therefore, the identification of novel biomarkers that are linked to reproductive aging is the subject of this study. FF was obtained from healthy younger (20–32 years old) and older (38–42 years old) women undergoing intracytoplasmic sperm injection (ICSI) due to male factor infertility. In this study, we investigated the protein composition of human FF obtained from females undergoing ICSI using the matrix-assisted laser desorption-ionization time-of-flight/time-of-flight (MALDI-TOF-TOF) mass spectrometry technique. Twenty-three protein spots showed reproducible and significant changes in the aged compared to the young group. Of these, 19 protein spots could be identified using MALDI-TOF-TOF-MS. As a result of MASCOT search, five unique downregulated proteins were identified in the older group. These were identified as serotransferrin, hemopexin precursor, complement C3, C4 and kininogen. A number of protein markers were found that may help develop diagnostic methods of infertility.

Qurat-ul-Ain, is a Ph.D student at Dr.Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi. She is collaborative Research Student at Department of Dermatology and Allergy University of Ulm Germany, Ms. Qurat-ul-Ain has characterized a variety of newly designed chemical compounds in term of their antioxidant and pro-oxidant properties. She studies these in melanoma cell and melanocytes. Some of the studied compounds reveal an inhibitory effect on melanoma cells, but not on their benign counterpart, the melanocyte. The mechanisms of action of these compounds are being investigated.Qurat-ul-Ain has authored 19 articles published in international journals.

Melanoma, the most dangerous skin cancer, originates from the melanocytes and has a high tendency to invade neighboring tissues, and metastasize. Both bioactive compounds appear to be involved in the modulation of melanocyte transformation and melanoma progression as well as invasion. Consequently, potent bioactive compounds may prevent transformation and progression of the tumor. Melanoma is also the most common malignancy diagnosed in United States. Out of 3.5 million, 2 million cancer cases diagnosed in US annually, resulting mostly in-patient death and poor survival. With emerging new therapies early detection and treatment has resulted in high survival rates with 85% of patients surviving for at least 10 years. One of these upcoming therapeutics is the use of bioactive compounds, which have proven to show increase response rate (IRR) and overall survival (OS) rates. In fact, dacarbazine is the only FDA approved chemotherapeutic bioactive compound for melanoma treatment. Therefore, we have identified eight bioactive compounds of four different new synthetic classes synthesized by our collaborator as anti-melanoma/anti invasion agents. These compounds were previously found to posse’s antioxidant and prooxidant in an in vitro antioxidant assay. Compounds 1, 2, 3, 4, 5, 6, 7 and 8 were found to be most potent anti-melanoma agent. We are now testing these compounds for their migration inhibition role in skin melanoma as well as skin stem cells in vitro and their ability to reduce proliferation and spreading. We are currently analyzing the influence of these compounds on the molecular pathways, involved in the proliferation-invasion inhibition. Recent Publication: 1. Barakat A, Ghabbour H A, Al-Majid A M, Imad Qurat-ul-Ain R, Javaid K, Shaikh N N and Wadood A (2016) Synthesis, X-ray crystal structures, biological evaluation, and molecular docking studies of a series of barbiturate derivatives. Journal of Chemistry 1-11. 2. Donat-Vargas C, Berglund M, Glynn A, Wolk A and Åkesson A (2017) Dietary polychlorinated biphenyls, long-chain n-3 polyunsaturated fatty acids and incidence of malignant melanoma. European Journal of Cancer 72:137-143.

Introduction: Alzheimer’s disease (AD) is the most common form of dementia. Amyloid beta(1-42) is prone to aggregate and found in plaque interacting with various proteins. Low molecular weight oligomeric form of amyloid beta is found as most toxic and responsible for disease process. Hippocampus is the primary region of the brain affected by AD. In this study, interaction profiles of oligomer and monomer form of amyloid-beta binding hippocampal neuron intracellular and cytosolic proteins were obtained. Methods: Amyloid beta (1-42) peptide- monomer and oligomer forms separated using gel-filtration chromatography. These were allowed to pull-down separately with hippocampal tissue neuron plasma membrane and cytosolic proteins using affinity chromatography in proteins native form. Interacting proteins were digested in-solution by trypsin and identified using mass spectrometry ESI-Triple-TOF5600, searched Uniprot database using software Protein pilot 4.2. Gene ontology and pathway analysis software Cytoscape was used for classification and interactions of proteins with respect to AD and apoptosis pathways. Result: Proteins found unique binding amyloid beta peptide monomer are synuclein-beta, SNAP25, lipophilin, EAAT-2 and SRPRB. Proteins found unique binding amyloid beta peptide oligomer are tubulin-beta, Tau (MAPT), 14-3-3 and phospholipase A2. Conclusion: Oligomer binding proteins may help in understanding the disease toxicity mechanism. Whereas, 14-3-3 protein could be possible novel therapeutic target for diagnosis, treatment and in understanding progression of AD.

Enass Y Osman is a Lecturer of Pharmacology and Toxicology, Faculty of Pharmacy, Tanta University, Egypt. Her expertise lies in pharmacotherapy and improvement of patients’ compliances especially those with psychiatric disorders. My publications are directed toward introduction of new drugs for treatment of schizophrenic patients for improving their life. The paper is based on previous publications by Abekawa et. al. (2008) who used amphetamine for induction of schizophrenia in animals. Our researches aimed to investigate potential effects of drugs other than classical antipsychotics as adjuvant therapies in schizophrenia.

Schizophrenia is a complex psychiatric disorder which markedly diminishes quality of life by its effects on cognitive, behavioral and emotional areas of functioning. The exact mechanism by which schizophrenia evolves is still unknown. Genetic, environmental factors, neurotransmitter, inflammation and oxidative stress are involved in pathophysiology of schizophrenia. β-glucuronidase is a member of the lysosomal glycosidase family that catalyzes breakdown of complex carbohydrates (hydrolysis of β-D-glucuronic acid residues) from the non-reducing end of mucopolysaccharides. The present study aimed to investigate the possible effects of celecoxib and omega-3 fatty acids on inflammation and lysosomal integrity as pathophysiological markers of schizophrenia. In the present study, amphetamine-treated rats received either ripseridone, celecoxib, omega-3 fatty acids, ripseridone plus celecoxib or ripseridone plus omega-3. The effects of treatment on brain β-glucuronidase enzyme activity and inflammatory markers including IL-6, Cox-2 and NF-kB were evaluated. Treatment with celecoxib or omega-3 fatty acids alone significantly reduced neurotoxicity which was indicated by reduction of brain β-glucuronidase enzyme activity. The anti-inflammatory effects of celecoxib and omega3 fatty acids were indicted by reduction of brain IL-6 level and decreased expression of brain Cox-2 and NF-kB. Addition of celecoxib or omega-3 fatty acids to risperidone also potentiated its effects on the measured parameters. In conclusion, celecoxib and omega-3 may be promising candidates as adjuvant therapy with risperidone to enhance its outcomes in schizophrenia. Recent Publications: 1. Shakoor S, McGuire P, Cardno AG, Plomin R, Ronald A (2015) A shared genetic propensity underlies experiences of bullying victimization in late childhood and self-rated paranoid thinking in adolescence. Schizophr. Bull. 41(3):754-763. 2. El Sisi A E, Sokkar S S, ElSayad M E, Ramadan E S, Osman E Y (2016) Celecoxib and omega-3 fatty acids alone and in combination with risperidone affect the behavior and brain biochemistry in amphetamine-induced model of schizophrenia. Biomedicine & Pharmacotherapy. 82:425-431. 3. Goddard A, Leisewitz A, Kjelgaard-Hansen M, Annemarie T et. al. (2016) Excessive pro-inflammatory serum cytokine concentrations in virulent canine babesiosis. PLoS ONE. 11(3):e0150113. 4. Messamore E and McNamara R K (2016) Detection and treatment of omega-3 fatty acid deficiency in psychiatric practice: Rationale and implementation. Lipids Health Dis. 15:25. 5. Ettinger U, Meyhöfer I, Steffens M, Wagner M, Koutsouleris N (2014) Genetics, cognition, and neurobiology of schizotypal personality: a review of the overlap with schizophrenia. Front. Psychiatry 5:18.

Dhingra G is an Assistant Professor of Zoology at the University of Delhi, Kirori Mal College - Department of Zoology, and has been involved in undergraduate teaching since past 13 years. She completed her PhD under supervision of Prof. Rup Lal, Department of Zoology in 2005 on Manipulations of Rifamycin Biosynthetic Gene Clusters in Amycolatopsis mediterranei. Presently she is working with Rup Lal’s group focusing on metagenomic diversity of pesticide contaminated sites.

A HCH tolerant strain, R11HT was isolated from the soil sample of HCH dumpsite located at Ummari village, Lucknow, Uttar Pradesh, India. On the basis of 16S rRNA gene similarity, the strain was identified as the member of genus Sphingopyxis with highest identity with Sphingopyxis indica DS15T (97.85 %). In addition, three more strains were identified with similarity >97%. The pairwise DDH analysis revealed that the strain R11HT belongs to a separate species. Further biochemical and chemotaxonomic studies confirmed the novelty of the strain and thus designated as Sphingopyxis flava R11HT. Due to the HCH tolerance ability, strain R11HT was selected for genome sequencing using Illumina Hiseq technology. It has a genome size of 4.15 Mbp, with G+C content of 63.75% and 90.40% coding potential. The strain was found to code for 4185 protein coding sequences. The total number of RNA coded by the strain is equal to 58 with a single copy of 5S, 16S and 23S rRNA and 46 tRNAs. The pfam analysis revealed 3219 protein sequences engaged in variety of metabolic functions, dominated by amino acid transport and metabolism, energy production and conversion, lipid transport and metabolism, replication, transcription and translation. The strain was also found to harbor five biosynthetic gene clusters including terpene and ectoine. The KEGG pathway genes include degradation pathways for number of compounds including amino-benzoate, benzoate, bisphenol, caprolactlam, chloroalkene, chlorohexane but lin genes which are known for HCH degradation were not annotated in the genome. It will be interesting to further analyze the probable metabolic pathways of strain R11HT which helps the strain to withstand in such high concentration of HCH. Recent Publications 1. Verma H, Bajaj A, Kumar R, Kaur J, Anand S, Nayyar N, Puri A, Singh Y, Khurana JP, Lal R (2017) Genome organization of Sphingobium indicum B90A: an archetypal hexachlorocyclohexane (HCH) degrading genotype. Genome Biol Evol. DOI: 1093/gbe/evx133. 2. Mahato NK, Gupta V, Singh P, Kumari R, Verma H, Tripathi C, Rani P, Sharma A, Singhvi N, Sood U, Hira P, Kohli P, Nayyar N, Puri A, Bajaj A, Kumar R, Negi V, Talwar C, Khurana H, Nagar S, Sharma M, Mishra H, Singh AK, Dhingra G, Negi RK, Shakarad M, Singh Y, Lal R (2017) Microbial taxonomy in the era of OMICS: application of DNA sequences, computational tools and techniques. Antonie Van Leeuwenhoek. doi: 10.1007/s10482-017-0928-1. 3. Kumar R, Verma H, Haider S, Bajaj A, Sood U, Ponnusamy K, Nagar S, Shakarad M, Negi R, Singh Y, Khurana J, Gilbert J, Lal R (2017) Comparative genomic analysis reveals habitat specific genes and regulatory hubs within the genus Novosphingobium. mSystems. 10.1128/mSystems.00020-17. 4. Verma H, Rani P, Singh AK, Kumar R, Dwivedi V and Lal R (2015) Sphingopyxis flava sp. nov., isolated from an hexachlorocyclohexane (HCH) contaminated soil, India. Int. J. Syst. Evol. Microbiol. 65: 3720-3726. 5. Verma H, Kumar R, Oldach P, Sangwan N, Khurana J P, Gilbert J A, Lal R (2014) Comparative genomic analysis of nine Sphingobium strains: Insights into their evolution and Hexachlorocyclohexane (HCH) degradation pathway. BMC Genomics, 15:1014.

Seo Hyein received the BS and MS degrees from the School of Electrical Engineering (EE), KNU, Daegu, Korea in 2014 and KAIST, Daejeon, Korea in 2016. Her research interests include WLAN, sensor network and bioinformatics. She is now a Ph.D. student of the School of EE, KAIST.

Statement of the Problem: Since the development of the Next Generation Sequencing (NGS), mutations in whole genome of human are investigated and the relationship between mutations and diseases, especially cancers, is studied. Insertion and deletion (Indel) is one of the important mutations. However, analysis result about the relationship between indel and cancer using NGS data is not sufficient. In this research, we want to derive the indel based biomarker that can distinguish whether the sequence is extracted from the cancer cell or not. Among indels, we use the duplicated-indel, which has similar property to microsatellite and exits in gene. Methodology & Theoretical Orientation: We obtained mutations from all genes of 100 sequences using GATK tool. Sequences were provided by the TCGA project and were sequenced from the cancer cell and the normal cell for 50 Acute Myeloid Leukemia (AML) patients. Among mutations, duplicated-indels, which are frequently found at the cancer cell but not in the normal cell, were listed. By counting the number of listed duplicated-indels, we could generate the biomarker of the cancer. Findings: In Fig. 1, we used 50 frequently existing duplicated-indels for the cancer distinction. By selecting the diagnosis threshold as 9 (Th1), we could accurately find 12 cancer sequences. Otherwise, if the threshold was 5 (Th2), 38 sequences were rightly extracted as the cancer but there was one wrong diagnosis. Conclusion & Significance: We showed the probability of the cancer biomarker using the duplicated-indel from NGS data. With optimization of threshold, more accurate biomarker can be derived. Also, we can extend our research to the analysis of the relationship between microsatellite and diseases. Recent Publications: 1.Sun Q Y, et al. (2017) Ordering of mutations in acute myeloid leukemia with partial tandem duplication of MLL (MLL-PTD). Leukemia 31(1): 1-10. 2.Papaemmanuil E, et al. (2016) Genomic classification and prognosis in acute myeloid leukemia. New England Journal of Medicine 374(23): 2209-2221. 3.Rabbani B, Nakaoka H, Akhondzadeh S, Tekin M and Mahdieh N (2016) Next generation sequencing: implications in personalized medicine and pharmacogenomics. Molecular BioSystems 12(6): 1818-1830. 4.Carethers J M and Jung B H (2015) Genetics and genetic biomarkers in sporadic colorectal cancer. Gastroenterology 149(5): 1177-1190. 5. Ahmed D, et al. (2013) Epigenetic and genetic features of 24 colon cancer cell lines. Oncogenesis 2(9): e71.

Yuko Sakajiri has her expertise in bioinformatics of protein structure prediction and has passion in visual restore. In a previous study, she studied the protein folding prediction of the beta barrel protein and found several folding patterns in the early stages of protein folding using the average distance map technique. Then, she starts the study for visual restore and has predicted the structure of the rhodopsin-like protein and the ion pathway inside the protein. These studies are expected to lead to the development of modified rhodopsin for the improvement of visual restore.

In this study, we aim for advanced visual restoration of enhanced contrast by light-driven halorhodopsin into retinal photoreceptor cells and hyperpolarization of optic nerve by light absorption. However, strong light is necessary for the light driving, because halorhodopsin has low photoresponsiveness. Therefore, it is necessary to develop a functionally enhanced halorhodopsin for visual restoration. As basic research, we analyzed the amino acid residues essential for chloride ion pump of halorhodopsin. Natronobacterium pharaonis halorhodopsin (NpHR) is a light-driven chloride ion pump. It is necessary to load chloride ions at the binding site-1 (BS1) of Thr126 near the protonated Schiff base in order to make chloride ions to pass through the cell membrane at light absorption. However, the network of hydrogen bonds near the BS1 is complicatedly intertwined, and it is not known well yet how chloride ions are retained at the BS1. In this study, we performed a molecular dynamics simulation for wild type and S81A mutant of NpHR structures, respectively to obtain dynamic information of chloride ion at the BS1. As a result, the Thr126 of the wild type retained binding to the chloride ion by hydrogen bond. While, the S81A mutant was unable for chloride ion to retain the position of the BS1, and then the chloride ion was released from there. We found that the side chain of Thr126, which was fixed by hydroxyl group of the Ser81, rotated other direction. Furthermore, NpHR S81A recombinant cell was actually prepared and then was recorded by the patch clamp. It was confirmed that the NpHR recombinant cell did not occurred hyperpolarization, and thus it was found that the NpHR S81A did not transport the chloride ion toward cytoplasmic side. Recent Publications 1. Analysis of the Local Sequences of Folding Sites in beta Sandwich Proteins with Inter-Residue Average Distance Statistics. The Open Bioinformatics Journal 2011, 5:59-68 Yuko Ishizuka and Takeshi Kikuchi

Sotiris Avgousti, is currently working as an instructor at Cyprus University of Technology. He has done masters in Computer Systems Networking and Telecommunication from Brunel University, London. He has done PhD from the University of Oreland France in Telerobotics.

A wearable tele-echography robot (MELODY) with four degrees-of-freedom that permits a medical expert to examine at a distance a patient by ultrasound was evaluated and tested over 4G mobile networks. At the expert side, the medical expert uses a dummy probe to control the real probe which is controlled by the robotic arms at the patient side and positioned on the patient’s body by paramedic personnel. The communication between the two sites is facilitated by a videoconferencing link. The telerobotic system has now been clinically tested and commercialized. The experimental setup of a wearable tele-echography robot, the MELODY system over a 4G connectivity link used to measure the system performance is described. The evaluation and investigation of the relevant medical ultrasound video and the relevant issues defined in terms of the average throughput, and jitter delay are investigated. A comprehensive video coding standards comparison for cardiac ultrasound applications is performed, including H.264/AVC and HEVC using a data set of nine cardiac ultrasound videos. Both objective and subjective (clinical) video quality assessment were performed.

Pushpanjali Dasauni is pursuing her PhD from University of Delhi South Campus, New Delhi, India and will submit the same by this year-end. She is expert in most of the proteomics tools like MALDI TOF-TOF and 2D-DIGE and works with various biophysical tools like FTIR etc. She is developing novel diagnostics tools for fast, cost-effective and accurate detection of hemoglobin disorders. She has published papers in reputed journals and she is a Life Time Member of Protein Society, India.

Around 7% of the global population carries an abnormal hemoglobin gene. Over 330,000 infants are born annually with hemoglobinopathies and it is the major cause of morbidity and mortality in early childhood. The treatments rely heavily on the diagnosis of hemoglobin variants. The routine/conventional techniques used for the identification of mutation in hemoglobin variants have their own limitations like co-migration of variants in electrophoresis and co-elution in HPLC. The WHO (2002) report on Genomics and Health has emphasized on the development of precise molecular techniques for screening of hemoglobin disorders. A sensitive, robust and reproducible method was thus developed to identify single substitution mutations in the hemoglobin disorders from sequence of the entire globin chains. The method was MS compatible and dealt with certain limitations like difficulty in getting complete sequence coverage. Different methods like using organic solvent, digestion with a different protease and combining results, treating the digestion mixture with 10% acetonitrile prior to incubation and combining the separation power of LC coupled with MALDI MS/MS were tried for standardization and optimization of protocol. Finally, we optimized a method using an organic solvent and heat denaturation step prior to digestion resulting in 100% sequence coverage in the β chains and 95% sequence coverage in the α chains. A hemoglobin variant database was created to specify the search and reduce the search time. All the mutations were thus identified using a non-targeted approach and this method could be used in future for regular screening of any single mutation in hemoglobin variants.

Sung Han Kim has completed his MD from Seoul National University of Medicine, Seoul, Korea and Postdoctoral studies from National Cancer Center, Goyang, Korea and Seoul National University of Medicine, Seoul , Korea. He is the Clinical Staff and Associate Researcher and Director of Jinsoo Chung, Prostate Cancer Center, National Cancer Center, Goyang, Korea. He has published more than 30 papers in reputed journals.

The study was aimed to identify targetable genes in PC from The Cancer Genome Atlas (TCGA), and to validate the significance of the genes identified in clinical studies using immunohistochemistry in PC patients’ prostatectomy microarray. Omics data and clinical data of 550 PC patients were obtained from TCGA. Several significant genes were identified from TCGA dataset having the most number of point mutation to exhibit significantly strong positive relationship in expression values with the most frequently mutated gene. Further validation of different expression values for the list of genes between tumor and normal lesions was performed to evaluate their prognostic significance using tissue microarray of 514 prostatectomy specimens by performing immunohistochemistry in clinical setting from a single cancer institution. Prognostic powers of these genes were investigated on the NCC dataset. Immunohistochemistry were performed on the genes associated with the most mutated gene. The gene markers’ prognostic factors were analyzed using Cox proportional hazard analysis with a significant p-value<0.05. FRG1B gene was found lineage-specific mutation with ESRP1, RAD51, and CHEK2 genes in the TCGA dataset. The union of samples with these three up-regulated markers with FRG1B mutation showed significant differences in disease-free survival compared to the samples without expression of two combinational series (p<0.05). Analysis of the clinicopathological factors related to three markers suggested that expression of ESRP1 was a significant risk factor for biochemical recurrence (BCR, HR 1.003) and cancer-specific survival (HR 1.048), even after adjusting for significant prognostic clinicopathological factors of BCR and CSS (p<0.05). On the other hand, CHEK2 was not significant in any BCR and CSS. RAD51 could not be evaluated because of its overall overexpressed in specimens. The study identified that ESRP1 was a potentially significant target gene of survival prognoses in PC.

Mohammed Al-Hajouj, Master Student – Clinical Chemistry, Clinical Laboratory Science College of Applied Medical Science, King Abdulaziz University

Urinary tract infection (UTI) is considered to be one of the most prevalent bacterial infections in the world predominantly affecting the bladder and the kidney; according to research, one in three women is affected by UTIs. Gram-negative bacteria are a major cause of such infections, particularly Escherichia coli (E. coli). E. coli was the main causative agent of 80-90% of community-acquired infection, about 40% of nosocomial UTI, and is responsible for 25% of recurrent infections. The field of proteomics has emerged as a great tool to analyze expressed proteins and to identify possible biomarkers associated with a number of pathological states, and to the same extent associated with bacterial pathogenesis. Researchers elsewhere are investigating E. coli proteomics profiles to identify possible biomarkers, however, protein profiles could vary environmental stress created by subculturing. Here we propose to answer the research questions, are there differences in protein profiles of E. coli originated from a sequential passage? To conduct this research, urine samples will be collected from individuals with recurrent UTI, sequentially subcultured, and analyzed using two-dimensional gel electrophoresis and mass spectrometry to identify any significant change in the protein profile of the bacteria. We hope to elucidate to the effect of passage on the protein profile of this common pathogen

Sung Han Kim has completed his MD from Seoul National University of Medicine, Seoul, Korea and Postdoctoral studies from National Cancer Center, Goyang, Korea and Seoul National University of Medicine, Seoul, Korea. He is the Clinical Staff and Associate Researcher of Director of Jinsoo Chung, Prostate Cancer Center, National Cancer Center, Goyang, Korea. He has published more than 30 papers in reputed journals.

Multilocular cystic renal neoplasm of low malignant potential (MCRNLMP) and multicystic renal cell carcinoma (MCRCC) are morphologically indistinguishable. MCRNLMP is a tumor composed entirely of numerous cysts, the septa of which contain individual or groups of clear cells without expansive growth. However, unlike MCRCC, neither recurrence nor metastasis have been reported in MCRNLMP. The aim of this study was to identify significant differential pathological characteristics in resected specimens from patients with MCRNLMP (n = 13) and MCRCC (n = 17) using immunohistochemistry of 25 tissue markers. Staining interpretation was performed semi-quantitatively using the H-score (0–300) or intensity score (0–3), and differences between groups were evaluated using the Fisher exact and Wilcoxon rank-sum tests. During a median follow-up of 66.2 months (1–141.9 months), there was only one case of recurrence in MCRCC among 30 patients. There were 19 (63.3%) at stage pT1a, 8 (26.7%) at stage pT1b, and 3 (10%) patients at stage pT2. Tumor necrosis rate (0% vs. 52.9%) and median tumor size (3.2 cm vs. 4.1 cm) significantly differed between MCRNLMP and MCRCC samples. Among the 25 tissue markers, only HIF1a, PDGFRα, SMA, VEGFR1, VEGFR2, VEGFR3, CD10, CD31, CD34, CK7-tubule, TGAse-2, and Ki-67 showed significantly different expression between the groups. These tissue markers with differential expression between MCRNLMP and MCRCC can provide a clue to understanding their distinct pathophysiology.

Juliana Guimarães Fonseca is a Biotechnologist graduated from Federal University of São Carlos, Brazil, in 2012. She has Master’s degree in Science from University of Sao Paulo, in 2014. Currently, she is PhD candidate at University of Sao Paulo and her research is on proteomics, more specifically, characterization of the protein profile of contaminating bacteria present in the first-generation ethanol fermentation process by MALDI TOF. She has already published papers in reputed journals and wrote book chapters.

Bioethanol has gained space in the global energy sector in recent years, wherein Brazil is the second largest producer of this fuel. The process responsible for ethanol production is fermentation, in which sugars available in sugarcane are turned into alcohol by fermenting microorganisms. Nonetheless, large-scale fermentation does not occur in an aseptic environment. In this way, presence of contaminants, mainly acid-lactic bacteria (LAB), is a recurring problem in the process, which can cause a decrease in ethanol yield. Thus, identification of contaminating bacteria by mass spectrometry techniques allows a rapid and efficient identification of contaminating microorganisms, which can prevent drastic falls or interruption of fermentation process. We isolated and identified contaminating microorganisms from fermentative process by Sanger sequencing of gene 16S rRNA. We also characterize protein profile of these bacteria through matrix-assisted laser desorption/ionization (MALDI). We identified 13 bacteria that belonged to Lactobacillus genus. We also optimized the methodology used for MALDI to identify LAB from a small number of bacteria grown in MRS media using a 1 μL loop and suspended in 10% formic acid. For the identification of protein characteristic spectral profile, the best results were obtained when 1 μL of the mixture was spotted onto a polished steel target plate and overlaid with 0.5 μL of ethanol. The matrix used was saturated solution of α-cyano-4-hydroxycinnamic acid 50% acetonitrile – 2.5% trifluoroacetic acid. This is the first time that mass spectrometry was used to identify bacterial contaminants from fermentation tanks in large scale ethanol production.

Siti Sarah Hamzah is a final year PhD student at University of Warwick, United Kingdom. She received a Bachelor degree in Biochemistry and Molecular Biology from The University of Melbourne, Australia and an Honours degree in Pharmaceutical Sciences from Monash Institute of Pharmaceutical Sciences, Australia. After 2 years as Medical Scientist in the Biochemistry Dept. of Institute for Medical Research, Ministry of Health Malaysia, she is now serving in the Endocrinology Dept. of the same institute. Her current research involves study of the role of alternative splicing (AS) in epithelial-to-mesenchymal transition (EMT) in breast cancer models.

Studies show that 70% of breast cancers are estrogen receptor-positive (ER+) and activation of cellular processes involved in several tumorigenesis-associated events are detected predominantly in ER+ breast cancer. To characterize the global proteomic alterations affected by sex hormone estrogen, a label-free quantitative proteomic method was used to identify and quantify the differentially expressed proteins in the hormone-responsive MCF7 cells exposed to 17b-estradiol (E2) for 24 h. Using a selection filter cut-off of >2-fold change and p value<0.01, 3,000 proteins were identified: 93 of them were upregulated whereas 64 were downregulated by E2. The list of upregulated proteins included the 91 kDa serine-arginine protein kinase 1 (SRPK1), a key kinase involved in the phosphorylation of serine-arginine proteins (SRps) during pre-mRNA alternative splicing that also found to be overexpressed in malignant cancer cells. Follow up studies employing qRT-PCR and Western blots revealed increased phosphorylation signal of SRp40 and SRp30 as well as increased production of aberrant CD44 mRNA isoforms. In cellular models of ER+ breast cancer, SRPK1 expression was also positively regulated by corticotropin-releasing hormone (CRH) a hypothalamic hormone involved in adaption to stress. In contrast, proteome analysis using Nano-flow Ultra HPLC coupled to Orbitrap fusion demonstrated that CRH did not affect SRPK1 expression in ER-breast cancer and phosphosites analysis in cells depleted with SRPK1 kinase resulted in reduced detection of signal specific for phosphorylation site of SRp40 and SRp30. Altogether, these results identify potential targets of hormone-altered proteome profiles in different types of cancer cells hence triggering signaling networks that could enrich proteome diversity by producing distinct oncogenic protein isoforms.

Kyoungsook Park has completed her PhD at the University of Pennsylvania, Philadelphia, USA. She is a Research Professor at Sungkyunkwan University in Republic of Korea and she has published many papers in reputed journals and has been serving as an active Member of AACR and a representative Committee Member of KSBMB.

Glycosylation is a major post-translational gene regulation and is involved in many aspects of cellular processes. It plays pivotal functional roles in immune surveillance, inflammation, and drug responses among many other biological processes. Establishment of a mouse model which mimics a human glycosylation profiling is urgent and is instrumental to accelerate the non-clinical tests prior to the human clinical trials for a potential novel drug candidate. To this end, we set out to identify the glycosylation-regulating genes (GRGs) which were differentially regulated in human liver compared to the mouse counterpart. Among major organs, we chose a liver due to its critical roles in metabolism. To facilitate the screening of differentially expressed GRGs, Glycosylation Profiler PCR array expression panel was utilized as an initial screening approach with the total RNAs derived from commercially available normal human liver tissues and B6 mouse liver tissues. Candidate GRGs were further confirmed by RT-PCR analysis with individually designed specific primer sets. Our findings would provide crucial information for construction of a non-clinical mouse model with humanized glycosylation profiling, which is critical for cell-cell interaction and signaling in immune responses, and drug responses.

Sulhee Kim is a PhD student at Biosystems & Biotechnology Department of Korea University in South Korea. Recently, she have published more than 5 papers in reputed journals, such as Autophagy, Nucleic acids research, and so on.

Schistosomiasis (or bilharzia) is the most common cause of death from a parasitic disease after malaria. The disease can be treated effectively with the drug praziquantel (PZQ). The tegumental allergen-like (TAL) proteins from Schistosoma mansoni (SmTAL) are part of a family of calcium binding proteins found only in parasitic flatworms. These proteins have attracted interest as potential drug or vaccine targets, yet comparatively little is known about their biochemistry. For elucidating the exact mechanism of drug-interaction with tegument associated proteins from parasites (TALs), here, we had grown the suitable crystals of TALs from Schistosoma mansoni. The crystals were diffracted at 2.1 Ã… and 2.5 Ã… at synchrotron radiation, respectively. The spacegroup of smTAL1 and smTAL2 are hexagonal system (P64 and P6422), respectively. They consist of two domains, calmodulin-like (EF hand) and dynein-like (DLC domain). We will discuss the difference between smTAL1 and smTAL2. Recent Publications 1.P Steinmann, J Keiser, R Bos, M Tanner and J Utzinger (2006) Schistosomiasis and water resources development: systematic review, meta-analysis, and estimates of people at risk. Lancet Infect. Dis. 6(7):411e425. 2.J Utzinger, S L Becker, S Knopp, J Blum, A L Neumayr, J Keiser, C F Hatz (2012) Neglected tropical diseases: diagnosis, clinical management, treatment and control. Swiss Med. Wkly. 142:w13727. 3.D Cioli, L Pica-Mattoccia, A Basso and A Guidi (2014) Schistosomiasis control: praziquantel forever? Mol. Biochem. Parasitol. 195:23e29.

Ms. Radostina Velikova is currently she is working in the Institute for Organic Chemistry with Center for Phytochemistry, Bulgarian Academy of Sciences.

Hemocyanins (Hcs) are copper-containing glycoproteins that act as oxygen transporting proteins in many arthropods and mollusk species. Hemocyanins from the molluscs Helix aspersa (HaH), Helix lucorum (HlH) and Rapana venosa (RvH) exhibiting different oligosaccharide structures have been investigated for potential use in therapy of bladder cancer permanent cells,. In vitro studies on the antitumor activities of these proteins were performed in T-24 cells and compared to doxorubicin and mitomycin-C. Control experiments were performed using normal urothelial HL 10/29 cells. The obtained results show that the human tumor T24 cell lines are sensitive to the action of the tested hemocyanins and their isoforms. The inhibition of the tumor cell growth was dose and time dependent and was observed after incubation with native HaH and HlH, and FUs (βc-HlH-h and RvH-c. Cells treated with both FUs, βc-HlH-h and RvH-e, showed apoptotic and necrotic cells and this inhibition was stronger than the effect measured for doxorubicin treated cells. No growth inhibition of the normal urothelial cell line HL 10/29 was observed after treatment with HlH, HaH, RvH and their isoforms. The impact of hemocyanins on tumor cells was investigated by 2D-gel PAGE and several proteins showed indeed altered abundancies. The most effective inhibition of tumor cells is probably caused by a specific novel and unusual N-glycan oligosaccharide structure on HlH with methylated hexoses, an internal fucose residue connecting one GalNAc (ß1-2) and one hexuronic acid.

Ondřej Pastva is a PhD student in the Biochemistry group at the Institute of Hematology and Blood Transfusion, Prague, Czech Republic. His main research interest is in utilizing of optical biosensors and bioassays for improving of diagnostics in Leukemias.

The Hsp70s (heat shock 70kDa) proteins are ubiquitous molecular chaperones forming the center of protein folding, refolding, and trafficking in all organisms. Hsp70 interacts with hydrophobic peptide segments of non-folded chains, as well as near-native, misfolded, and aggregated proteins (clients), both at normal and at stressed conditions. To date, mostly the ADP-affinity chromatography or affinity purification chemical tool is generally used to detect the Hsp70 substrates. These techniques are time consuming and samples may contain non-specific ADP-like proteins or should be modificated before subsequent identification through biochemical techniques. We designed a new assay which allows real-time monitoring of the (i) trapping and retention of Hsp70 client proteins from blood plasma samples and (ii) highly efficient elution (>90%) of retained proteins. The Hsp70 trap assay has been implemented using a multichannel surface plasmon resonance (SPR) biosensor functionalized by Hsp70. Trapping and elution of client proteins is controlled by ATP/ADP exchange. The nucleotide and cations requirements were investigated and set up. In the three-step assay, the reference channel represents non-specific proteins was designed to control of elution. The SPR biosensor was used for the screening of healthy controls and clinical samples – myelodysplastic syndromes patients (MDS, subgroups – RARS, RAEB, and AML). We observed significant differences between the tested groups and that the amount of misfolded proteins correlated with the progression of the disease. Our results are in a good agreement with the fact that oxidative stress as one of the main factor in MDS disease progression leads up to covalent modifications that destabilize and inactivate proteins. To the best of our knowledge, this is the first biosensor using Hsp70 to reveal a misfolded protein complexes. The Hsp70 trap assay seems to be a promising tool for general profiling of disease pathogenesis and progression. Using three-step assay, Hsp70 client proteins were detected in blood plasma in ~35 min at 25 ng/cm2 to 150 ng/cm2 concentration for healthy controls and AML patient, respectively.

Abdullah Essa Alsubhi completed hisBachelor’s Degree from Umm Alqura, KSA in 2011 and Master’s Degree from King Abdulaziz University, Faculty of Applied Medical Sciences, Department of Clinical Laboratory Science. He have been working in Saudi Health Ministry for six years. He has worked his practical master research in Aberdeen University, Scotland.

Urinary tract infection (UTI) is one of the most prevalent bacterial infections in the world. It affects urinary tract system including bladder and kidney. Gram-negative bacteria is a major cause, particularly Escherichia coli (E. coli), which is considered a main causative agent for 80-90% of community-acquired infection and for about 40% of nosocomial UTI. Moreover, it is responsible for 25% of recurrent infection. The study of the genome identified and sequenced three E. coli strains causing UTIs and all strains showed higher expression of certain proteins; such as adhesion protein p, and toxin such as hemolysin and high expression of proteins responsible for iron acquisition. Proteomics is used to analyze and identify complete components of proteins and it can be used to distinguish between bacteria based on synthesized protein. In addition, proteomic is applicable to identify possible target of therapy. This study aims to compare protein profiles of E. coli from different UTI patients and identify possible unique proteins signature for future biomarker studies. Seven urine samples were taken from different UTI patients and the pathogenic agent among those patients was E. coli. Urine E. coli isolates were analyzed by 1D SDS-PAGE, 2DGE and LC-MS/MS and three interesting spots were selected for protein identification by LC-MS/MS. Many significant differences were observed in protein profiles of E. coli isolates in both 1D SDS-PAGE and 2DGE regardless of type of E. coli species. Finally, it was concluded that E. coli isolates obtained from the different UTI patients had different protein profiles.

Joanna Tracz has received his/her Bachelor’s degree in 2015 and completed his/her Master’s degree in Chemical Science in 2016 and Biological Science in 2017. Presently, She/he is a PhD student in Laboratory of Mass Spectrometry at the Polish Academy of Sciences. She/he is involved in project concerning the molecular mechanism of atherosclerosis progression in chronic kidney disease.

The major cause of mortality in patients with chronic kidney disease (CKD) is atherosclerosis related to traditional and non-traditional risk factors. However, the understanding of the molecular specificity that distinguishes the risk factors for classical cardiovascular disease (CVD) and CKD-related atherosclerosis (CKD-A) is far from complete. Although dyslipidemia is common in CKD patients, epidemiological data show that in CKD the link between cholesterol and its fractions is not as straightforward like in the general population. CKD is frequently accompanied by reduced of plasma HDL concentrations, and normal or even low serum total cholesterol and LDL concentrations. Normal HDL function is reverse cholesterol transport from peripheral cells and its transport to the liver. HDL protects of LDL against oxidation and suppress of systemic inflammation. Therefore, HDL deficiency is the key in perpetuating chronic inflammation and oxidative stress leading to atherosclerosis. On the other hand, it is suggested that lipid abnormalities in CKD are characterized by more qualitative abnormalities and may be related to HDL function rather than HDL deficiency. Mass spectrometry-based proteomic analysis is excellent, powerful tool for tracking molecular changes during progression of CKD. In this study we investigated the alterations in leukocytes protein accumulation in patients with CKD and classical cardiovascular disease (CVD) without CKD. Cells collected from patients in various stages of CKD, CVD patients without symptoms of kidney dysfunction and healthy volunteers (HVs), were analyzed by a label-free proteomic approach. Obtained cells were also analyzed in term of inflammation modulators and the oxidative status enzymes. Label-free quantitation analysis revealed characteristic proteins of particular stage of atherosclerotic plaque formation process and CKD progression. All proteomic data were subjected to bioinformatic analysis for identification of specific for CKD and CVD pathways. Further research should focus on precise profiling of metabolites and/or lipids present in cells during the atherosclerosis development.