Day 2 :
Keynote Forum
Ada Yonath
Weizmann Institute, Israel
Keynote: Novel antibiotics against species-specific resistance, microbiome conservation and environmental preservation
Time : 09:30-10:30
Biography:
Ada Yonath is focusing on protein biosynthesis and the antibiotics hampering it. In the seventies she established the first structural-biology laboratory in Israel. She is the Director of Kimmelman Center for Biomolecular Structure. During 1986-2004 she was the Head of Max-Planck Research Unit for Ribosome Structure in Hamburg. She is a Member of US National Academy of Sciences, Israel Academy, German Science Academy and Pontificia Accademia-delle-Scienze (Vatican). She holds honorary Doctorates from Oslo, NYU, Mount-Sinai, Oxford, Cambridge, Hamburg, Berlin-Technical, Patras, De-La-Salle, Xiamen, Lodz universities. Her awards include the Israel Prize, Louisa-Gross-Horwitz Prize, Linus-Pauling Gold Medal, Wolf-Prize, UNESCO/L’Oreal Award, Albert-Einstein World Award for Excellence and Nobel Prize for Chemistry.
Abstract:
The current global escalation in resistance to antibiotics is a serious threat, as it seems that the world is headed for a post antibiotic era, in which common infections and minor injuries that have been treatable for decades could become fatal again. Ribosomes, the universal cellular machines that translate the genetic code into proteins, are paralyzed by many clinically useful antibiotics. The structures of ribosomes from non-pathogenic bacteria, used as models for genuine pathogens, illuminated the antibiotics binding modes, inhibitory actions, synergism pathways, the differentiation between patients vs. pathogens and mechanisms leading to bacterial resistance. However, as species specific diversity was detected in susceptibility to infectious diseases and in developing specific resistance mechanisms, our structural studies have been extended to ribosomes from genuine pathogens. The high resolution structures of ribosomal particles from multi-resistant pathogens and from eukaryotic parasites with several antibiotics, highlighted subtle, albeit highly significant structural elements that can account partially or fully for species specificity and may be exploited for improving known antibiotics and for the design of novel compounds.
Keynote Forum
Reiko Kuroda
Tokyo University of Science, Japan
Keynote: How is the chirality information transferred during the mollusk development?
Time : 10:30-11:00
Biography:
Reiko Kuroda has obtained her PhD in Chemistry from The University of Tokyo and carried out Postdoctoral studies at King’s College London. Her research focuses on chirality both in the field of chemistry and biology: Chirality recognition, transfer and amplification in the solid state, development of chiroptical spectrophotometers to follow aggregation processes of e.g. β-amyloids and the molecular basis of snail coiling. She has 320 papers published to her credit.
Abstract:
Body handedness of Gastropod Lymnaea stagnalis is determined by a single gene locus that functions maternally. We have previously shown that the gene dictates the cytoskeletal dynamics at the third cleavage and have created fertile snails of mirror-image body plan by mechanically manipulating the blastomeres at this stage. In this talk, we shall show that nodal expression started at the 33-49 cell stage and was confined only to the left or the right side of embryos, in a mirror-image manner for the sinistral and the dextral snails, throughout the development until the shell was getting formed. The mechano-manipulation reversed the entire expression. Thus, the blastomere arrangement at the 8-cell stage regulates the asymmetric expression of nodal/Pitx genes. At the 24-cell stage, the organizer macromere 3D moved to the central location of vegetal side, filled almost entire cleavage cavity where it contacted with micromeres. MAPK (mitogen-activated protein kinase) was activated in 3D macromere 30 - 60 min. after embryo reached the 24 cell stage. Treatment with U0126, a specific inhibitor of MEK (MAPK/ERK kinase), at the 4-8 cell stage completely inhibited the expression of nodal and its downstream Pitx, whereas, similar treatment at the 24-cell stage after the activation of MAPK did not inhibit the gene expressions. These results clearly indicate that chirality determined at the 8-cell stage is transferred to the 24-cell stage via spiral cleavage and MAPK at the 24-cell stage controls the left-right asymmetric expression of nodal/Pitx genes.
- Cell Biology | Developmental Biology | Stem Cell Biology | Tissue Biology
Location: Experience II
Chair
Anja Nohe
University of Delaware, USA
Co-Chair
Jamila Chakir
Laval University, Canada
Session Introduction
Yu Haijun and Yunfeng Zhou
Zhongnan Hospital of Wuhan University, China
Title: Radio-sensitization of clioquinol and zinc ion in human cancer cells
Time : 15:30-15:50
Biography:
Yunfeng Zhou is a Professor of Radiation Oncology and he was the Dean of Medical School and the President of Zhongnan Hospital, Wuhan University. From 1986 to 1991, he studied for his Oncology Diploma (DIS) in Lyon, France. He has been working at the Department of Radiation Oncology and Medical Oncology as a Director of Hubei Cancer Clinical Study Center, Hubei Key Laboratory of Tumor Biological Behaviors and Hubei Radio-therapeutic Quality Control Center. His main research fields including radiation biology which focuses on the radio-sensitivity modified by telomere/telomerase and radiation-guided gene therapy of cancer. He has published more than 100 papers in international and national journals. Due to his outstanding contributions for Sino-France medical education exchange, the French Government awarded him French Knight Badge (2006) and National Order of the Legion of Honor (2009).
Abstract:
Objective: We have reported that the anticancer activity of Clioquinol and Zinc in different cancer cells, Clioquinol and Zinc can inhibit the cancer cell viability by down-regulation of NF-kb activity. Re-activation of NF-kb plays an important role in radio-resistance of human cancer cells. Here we investigated the radio-sensitization of Clioquinol and zinc in different human cancer cells.
Methods: The toxicity of 1 μM Clioquinol (CQ) and 10 μM ZnCl2 (Zn) in human cancer cells of Hep-2 and human normal cells MRC-5 was determined by MTS assay. The radio-sensitization of CQ+Zn in Hep-2 and Hela cells was detected by colon formation measure. The effect of CQ+Zn on the NF-kB activity in Hep-2 and Hela cells is measured by the luciferase activity assay. The ATM RNA and protein expression level were determined by RT-PCR and Western blot methods.
Results: The cell viability of Hep-2 and MRC-5 treated with 1 μM CQ and 10 μM Zn for 72 hours were 104.0% and 114.3% respectively compared to the control groups (Hep-2 cells: CQ+Zn vs. Control, P=0.8850; MRC-5 cells, CQ+Zn vs. Control, P=0.8204). Colon formation measure indicated that 1 μM CQ and 10 μM Zn can significantly enhance the radio-sensitivity of Hep-2 and Hela cell (Irradiation group vs. Irradiation+CQ+Zn group: P<0.001 in Hep-2 cells and P<0.001 in Hela cells), SERSF2 for Hep-2 and Hela were 1.33 and 1.75 respectively. One μM CQ and 10 μM Zn inhibited the activity of NF-kB after 2 Gy γ-Ray irradiation in Hep-2 and Hela cells (Irradiation group vs. Irradiation+CQ+M Zn group: For Hep-2 cells, 151.10% vs. 108.60%, P<0.001; for Hela cells, 156.30% vs. 104.20%, P<0.001). We further detected the ATM mRNA and protein expression level after 2Gy irradiation with or without pre-treatment of 1 μM CQ and 10 μM Zn for 6 hours. ATM mRNA expression level in Hep-2 after 24 hours of irradiation in the group of with the 1 μM CQ and 10 μM Zn was 67.78% of that in the irradiation along group (P=0.017). ATM protein expression level after 48 hours of irradiation in the group of with the 1 μM CQ and 10 μM Zn was 69.38% of that in the irradiation along group (P=0.039).
Conclusion: Clioquinol and zinc can enhance the radio-sensitivity of human cancer cells, the inhibition of NF-kB and ATM may mediate the radio-sensitization in human cancer cells.
Mohammed Nabih Baeshen
University of Jeddah, KSA
Title: The effect of biosynthesized Rhazya stricta leaf extracts with gold nanoparticles on breast cancer cell lines
Time : 18:20-18:35
Biography:
Mohammed Nabih Baeshen is an Assistant Professor of Genomics and Biotechnology, Department of Biology, Faculty of Science, University of Jeddah since 2014 to till date. He has completed his PhD in 2010 from King Abdulaziz University (KAU) and been assigned as an Assistant Professor at the Department of Medical Laboratories at the Faculty of Health Sciences, KAU. He was also assigned as Consultant in the Center of Nanotechnology at KAU. He has three reference books in practical and theoretical introductory biology and up to 29 publications to his credit.
Abstract:
Rhazya stricta is a popular plant used in folkloric medicine around many parts of Asia. Recent studies proved its medicinal properties against many diseases, inflammations and abnormal conditions. Many in vivo and in vitro studies showed the ability of plant extracts against different types of cancer. Our study is representing new records and novel techniques were first used for R. Stricta. All previous studies used whole leave extracts and alkaloidal fractions according to their famous medicinal reputation, while our present study also showed a cytotoxic effect of the non-alkaloidal fraction of the leaf extract against breast cancer MFC-7 cell line. On the other hand, we introduced in our study for the first time the cytotoxic effect of the biosynthesized extracts of R. Stricta leaves with gold nanoparticles against MFC-7 cell lines as aqueous whole extract, alkaloidal and non alkaloidal fractions of the extract. MTT test results showed cytotoxic effect of all nano-biosynthesized plant extracts when compared to non treated control group as represented by the percentage of cell death as follows: 82% non-alkaloidal fraction, 70% alkaloidal fraction, 52% whole aqueous extract and 0% for the control group. These results showed that the fractionations of the plant extracts were more effective than the whole aqueous extract against MFC-7 cell line and non-alkaloidal fraction as not expected gave the strongest effect against MFC-7 cell lines. In conclusion, our results were promising for the treatment of cancer and we recommend to apply it more in vivo and in vitro studies against more types of cancer with more experiments of the biosynthesis of R. stricta extracts alone or mixed with other medicinal plant extracts with more types of nanoparticles in different physical and chemical conditions to get the best results for this promising plant.
Arezou Pakfar
Islamic Azad University, Iran
Title: Chondrogenic and possible pathologic effects of PRP on adipose derived
Time : 18:05-18:20
Biography:
Arezou Pakfar holds a Master degree in Cellular and Molecular Biology at Islamic Azad University, Iran. Her thesis was about Tissue Engineering and Stem Cells. She is currently working as a Researcher at Stem Cell Technology Research Center since 2014.
Abstract:
Introduction: Application of activated Platelet-Rich Plasma (PRP) with its vast range of cytokines and growth factors has achieved a considerable attention for chondrogenic differentiation in tissue engineering fields. Therefore, the aim of this study was to investigate the effects of PRP on human adipose derived MSC chondrogenesis.
Material & Methods: MSCs were differentiated using different PRP concentrations (5% and 15%). Changes in gene expression levels for cartilage and bone specific markers (COLII, AGC, SMAD2, SOX9) and (RUNX, Osteocalcin), respectively, were appraised by real time PCR. Also chondrogenesis was assessed by measuring secreted glucosaminoglycan in the medium or that kept in cell ECM. The expression of pathologic markers was evaluated by measuring the VEGF, TNFα secretion and alkaline phosphatase activity and calcium deposition.
Results: The most secreted VEGF (p<0.05) in 5% and 15% concentration were anti-angiogenesis. The inflammation factor (TNF-α) quantity of 5% PRP was the lowest (p<0.05) on 21st day but chemotaxic characteristics of the mentioned group was the highest. The expression levels of AGC, SOX9, COLII and RUNX were significantly (p<0.05) down-regulated while Osteocalcin was up-regulated. In addition, hypertrophy was seen in chondrogenic differentiation.
Conclusion: Due to having vast range of biologic active factors, PRP based chondrogenesis of human adipose derived MSC is dose dependent and the undesired outcomes due to absence of regulatory factors, should be suppressed by further optimizing the formulation of chondrogenic differentiation media.
Jun Wu
Southeast University, China
Title: Proteolytic maturation of Drosophila neuroligin3 in central nervous system
Time : 17:45-18:05
Biography:
Jun Wu is currently pursuing PhD in Life Science at Southeast University, China. His research interest focuses on the molecular mechanism of neurological disorder diseases, such as autism spectrum disorders.
Abstract:
Neuroligins are postsynaptic adhesion molecules that are essential for synaptic function and regulation by binding to their presynaptic ligands, Neurexins. Mutations in neuroligin and neurexin genes have been implicated in cognitive diseases such as autism. Previous study shows more than two isoforms of endogenous neuroligin3 in Drosophila. Here, we report that Drosophila neuroligin3 (DNlg3) is proteolytically activated in the central nervous system specifically, which is essential for an interesting behavior. A protease belonging to ADAMs (a disintegrin and metalloproteinases) family is responsible for DNlg3 processing in vivo and in vitro. Interestingly, as a membrane protein, DNlg3 is processed intracellularly rather than at the cell surface. DNlg3 is cleaved at its extracellular AchE-like domain to generate the N-terminal fragment (NTF) and the cleaved membrane-anchored fragment (cDNlg3). After cleavage, the cDNlg3 rather than full-length (FL) or NTF can rescue defect in DNlg3 mutants, suggesting that proteolytic cleavage of DNlg3 is required for keeping normal behavior. Our study broadens our knowledge of the scope of Neuroligins function, as well as provides a novel cleavage paradigm for studying other membrane proteins.
Yu Liu
Zhongnan Hospital of Wuhan University, China
Title: Neogenin expression may be inversely correlated to the tumorigenicity of human lung cancer
Time : 17:25-17:45
Biography:
Yu Liu is currently working as an Associate Professor in the Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China. Her research interests include the study of key signaling pathways involved in liver metastasis of colorectal cancer by exploring the molecular mechanisms mediated filopodia growth of tumor cells to provide new thinking direction and theoretical basis for effective prevention and treatment of colorectal cancer liver metastases. She also works on the study of key proteins involved in the communications between stomach cancer cells and bone lesion to investigate the mechanism of pre-metastatic communication between primary tumors and bone.
Abstract:
Despite advanced screening technology and cancer treatments available today, metastasis remains an ongoing major cause of cancer-related deaths worldwide. Typically, lung cancer is one of the cancers treatable by surgery in conjunction with chemotherapy when it is detected at an early stage. However, it still ranks as the highest modality and mortality of cancer types in the world and this is mostly due to a recurrence of metastatic lung cancer post-resection of the primary malignancy. Lung cancer metastases predominantly occur in the liver and bone and yet the molecular mechanisms that regulate these organ-specific lung cancer metastases are largely unknown. Therefore, the identification of any critical molecule, which triggers malignancy in lung cancer, would be an excellent target for treatment. There is growing evidence that cytoskeletal proteins and actin-based protrusions have central roles in cancer biology, particularly in metastasis. Our previous study showed neogenin, a receptor of chemotropic neuronal guidance molecule Netrin, can directly interact with myosin X, one of key filopodia regulators and regulates in myosin X movement and functions in inhibition of filopodia formation. However neogenin's relationship to tumorigenesis remains to be elucidated. We report here neogenin expression in human lung cancer samples and its association with different clinicopathologic characteristics relationship. Immunohistochemically, compared with adjacent normal tissues, neogenin staining was significantly lower in tumor tissues (P<0.001). Loss of neogenin sub-cellular localization in lung cancer tissue was correlated with pathological stage, differentiation extent (P<0.001), but not with the age or smoking history, lymphatic invasion, vascular invasion, pleural invasion and gender (P>0.05). Conversely, RGMc, one of ligands of neogenin, expression is not differential between lung cancer tissue and normal tissue. More importantly, membranous staining of neogenin was significantly correlated with a better overall survival of either stage I or stage II/III lung cancer patients and multivariate analysis confirmed that membranous expression of neogenin was an independent positive prognostic indicator (P<0.05). Together, these observations establish neogenin may play a role in lung carcinogenesis as well as morphogenesis and the expression may be inversely correlated with lung carcinogenicity. It is valuable as a potential prognostic factor.
E. Sacide Çaglayan
Yıldırım Beyazıt University, Turkey
Title: Importance of Myc-related microRNAs in induced pluripotency
Time : 17:05-17:25
Biography:
E Sacide Caglayan has completed her PhD on Medical Genetics in Afyonkocatepe University in 2010 and worked as a Visiting Scholar on induction of pluripotency from fibroblasts by using microRNAs in Ruohola-Baker Lab, Institute of Stem Cell and Regenerative Medicine in University of Washington. Presently, she is working as an Assistant Professor in Health Science Faculty, Yildirim Beyazit University, Turkey.
Abstract:
Pluripotent stem cells (PSCs) have the capacity to differentiate into any cell type of the body. Therefore, induced pluripotent stem cells (iPSCs) are seen as a promising solution for patient-specific cell therapies. However, the safety is major issue for in vitro methods that are used in induction of pluripotency and also in differentiation of PSCs toward specific cell types. In pioneer studies of iPSC generation, the role of c-Myc has been highlighted as a possible master regulator of pluripotency, but direct c-Myc overexpression is known to prompt drawbacks, especially in human cells. In recent studies, the role of non-protein coding RNA molecules such as microRNAs (miRNAs) has been shown in enhanced reprogramming efficiency. In addition, new reprogramming methods have been ultimately improved by adding miRNAs, in the absence of previous factors. Cross interaction between miRNAs and c-Myc has been also found in differentiation of iPSCs, as well as in reprogramming and self-renewing the pluripotent state. Thence, miRNAs are promising solution for efficiency and safety of iPSC derivation and differentiation methods. The purpose of the present review is to evaluate interaction mechanisms of miRNAs with c-Myc and in iPSC technology.
Jamila Chakir
Laval University, Canada
Title: Tissue engineering concept of a model of airway bronchial mucosa
Time : 16:45-17:05
Biography:
Jamila Chakir is a full Professor at the Department of Medicine at Laval University and Institut Universitaire de Cardiologie et Pneumologie de Québec. She has obtained her PhD degree in Immunology in France. She has received her Postdoctoral research training at Laval University and McGill University, Canada in inflammation and remodeling in asthma. Her research focuses on cellular and molecular mechanisms of airway remodeling particularly the role of structural cells in airway remodeling and their interaction with and inflammatory cells. She has published more than 200 papers, communications and book chapters in the respiratory and immunology field and holds grants from Canadian agencies. She is a Member of different national and international scientific committees and has received several awards from national and international organisms.
Abstract:
Asthma is an inflammatory disease characterized by an injury-repair cycle in the bronchial wall leading to airway remodeling. Cellular interactions between epithelial cells and underlying fibroblasts play a key role in this remodeling. The available information on resident cells in the bronchial mucosa were obtained from studying fixed bronchial biopsies or from studies conducted on cells grown in monolayers. However, isolated cells can only simulate a small part of the body’s complexity and often lose their morphology and functional properties. Tissue engineering is a field, which applies the principles of biology and engineering to the development of functional substitutes for damaged tissue. The two major goals of tissue engineering are the production of functional tissues that can be grafted into human and the development of in vitro models that are superior to conventional cell cultures mainly because monolayer cultures lack an adequate extracellular matrix. These in vitro models offer the possibility to study different mechanisms involved in many diseases such as asthma. We developed a bronchial mucosa model by tissue engineering using primary fibroblast and epithelial cells isolated from normal and asthmatic human bronchial biopsies. We observed that this model exhibits morphological, histological and functional features of bronchial mucosa. In engineered tissue from normal volunteers, fibroblasts were well organized in the extra-cellular matrix and the epithelial cells proliferate and differentiated to produce a pseudo-stratified structure. Epithelial cells and fibroblasts in this model were able to produce basement membrane proteins. This confirmed that there was functional in vitro cooperation between cells through laminin and type IV collagen synthesis. We used this model to study communication between inflammatory and resident bronchial cells. We found that T cell survival was greater in asthmatic engineered bronchial mucosa and that epithelial cells are more effective than fibroblasts in ensuring T cell survival. We also showed that fibroblasts from asthmatic subjects regulate epithelial cell proliferation and TGF-β signaling may represent one of the pathway involved in these interactions. This sophisticated three dimensional model could be a valuable tool to a better understand key mechanisms involved in inflammation and airway repair in asthma
Chasserot-Golaz Sylvette
Institute of Cellular and Integrative Neurosciences, France
Title: Actin and annexin A2: Essential partners of neuroendocrine secretion
Time : 16:25-16:45
Biography:
Chasserot-Golaz Sylvette has completed her PhD from University of Strasbourg, France which is centered on the mechanism of action of steroids antiglucocorticoids in hepatocytes and hepatoma cells at Institut de Biologie Moléculaire et Cellulaire (IBMC) in 1985. She has been working as a permanent Research Scientist at INSERM since 1988 and moved to the Institut des Neurosciences Cellulaires et Intégratives (INCI) in Strasbourg in 1993 where her research is dedicated to elucidating the molecular mechanisms underlying exocytosis in neuroendrine cells. She is an expert in the molecular and cellular implication of annexin A2 in chromafin cells and more generally in cellular neurobiology. She has published more than 84 papers in renowned journals.
Abstract:
The neuroendocrine system depends on elaborate cellular communication provided by intense membrane trafficking. Calcium regulated exocytosis results in the release of molecules such as neurotransmitters and hormones contained in secretory granules. In neuroendocrine cells, the recruitment and subsequent fusion of secretory granules at the plasma membrane occur at specific sites dedicated to exocytosis. Annexin A2 was the first protein identified at these exocytotic sites in chromaffin cells. It binds two major actors of exocytosis, actin and phospholipids and mediates the formation of lipid microdomains required for the spatial organization of fusion sites at the plasma membrane. To understand how annexin A2 promotes this membrane remodeling, the involvement of cortical actin filaments in lipid domain organization was investigated. Electron tomography of chromaffin cells, together with amperometric measurements of single cell catecholamine release showed that cortical actin bundled by annexin A2 connects docked secretory granules to the plasma membrane and contributes to the formation of GM1-enriched lipid microdomains at exocytotic sites. When an annexin A2 mutant with impaired actin filament-bundling activity was expressed, the formation of plasma membrane lipid microdomains and the number of docked granules decreased and fusion kinetics slower, whereas the pharmacological activation of the intrinsic actin-bundling activity of endogenous annexin A2 had the opposite effects. Thus, annexin A2-induced actin bundling is essential for generating active exocytotic sites. Our results reveal that annexin A2 and the actin cytoskeleton are essential partners in the formation of lipid platforms for granule docking and fusion. This challenges the classical passive role depicted for the cortical actin cytoskeleton in calcium-dependent exocytosis and represents a major advance in our understanding of neuroendocrine secretion.
Avinash Patel
Max Planck Institute of Molecular Cell Biology and Genetics, Germany
Title: Dissecting the mechanisms of liquid to solid phase transition associated with neurodegenerative diseases
Time : 15:50-16:10
Biography:
Avinash Patel has completed his PhD from the Manchester Cancer Research Institute, UK in 2012. He is currently pursuing Post doctoral research in the lab of Prof Tony Hyman, Max Planck Institute for Cell Biology and Genetics, Dresden, Germany. He has recently published a paper in the journal Cell, which showed general principles underlying Liquid-to-Solid phase transitions might be a key mechanism behind neurodegenerative diseases.
Abstract:
FUS/TLS is a prion-like protein that contains intrinsically disordered domains and is associated with neurodegenerative disease. We recently showed that intracellular FUS/TLS compartments form under various cellular conditions and that these compartments exhibit liquid-like properties in vivo and in vitro. “Aging” experiments revealed that FUS/TLS liquid droplets undergo a phase transition to a solid-like state which is accelerated by disease mutations. We discovered that concentrating proteins by phase separation comes with the trade-off that can also promote protein aggregation. Solid-like aggregates of prion-like proteins are a hallmark of many aging-associated diseases. Aberrant phase transitions might be one trigger causing aging-associated diseases. However, the molecular mechanisms underlying this aberrant phase transition and the strategies cells have developed to sustain the function of these aggregation-prone proteins remain largely enigmatic. Here, we present recent advances we made in understanding the mechanisms cells might have developed to prevent the liquid-solid phase transitions by using a wide range of biochemical, biophysical and cell biology techniques. We find that electrolytes, small compounds and protein interactors affect the liquid-liquid, as well as liquid-solid transitions. Insights gained from studying liquid-solid phase transition might help us developing drugs targeted to treat age-associated diseases.
Eva Collakova
Virginia Tech, USA
Title: Potential targets of VIVIPAROUS1/ABI3-LIKE1 (VAL1) repression in developing Arabidopsis thaliana embryos
Time : 12:00-12:20
Biography:
Eva Collakova has obtained her PhD in 2003 from Michigan State University, where she has also completed her Postdoctoral studies. In 2009, she became an Assistant Professor at Virginia Tech, USA. She is currently an Associate Professor at the Department of Plant Pathology, Physiology and Weed Science at Virginia Tech. She has published over 20 manuscripts in peer-reviewed journals, including top plant research-related journals, e.g., Plant Cell, Plant Physiology and Plant Journal and has served as a Reviewer of over 25 manuscripts for international journals and as a Panelist and an ad-hoc Reviewer for Federal Grant Agencies in the US.
Abstract:
Seed development and metabolism in Arabidopsis are regulated by leafy cotyledon1 (LEC1), Abscisic acid-insensitive3 (ABI3), Fusca3 (FUS3) and LEC2. These transcription factors are part of the core LAFL (LEC1, ABI3, FUS3, and LEC2) regulatory network central to seed development. The action of the LAFL transcription factors is inhibited in germinating seedlings by VAL1 and 2 to suppress the embryonic program during the transition from the embryonic to vegetative state. However, the VALs are also expressed in maturing seed, which appears controversial, considering their role in suppressing the embryonic program. Two VAL1 splice variants were identified through RNA sequencing in developing Arabidopsis embryos: A full-length form containing four domains known to be involved in transcriptional and/or epigenetic regulation and a truncated form lacking the plant-homeodomain-like domain associated with epigenetic repression. Reverse genetics revealed limited influence of the VAL1 absence on seed and embryo metabolomes. However, 3,293 and 2,194 transcripts were up and down-regulated, respectively, in developing val1 mutant embryos relative to the wild type, suggesting that VAL1 is a global regulator of gene expression in developing embryos. Interestingly, none of the transcripts encoding the core LAFL network transcription factors were affected in val1 embryos. Instead, activation of VAL1 by FUS3 appears to result in repression of a subset of seed maturation genes downstream of core LAFL regulators. Transcripts that were not LAFL targets were also de-repressed in developing val1 embryos. Taken together, VAL1 appears to repress its targets through LAFL-dependent and independent mechanisms through epigenetic and/or transcriptional regulation.
Hila Toledano
University of Haifa, Israel
Title: microRNAge: The role of microRNAs in aging of the Drosophila germline stem cell niche
Time : 15:10-15:30
Biography:
Hila Toledano has received her PhD from The Weizmann Institute Israel (2003) and completed her Postdoctoral studies at the Salk Institute, San Diego CA (2012). She is a PI at University of Haifa, Israel and her lab is focused on post-transcriptional regulation of adult stem cells.
Abstract:
Highly regenerative tissues are supported by rare populations of tissue-specific stem cells that continuously divide to both self-renew and generate differentiated progeny. Aging is characterized by aberrant tissue regeneration that is attributed to deteriorated function of stem and its surrounding cells; however it is not clear whether this process is genetically regulated. Heterochronic microRNAs (controlling the timing of events) were initially described to control the timing of developmental stages; however their role in the regulation of aging is just beginning to be studied. Previously we have linked the role of the heterochronic miRNA let-7 to the declined function of the germline stem cell in aged Drosophila males. Our recent findings indicate that the expression of the evolutionary conserved miR-9a increases significantly during aging in both stem and progenitor germ cells. We further show that miR-9a directly down regulates the levels of N-cadherin, which is required to enable stem cells detachment from the niche. Thus we conclude that miR-9a promotes differentiation and attenuates tissue degeneration. Characterizing the microRNA based posttranscriptional regulatory network and its temporal modulation is critical towards understanding the role of regulation in driving and responding to aging.
Claire Wyart
Institut du Cerveau et de la Moelle épinière-UPMC CNRS, France
Title: Investigation of sensory interface relaying information from cerebrospinal fluid to motor circuits
Time : 14:50-15:10
Biography:
Claire Wyart has completed her PhD in Strasbourg, France and her Postdoctoral Fellowship in UC Berkeley, California, USA. She has trained in neuroscience, physiology and biophysics. She has started her lab in the Brain and Spine Institute in Paris in 2011. Her main interest is to unravel the circuits located in hindbrain and spinal cord that underlie locomotion. In particular, she has developed new optical and ontogenetic technologies to probe the role of sensory feedback during active locomotion.
Abstract:
The cerebrospinal fluid (CSF) is a complex solution circulating around the brain and spinal cord. Behavior has long been known to be influenced by the content and flow of the CSF, but the underlying mechanisms are completely unknown. CSF-contacting neurons by their location at the interface with the CSF are in ideal position to sense CSF cues and to relay information to the nervous system. By combining electrophysiology, optogenetics, bioluminescence monitoring with calcium imaging in vivo, we demonstrate that neurons contacting the CSF in the spinal cord detect local bending and in turn feedback GABAergic inhibition to multiple interneurons drives locomotion in the ventral spinal cord. Behavior analysis of animals deprived of this mechano-sensory pathway reveals its contribution in modulating frequency and duration of locomotion. Altogether our approach developed in a transparent animal model shed light on a novel pathway enabling sensory motor integration between the CSF and motor circuits in the spinal cord.
Haya Lorberboum-Galski
Hebrew University of Jerusalem, Israel
Title: Protein replacement therapy for mitochondrial disorders: New hopes for incurable diseases
Time : 14:30-14:50
Biography:
Haya Lorberboum-Galski is a full Professor of Biochemistry at the Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada (IMRIC), Faculty of Medicine, the Hebrew University of Jerusalem, Israel. She has published over 60 publications in peer-reviewed journals in her fields of expert, as well as review articles and edited a book on chimeric proteins. She serves as an ad-hoc Referee for peer-reviewed journals. She is currently the Chairman of the Institute for Medical Research Israel-Canada (IMRIC).
Abstract:
Modern medicine offers no cure for genetic mitochondrial disorders and the usual treatment is mostly palliative. We developed a novel concept for the treatment of mitochondrial disorders using Cell/Organelle-Directed Protein Replacement Therapy; the delivery of a wild type mitochondrial protein/enzyme directly to its sub-cellular location and into its natural complexes, in the form of a fusion protein. Our approach is to fuse a wild type mitochondrial protein, including the Mitochondrial Targeting Sequence (MTS) with the delivery peptide TAT [HIV-transactivator of transcription (TAT) peptide], which will lead the protein/enzyme into the cells and their mitochondria, where it will substitute for the mutated endogenous protein. We tested this novel approach using a number of mitochondrial proteins, implicated in mitochondrial human diseases: Lipoamide Dehydrogenase (LAD), C6ORF66 and Frataxin were evaluated in vitro, in patients’ cells and in vivo, in mouse models. TAT-MTS-Mitochondrial fusion proteins are rapidly and efficiently internalizing into cells and their mitochondria both in patients’ cells and in mice tissues, including the brain. Treatment with the new TAT-MTS-Mitochondrial fusion proteins, improves mitochondrial functions and life span in animal models. Interestingly, when we replaced the MTS sequence of the exogenous protein with a heterogeneous MTS sequence, both mitochondrial penetration and biological activity significantly increased. This novel approach may open new inroads in the management of many incurable mitochondrial diseases.
Talila Volk
Weizmann Institute of Science, Israel
Title: The mechanobiology of muscle nuclei: Mechanism and functional significance
Time : 14:10-14:30
Biography:
Talila Volk gained a BSc in Biology at Tel Aviv University. She continued her scientific training at the Weizmann Institute of Science, Rehovot, where she completed her MSc and PhD degrees in the laboratory of Benjamin Geiger. She then moved to the laboratory of John Fessler at UCLA for her postdoctoral studies. In 1990, Talila returned to Israel and, during the years that followed, she became a faculty member in the Department of Molecular Genetics at the Weizmann Institute, where she currently works.
Abstract:
Nuclear shape and morphology is essential to maintain the epigenetic state of the genome and is robust in differentiated cells. In contrast to nuclei in non motile tissues, nuclei in differentiated skeletal and cardiac muscles are facing iterated and altered cytoplasmic mechanical forces, produced by muscle contraction/relaxation waves. Recent findings from several labs (including ours), uncovered a muscle-specific network of nuclear associated cytoskeletal proteins, which is essential to protect muscle nuclei from the variable cytoplasmic strain induced by muscle contraction/relaxation and consequently is essential for the maintenance of myonuclear shape. We are studying Nesprin-related mechanisms essential for maintenance of robust muscle nuclear structure. Our recent studies identified intra-nuclear alterations in the distribution of chromatin elements and DNA within the muscle nuclei of Nesprin/MSP-300/Klar mutants. These proteins were shown to be essential for linking the nuclear membrane with the microtubule network, as well as with muscle sarcomeres, in order to maintain robust myonuclear shape. Furthermore, we have identified a novel membrane protein, (Muscle-specific-alpha2delta), which is essential for keeping Nesprin/MSP-300 in the nuclear membrane preventing its re-translocation to the ER. Live imaging of muscles within intact Drosophila larvae with fluorescently labeled nuclei and Z-lines enabled imaging of myonuclei during muscle contraction/relaxation waves. A general recovery of myonuclear shape is detected in the course of contraction/relaxation waves of wild type larvae. In contrast, mutant nuclei became fluidic and exhibited significant deformation. We suggest that this deformation is the basis for defects in the intra-nuclear organization of chromatin, which further leads to aberrant transcriptional alterations in the mutant muscles. Such alterations might represent the cause for the numerous muscle diseases associated with mutants of the LINC complex in humans.
Anja Nohe
University of Delaware, USA
Title: New treatments for articular cartilage formation and repair
Time : 13:50-14:10
Biography:
Anja Nohe is an Associate Professor in the Department of Biological Sciences at the University of Delaware, USA. She has received her PhD in Chemistry in 2000. After a Postdoctoral fellow at the University of Western Ontario in Canada, she accepted a first faculty position at the University of Maine in Chemical and Biological Engineering. In 2008, she relocated to the University of Delaware, USA. She is a Member of several Editorial Boards. She uses novel imaging approaches such as AFM and the family of Image Correlation Spectroscopy to define cellular processes during stem cell differentiation and skeletal formation. Moreover, utilizing novel techniques and tools such as real time imaging and nanoparticles, she focuses on protein dynamics in cells as well as on protein distribution in mice.
Abstract:
Osteoarthritis (OA) is characterized by the progressive degradation of articular cartilage. There are no treatments today that can stop or reverse the loss of cartilage degradation. A desperate need for treatment options are on the rise as does the OA cases on an annual basis. Growth factors like Bone Morphogenetic Proteins (BMPs) are known to be present throughout the chondrocytic lineage and influence their secretion of extra cellular matrix (ECM) that is essential for the formation of articular cartilage. However, BMPs usage as a therapeutic has many drawbacks as they are known to initiate chondrocyte hypertrophy and cartilage degradation. In order to develop a more specific treatment we designed a peptide CK2.1. Using state of the art imaging techniques and system biology approaches we designed a peptide that activates a very specific BMP2 signaling pathway without the induction of chondrocyte hypertrophy. Injection into the tail vein of mice reveals increased articular cartilage formation. Additionally, markers for cartilage formation such as collagen type IX are up-regulated. This is in sharp contrast to BMP2 injection. BMP2 injection up-regulated collagen type X and MMP13 markers for hypertrophy. Second harmonic imaging of the cartilage shows a more improved structure of the cartilage. These data make CK2.1 a peptide that can restore cartilage without induction of hypertrophy and a useful therapeutic for OA treatment.
Eva E Qwarnstrom
University of Sheffield, UK
Title: Regulation of inflammatory and anti-apoptotic responses through the IL-1RI/TILRR complex
Time : 12:40-13:00
Biography:
Eva E Qwarnstrom is a Professor of Cell Biology at the University of Sheffield and holds an honorary affiliated Associate Professorship at the University of Washington, Seattle. She has obtained her PhD degree from the University of Lund, Sweden, following a Fellowship at the National Institute of Health, Bethesda, USA. She is a Member of Editorial Boards and scientific advisory committees.
Abstract:
Members of the toll-like and IL-1 receptor family (TIR) are central regulators of immune and inflammatory responses. Signal activation is induced through ligand binding and controlled by system specific co-receptors. The IL-1RI co-receptor TILRR is a splice variant of FREM1. TILRR association with the signaling receptor magnifies IL-1 induced activation of the canonical and non-canonical NF-ï«B network by enhancing signal amplification at the level of the receptor complex and potentiates recruitment of the MyD88 adapter and PI3 kinase. TILRR controlled MyD88 dependent activation of the canonical pathway is regulated in a Ras-dependent manner, reflected in alterations in cytoskeletal structure and cell adhesion. The changes induced provide a process for rapid control of NF-ï«B, involving sequestration and release of cytoskeletal bound Iï«Bα through a mechanism controlled by TILRR signal amplification. In silico simulations using agent based modeling of the NFï«B network predict cytoskeletal control of inhibitor levels to provide a mechanism for signal calibration and to enable activation-sensitive regulation of NFï«B induced inflammatory responses. Our studies have identified two functional sites within the TILRR core protein, which selectively control inflammatory and anti-apoptotic responses. The mechanisms underlying distinct network amplification and the relevance of pathway-specific regulation of canonical and non-canonical NFï«B activation will be discussed.
Hilal Turkoglu Sasmazel
Atilim University, Turkey
Title: Hybrid PCL/chitosan scaffolds with micro and macro porosity
Time : 12:20-12:40
Biography:
Hilal Turkoglu Sasmazel is working in Metallurgical and Materials Engineering Department at Atilim University, Ankara, Turkey since 2007. Her areas of interest are biomaterials, nanomaterials, tissue engineering, polymeric and composite materials, materials surface modifications and characterizations. She was honored with TUBA-L’Oreal-UNESCO Young Women in Science Award in Materials Engineering in 2009. She has published 21 SCI research articles and has 31 conference presentations in the last 15 years. She is the Director of Polymer Composite Materials, Biocompatibility of Biomaterials and Antibacterial Property Testing Laboratories at Atilim University. She is an MC Member and representative of Turkey in EU-COST MP1101, MP1206 and FP1405 actions.
Abstract:
In this study, hybrid PCL/chitosan polymeric scaffolds have been developed by combining electrospinning, solvent casting and freeze drying techniques. The aim was to obtain a hybrid structure with micro and macro porosity. The fabrication of the scaffolds has been designed in three steps. In the first step, PCL solution, prepared by dissolving 15 weight% PCL in chloroform/methanol solvent (v/v, 75/25), was electrospun in order to obtain fibrous mats with microporous structure. In the second step, chitosan solution, dissolved in acetic acid, was cast into a Petri dish and the prepared PCL fibrous mat was immersed into the solution to combine PCL with chitosan. For a better integration of the chitosan solution to the pores of the PCL fibrous network, pressure was applied on top of the PCL mat. Finally, the samples were freeze-dried with two different pre-drying step, refrigerating and vacuum incubating, to obtain macropores, accompanying the micropores of the fibrous structure. These prepared scaffolds were found to have a structure similar to the natural extracellular matrix (ECM) with an average contact angle of 68.93±2.18o. The optimization of the fabrication parameters was carried out with naked eye observations, SEM analysis and mechanical testing. It was found that the scaffold, freeze dried for 24 hours, showed the highest Young’s modulus and yield strength values. Additionally, thickness and water contact angle (CA) measurements, Fourier Transform Infrared Spectroscopy (FTIR) and PBS absorption/shrinkage studies were carried out to define physical and chemical properties of the developed scaffolds. Finally, the biocompatibility of the scaffolds was tested in vitro with MRC5 fibroblast cells regarding cell attachment and growth and the developed scaffold was found to have better biocompatibility than commercial tissue culture polystyrene.
- Molecular Biology | Structural Biology
Location: Experience II
Chair
Michael Kolbe
Max Planck Institute for Infection Biology, Germany
Co-Chair
Alexei V Finkelstein
Russian Academy of Sciences, Russia
Session Introduction
Alexei V Finkelstein
Russian Academy of Sciences, Russia
Title: There and back again: Two views on the protein folding puzzle
Time : 11:15-11:35
Biography:
Alexei V Finkelstein was graduated in 1970 and received his PhD degree in 1976 from the Moscow Institute of Physics and Technology. He is the Head of the Protein Physics Lab at the Institute of Protein Research, Russian Academy of Sciences and is a Professor of the Lomonosov Moscow University awarded by the State Prize of Russia; elected to the Russian Academy of Sciences, Alumnus of LMB MRC (Cambridge) and HHMI Scholar (1995-2010). He has published 200+ papers in reputed journals. His two books on protein physics has been published in English, Russian and Chinese. He is serving as an Editorial Board Member of several reputed journals.
Abstract:
The intricate protein 3D structure results from spontaneous folding (both in vitro and in vivo), though more than the life-span of the Universe would have been required to find it by sampling of amino acid conformations, this is called "the Levinthal's paradox". To resolve it, various models of folding were proposed during decades. However, they fail to overcome this paradox when the 3D structure’s stability is close to that of the unfolded chain, as it is in reality. The folding rate problem was first solved using unfolding (not folding!). The trick is that, firstly, the rates of the forward and reverse reactions coincide when the structure stability equals to that of the unfolded chain (according to the “principle of detailed balance” well-known in physics) and it is much easier to imagine and investigate how the thread unfolds than how it obtains a certain fold. Recently, the folding problem has been also solved “from the viewpoint of the folding chain”: it has been proved that the necessary, search for the most stable fold, sampling is by many orders of magnitude smaller when considered at the level of formation and packing of secondary structures than at the Levintal-considered level of amino acid conformations. The estimated rate of such a sampling turned out to be physically and biologically reasonable for proteins of various sizes.
Michael Kolbe
Max Planck Institute for Infection Biology, Germany
Title: The bacterial type 3 secretion system: Structure function analysis of a molecular syringe
Time : 11:35- 11:55
Biography:
Michael Kolbe has studied Chemistry at the Universities of Paderborn and Hamburg. Thereafter he has completed his Doctorate on the structure and function of the chloride pump Halorhodopsin at Max-Planck-Institute for Biochemistry and the Ludwig-Maximilians University in Munich. After his Postdoc at the Max-Delbrück Centre in Berlin he joined the Max-Planck-Institute for Infection Biology as Leader of a Junior Research Group. Since the beginning of the year 2015, he is a Professor at the University Hamburg and Head of the Department for Structural Infection Biology at Helmholtz Center for Infection Research.
Abstract:
Many different bacterial pathogens use protein secretion systems to transport effector molecule into host cells. Effector transport through these systems is essential to establish and maintain host cell infection. To understand host-pathogen interaction and pathogenesis during infection, we analyzed the structure and function of the type 3 secretion system (T3SS) of Gram-negative bacteria including Shigella flexneri and Salmonella typhimurium. The T3SS is a highly conserved virulence machinery of Gram-negative bacteria that initiates infection by subverting host cell defense mechanisms. Although great efforts were made to elucidate the structure of the T3SS in the last decades, the mechanistic details of the protein transport remains elusive. By using structural biology methods in combination with biochemical and cellular assays we analyzed the assembly and the architecture of the T3SS. Our studies explain the assembly of the T3SS needle and they provide a model of substrate molecule transport. We also developed tools to block substrate molecule transport through the T3SS channel which might help to characterize important steps in the secretion process.
Biography:
Cordula Enenkel has completed her PhD at the University of Stuttgart, Germany and Postdoctoral studies from Rockefeller University, New York, USA. She has worked as Privatdozent at the Humboldt University, Berlin, Germany, before she joined the University of Toronto as an Associate Professor in 2011. She has published 24 papers in reputed journals and has been serving as Reviewer for journals and funding agencies.
Abstract:
Proteasomes are key proteases in regulating protein homeostasis. During cell cycle progression, proteasomes exist as holo-enzymes in the nucleus and are engaged in the degradation of poly-ubiquitylated proteins. Proteasomes can be imported into the nucleus as mature or immature sub-complexes dependent on the growth conditions. Most of our body’s cells do not proliferate and remain in quiescence during aging. The transition from proliferation to quiescence is accompanied by significant metabolic changes and the rearrangement of sub-cellular structures. Proteasomes are exported from the nucleus into reversible and motile granules in the cytoplasm. Studies in quiescent yeast revealed that proteasome granules are not surrounded by membranes and rapidly resolve upon exit from quiescence. Proteasome granules either represent proteolytic centers for unwanted and toxic proteins or serve as storage compartments, thus names proteasome storage granules (PSGs). Their presence strengthens the resilience of quiescent yeast towards proteo and genotoxic stress and confers fitness during aging. The organizing principle of PSGs remains a mystery. We searched for proteins orchestrating PSG formation and performed high throughput microscopy screens in the yeast null mutant collection and GFP library. The hit genes involved in PSG organization are required for the regulation of nuclear transport, ubiquitin concentration, genotoxic stress and metabolic energy. We purified cross-linked PSGs and subjected them to mass spectrometry analysis. Our data suggest that PSGs mainly consist of proteins of the ubiquitin-proteasome-system and provide an interesting link between PSG formation and the availability of free ubiquitin.
Hermona Soreq
The Hebrew University of Jerusalem, Israel
Title: Non-coding RNAs: An integrative biology hope for anxiety-related syndromes
Time : 12:15- 12:35
Biography:
Hermona Soreq was trained at The Weizmann Institute of Science and the Rockefeller University. In 1980, she has joined the Weizmann Institute as a Senior Lecturer and joined the Faculty of The Hebrew University in 1986. She pioneered the application of molecular biology and neurogenomics to the study of cholinergic signaling with a recent focus on the evolutionary and functional aspects of brain microRNA regulation over cholinergic coding genes and pseudogenes under stress and in mental diseases. She has authored over 300 publications and won Advanced ERC Award and Israeli I-Core Center of Excellence Award on Mass Trauma.
Abstract:
The discovery of non-coding RNAs revolutionized our view of how the brain works and holds great promise for rapid progress in the run for therapeutics of anxiety-related diseases. We now know, unlike previous beliefs that our DNA includes several families of non-coding genes with regulatory functions; that these functions are differentially impaired under diverse anxiety reactions and most importantly, that the new genes can serve as scaffolds for developing new diagnostic tools and synthesizing novel therapeutics. I will discuss the family of microRNAs, tiny blockers of brain signaling pathways that govern cognition and anxiety reactions and will focus on those microRNAs that malfunction in mental diseases and their target genes with a special emphasis on the pathway of cholinergic signaling.
Byung-Dong Kim
Seoul National University, South Korea
Title: The foldback intercoil DNA
Time : 12:35- 12:55
Biography:
Byung-Dong Kim is a Professor Emeritus of the Seoul National University and a Member of the Korean Academy of Science and Technology. He is the chair of the Advisory Board of the Plant Genomics and Breeding Institute of Seoul National University. He has authored a book entitled “Foldback Intercoil (FBI) DNA” in 2008. Currently he is pioneering the biological meaning of the FBI DNA in the age of genomics and epigenetics.
Abstract:
Foldback intercoil (FBI) DNA is a unique and transient configuration of duplex DNA that consists of four functional parts: Foldback head, intercoil stem, intercoil blunt end tail and heteroduplexes. FBI DNA was first found in rare TEM configurations of pearl millet mtDNA and was tested out for its feasibility by space-filling model of DNA. FBI DNA is formed by foldback bending at one location of a duplex DNA, to lead the flanking anti-parallel double helixes to intertwine in each other’s major groove to form an intercoil. Repeat sequences in the intercoil make four-stranded base pairing. Base flipping of the repeats leads to heteroduplexes formation and homologous recombination. This subtle transformation of the double helix into FBI DNA structure is instrumental in mediating four major DNA-DNA transactions, namely, α deletion by direct repeats, Ω site-specific inversion by inverted repeats, FBI tip insertion in site-specific insertion and non-homologous end joining and gap filling (EHEJ-GF) in transposition. Most significantly, FBI DNA transfiguration into heteroduplexes offers an effective mechanism of paranemic separation of daughter strands after DNA replication which otherwise would get stuck after unwinding a plectonemic double helix DNA at the replication fork. Biochemical and bioinformatics evidences in the literature that support the FBI DNA for the inevitable presence and working in the real biology will be presented. Put together, realization of the dynamic and diverse transformation of the FBI DNA structure would allow a new understanding of diverse DNA function, their interaction at genome level and at cellular differentiation. Suggestions for future research strategies would be discussed.
Larry Mark Fisher
St George’s, University of London
Title: Structural basis of DNA gating by gyrase and topoisomerase IV and its inhibition by antibacterial therapeutics
Time : 12:55- 13:15
Biography:
Larry Mark Fisher has obtained his PhD in Chemistry from Harvard University and was a Damon Runyon Walter Winchell Cancer Fellow at NIH working with Dr Martin Gellert. He is the Dean of Research at St George’s, University of London. He has published more than 100 papers on DNA topoisomerases and DNA supercoiling in bacteria, yeast and human cell systems.
Abstract:
Gyrase and topoisomerase IV (topo IV) are bacterial type II topoisomerases that regulate cellular DNA topology and are key targets of antimicrobial therapeutics. The enzymes share close mechanistic and architectural similarity notably a DNA gating mechanism that involves the formation of a covalent enzyme-DNA complex known as the ‘cleavage complex’. Antibacterial fluoroquinolones and quinazolinediones stabilize the cleavage complex triggering cell death. To gain insight into the reaction cycle and drug action and resistance, we solved the first crystal structures of drug-DNA cleavage complexes with several different quinolones. We present structures for topo IV and gyrase revealing details of the cleaved DNA gate and drug binding pockets. Recently, we have also solved structures for the three-gate ‘open clamp’ state of topo IV, a key intermediate that suggests a mechanism for how DNA is captured and transported through the enzyme complex. Our studies provide new insights on how DNA is manipulated by these complex molecular machines to mediate DNA supercoiling and chromosome segregation.
Tali E Haran
Technion-Israel Institute of Technology, Israel
Title: The relationship between the structural properties of p53 binding sites and p53-dependent gene expression
Time : 14:05- 14:25
Biography:
Tali E Haran is an Associate Professor at the Department of Biology, Technion-Israel Institute of Technology. She holds PhD and Master Degree from the Weizmann Institute of Science, studying the crystal structure of DNA oligomers. She has completed her Postdoctoral studies at Yale University, studied DNA bending and indirect recognition in protein-DNA interactions. She has been a Visiting Scientist at the Department of Biochemistry, Cambridge University, UK at the Department of Biochemistry and Molecular Biology, Columbia University, USA and at the Centre for Integrative Biology, University of Trento, Italy. Her main research interest is the interactions between sequence-specific transcription factors and their DNA binding sites, focusing on the mechanism by which DNA structure contributes to the recognition of particular sites by regulatory proteins.
Abstract:
The tumor suppressor protein is a central hub protein in human cells. In response to stress, it functions mainly as a transcription factor (TF), binding to more than 200 response elements (REs), activating and repressing adjacent genes. The REs are made of two sequence-specific half-sites, separated by a variable number of base pairs. It is currently unclear how p53 chooses its target sites, however, p53 multi-functional activities are directly linked to its ability to function as a sequence-specific TF. It is now well appreciated that the intrinsic physical properties of the DNA double helix can affect binding of TFs and transactivation of adjacent genes. We have previously shown that DNA structure and flexibility vary among p53 REs, affecting their binding characteristics. We carried out experimental measurements of global structure and flexibility properties of p53 REs using cyclization kinetics of DNA minicircles, together with binding studies and transactivation assays in yeast and human cells. We propose that functional selectivity is conferred at least in part through p53/DNA binding and that differential structural characteristic of p53 REs play a role in this selectivity. I will present recent experimental results showing how p53 uses the structural properties of its binding sites to differentiate between functional classes of p53 REs, that p53 REs are allosteric effectors of p53 transactivation and the novel role of the spacer sequences in these interactions. These recent findings reveal how non-canonical sites, such as half-sites can be functional and hence expand the “universe” of p53 binding sites.
Gali Prag
Tel Aviv University, Israel
Title: Bacterial genetics and structural biology for decoding the ubiquitin code
Time : 14:25- 14:45
Biography:
Gali Prag has earned his PhD from the Hebrew University, Israel. With his supervisor Prof. Oppenheim, he has studied bacterial genetics and obtained two EMBO Fellowships to determine the structures of several chitin-degrading enzymes in complex with their native substrates. He has completed his Postdoctoral studies at the NIH with Professor James Hurley, where he determined the first structures of ubiquitin-receptor complexes with ubiquitin and some of the ESCRT complexes. In 2008, he returned to Israel and established a structural-biology and bacterial genetic laboratory in TAU.
Abstract:
Ubiquitin (Ub)-signals virtually regulate all cellular pathways. However, two major challenges impede our ability to identify and characterize associations within ubiquitylation cascades: Ubiquitylation cascades are multiplex, i.e., few E1s, dozens E2s and hundreds of E3s ubiquitylate thousands of substrates. Moreover, many substrates possess more than one cognate E3-ligase. About a hundred deubiquitylases rapidly and efficiently reverse the ubiquitylation. To circumvent these limitations we took an integrating biology approach including structural based in silico search, bacterial genetics, biochemical, biophysicals and X-ray crystallography to establish a productive interdisciplinary research. A novel bacterial genetic selection system for ubiquitylation and its utilization in identifying and characterizing new E3s, Ub-receptors and ubiquitylation substrates will be presented. Using bacterial expression of a functional ubiquitylation apparatus we purified and crystallized and determined the structure of an ubiquitylated-Ub-receptor for the first time. We took a multidisciplinary approach and uncovered a novel UBD within this receptor. A surprising function of the Ub-receptor ubiquitylation will be presented. As the findings derived from the genetic selection system we developed and the crystal structure of ubiquitylated-ubiquitin-receptor are still under review so I will share the full result and discussion at presentation time.
Sapun H Parekh
Max Planck Institute for Polymer Research, Germany
Title: Mechanically-induced protein structural changes in fibrin hydrogels using hyperspectral CARS microscopy
Time : 14:45-15:05
Biography:
Sapun H Parekh has joined the MPIP in February 2012. Before coming to the MPIP, he has worked as a Science Policy Fellow in the National Science Foundation in Washington, DC and as a Visiting Scientist at the National Institutes of Health. Prior to this, he was a Postdoctoral Researcher in the Biomaterials Group at the National Institute for Standards and Technology where he has worked on mechanobiology of stem cell differentiation and development of label-free imaging techniques. He has received his BS in Electrical Engineering from the University of Texas at Austin in 2002 and his PhD in Bioengineering from the University of California at Berkeley, San Francisco in 2008. His PhD thesis focused on force generation and mechanics of semi-flexible actin networks that are ubiquitous in biology. During his PhD, he has developed and applied a new atomic force microscopy system with improved long-term stability to measure these biophysical systems. At the MPIP his group focuses on molecular imaging and his research interests include applications of non-linear microscopy in biology and molecular biophysics.
Abstract:
Fibrin is a protein hydrogel material responsible for stabilizing the platelet-rich blood clot over a wound in blood coagulation. Its utilitarian mechanical properties: Being stiff or deformable as needed result from the unique hierarchical organization of the polymer network. Experimental and theoretical studies have shown that single filament stretching, network rearrangements and protein unfolding are responsible for this unique mechanical behavior. In this work, we investigate the biophysics of fibrin unfolding in response to uniaxial stretch in situ using coherent Raman imaging. Fibrin hydrogels are stretched to regime where unfolding transitions of α-helical structures to β-sheet occur and spatially resolved broadband coherent anti-Stokes Raman scattering (B-CARS) spectra of fibrin gels are acquired and analyzed. The secondary structure is calculated from peak analysis of the amide I and amide III regions, which are sensitive to subtle changes in protein structure. Experiments on gels of different polymer concentration and cross-linker density show unfolding transitions that correlate with non-linear effects seen in shear rheology. Finally, imaging results show an inhomogeneous unfolding distribution near inert beads in the gel, suggesting that local stresses on platelets within biological clots is different from the bulk mechanical response. This demonstrates the use of hyperspectral B-CARS microscopy to measure local, mechanically-induced conformational changes in proteins.
Henrik Devitt Møller
University of Copenhagen, Denmark
Title: Extrachromosomal circular DNA: A key player in creation of copy number variation
Time : 15:05-15:25
Biography:
Henrik Devitt Moller has completed his PhD at the University of Copenhagen, Denmark in 2015 and continued his work on extrachromosomal circular DNA as Post doctorate in the Regenberg Laboratory. He has published 8 papers in peer-reviewed journals.
Abstract:
Numerous human cancers are caused by copy-number variations (CNVs) of proto-oncogenes. Yet, detecting chromosomal CNVs before they reach establishment in large cell populations is a major challenge. By screening for a potential deletion-byproduct of CNVs, the so-called extrachromosomal circular DNA (eccDNA), we reasoned that we might elucidate some of the early ongoing processes in genomic rearrangements. We developed a highly sensitive eccDNA purification method, Circle-Seq that relies on removal of all linear DNA and next-generation sequencing of circular DNA. More than a thousand eccDNAs larger than 1 kb were recorded in the eukaryotic model Saccharomyces cerevisiae (yeast) increasing the number of known eccDNAs in eukaryotes more than a hundred fold. Now we present hundreds of eccDNA profiles from a distant related yeast subspecies. A number of eccDNAs are found to be identical between the two yeast strains, advocating for conserved hotspots for DNA circularization and potential genomic reintegration. We reveal that CNVs in the form of eccDNAs are common in S. cerevisiae and we hypothesize that eccDNAs could be important players in genetic variation and evolution of eukaryotic genomes.
Nadine Provencal
Max Planck Institute of Psychiatry, Germany
Title: Exposure to early life stress and glucocorticoids: Mechanisms of system-wide epigenetic effects
Time : 15:25-15:45
Biography:
Nadine Provencal has completed her PhD in Epigenetics at McGill University in collaboration with the Research Group on Psychosocial Maladjustment in Children (GRIP) in 2013. Thereafter, she continued her training through Post-doctoral research at the University of Montreal and Max-Planck Institute of Psychiatry. She has published more than 15 papers in high impact international journals and received a prestigious Postdoctoral Fellowship from the Canadian Institute of Health Research (CIHR) and has been awarded the 2014 Richard Todd Award from the International Society of Psychiatric Genetics for her outstanding contribution to the genetics of child psychiatry.
Abstract:
Exposure to early life stress (ELS) is a well-known major risk factor for developing psychiatric and behavioral disorders later in life. Both prenatal and postnatal stressors have long-lasting impact on adult pathological states. Epigenetic mechanisms have been shown to be involved in the embedding of these long-term changes. In a model of early life adversity in rhesus macaques, we have shown that differential rearing leads to long-lasting epigenetic alterations in two different tissues, the prefrontal cortex (PFC) and T cells. One of the mechanisms that might lead to these epigenetic alterations in multiple tissues is a long-lasting disruption of the stress hormone system by excessive glucocorticoids (GCs) release after ELS exposure. Using human hippocampal progenitor cells (HPCs), we have recently identified long-lasting DNA methylation alterations induced by GCs exposure, where a significant portion of these marks were initiated early during cellular proliferation and differentiation stages and persisted in mature neurons. Moreover, a significant overlap was observed between our GR-induced epigenetic changes in HPCs and sites previously associated with child abuse in postmortem human hippocampus and blood cells, suggesting similar long-lasting GR-induced epigenetic alterations in the brain and in peripheral tissues reflecting GC actions during ELS. A mechanistic understanding of the long-term epigenetic consequences of stress using a translational approach may allow novel, targeted intervention and prevention strategies for behavioral, psychiatric and other stress-associated disorders.
Jinyan Du
Merrimack Pharmaceuticals Inc., USA
Title: Identification of non-intuitive biomarkers predicting dependency on AKT vs. MAPK signaling of ERBB2+ cancer cells using an integrated experimental and computational framework
Time : 16:20-16:40
Biography:
Jinyan Du has completed her PhD at Harvard University and Postdoctoral training at the Broad Institute. She is currently a Principal Scientist at Merrimack Pharmaceuticals, a fully integrated biopharmaceutical company that is building one of the most robust oncology pipelines in the industry. She has published over 30 papers in reputed journals.
Abstract:
Understanding the molecular pathways by which oncogenes drive cancerous cell growth and how dependence on such pathways varies between tumors, could be highly valuable for the design of anti-cancer treatment strategies. In this work, we study how dependence upon the canonical PI3K and MAPK cascades varies across HER2+ cancers and define biomarkers predictive of pathway dependencies. A panel of 18 HER2+ (ERBB2-amplified) cell lines representing a variety of tumor types was used to characterize the functional and molecular diversity within this oncogene-defined cancer. PI3K and MAPK-pathway dependencies were quantified by measuring in vitro cell growth responses to combinations of AKT (MK2206) and MEK (GSK1120212; trametinib) inhibitors, in the presence and absence of the ERBB3 ligand heregulin (NRG1). A combination of three protein measurements comprising the receptors EGFR, ERBB3 (HER3) and the cyclin-dependent kinase inhibitor p27 (CDKN1B) was found to accurately predict dependence on PI3K/AKT vs. MAPK/ERK signaling axes. Notably, this multivariate classifier outperformed the more intuitive and clinically employed metrics, such as expression of phospho-AKT and phospho-ERK and PI3K pathway mutations (PIK3CA, PTEN and PIK3R1). The predictability of the three protein biomarkers for differentiating PI3K/AKT vs. MAPK dependence in HER2+ cancers was confirmed using external datasets (Project Achilles and GDSC), again out-performing clinically used genetic markers. Measurement of this minimal set of three protein biomarkers could thus inform treatment and predict mechanisms of drug resistance in HER2+ cancers. More generally, our study provides an integrated framework for identifying non-intuitive biomarkers in cancer patients.
Chaohui Dai
Yangzhou University, China
Title: Effect of porcine CD14 gene RNAi on the expression of toll-like receptor 4 pathway-related genes, the level of pro-inflammatory cytokines and adhesion ability to Escherichia coli
Time : 17:00-17:20
Biography:
Chaohui Dai is currently a Postgraduate student of Yangzhou University, China. She is mainly engaged in pig disease-resistant breeding and reproduction.
Abstract:
Three full-sib individuals of the resistance and susceptibility to E. coli F18 in Meishan piglets were obtained by challenging with the pathogens through feeding F18ab and F18ac strains and then the transcriptome sequencing of intestinal tissue in sensitive and resistant pigs to E. coli F18 was analyzed. The pig small intestinal epithelial cell line (IPEC-J2) with CD14 gene silencing were established by Lentivirus-mediated RNAi and the transcription and protein expression level of TLR4 pathway-related genes (MyD88, IFN-α, IL-1β, TLR4 and TNF-α) were detected; the levels of proinflammatory cytokines IL-6, IL-8, IL-12, MIP-1α and MIP-1β in cell culture supernatants were measured; the E. coli F18ab and F18ac’s adhesion ability to IPEC-J2 were detected. The transcriptome sequencing results revealed that toll-like receptor 4 (TLR4) signaling pathway especially CD14 gene played important roles in immune process of E. coli F18-invasion. After CD14 gene silencing, the transcription and protein expression levels of IFN-α, IL-1β, TLR4 and TNF-α were significantly down-regulation (P<0.05); the levels of IL-6 and IL-12 in cell supernatants were significantly reduced (P<0.05); the E. coli F18ab’s adhesion to IPEC-J2 enhanced highly significantly (P<0.01). In summary, the establishment of IPEC-J2 cell line with CD14 gene silencing stably mediated by Lentivirus offered important material for mechanism research of CD14 gene and TLR4 signal pathway. These results suggested that CD14 gene played an important role in not only TLR4 signaling pathway but also regulating the immune process of E. coli F18-invasion.
Ying Liu
Yangzhou University, China Panel
Title: MicroRNA transcriptome of duodenum tissues in Chinese Meishan weaned piglets challenged with E. coli F18
Time : 17:20-17:40
Biography:
Ying Liu is a Doctor of Yangzhou University, China. She is mainly engaged in pig disease-resistant breeding and reproduction.
Abstract:
Escherichia coli F18 is mainly responsible for post-weaning diarrhea (PWD) in piglets. The molecular regulation of E. coli F18 resistance in Chinese domestic weaned piglets is still obscure. We used Meishan piglets as model animals to test their susceptibility to E. coli F18. Small RNA duodenal libraries were constructed for E. coli F18-sensitive and resistant weaned piglets challenged with E. coli F18 and sequenced using Illumina Solexa high-throughput sequencing technology. Sequencing results showed that 3,475,231 and 37,198,259 clean reads were obtained with 305 known and 681 novel microRNAs (miRNAs) differently expressed in resistant and sensitive groups, respectively. Twenty-four miRNAs including 15 up-regulated and 9 down-regulated demonstrated more than a 2-fold differential expression between the F18-resistant and sensitive pigs. Stem-loop RT-qPCR validation indicated that most of the differently expressed miRNAs were consistent with the high-throughput sequencing data, including significantly expressed miRNAs, such as miR-136, miR-196b, miR-499-5p and miR-218-3p (p<0.05). KEGG pathway analysis for target genes revealed that differently expressed miRNAs were involved in infectious diseases, signal transduction and immune system pathways. According to the function of the target genes and previous sequencing results, miR-196b, miR-499-5p and miR-218-3p appear to be very promising candidates for miRNAs involved in response to E. coli F18 infection. The present study provides improved database information on pig miRNAs, better understanding of the genetic basis of E. coli F18 resistance in local Chinese pig breeds and lays a new foundation for identifying novel markers of E. coli F18 resistance.
- Systems Biology | Bioinformatics | Bioengineering | Bioimaging
Location: Experience II
Chair
Bernard Korzeniewski
Jagiellonian University, Poland
Co-Chair
Mahmoud Rouabhia
Laval University, Canada
Session Introduction
Bernard Korzeniewski
Jagiellonian University, Poland
Title: Regulation of oxidative phosphorylation during work transitions and bioenergetic background of mitochondrial diseases
Time : 09:00-09:20
Biography:
Bernard Korzeniewski has completed his PhD and Postdoctoral studies from Jagiellonian University. He has published more than 75 papers in reputed journals.
Abstract:
It was proposed that the main mechanism responsible for the regulation of the cell bioenergetic system in skeletal muscle and heart during work transition is each-step activation (ESA) of all oxidative phosphorylation (OXPHOS) complexes, NADH supply and glycolysis in parallel with the activation of ATP usage (actomyosin-ATPase and Ca2+-ATPase) by Ca2+ ions. A widely-validated computer dynamic model involving this mechanism is able to explain numerous, frequently apparently unrelated to each other, properties of the system behavior under various conditions. Computer simulations demonstrate that in intact working skeletal muscle metabolite (PCr, ADP, Pi) concentrations and cytosolic pH begin to change significantly at much higher OXPHOS (complex) activities than the respiration rate (VO2). Consequently, it is postulated that inborn deficiencies of particular OXPHOS complexes and entire OXPHOS as well as ESA dysfunction can lead to mitochondrial myopathies not by compromising mitochondrial VO2 and oxidative ATP production per se, but through increase in cytosolic Pi, ADP and H+ concentrations. This increase can account for such mitochondrial myopathy syndromes as muscle weakness, exercise intolerance (exertional fatigue) and lactic acidosis.
Vanathi Gopalakrishnan
University of Pittsburgh School of Medicine, USA
Title: Novel methods for integrative modeling of biomedical data
Time : 09:20-09:40
Biography:
Vanathi Gopalakrishnan is a tenured Associate Professor of Biomedical Informatics in the School of Medicine at the University of Pittsburgh and has a PhD in Computer Science. She has secondary appointments in the Intelligent Systems Program and the Department of Computational and Systems Biology. She directs the PRoBE Laboratory for Pattern Recognition from Biomedical Evidence. Her research involves predictive modeling from big biomedical datasets with a focus on transforming imaging and biomarker data into actionable knowledge to enable precision medicine and translational bioinformatics. She is a Guest Editor for a special edition on Biomedical Informatics in the journal data.
Abstract:
Molecular profiling data from scientific studies aiming for early detection and better management of diseases such as cancer has accumulated at rates far beyond our abilities to efficiently extract knowledge of value to the practice of precision medicine. A major challenge is that these data are often generated using multiple high-throughput technologies giving rise to panomics data such as gene expression and DNA methylation for the same or related classification task. In this talk, I will present novel computational methods and tools that are being developed in my laboratory for the integrative modeling of panomics data to improve disease state classification from related molecular profiling studies. We are extending the novel Transfer Rule Learning (TRL) methods that were previously developed to deal with sparse data from biomarker profiling studies, by automatically learning classification rules from one dataset, transferring that knowledge and using it when learning rules from a related dataset. The extensions include methods for knowledge transfer using ontological or taxonomic hierarchies along with classification rule learning. Preliminary results from collaborative studies involving biomarker profiling data for the early detection of lung cancer and microbiome data for infectious disease classification will be presented.
Max von Kleist
Freie Universität Berlin, Germany
Title: Mutational interference mapping experiment (MIME) for studying RNA structure and function
Time : 09:40-10:00
Biography:
Max Von Kleist has an undergraduate background in Bioinformatics and holds a PhD in Mathematics, which he has completed in 2009 at the Hamilton Institute, National University of Ireland. After a short Postdoctoral phase at the Freie Universität Berlin (2010-2011), he gradually built up an own research group. He has published over 30 papers to date.
Abstract:
RNA has long been believed to mainly serve as a blueprint for proteins. However, a large diversity of so called non coding RNAs has been discovered lately to regulate virtually all cellular processes. Characterizing functional domains and structure-function-relationships in RNA is a major challenge as classical experimental approaches are time-consuming and require substantial investigator expertise. To overcome these obstacles we recently developed MIME which coupled to a bioinformatics analysis pipeline implemented in the cross-platform software MIMEAnTo allows to identify domains and structures in RNA that are important for its function. In MIME, target RNAs are randomly mutated, selected by function, physically separated and sequenced using next-generation sequencing (NGS). Consequently, quantitative effects of mutations at every nucleotide position are recovered. While the location of function-disrupting mutations in the RNA allows identifying binding domains, permitted patterns of mutations reveal the functional role of each nucleotide. Moreover, through co-variation analysis it is possible to de novo model the structure of the RNA that is associated with the analyzed function.
Karen Lipkow
University of Cambridge, UK
Title: Cellular systems biology of chromosome dynamics
Time : 10:00-10:20
Biography:
Karen Lipkow was originally trained as a Molecular Biologist with undergraduate degree and research at the University of Konstanz, Germany and Rockefeller University, New York and has obtained his PhD degree from the University of Oxford, UK. For her Post doctorate at the University of Cambridge, she switched to computational biology. Since becoming a Group Leader in Cambridge, she is combining both computational and experimental approaches to study the mechanisms that shape cellular architecture. She is also an Editorial Board Member of the world's oldest scientific journal.
Abstract:
The questions of how genes are regulated remains fundamental even after many decades of intense study. Rather than just studying the linear, one-dimensional sequence of DNA to inform us about regulatory mechanisms, we can now investigate the complex 3-dimensional organization of whole genomes. It has become clear that this organization is non-random and highly dynamic. To address new questions in genome architecture, we are taking a systems biology approach, combining the bioinformatic determination of chromatin states with quantitative experiments and dynamic, stochastic models of whole genome organization. Comparing these results with our experimental data has led us to understand how biophysical properties of the chromatin fibre lead to significant and biologically relevant self-organization of the genome.
Jorn M Werner
University of Southampton, UK
Title: MHC I and antigen selection: Immune system modeling integrates cellular function with structural plasticity
Time : 10:35-10:55
Biography:
Jorn M Werner has received his PhD in Biochemistry from the University of Oxford and established his own research group at the University of Southampton in 2003. His interdisciplinary research group integrates structural biochemistry with cellular function using systems model approaches. He has published over 50 peer reviewed papers and is serving as an Editor for Science Reports as well as Frontiers in Structural Biology.
Abstract:
The control of the immune system plays a key role in both healthy and diseased states and the presentation of peptides at the surface of most nucleated cells by major histocompatibility complex class I molecules (MHC I) is crucial for eliciting or evading an immune response. Since the pool of surface presented peptides only presents a small sample of all possible peptides understanding their selection process is crucial for the development of treatments such as vaccines, which rely on the selection of specific peptides. The peptide selection process is mediated primarily by a weakly interacting multi-protein peptide loading complex (PLC) at the centre of which is the modulation of MHC class I conformation. To gain a better understanding of the mechanisms of peptide selection by MHC I, we developed computational systems models encoding distinct mechanistic hypotheses of PLC function. Using in vivo biochemical data we were able to infer that the system is under kinetic control and that a conformational intermediate of MHC I is significant for peptide selection. We investigate the molecular determinants of peptide selection using a combination of X-ray, NMR and biophysical techniques together with molecular dynamics simulations. Using this approach we show that peptide selector function correlates with protein plasticity rather than structure. This in turn was tested experimentally in vivo and extended to the PLC resident chaperone tapasin. By combining computational systems models with in-cell biochemical data and structural methods we identify a previously undetected correlation between protein plasticity and in vivo peptide selector function of MHC I, with implications for host defense and immunotherapy.
Erchin Serpedin
Texas A&M University, USA
Title: Investigating functional relationships of five critical genes present in the familial nonsynonymous loci with risk of having acute lymphoblastic leukemia
Time : 10:55-11:15
Biography:
Erchin Serpedin has completed his specialization degree in Signal Processing and Transmission of Information from Ecole Superieure D’Electricite (SUPELEC), Paris, France, in 1992. He has received his MSc degree from the Georgia Institute of Technology, Atlanta, in 1992 and the PhD degree in Electrical Engineering from the University of Virginia, Charlottesville in 1999. He is currently a Professor in the Department of Electrical and Computer Engineering at Texas A&M University, College Station. He is the author of 2 research monographs, 1 textbook, 75 journal papers and 120 conference papers.
Abstract:
A recent whole exome sequencing of Acute Lymphoblastic Leukemia (ALL) revealed that common variations in particular non-synonymous homozygous variants affects disease risk. The present work researches into the functional consequences of the polymorphisms in the following genes: B3GALTL (rs1041073), GEN1 (rs16981869), CA9 (rs2071676), CHIT1 (rs2297950), CHRNB1 (rs17856697), ERBB2 (rs1058808) and ZNF207 (rs3795244). The Polyphen scores were evaluated using the residue changes due to missense variations and protein identifiers generated GlobPlots to predict inherent protein disorders and ProtParam provided the ‘instability indices’. Furthermore, metabolic pathways and protein networks were studied by Reactome Pathway Browser and String-db.
Daniel H Shain
Rutgers University, USA
Title: Energy anabolism as a modulator of adaptation across domains of life
Time : 11:15-11:35
Biography:
Daniel H Shain has completed his PhD from Colorado State University and Postdoctoral studies from the University of California, Berkeley. He has published more than 50 papers in reputed journals.
Abstract:
Adenosine 5’-trisphospate (ATP) is the universal currency of energy in living cells. We have determined that elevated ATP confers environmental stress resistance in disparate organisms. For example, glacier ice worms (Annelida) display atypically high ATP levels that paradoxically increase as temperatures decline, comparable with other cold-adapted taxa. By manipulating key targets in purine metabolism, we have generated strains of bacteria and algae with elevated ATP that are cold tolerant. The F1F0 ATP synthase complex is the primary producer of energy and is the most functionally conserved molecular machine across domains of life. We have identified two ice worm-specific accessory domains in subunits ATP6 and epsilon that likely enhance ATP production. We propose that manipulation of these targets will lead to translatable applications ranging from stress-resistant crops to the treatment of mitochondrial disease.
Bruno César Feltes
Federal University of Rio Grande do Sul, Brazil
Title: Conformational study of a mutated protein complex in xeroderma pigmentosum disease using molecular dynamics and residue interaction networks
Time : 11:35-11:55
Biography:
Bruno Cesar Feltes is currently a PhD candidate in Cellular and Molecular Biology at the Federal University of Rio Grande do Sul, Brazil. His studies have been focused in bioinformatics with emphasis on systems biology, systems toxicology and systems pharmacology to answer biological questions related to developmental biology and aging mechanisms; he has published most of his works in these fields. Presently, he works with molecular dynamics simulations and network analysis applied to structural biology and diseases. His collaborations also extend to microarray and RNA-seq data analysis.
Abstract:
Xeroderma Pigmentosum (XP) is a rare autosomal recessive disorder caused by mutations in seven genes that codify Nucleotide Excision Repair (NER) pathway proteins, named XPA to XPG. As a result of this, XP patients produce mutant proteins that compromise DNA lesion removal, resulting in a broad range of pathological symptoms. However, little is known about XP proteins structure or how these mutations affect NER complex assembly. Thus, to understand how these mutations impact on XP proteins, we obtained DDB2(XPE)-DDB1 protein complex (DDB-complex) PDB data, since this complex is necessary for damage recognition in NER and performed multiple molecular dynamics simulations. Simulations were performed in triplicates for wild-type DDB2, DDB1 and DDB-complex, as well as for the naturally-occurring mutations found in XP, namely DDB2R273H, which impair DDB2 DNA binding and DDB2L350P, which affect the DDB-complex (all simulated alone and assembled with DDB1). We also applied dynamic Residue Interaction Networks (RINs) analyses to observe how these mutations impact on structurally important residues and communities formation over simulated periods and combined these results with systems biology analysis of RINs. Hence, it was possible to observe conformational differences between wild-type and mutated proteins/complex, such as reduced local flexibility, residues imperative for communication between communities, complex instability, structurally critical residues and loss or gain of communities. The combination of in silico analyses employed arises as a promising method for studying protein structure and could be assigned to other relevant investigations, such as small molecules impact on proteins and recombinant proteins design.
Ken-ichro Ogawa
Tokyo Institute of Technology, Japan
Title: Robust patterning of gene expression based on internal coordinate system of cells
Time : 11:55-12:15
Biography:
Ken-ichro Ogawa has completed his PhD (Doctorate of Science) in 2011 from Tokyo Institute of Technology and was engaged in scientific pursuits as a Research Associate at Tokyo Institute of Technology from 2011 to 2012. He is currently an Assistant Professor in the Department of Computational Intelligence and Systems Science at Tokyo Institute of Technology. His research interests lie in the field of modeling embryogenesis of multicelluar organisms and embodied interaction in human communication.
Abstract:
Cell-to-cell communication in multicellular organisms is established through the transmission of various kinds of chemical substances. It is known that gene expression triggered by a chemical substance in individuals has stable spatial patterns despite the individual differences in concentration patterns of the chemical substance. This fact reveals an important property of multicellular organisms called “robustness”. Robustness has been conventionally accounted for by the stability of solutions of dynamical equations of chemical substances. However, any biological system is composed of autonomous elements, in which each element does not merely accept information on the chemical substance from the environment; instead, it accepts the information based on its own criteria for reaction. Therefore, this phenomenon needs to be considered from the viewpoint of cells. This study aims to explain theoretically the robust patterning of gene expression from the viewpoint of cells. For this purpose, we introduced a new operator for transforming a state variable of a chemical substance from an external coordinate system to an internal coordinate system of each cell. Then, this operator is applied to the simplest reaction diffusion model of the chemical substance. This extended model indicates that the robust patterning of gene expression against individual differences in concentration pattern of the chemical substance can be explained from the viewpoint of cells if there is a regulation field that compensates for the difference between cells seen in transformation. This result provides a new insight into the investigation of the mechanism of robust patterning in biological systems composed of individual elements.
Susanne Franziska Fenz
University of Wurzburg, Germany
Title: Super-resolution imaging of intrinsically fast moving flagellates
Time : 12:15-12:35
Biography:
Susanne Franziska Fenz has studied Physics in Wurzburg and Heidelberg. She has received her PhD in 2009 from the University of Bonn, Germany. As a Post-doctoral fellow she moved to Leiden University in the Netherlands to work on single-molecule fluorescence microscopy of living cells. Her current interests include biomimetics, cell adhesion and diffusion in crowded membranes as well as super-resolution microscopy.
Abstract:
Recent developments in super-resolution microscopy made it possible to resolve structures in biological cells at a spatial resolution of a few nm and observe dynamical processes with a temporal resolution of ms to µs. However, the optimal structural resolution requires repeated illumination cycles and is thus limited to fixed cells. For live cell applications substantial improvement over classical Abbe-limited imaging can be obtained in adherent or slow moving cells. Nonetheless, to our knowledge a large group of cells, intrinsically fast moving flagellates could not yet be addressed with super-resolution microscopy. These include pathogens like trypanosomes, the causative agents of sleeping sickness in humans and Nagana in cattle. Attempts to immobilize these cells include drug treatment or embedding in agarose or gelatin gels. However, these methods either have unwanted side effects or are not sufficient for super-resolution imaging because they do not efficiently suppress the flagellar beat. Here, we present a novel hydrogel embedding and quantify its biocompatibility and immobilization efficiency. We characterize both the cells and the gel with respect to their autofluorescence properties and find them suitable for single-molecule fluorescence microscopy (SMFM). We apply SMFM to track individual Atto647N-labeled membrane proteins on the surface of immobilized trypanosomes and achieve a localization precision of 30 nm and a temporal resolution of 25 ms.
Tso-Fu Mark Chang
Tokyo Institute of Technology, Japan
Title: Fabrication of high biocompatible Pt-nylon and Pt-silk composite materials by supercritical carbon dioxide-assited metallization method
Time : 13:25-13:45
Biography:
Tso-Fu Mark Chang has received his BSc in Chemical Engineering from the University of Toronto (2004), MS in Chemical Engineering from National Tsing Hua University (2007) and PhD in Materials Science and Engineering from Tokyo Institute of Technology (2012). He is currently an Assistant Professor of Precision and Intelligence Laboratory at Tokyo Institute of Technology. His research interests include pressure and solvent effects on reactions in supercritical CO2 and characterization of the materials fabricated in supercritical CO2. He has published more than 50 papers in reputed journals.
Abstract:
As the medical technology advances, the next-generation healthcare devices are urgently demanded. Implantable and wearable medical devices are the latest applications over the decades. Nickel, copper and aluminum are widely used in aforementioned medical devices because of the simple process and low cost, however, adverse reactions such as allergies and Alzheimer's disease might take place due to the releasing of the metal ions. A biocompatible electronic material, thus, becomes the most urgent demand. Platinum is considered to be the most promising material owing to its irreplaceable biocompatibility. Moreover, nylon and silk are the common materials used in clothes. The combinations of Pt with nylon and silk textiles are considered to be promising candidates for the medical devices. Electroless plating can put these composite materials into practice and further achieves homogeneous metallized-surface due to the low deposition rate. Typical electroless plating consists of pretreatment to clean and roughen the surface, catalyzation to embed the catalysts as a nucleation site into the substrate and the plating step for the metallization. In spite of the dominance of Pt, electroless plating of Pt remains less studied due to the difficulties in controlling the catalyzation step in the electroless plating process. An up-to-date technique of supercritical carbon dioxide (sc-CO2) assisted catalyzation is practiced in this study to overcome the instinct difficulty of Pt metallization. With the help of the sc-CO2, the Pt catalyst can be inlaid into the textile structure and uniform Pt coatings can be deposited on the textile.
Mahmoud Rouabhia
Laval University, Canada
Title: Electrical stimulation as a tool to accelerate cutaneous regeneration and wound repair
Time : 13:45-14:05
Biography:
Mahmoud Rouabhia is a full Professor at the Faculty of Dentistry of Laval University. He is a Senior Scientist in the field of Immunology, Cell Biology and Tissue Engineering. He has obtained his PhD in France, followed by a Postdoctoral training for four years in Canada. His research interest includes wound healing under chemical and physical stimulations that include growth factors but also electrical stimulation, stem cell differentiation for tissue regeneration, the interaction between host & oral microorganisms related to the oral cavity, the role of local innate immunity reducing oral infections, etc. He has more than 130 pair reviewed scientific publications. He is the Editor/Co-editor of three books. He has published over 15 book chapters/review articles and two patents.
Abstract:
Electrical stimulation (ES) in its various forms has been shown to promote wound healing by increasing the migration of keratinocytes and macrophages, enhancing angiogenesis and stimulating dermal fibroblasts. Delivery of ES to the wound can be through biocompatible conductive biomaterials such as conductive membranes made of 5% polypyrrole (PPy) and 95% polylactide (PLA), as well as an electronic system that enables cells to be cultured on the surface of the conductors and then electrically stimulated. One of the key cells in wound healing is fibroblast contributing to extracellular matrix synthesis and interaction with epidermal cells thus contributing to wound closure. Fibroblast activities during wound healing were reported to be modulated by multiple agents including ES. However, the underline molecular mechanisms are not clear and the approach to apply electrically activated fibroblasts to assist skin wound healing needs to be explored. With this conference, we will be presenting cell response/cell signaling pathway following exposed to ES; demonstrating the advantages of ES on in vitro and in vivo skin tissue regeneration. To generate original data related to ES promoting wound healing we used a sophisticated conductive membrane that combines polylactide (PLLA) or polyester fabrics (PET) with polypyrrole (PPy) as a conductive polymer. With these conductive membranes, we demonstrated that both continuous and pulsed ES-induced fibroblast adhesion and proliferation. Furthermore, ES promoted fibroblasts to myofibroblast differentiation confirming what has been reported previously. Interestingly, the myofibroblast phenotype acquired following ES can be transferred to daughter cells. The effects of ES on human fibroblasts lead to an increased production of TGFβ1 by activating ERK and NF-κB signaling pathway. The ES-modulated fibroblasts adequately interacted with keratinocytes leading to a well-structured EHS tissue expressing basement membrane (BM) glycoproteins, including laminin and type IV collagen. Tissue organization was superior under 200 mV/mm of ES compared to 50 mV/mm. This confirms the previously reported study suggesting that exogenous ES maintains the ex vivo epidermal integrity and cell proliferation of a human skin explants. Following 20 and 30 days of grafting, the newly regenerated skin was well vascularized, showing BM formation through laminin and type IV collagen secretion and was wholly formed by the implanted human cells. In conclusion, we demonstrated that electrically activated fibroblasts interacted with keratinocytes leading to in vitro/in vivo well-structured engineered skin. This study thus provides an innovative way to use electrically activated cells for skin regeneration and wound repair.
Rajeshkumar Anbazhagan
National Taiwan University of Science and Technology, Taiwan
Title: Synthesis of molybdenum disulphide (MoS2 ) gadolinium complex with core shell structure used as in vivo MRI
Time : 14:05-14:25
Biography:
Rajeshkumar Anbazhagan has completed his Master’s degree from Annamalai University and studying PhD in National Taiwan University of Science and Technology, Taiwan. He has published 2 papers in reputed journals.
Abstract:
In this paper, water soluble core shell molybdenum disulphide (MoS2) gadolinium complex was synthesized and used as in vivo MRI contrast agents. Briefly, monolayer MoS2 nanosheets were exfoliated with help of thioglycolic acid (TGA) as stabilizing agents by room temperature stirring followed by the sonication in water. Subsequently, luminescent MoS2 quantum dots with sustained fluorescence emission, which were fabricated through hydrothermal treatment of exfoliated MoS2 and could be utilized as cell biomarkers. These primary in vitro cell imaging results proved the biocompatibility of the nanomaterials, it could be used as in vivo imaging candidate in future. Therefore, we develop core-shell molybdenum disulfide and gadolinium complex, as an alternative in vivo MRI candidate. The synthesized core-shell contrast agents’ exhibits enhanced paramagnetic property; compared to commercial gadolinium contrast agents core-shell MoS2 chelate has 4.5-times longer water proton spin-lattice relaxation time (T1); as well as lowered toxicity, extended blood circulation time, increased stability and desirable excretion characteristic. Transmission electron microscopy (TEM) proved core-shell nanoparticles 100 nm in size. These findings suggest that the synthesized nanomaterials possess high potential as a positive contrast agent for the enhancement of MRI imaging.
- Poster Presentation
Session Introduction
Nehad Mahmoud Gumgumjee
King Abdulaziz University, KSA
Title: Synergistic antimicrobial effects and GC-MS analysis of phytocomponents of Commiphora quadricincta
Biography:
Nehad Mahmoud Gumgumjee has completed her PhD and Postdoctoral studies from King Abdulaziz University, Saudi Arabia. She has published more than 10 papers in reputed journals and has been serving as an Editorial Board Member of repute.
Abstract:
The Commiphora quadricincta, a small tree, belong to Burseraceae family is traditionally known for its medicinal properties. The present study was therefore carried out to investigate the synergistic antimicrobial activities and the phytochemicals of the bioactive components in the extract of this plant species. The antimicrobial activities of stem bark and leaves extract was investigated against 7 medically important bacterial strains, namely Bacillus subtilis, MRSA, Micrococcus, Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aurues and Klebsella pneumoniae and five fungi (Aspergillus niger, A. fumigatus, A. flavus, Candida albicans and Saccharomyces spp.). The antibacterial activity was determined using agar well diffusion method. The most susceptible bacteria to this extract were Escherichia coli, while the most susceptible fungi were A. flavus. GC-MS analysis revealed that the ethanol extract of Commiphora quadricincta contained mainly; 2-Methyl-3-pentanol (2.84%); Butyl hydroxy toluene (22.32%); 9,12,15-Octadecatrienoic acid, 2-phenyl-1, 3-dioxan-5-yl ester (5.90); Ethyl isoallocholate (11.21%); à-Amyrin (2.22%) and Flavone 4-OH,5-OH,7-dioglucoside (11.21%). Most identified compounds are known to have antimicrobial activity.
Biography:
Abdul Rahman Hajar has completed his PhD and Postdoctoral studies from King Abdulaziz University, Saudi Arabia. She has published more than 45 papers in reputed journals and has been serving as an Editorial Board Member of repute.
Abstract:
Qutran (Wood tar) oils and vapor of Olea europaea subsp. cuspidate extracted medicinal plants were screened for their activity against seven strains of bacteria. Bacillus subtilis, methicillin-resistant Staphylococcus aureus (MRSA), Micrococcus, Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa and Klebsiella pneumonia using agar well diffusion method were investigated. Results showed that the effect of oils extract was higher than that of vapor. The tar oils have great antibacterial activity against all the investigated strains. The growth inhibition rate ranged from 16.33 to 46.00 mm .The wood tar oil showed higher activity against tested organisms than Streptomycin. In this study the most pronouns effect was shown by that of Olea europaea subsp. cuspidata wood tar oil. The most susceptible bacteria was Pseudomonas aeruginosa, flowed by Micrococcus luteus, while the most resistant bacteria was Staphylococcus aureus with 16.33 mm of inhibition zone. The results showed that wood tar oil of Olea europaea subsp. cuspidate was more effective than Streptomycin. GC-MS analysis revealed that the Qutran (Wood tar) oils contained mainly Octadecenamide (5.77%); Lucenin 2 (5.46%); Docosane and Nonacosane (3.75%); Cyclopropene (3.50%); Hematoporphyrin (2.68%); Tetratetracontane (2.36%); Dotriacontane (1.57); Acetic acid (1.53); N-methylglycine (1.49%); Propyne antimicrobial (1.41%). All identified compounds are known to have antimicrobial activity.
In-Su Park
Dankook University, South Korea
Title: Adipose-derived stromal cell cluster with light therapy enhance angiogenesis and skin wound healing in mice
Biography:
In-Su Park is currently working in Stem Cell Biology/Tissue Engineering Department at Korea Institute of Science and Technology (KIST) in Seoul, South Korea. He has completed his PhD in 2012 at Korea University. He has developed growth factor-immobilized substrate (fibroblast growth factor, heparin-binding peptide substrate) as a bioartificial material for stem cells differentiation. He has published more than 10 papers in reputed journals.
Abstract:
Human adipose-derived mesenchymal stem cells (hASCs), which are found in adipose tissue, are an attractive cell therapy source for the regeneration of damaged tissues because they are the
ability of self-renewal and the ability to differentiate into various cell lineages. Transplanting hASCs induces neovascularization and improves blood flow to ischemic tissue in animal models. In spite of the angiogenic potential of hASCs for treatment of ischemic wounds, these cell sources have limitations for therapeutic angiogenesis. Although ASCs are favorable with regard to obtaining the number of cells required for transplantation, few transplanted stem cells have been found to differentiate into endothelial cells (ECs) and incorporate into vascular structures in ischemic sites. Thus, the foremost mechanism by which stem cells participate in tissue repair seems to be related to their trophic factors. Indeed, stem cells provide the microenvironment with a wide range of growth factors, cytokines and chemokines, which can broadly defined as the stem cells secretome. In in vitro condition, these molecules can be traced from the conditioned medium or spent media harvested from cultured cells. Conditioned medium now serves as a new treatment modality in regenerative medicine and has shown a successful outcome in some diseases. Low-level light therapy (LLLT) has been used for a long time for various purposes, such as reduce inflammation and improvement in the local circulation. Moreover, many studies have demonstrated positive bio-stimulatory effects of LLLT on stem cells. The aim of this study was to investigate the effects of low-level light therapy (LLLT) on stem cells secretome. With the emergence of this approach, we described the possibility of using stem cells conditioned medium as a novel and promising alternative to skin wound healing treatment.
Daniel Neiman
The Hebrew University-Hadassah Medical School, Israel
Title: Identification of tissue specific cell death using methylation patterns of circulating DNA
Biography:
A Phd student under the guidance of Prof Aharon Razin & Prof Yuval Dor lab & Ruth Shemer at The Hebrew University-Hadassah Medical School, Israel.
Abstract:
Minimally-invasive detection of cell death could prove an invaluable resource in many physiologic and pathologic situations. Cell-free circulating DNA (cfDNA), released from dying cells, is emerging as a diagnostic tool for monitoring cancer dynamics and graft failure. However, existing methods rely on DNA sequence differences in source tissues, so that cell death in tissues with a normal genome cannot be identified. We developed a method of detecting tissue-specific cell death in humans, based on tissue-specific methylation patterns in cfDNA. We interrogated tissue-specific methylome databases to identify cell type-specific DNA methylation signatures, and developed a method to detect these in mixed DNA samples. We isolated cfDNA from plasma or serum of donors, treated with bisulfite, PCR-amplified and sequenced to quantify cfDNA carrying the methylation markers of the cell-type of interest. Pancreatic beta-cell DNA was identified in the circulation of recently diagnosed type-1 diabetes patients and islet graft recipients, oligodendrocyte DNA in patients with relapsing multiple sclerosis, neuronal/glial DNA in patients after traumatic brain injury or cardiac arrest, and exocrine pancreas DNA in patients with pancreatic cancer or pancreatitis. This proof-of-concept study demonstrates that the tissue origins of cfDNA and thus the rate of death of specific cell types can be measured in humans. The approach can be adapted to identify cfDNA derived from any cell type in the body, offering a minimally-invasive window for monitoring and diagnosis of a broad spectrum of human pathologies, as well as better understanding of normal tissue dynamics.
Joice de Faria Poloni
Federal University of Rio Grande do Sul, Brazil
Title: Evaluation of somatic point mutations associated to splicing mechanisms in colorectal cancer
Biography:
Joice de Faria Poloni is currently a PhD candidate in the Cellular and Molecular Biology Post-graduation program of the Federal University of Rio Grande do Sul, Brazil. Her area of expertise is in the bioinformatics field with emphasis on systems biology, systems chemo-biology and transcriptomic analysis to study tumoral processes and developmental mechanisms. She also works with somatic point mutations and alternative splicing isoforms in different tissues. In this sense, her scientific production involves book chapters, research and review articles in these fields.
Abstract:
Coloretal cancer (CRC) is a multifactorial disease and the third more common cancer worldwide. Cancer development involves numerous abnormal regulations, such as gene expression, mRNA processing and somatic point mutations. To improve the comprehension of these factors, we evaluated the correlation of differential splicing with differentially expressed genes (DEG), differentially exon usage (DEU) and somatic point mutations through interatomic network analysis. For this purpose, the RNA-seq dataset (GSE50760) of 12 paired tumor and adjacent normal tissue samples was employed. After reads alignment on the reference genome, the data was submitted to DEG analysis supported with gene and transcripts quantification and DEU analysis assisted with exonic quantification. Additionally, samples were analyzed for somatic point mutations detection. The results were integrated in an interatomic network for the proceeding analysis. Furthermore, the variants effects prediction was estimated to understand their impact in the splicing mechanisms of CRC. According to the obtained results, it was possible to elaborate an interatomic network composed by DEG, which was assigned to gene ontology, hub-bottlenecks and clustering analysis. These analyzes allowed the detection of DEG that are highly representative for CRC development and maintenance. The DEG was mainly involved in processes such as cell cycle regulation, extracellular matrix organization and immune response. The data also permitted the identification of DEG with specific somatic point mutations in essential regions for splicing mechanism. Hence, the methods employed in this work promoted a better and innovative understand of cancer development.
Biography:
Nermeen M. Arafa has completed her PhD at the age of 34 years from faculty of Agriculture, Cairo university and postdoctoral studies from National Research Center. She has published three papers in reputed journals.
Abstract:
Cassava (Manihot esculenta) is a major industrial crop which are rich in lot of therapeutic applications such as antitumor activity. Leaf, stem and petiole of Cassava in vitro plantlets were cultured on solid MS-medium containing different combinations and concentrations of 2.4-D, picloram or NAA as auxins and BA as cytokinins. Stem was chosen as the best explant for callus induction, stem derived calli (25.892 ± 0.117g) on the best selected medium for callus production (5 mg/l 2.4-D and 0.2 mg/l BA) with subculture intervals each 40 days of culture. The phytochemical components such as fatty acids and their ester derivatives constituents were extracted from calli of cassava using different solvents, ethylacetate as aprotic polar solvent, chloroform and hexane as non-polar solvent to examine the efficiency of these extracts for inhibition the growth of the breast cancer cell. All extracts recorded positive results for inhibition cancer cell proliferation. Ethylacetate extracts have maximum efficiency for inhibition breast cancer (2.63 ug IC50), followed by hexane extracts (3.44 ug IC50), then chloroform extracts (6 ug IC50) recorded the least value. The objective of this study was analysed the composition of lipid profile components for ethylacetate extract, chloroform extract and hexane extract by GC-Mass and determine the efficiency of these extracts as anti-breast cancer cell growth. Ethylacetate extracts showing higher concentration of the total fatty acids (76.53%), also, included caprylic acid (14.52%) and caproic ester (3.10%), while that hexane and chloroform extracts recorded less values of total fatty acids (69.26% and 39.77%, respectively) and recorded no value of both of caprylic acid and caproic ester. Therefore it could be recommended to use ethylacetate as aprotic solvent for the extraction of calli, as including most amounts of fatty acids and their derivatives compounds due to the most effect as anti-breast cancer.