Biography:

Robin Ketteler has studied biochemistry at the Free University Berlin and completed his PhD in 2002 at the Max-Planck Institute for Immunobiology in Freiburg, Germany. He completed his postdoctoral studies from Massachusetts General Hospital in Boston and since 2009 is group leader at University College London. He is the the manager of the Translational Research Resource Center, a high-content screening facility at UCL.     
 

Abstract:

Autophagy is a catabolic process that encloses cytoplasmic content in a double membrane vescicle, the autophagosome, and degrades it through fusion with the lysosome. The modulation of autophagy has been implicated in multiple diseases including pathogen infection, neuro-degenerative disorders and cancer. Although the main components of the autophagy machinery have been identified by yeast genetics and in mammalian cells, the identification of entry points for drug targeting in this pathway has proven challenging. Recent findings suggest that autophagy protease ATG4B and proteins that regulate ATG4B activity are potential drug targets in cancer. In order to study the regulation of ATG4B, we took advantage of our recently developed assay to measure ATG4B activity in cells by assessing the amount of secreted luciferase in cells expressing the reporter Actin-LC3-DeltaNluciferase. We used this assay to identify small molecule inhibitors of ATG4B that may have therapeutic potential in breast cancer. Further, we used kinase and phosphatase siRNA and cDNA libraries and identified genes that enhance or suppress cellular ATG4B activity. We identified an inhibitory phosphorylation of ATG4B at the forming autophagosome that allows the spatio-temporal control of autophagosome maturation. Finally, we provide preliminary data using CRISPR-Cas9 genome editing to study the function of ATG4 isoforms in mammalian cells. Overall, our results shed light on the complex regulation of ATG4B in cells and will inform therapeutic strategies targeting this protein.

Biography:

Anthony Uren completed his PhD at the Walter and Eliza Hall Institute, followed by postdoctoral positions at Genentech and at the Netherlands Cancer Institute. He is currently a principal investigator at the MRC London Institute of Medical Sciences at Imperial College.

Abstract:

Determining whether recurrent but rare cancer mutations are bona fide driver mutations remains a bottleneck in cancer research. Here we present the most comprehensive analysis of retrovirus driven lymphomagenesis produced to date, sequencing 700,000 mutations from >500 malignancies collected at time points throughout tumor development. This enabled identification of positively selected events, and the first demonstration of negative selection of mutations that may be deleterious to tumor development (e.g. Smyd3) indicating novel avenues for therapy. Customized sequencing and bioinformatics methodologies were developed to quantify subclonal mutations in both premalignant and malignant tissue, greatly expanding the statistical power for identifying driver mutations and yielding a high-resolution, genome wide map of the selective forces surrounding cancer gene loci. Screening two BCL2 transgenic models confirms known drivers of human B-cell non-Hodgkin lymphoma, and implicates novel candidates including modifiers of immunosurveillance such as co-stimulatory molecules (Cd86, Icosl, PD-1) and MHC loci. Correlating mutations with genotypic and phenotypic features also gives robust identification of known cancer genes independently of local variance in mutation density. An online resource http://mulv.lms.mrc.ac.uk allows customized queries of the entire dataset.

Biography:

Mireille Claessens obtained her PhD training in the laboratories of Physical Chemistry and Colloid Scieces and Plant Physiology at Wageningen University, the Netherlands. After receiving her PhD degree in 2003 she did postdoctoral studies at the Technical University of Munich where she investigated the physical properties of cytoskeletal networks. In 2008 she joined the Nanobiophysics group at the University of Twente, the Netherlands as an assistant professor, in 2013 she became chair of the Nanobiophysics group-group.

Abstract:

The formation of α-synuclein (aS) amyloid aggregates, called Lewy bodies (LBs), is a hallmark of Parkinson’s disease (PD). The role of LBs in PD is however still unclear; they have been associated with both neuroprotection and toxicity. In an attempt to resolve this contradiction, we studied the aggregation of aS in cell model systems and in the test tube. 

We induced the formation of aS inclusions, using three different methods in SH-SY5Y cells and rat-derived primary neuronal cells. Using confocal and STED microscopy we observed method dependent differences in aS inclusion morphology, location and function. The aggregation of aS in functionally different compartments correlates with the toxicity of the induction method measured in viability assays. The most cytotoxic treatment largely correlates with the formation of proteasome associated juxta-nuclear inclusions. Cytosolic deposits formed by less toxic methods are not associated with the proteasome and are more prevalent.

The formation of inclusions is however not necessarily an active process governed by the cells biochemical machinery. In the test tube, we observed that, under physiological salt conditions aS spontaneously self-assembles into micrometer-sized suprafibrillar aggregates (SFAs) that are reminiscent of LBs. The assembly of these SFA is very sensitive to physicochemical conditions such as ionic strength. This sensitivity leads to the formation of anisotropic SFAs in vitro and may also be the cause of the anisotropy observed in their in vivo counterparts. The onset of disease may trigger changes in the physicochemical conditions within the cell which are reflected in the architecture of LBs.

Biography:

Kristina Djinovic Carugo has completed her PhD at the age of 29 years from Ljubljana University and postdoctoral studies from University of Pavia and EMBL-Heidelberg. She is the head of the  Department of Structural and Computational Biology at the University of Vienna, and director of Laura Bassi Center for Optimised Structural Studies. The main area of her research is structural biology of actin based cystoskeleton with focus on striated muscle Z-disk. She uses an integrative structural biology approach, combining high resolution studies with complementary lower resolution biophysical and biochemical approaches. He has published more than 100 papers in international peer reviewed journals and is serving as a member of scientific advisory boards of repute.

Abstract:

The sarcomere is the minimal contractile unit in the cardiac and skeletal muscle, where actin and myosin filaments slide past each other to generate tension. This molecular machinery is supported by a subset of highly organised cytoskeletal proteins that fulfil architectural, mechanical and signalling functions, including the giant proteins titin, obscurin and nebulin as well as the cross-linking proteins α-actinin and myomesin.

The cross-linking of actin and myosin at the boundaries of their filamentous structures is essential for the muscle integrity and function. In the Z-disks – the lateral boundaries of the sarcomere machinery – the protein α-actinin-2 cross-links antiparallel actin filaments from adjacent sarcomeres, and additionally serves as a binding platform for a number of other Z-disk proteins. In striated muscle cells, the Z-disk represents a highly organized three-dimensional assembly containing a large directory of proteins orchestrated in a multi-protein complex centered on its major component α-actinin, with still poorly understood hierarchy and three-dimensional interaction map. On the way to elucidate the molecular structural architecture of the Z-disk, the hierarchy of its assembly and structure-function relationships, we are studying binary and higher order sub-complexes of α-actinin using biophysical, structural and cell biological approaches.

Here we will present recent data on interaction of muscle α-actinin and filamin C with an adaptor proteins ZASP, myotilin and FATZ-1, forming a fuzzy complex with the latter, and discuss findings in view of muscle Z-disk architecture and assembly.

Biography:

Clifford Lingwood completed his PhD at the University of London in1974, and postdoctoral studies at the Universities of Washington and Toronto.  He has been a full professor at the University of Toronto since 1997 and is a senior scientist within the Molecular Medicine program, Research Institute, Hospital for Sick Children, Toronto Dr Lingwood’s research program concerns the biochemistry, chemistry, metabolism and function of glycosphingolipids with a view to the therapy of diseases in which they are involved.  He has published more than 200 papers in reputed journals.

Abstract:

Glycosphingolipids (GSLs) and cholesterol accumulate in membrane lipid rafts and play a central role in these foci of signal transduction. However within the GSL/cholesterol complex, an H-bond network is formed which alters the conformation of the GSL carbohydrate from a membrane perpendicular, to a membrane parallel format. This latter GSL conformation is largely unavailable for exogenous ligand binding-“invisible GSLs”.

Due to the increased cholesterol levels typical of cancer cells, we studied the prevalence of cholesterol-masked GSLs in human primary tumour biopsies (prostate, neuroblastoma, colon, breast, testicular, pheochromocytoma, ovarian and ganglioneuroma). We found that such ‘invisible’ GSLs were widely present in these tumour serial cryosections, e.g SSEA1, SSEA3, SSEA4, globoH and Gb3. We propose that such masking can prevent immunosurveillance of tumour–associated GSL antigens and thereby compromise natural tumour immunity to block progression. Moreover, anti GSL Mabs in development or clinical use for treating cancer (F77 for prostate and Unituxin-antiGD2 for pediatric neuroblastoma) were highly subject to such masking, and prior tumour cholesterol extraction with b-methylcyclodextrin, resulted in a remarkable increase in antiGSL tumour staining. This suggests that tumour cholesterol depletion would increase the antineoplastic activity of these therapeutic Mabs.

We also found that the order in which the binding ligands were added was of major significance. Prior Gb3 binding promoted ligand-cholesterol binding and vice versa. This provides the means for amplification and/or diversification of GSL-dependent signal transduction and thus is the first example of a native cell based membrane “transistor”.

Biography:

Sakae Tsuda has completed his PhD at Hokkaido University, Japan and Post-doctoral studies at University of Alberta (Canada). He did his research on Biomolecular NMR, which gave him the skills of biochemistry, biophysics and structural biology. He is a Chief Senior Researcher of National Institute of Advanced Science and Technology (AIST), Japan. His current research target is the antifreeze proteins, which have originally been explored from Japanese organisms in the last 15 years.

Abstract:

The general ice crystal is a polycrystalline state composed of numerous single ice nuclei, which undergo crystal growth and are combined together to form a larger ice block below 0°C. Antifreeze protein (AFP) has an ability to bind to a set of waters constructing an ice surface, and disturbs formation of the polycrystalline ice, since the AFP-adsorbed ice surfaces are inhibited their growth and integration. A hyperactive species of AFP that can bind to any set of the waters of the ice is extremely powerful in such function, compared with general AFPs that only bind to specific ice surfaces. Here, we discovered a new 40-residue antifreeze protein (AFP) from a right eye flounder barfin plaice (BpAFP), which uniquely showed two manners of ice binding at different concentrations. The BpAFP bound to prism and pyramidal surfaces of an ice crystal to shape it into hexagonal trapezohedron at the concentrations below 0.01 mg/mL, while underwent further binding to whole ice crystal surface including the basal planes at the concentrations above 0.01 mg/mL. In the latter, the ice crystal became smaller and lost their facets in keeping with the concentration, and finally changed into a tiny lemon-shaped morphology, as similarly observed for the known hyperactive AFPs. The basal plane binding further caused the bursting ice crystal growth normal to the c-axis, for which it detected 3.2°C of high thermal hysteresis activity. The BpAFP is an alanine-richest isoform of type I AFP composed of three tandem repeats of the 11-residue consensus sequence TX₁₀ (where X is mostly alanine), which presumably constructs the monomeric -helical structure so as to encompass an extremely continuous alanine-assembled surface. These remarkable properties distinguish BpAFP from all the known macromolecules, thereby offering an epoch to advance our understanding of ice-protein interaction.

Biography:

Marta Leonor Marulanda is a Biologist with a PhD degree in Agricultural Sciences from Universidad Agraria de La Habana (Cuba), with over 25 years of experience as main Researcher in Plant Biotechnology and 20 years of experience as Professor of Biotechnology- and biology-related courses at undergraduate and graduate levels at different universities in Colombia’s Coffee Belt. She is an Author and Co-author of more than 20 articles published in national and international journals. Currently, she is responsible for seven research projects conducted under different collaborative agreements, mainly with the Colombian Ministry of Agriculture and Rural Development.

Abstract:

In Colombia, the Andean blackberry (Rubus glaucus Benth) is one of the products with the greatest development potential in the Colombian Andes. It has a share of 0.7% in cultivated area and 0.4% in national production of permanent crops; its annual growth rate is 8.8% in production and 7.8% in area. Anthracnose caused by several species of Colletotrichum fungi is considered a major Andean blackberry pathogen (Rubus glaucus) in Colombia. Plants with fungal tolerance are promising material for growers to avoid pest control through fungicides, which are also detrimental to the environment. By using RNA-seq in R. glaucus tolerant and susceptible accessions to Colletotrichum a large number of differentially expressed genes (DEGs) in tolerant R. glaucus material were identified. A total of 44,660 genes were up-regulated in R. glaucus tolerant material challenged with Colletotrichum when compared to susceptible material also inoculated with the fungus. The largest numbers of identified up-regulated genes were classified as having catalytic and binding activities. In addition over 2,000 SNPs and 4,799 SSR markers that are potential candidates to distinguish between tolerant and susceptible material were also determined. In order to have significant advances in the characterization and selection processes, SSR and SNP markers were evaluated.

Biography:

Oara Neumann completed her MS at Weizmann Institute of Science, Israel; PhD at Rice University and; Post-doctoral studies at Rice University. She is a Scientist in Naomi Halas Group at Rice University. She has published more than 25 papers in reputed journals

Abstract:

Multifunctional plasmonic nanostructures have enormous potential in the treatment of solid tumors; however, tracking particles with drug cargo and triggering the release of the cargo in mapped tumors is still impossible. To overcome this challenge, we have developed an MRI active nanostructure called Gd-nanomatryoshka (Gd-NM). This new structure is composed of a 50 nm Au core surrounded by a Gd(III)-DOTA chelate doped SiO₂ inner-shell and an outer Au shell. The experimental results demonstrates an enhanced T₁ relaxation (r₁~24 mM^-1 s^-1 at 4.7 T) compared to the clinical Gd(III)-DOTA chelating agents (r₁~4 mM^-1 s^-1). This multifunctional nanosystem increases MRI sensitivity by concentrating Gd(III) ions into the Gd-NMs, reduces the potential toxicity of Gd(III) ions by preventing their release in vivo through the outer Au shell protection, and the terminal gold layer surface can then be functionalized to increase cellular uptake, circulation time, or thermal drug-release properties.

Biography:

Svetlana A Limborska completed her Graduation in Biology department at Moscow State University in 1969. She completed her PhD in Molecular Biology and; Doctor of Science in Genetics. She is a Professor of Genetics at Institute of Molecular Genetics, Russian Academy of Sciences. Since 1983, she has been a Chair of Human Molecular Genetics Department of the same institute. She has got Russia State Prize award in 1996. She has published more than 300 papers in reputed journals and has been serving as an Editorial Board Member of Russian Journal of Genetics, Molecular Genetics, Microbiology and Virology, Medical Genetics, and Proceedings of Latvian Academy of Sciences.

Abstract:

The application of pharmacogenomics approaches has become an integral part in the drug development. This report will demonstrate the notable examples of using pharmacogenomics to clarify the mechanism of action of compounds based on natural regulatory peptides. Genome-wide transcriptome analysis was employed to search gene expression alterations under Semax and Selank impact. Semax has neuroprotective and nootropic effects without hormone action. Semax used for the treatment of cerebral ischemia, stroke, traumatic brain injuries, Parkinson’s, Alzheimer’s and other diseases. The study of Semax action on the transcriptome of rat brain cells under experimental ischemia conditions has identified large-scale changes in gene expression, including genes, which provide functioning of immune and vascular systems. Selank has anti-anxiety effect, normalizes the emotional state, and also has antiviral activity. Selank used in neurology, pediatrics and for the treatment of viral diseases. We revealed the change in mRNA level of many genes in the rat hippocampus after Selank administration including genes involved in neurotransmission. The transcriptome analysis of mouse spleen cells after Selank treatment revealed many genes changing their expression including genes of immune system. Thus, the transcriptome analysis showed important influence of regulatory peptide drugs on cellular metabolism that may determine their positive effect on the treatment of the relevant diseases.

Biography:

Juan Cevallos-Cevallos completed his PhD in Food Science at University of Florida where he also carried out Post-doctoral studies in Food and Plant Microbiology. He is the Head of Microbiology and Plant Pathology laboratory at ESPOL University. He is a Scientist with more than 25 papers in reputed peer-reviewed journals and has been serving as an Editorial Board Member of important journals.

Abstract:

Cacao is the raw material of chocolate—one of the most consumed food worldwide and the spontaneous fermentation of cacao is a critical step in the making of chocolate. Despite the importance of cacao fermentation, no combined metagenomic and meta-metabolomics characterization of this process can be found in the literature. Cacao samples form three farms in Ecuador—the top fine-flavor cacao producer in the world—was taken after 0, 24, 48, 72, and 120 hours of fermentation. Culture-dependent microbial characterization, amplicon-based illumina sequencing, and GC-MS metabolite profiling were carried out on each sample. Productions of aroma compounds were then related to specific microorganisms through inoculation into sterile cacao beans. A total of 586 different microbial species were detected by NGS but only 42 were isolated. Correlation with metabolomics data showed that important aroma compounds were produced at each sampling time including ethanol by yeasts, 2, 3 butanediol by Lactobacillus nagelii; benzeneethanol by Saccharomyces cerevisiae, Acetobacter pasteurianus, Acetobacter ghanensis, and Lactobacillus nagelii; acetic acid by Acetobacter pasteurianus and Acetobacter ghanensis; benzaldehyde and phenylvinylacetylene by Bacillus subtilis. Interestingly, various microorganisms were related to the comsumption of important volatile compounds including benzaldehyde, acetophenone, and acetaldehyde by Lactobacillus nagelii, Acetobacter syzygii, and Acetobacter pasteurianus among others. The amount of each aroma compound was enhanced five folds or more by direct inoculation of the fermenting beans. Results show evidence of the importance of combined metagenomics and meta-metabolomics for characterizing the spontaneous fermentation of foods.

Biography:

Maria Gabriela Mariduena-Zavala is an Agricultural Engineer from Ecuador with a Master's degree in Biotechnology. She has been involved in Agricultural Research and carried out various studies in the Phytopathology Department at Espol University in Guayaquil, Ecuador. Her research has been directed towards the use of omics tools for the characterization of pathogenic fungi from the main crops in Ecuador. Among her studies, the morphological and genetic characterizations of Moniliophthora species from cocoa crops in Ecuador as well as the investigation of metabolomics profiles of isolates resistant to fungicides including Mycosphaerella fijiensis and Phytophthora infestans are noteworthy. Her current studies focus on “The use of metabolomics and metagenomics techniques for understanding of the behavior of fungal communities”.

Abstract:

Potato production is continuously being threatened by Phytophthora infestans, the most important potato pathogen worldwide. Applications of phenylamide fungicides including metalaxyl have been used to control this pathogen, causing the development of fungicide resistance in P. infestans. Despite the importance of the disease, no metabolomics-based characterization of fungicide resistance development in P. infestans has been reported. Isolates of P. infestans were obtained from the most important potato production areas in Ecuador. The resistance of Phytophthora infestans isolates to metalaxyl was evaluated in vitro and the GC-MS metabolite profile of all isolates was assessed at 0, 0.5 and 100 mg/L of metalaxyl. All metabolites were mapped to potential pathways using KEGG pathway mapping with Pseudocercospora fijiensis as the model organism. Only 30% of the isolates tested were sensitive to the low doses of metalaxyl and a total of 49 metabolites were differentially expressed in resistant isolates growing in the presence of the fungicide. Metabolites such as hexadecanoic and octadecanoic acids; glucose, fructose, proline, valine, butanedioic and propionic acids were overexpressed in resistant isolates. Potential resistance-related metabolic pathways were mostly involved in the regulation of the pathogen’s membrane fluidity and included the fatty acid biosynthesis as well as the glycerophospholipid metabolism pathways. No metalaxyl residues were found in resistant isolates, suggesting that the fungicide was not able to penetrate the membranes.

Biography:

Natalia Bakhtina has been a PhD candidate in the Department of Microsystems Engineering of the University of Freiburg, Germany under the supervision of Jan G. Korvink since 2012. The outcome of her investigations has resulted in several publications in journals with quality control. She was awarded by the very prestigious Outstanding Student Paper Award at IEEE MEMS conference in 2015 (Estoril, Portugal) and SPIE3D Printing Best Paper Award at SPIE Photonics West in 2016 (San Francisco, USA).

Abstract:

The combination of light-sensitive non-conductive photoresist, as a host network, with an ionic liquid brings superior advantages in terms of material characteristics [1−4]. Compatibility with the advanced two-photon (2-PP) nanolithography yields the opportunity to produce high-resolution (down to 150 nm) conductive structures in a single-step process and opens up a variety of potential applications. For example, real-time monitoring the motility of small model organisms, such as Caenorhabditiselegans, remains a key challenge for in situ manipulation and stimulation. Tracking of this motile microorganisms provides an efficient method of investigating a variety of biological processes through the miniaturization and functional integration of bioanalytical devices. The approach to this challenge includes the integration of electrodes, fabricated by 2-PP nanolithography, into a microfluidic platform. Transparency and conductivity of the presented material in combination with highly standardized electrodes inside microfluidic channels provides a simple means of creating electrofluidic chips to flexibly control the movement of C. elegansin a sensitive and reproducible manner without blocking optical visibility. As a result, performance of numerous experiments, including electrochemical impedance spectroscopy and microscopy-based imaging, in parallel on the same chip with fewer reagents, improved sensitivity and increased resolution has become possible. This will most certainly bring about more precise quantitative and qualitative in vivo analyses for novel true 3D applications in the near future.

1. Bakhtinaet al., patent DE 10 2014 016 802.6
2. Bakhtinaet al., Proc. IEEE MEMS 2015, pp. 97 – 101
3. Bakhtinaet al., Adv. Func. Mat. 2015, 25, 1683 – 1693
4. Bakhtinaet al., Proc. SPIE Photonics West 2016, ID 9738-10, 1 – 10