Day 2 :
- Track 7: Epigenetics, Track 11: Clinical Applications and Related Disorders
Location: Continental Ball Room 5 & 7
Chair
Max H Garzon
The University of Memphis, USA
Co-Chair
Yingwei Mao
Pennsylvania State University, USA
Session Introduction
Yingwei Mao
Pennsylvania State University, USA
Title: A critical role of an exon junction complex (EJC) factor in regulation of embryonic neurodevelopment and implications in neurodevelopmental disorders
Time : 09:00-09:20
Biography:
Yingwei Mao has completed his PhD at University of Michigan School of Medicine and postdoctoral studies from MIT Picower Institute of Learning and Memory. He is the assistant professor of Penn State University. His lab studies molecular mechanism of neurodevelopment and the relationship to psychiatric disorders. He has published more than 25 papers in reputed.
Abstract:
Nonsense-mediated mRNA decay (NMD) is an RNA surveillance mechanism that degrade mRNAs carrying premature termination codons (PTCs). This mechanism requires several key EJC factors to distinguish PTC from the normal stop codon. But how this mechanism modulates the embryonic neurodevelopment and behaviors is largely unknown In this study, we demonstrated that RBM8a plays a key role in neural progenitor proliferation and differentiation. First, RBM8a is highly expressed in the subventricular zone of early embryonic cortex, suggesting that RBM8a may play a role in regulating neural progenitor cells (NPCs). To test this hypothesis, we used in utero electroporation to overexpress or knock down RBM8a in mouse brain at E14. RBM8a stimulates embryonic neural progenitor proliferation and suppresses neuronal differentiation, indicating that RBM8a positively regulates NPC proliferation. Conversely, knockdown of RBM8a in the neocortex reduces NPC proliferation and promote premature neuronal differentiation. Consistently, Nes-cre; RBM8afl/+ mice show severe developmental defects including microcephaly and postnatal lethality. When RBM8a is overexpressed in the dentate gyrus of adult brain using stereotactic viral injection, mice showed altered anxiety and depressive-like behaviors. To uncover the underlying mechanisms, genome-wide RNAseq identifies potential substrates of RBM8a in the brain, which have been implicated in neurogenesis and plasticity. Interestingly, autism- and schizophrenia-risk genes are highly representative in RBM8a-associate transcripts. Taken together, we identify a novel role of RBM8a in regulation of neurodevelopment and behaviors. Our studies provide a deeper insight on causes of mental illnesses and will facilitate the development of new therapeutic strategies for neurodevelopmental illnesses.
Zsolt Boldogkoi
University of Szeged, Hungary
Title: Transcription Interference Networks examined by Single Molecule Long Read Sequencing Technology
Time : 09:20-09:40
Biography:
Zsolt BoldogkÅ‘i received his PhD degree (1999) in molecular biology from Szent Istvan University at GödöllÅ‘. He also worked at the Whistar Institute (Philadelphia, PA, USA) as a PhD student then had post-doctoral training at University of Bonn. He received his DSc degree (2008) at University of Szeged. His primary field of interest is the molecular biology of herpes viruses with special emphasis on the regulation of gene expression analysis and utilization of herpesviruses as tools in various fields of biology including neurobiology and cardiology. He and his group currently also work in different fields of genomics, focusing on human diseases. He has published more than 70 papers in reputed journals. Currently, Zsolt BoldogkÅ‘i is the head of Department of Medical Biology at Faculty of Medicine of University of Szeged.
Abstract:
Introduction
Gene expression is mainly controlled at the level of transcription initiation through the interaction between cis- and trans-acting regulatory elements and epigenetic processes. The Transcriptional Interference Network (TIN) hypothesis assumes the existence of a new layer of gene regulation, based on the confrontations between the transcriptional machineries of functionally linked genes located in the same cluster. Pseudorabies virus (PRV) is a neurotropic herpesvirus of swine, which – due to the characteristic genomic features – is a perfect model organism for the study of TIN. PRV is a compact, double-stranded DNA virus; the viral genome is relatively large (~ 143 kb), and the known 70 protein coding genes and the non protein coding transcripts are located in – convergent, divergent and nested - clusters.
Methods
In this study we have used a third generation single molecule sequencer (Pacific Biosciences RS II) to analyze and characterize the PRV transcriptome and to find evidences for the existence of TIN. Immortalized porcine kidney 15 (PK-15) cells were infected with PRV. Cells were harvested after 1, 2, 4, 6, 8 and 12 hours after infection. Total RNA was isolated and converted to cDNAs, followed by PacBio SMRTBell Library preparation and sequencing.
Results
Transcriptional read-through was found between the convergently oriented genes (gene clusters). The read-through efficiency and its orientation shows time dependence. Our data show inverse expression dynamics between the convergent clusters. Previously unknown interactions were found between the nested clusters as well as between the divergently oriented genes. Temporal changes of these gene interactions were also characterized. New long non-coding and overlapping RNAs were found which might give rise to transcription interference and serve as an added layer of regulation
Krzysztof Wieczerzak
University Rostock, Germany
Title: A comparative transcriptome provides candidate genes for determination the cause of males infertility.
Time : 09:40-10:00
Biography:
Krzysztof Wieczerzak finished his M.Sc. in Department of Genetics at Jagiellonian University in Kraków, Poland. Then he worked as young scientist in Institute of Pharmacology, Polish Academy of Science. Next, he has studied and completed his PhD from Institute of Human Genetics at Georg-August-University in Göttingen, Germany. He is interested in molecular aspects of reproduction biology, gene therapy and cancer biology. Now he is working as a post-doc in Institute of Experimental Gene Therapy and Cancer Research at Rostock University, Germany. He is working with CRISPR-Cas9 system in cancer aspects
Abstract:
Since most cases of male infertility remain idiopathic, analysis of the mechanism in which genes are involved in spermatogenesis control might help to better understand the reasons. During years we tested several knockout mouse line with disruption of genes important for human fertility. Now, we have analyzed the phenotype and determined the cause of males infertility from a multiple knockout mouse line with knockouted six germ cell-specific genes. We observed in about 20% of mice infertility, but in both, fertile and infertile males, increased number of spermatozoa with abnormal head and also reduction of sperm motility were found. In order to examine more thoroughly which genes might be involved in the infertility of males, we have performed transcriptome assay and compared the expression of genes in the testes of fertile and infertile animals. We identified 55 candidates genes and analyzed a new gene 4933400A11Rik. In wild type mice, 4933400A11Rik is expressed in germ cells, detected from 16dpp, when primary spermatocytes are produced. 4933400A11RIK has sequence similar to the actin filament capping protein family, which control the process of cytoskeleton growth by the regulation of actin filaments reorganization. The 4933400A11RIK colocalises with Factin capping protein subunit alpha-1. Dysregulation of germ cells actin cytoskeleton reorganization may be the underlying cause of male infertility in 6xKO mice, because 4933400A11Rik gene is expressed in testis of fertile, but not present in infertile males. In conclusion, the data obtained from comparative transcriptome provides candidate genes for analysis the cause of human males infertility.
Biography:
Dr. Yunlong Qin works at Morehouse School of Medicine, Cancer Biology Program as a senior researcher.
Abstract:
Aging in humans is irreversible, characterized by a decline of physiological functions in various organs and tissues, leading to multidimensional process of physical, psychological, and social change, causing most human diseases and an increasing probability of death. At present, the exact mechanism and biological basis of aging is unknown. The antagonistic pleiotropy theory and competing model of senescence explain the aging occurrence of some physiological functions of human body from different angles. The single nucleotide polymorphisms (SNPs) of genome suggest the individual’s difference of aging process is associated with SNPs-related individual’s sensitivity to diseases. As the naturally occurring DNA damages and ageassociated accumulation of DNA damage as well as decline in gene expression regulation indicate individual life expectancy, whereas the shortening mechanism of telomeric terminals of chromosomes and Hayflick limit of cell division determine human life span. The genomic aging exerts impact on various physiological functions, also imprints individual’s appearance, such as wrinkled, thinning skin, graying and loss of hair. Feeling helpless before slowing down senescence of the genetic materials people turn to anti-aging products, spending billions of dollars each year on such creams and lotions for decreasing signs of aging and nutrients for postponing decline of physiological functions. Indeed, recently, scientists carried out reversing muscle aging in mice model through feeding an experimental compound and made a comment that for humans the effect would be similar to a 60-year-old feeling like a 20-year-old, but still powerless for reversing of genomic aging, even a little Is there a possibility of U-turn in the highway of life progress? Recently, the discovery that mature cells can be reprogrammed to become pluripotent and the development of rehabilitative and regenerative medicine rekindle spark in hope of humans against aging. The induced pluripotent stem cells (iPSCs) hold great promise in the field of regenerative medicine because each individual could have their own pluripotent stem cell line and these unlimited supplies of autologous cells bypass body’s immune defense system, immune rejection, this will be a new milestone in transplantation medicine, one of the most challenging and complex areas of modern medicine. Nowadays, iPSCs are mainly used in medical research, including organ synthesis, disease modeling of cellular basis and drug development, tissue repair in animal model. Here is an opinion regarding the possibility and feasibility of iPSCs application in gerontology. The gerontology is the study of the social, psychological and biological aspects of aging, itself is a youthful field, its progress having been slowed by aging's daunting complexity and a tendency among scientists and doctors to consider diseases as entirely separate, rather than as manifestations of a common origin. In comparison to the complexity and difficulty of synthesizing other organs or systems through iPSCs, there is great advantage for iPSCs being applied into the immune system, the functions of which are mainly carried out by immune cells, same as red blood cells, these immune cells travel to everywhere of human body. The application of cell levels of iPSCs is more reliable and easier in technology. The aging process accompanies gradual deterioration of the immune system. This age-associated immune deficiency is ubiquitous, decreasing host’s capacity to respond to infections, increasing individual’s sensitivity to most human diseases, including autoimmune disorders. The functional capacity of T-cells is most influenced by the effects of aging. Since all the blood cells come from pluripotent hematopoietic stem cells (HSCs) of bone marrow, no matter what age you are, but these freshly produced immune cells from aging body are still senescent. The raised question is when is best time period to collect adult cells to be reprogrammed genetically into iPSCs? Here is a suggestion with the best timing for preparing the individual specific iPSCs should be a period of time of strongest function of immune system, thinking roughly 30 years of age. Comparing to the cord blood stem cells, unlimited supplies of iPSCs will have more attractive application prospect once its safety is more reliable and accepted and more mature in technology. There is an expectation to help elderly people re-establish a strong immune system to resist the attack of pathogens including bacteria and viruses and make them live in a higher level of health state. Interestingly, recently, type O red blood cells were synthesized at the Scottish National Blood Transfusion Service from iPSCs. Type O can be transfused into all patients, this is unprecedented brilliance in the transfusion history considering more than 100 million blood donations are collected globally every year. Where do we go on the journey against aging? It seems we see some light we could reach from the rapid progress of life sciences and biotechnology today. Hopefully, it is not star light.
- Workshop: Impact of variation in regulatory region on gene expression
Session Introduction
San Ming Wang
University of Nebraska Medical Center, USA
Title: Impact of variation in regulatory region on gene expression
Time : 10:00-10:45
Biography:
San Ming Wang finished his Master of Medicine 1986 from Shandong Medical University, Jinan, China. He pursued Doctor of Medicine at Genetic Unit, Swiss Institute for Experimental Cancer Research (ISREC)/University of Lausanne, Switzerland. He worked as Assistant Professor from 2004-2009 at Northwestern University. Later he got appointed as Director for Center for Functional Genomics, ENH Research Institute (Now named NorthShore University Health System Research Institute). From October, 2010–till date, he is working as an Associate Professor at Department of Genetics, Cell Biology & Anatomy, University of Nebraska Medical Center, Nebraska.
Abstract:
Promoter is the regulatory part of a gene. In promoters, the interactions between cis-regulatory elements, e.g., transcription-factor binding sites (TFBS), and trans-regulatory elements, e.g., transcription factors (TFs), spatially and temporally regulate gene expression to ensure homeostasis of biological functions. Alterations in promoter sequences can change cis-trans interactions resulting in modified gene expression, impacting downstream biological processes, and leading to the development of disease. In this workshop, I will give an introduction on the topic, show the data from my breast cancer studies, and then have a round table discussion/presentation for attendees to address the issue covering normal gene expression regulation, evolution conservation, alternation in disease, etc.
- Track 14: Transcriptomics and Proteomics of Microorganisms
Chair
Subha Bhassu
University of Malaya, Malaysia
Co-Chair
Ilana Kolodkin
Weizmann Institute of Science, Israel
Session Introduction
Claire Lemaire
National Center for Scientific Research, France
Title: Quantitative analysis of the mitochondrial proteome and phosphoproteome in the yeast Saccharomyces cerevisiae
Time : 11:00-11:20
Biography:
Claire Lemaire is biochemist specialized in membrane proteins. She began her career in the photosynthesis field on the assembly and regulation of photosynthetic complexes (I.B.P.C. ,Paris). She then joined the C.N.R.S. (French National Center for Scientific Research) where she acquired a solid expertise in the respiratory complexes. Over the last six years, she has developed a research project with her group focusing on the regulation of OXPHOS complexes by phosphorylation.
Abstract:
The mitochondrion is an organelle with multiple functions, the most important of these being to provide energy to the cell as a whole in the form of ATP, generated by oxidative phosphorylation catalyzed by the respiratory enzymes in the mitochondrial inner membrane. In humans, deregulation of mitochondrial functions, particularly with regard to the respiratory chain, is associated with several pathologies, including neurodegenerative diseases, neuromuscular diseases, type II diabetes and cancer. The activity of the respiratory enzymes may be modulated in response to metabolic demand and various types of stress. Several levels of regulation may be conceived, including changes in protein expression magnitudes, reversible interaction with effectors, and post-translational modifications, such as phosphorylation. The steadily increasing number of identified mitochondrial phosphoproteins, kinases and phosphatases suggests that reversible protein phosphorylation could be an important level of regulation in mitochondria. However, this hypothesis cannot be tested without quantitative data on variations in the abundance of mitochondrial proteins and their level of phosphorylation under different growth conditions. The yeast Saccharomyces cerevisiae is a powerful tool for studying various energetic and physiological states as it is a facultative aerobe which can grow on either fermentative or respiratory substrates. We present for the first time a quantitative study of both protein abundance and phosphorylation levels in isolated yeast mitochondria under respiratory and fermentative conditions. To focus our analysis specifically on mitochondrial proteins, we performed a subcellular fractionation and used LC–MS/MS to overcome the limitations of 2D gel electrophoresis. Protein abundances were quantified using a label-free method. The phosphoproteome was analyzed quantitatively using the multiplex stable isotope dimethyl labeling procedure. For all quantified phosphopeptides, protein abundance was determined, allowing normalization of the data and permitting analysis of the specific variation of phosphorylation status independent of changes in protein abundance. This study provided reliable information on how the yeast mitochondrial proteome and phosphoproteome adapt to different carbon sources.
Ilana Kolodkin-Gal
Weizmann Institute of Science, Israel
Title: Maintaining motile cells inside the biofilm through cell-to-cell signaling, transcription regulation and evolution
Time : 11:20-11:40
Biography:
Ilana Kolodkin Gal completed her PhD in the year 2009 form Department of Molecular Biology, The Hebrew University of Jerusalem, Israel. During 2009-2012 she was a post-doctoral research fellow under supervision of Prof. Richard Losick, department of molecular and cellular biology, Harvard and co-mentored by Prof. Kolter, department of microbiology and molecular genetics, Harvard Medical School, USA. Since 2012 till date, she is working as Senior Researcher, department of molecular genetics, Weizmann institute of Science, Israel.
Abstract:
Bacteria in nature are usually found in complex multicellular structures, termed biofilms, which protect them from numerous environmental threats. The biofilm structure is the end result of collective behavior of different cell types in a coordinated fashion, achieved by the accurate regulation of dedicated genetic programs. So far, it was well established that in the single-cell level once a bacterial cell commits to the biofilm state it represses motility both transcriptionally and post-translationally. However, at the population level, we found a motile cell sub-population that is tightly retained inside the biofilm of Bacillus subtilis, enabling fast occupation of new niches, as well as invasion of neighboring colonies of foreign bacterial species.This dogma-breaking phenomenon depends on a unique signal originating in the extracellular matrix (ECM) that surrounds the cells in the biofilm, maintaining a motile cell sub-population. This ECM-based signal acts to induce motility, as mutants deficient in ECM production show lower numbers of motile cells. When the ECM extracted from a wild type biofilm was externally added to the ECM mutants, motility level was restored. In particular, TasA, the proteinaceous component of B. subtilis biofilm, appears to be a specific chemical signal that strongly induces bacterial motility. Using evolutionary and genomics approaches we found striking evidence for the importance of maintaining motility in the biofilm. During the maturation of tasA mutant colonies hyper-motile suppressors appeared in high frequency. We suggest that in the absence of ECM-based induction of motility, a strong selective pressure acts to reinstate motility in the biofilm. We are currently using RNA-seq to compare between wild type and ECM mutants transcriptomes in order to identify the different genetic programs that are activated by ECM-derived signaling genome-wide.
Subha Bhassu
University of Malaya, Malaysia
Title: Transcriptomic and proteomic profiling of infectious hypodermal and hematopoietic necrosis virus (IHHNV) in giant freshwater prawns
Time : 11:40-12:00
Biography:
Subha Bhassu completed her graduation BSc (Biomedical Sciences) in the year 1996 from University Kebangsaan Malaysia, Kualalumpur. Later she did her PhD in Molecular Biology from University Putra Malaysia. In the year 2010 she got appointed as CEBAR Biosafety Committee (CBC) Member.
Abstract:
Prawn shrimp aquaculture which captured billions of dollars often affected by viral and bacterial diseases which have led to new technologies such as expression and proteomic profiling using Next Generation Sequencing and 2D proteomic being used as an empowerment measures to tackle these problems in a more rapid, cost and effective way. With advancement of these technologies, will next generation sequencing and proteomic profiling be sufficient to explain the actual physiological changes in prawns that are affected from the Infectious hypodermal and hematopoietic necrosis virus (IHHNV), a single stranded DNA virus which is found in host nucleus as membrane bound phagosomes that has cause slow growth in freshwater prawns, deformities in Peneaus monodon and death in Litopeneaus varnamei. This is the first presentation of the pond bred freshwater prawns that survived the disease outbreak and their bio-physiological changes were captured using Next Generation Sequencing and proteomic profiling. Using muscles of survived and and death prawn muscle transciptomes, there are five major pathways that are affected and showed significant differential expressed genes which are 312 genes in cellular macromolecular machines, 398 in motor neuronal related disease, 36 genes in antigen processing and presentations, 72 genes in viral myocardiatic viral diseases and 100 genes in muscle contraction and oxidative phosphorylation pathways. Protein profiling revealed that ten proteins were significantly up-regulated whereas ten other new proteins were significantly down regulated. The up-regulated protein plays an important role in innate immune system response to infection of M. rosenbergii whilst the down regulated protein indicated metabolite and cell function response to environmental changes. The given insights from transcriptome and proteomic results have shown the physiological changes at host level towards the viral infection which indicates why the post-larvae of freshwater prawns can face severe mortality due to these physiological changes that occur when they are young. Epizootic diseases have caused huge economical loses in shrimp and prawn culture. However, within the commercial fresh water prawn aquaculture industry, M. rosenbergii seems less susceptible to viral diseases in comparison to paneaids. This is a study that would lead future advance technologies such as CHIP-sequencing, immuno precipitation studies that can be conducted to elucidate the survival of these freshwater prawns in comparison to other peneaid species.
Dharmendra Kumar
Narendra Deva University of Agriculture and Technology, India
Title: Transcriptome analysis of nematode-trapping fungi during infection of plant-parasitic nematodes
Time : 12:00-12:20
Biography:
Dharmendra Kumar has completed his PhD from Banaras Hindu University, Varanasi, India in year 2003 on Predacity and bio-control potential of a nematode-trapping fungus Arthrobotrys dactyloides. He is working as Assistant Professor of Plant Pathology in Narendra Deva University of Agriculture and Technology, Kumarganj, Faizabad, India. He also worked as DST BOYSCAST Fellow at Microbial Ecology, Department of Biology, Lund University, Sweden under guidance of Professor Anders Tunlid and Dr Dag Ahrén in the year 2011. He has published 19 papers in refereed scientific journals.
Abstract:
Nematode-trapping fungi are a group of soil living carnivorous microorganisms that form unique infection structures called traps to capture and kill the vermiform nematodes. Majority of nematode- trapping fungi belong to a monophyletic group consisting of single family of the order Orbiliales (Ascomycota). We studied the transcriptome expressed by Arthrobotrys oligospora forming adhesive networks, Monacrosporiumcionopagum forming adhesive branches and constricting ring forming species Arthrobotrys dactyloides during infection of root-knot nematode Meloidogyne hapla and sugar beet cyst nematode Heterodera schachtii. Comparative transcriptome analysis during infection process including trapping, penetration and digestion of nematode hostby nematode-trapping fungi showed that the divergence in gene expression pattern associated with fungal species was significantly larger than that related to the host nematode species. Genes that were highly expressed in all nematode-trapping fungi encoded endopeptidases such as peptidase S8, peptidase M3 and aspartic proteases; cell-surface proteins containing the carbohydrate-binding domain WSC; stress response proteins; membrane transporters; transcription factors and cell singling genes containing the Ras domain. Transcripts containing the Ricin-B lectin and Atg8 domain were also highly expressed in all nematode- trapping fungi. Differentially expressed transcripts among the fungal species encoded various lectins such as the fungal fruit-body lectin and the D-mannose binding lectin; transcription factors; cell-signaling components; proteins containing a WSC domain and proteins containing a DUF3129 domain. Interestingly, DUF 3129 was highly expressed in M. cionopagum but not expressed at all in A. dactyloides. Differentially expressed transcripts during infection of different host nematodes; including peptidases, WSC domain proteins, tyrosinases and small secreted proteins with unknown function.
Dora Tombacz
University of Szeged, Hungary
Title: Characteristics of Pseudorabies virus transcripts analyzed by PacBio and Illumina sequencing techniques
Time : 12:20-12:40
Biography:
Dora Tombacz is MSc in Biology (Faculty of Sciences, University of Szeged - 2006) and PhD in Medical Sciences (Faculty of Medicine, University of Szeged - 2010). She works in the Department of Medical Biology as an assintant professor at the Faculty of Medicine at University of Szeged in the Boldogkoi’s group. Their primary field of interest is the analysis of herpesvirus gene expression and utilization of herpesviruses as tools in various fields of biology including neurobiology and cardiology. She currently works with next – and 3rd generation sequencing techniqes, focusing on virology and genomics of human diseases at the University of Szeged (Szeged, Hungary) and the Stanford University (Stanford, CA, USA).
Abstract:
Introduction
Pseudorabies virus (PRV) is an alpha-herpesvirus that causes Aujeszky’s disease of swine. The viral genome is double stranded DNA and contains protein-coding and non-coding genes. This virus is a widely used model for the study of neural circuits and it serves as gene delivery vector into mammalian cells. Thanks to its relatively small, compact genome, PRV is also a useful model organism for the analysis of gene expression regulation at different levels.
Materials and Methods
Immortalized porcine kidney 15 (PK-15) cells were infected with Kaplan strain (Ka) of Pseudorabies virus (PRV). For PacBio sequencing, infections were stopped after 1, 2, 4, 6, 8 or 12 hours after infection. Polyadenylated RNAs were isolated from the total RNA samples, then were converted to cDNAs with anchored Oligo(dT)20 primer. cDNAs were used for the SMRTBell library preparation. For Illumina sequencing, we mixed infected cells. Strand-specific total RNA libraries were prepared for random hexamer primed amplification and the sequencing of 2x100 bp fragments. Expression patterns were also examined by strand specific qPCR for validation.
Results
PacBio long read sequencing technology was used for the first time to analyze viral gene expression. With the PacBio sequencing technique, full-length transcripts of up to about 2 kb could readily be monitored with little sequence loss at the 5′ ends. We have detected 27 new transcript isoforms (alternative polyadenylation sites of protein coding genes). Previously unknown splicing sites (in the following genes: ep0; ul12; ul22; ul43; ul3.5), alternative splice variants of the genes (in: us1; ul15 genes) were also detected.
- Workshop: On the way to disentangling the enigma of angiosperm egg activation
Session Introduction
Zsolt Ponya
Kaposvar University, Hungary
Title: The unique characteristics of the angiosperm plant life cycle and their potential consequences on the developmental plasticity of nucellar cells using wheat as a model system
Time : 13:25-14:10
Biography:
Zsolt Pónya has completed his PhD at the age of 32 years from the Eötvös Lóránd University of Arts and Sciences, Budapest, Hungary, and following obtaining his degree, he has launched his postdoctoral studies at the University of Siena, Italy, followed by a postdoc research fellowship at the Ben-Gurion University of the Negev, Israel. He is currently a senior scientist at the University of Kaposvár, Hungary. He has published a number of papers in reputed international journals and is a member of the editorial board of several prestigious scientific journals.
Abstract:
Angiosperm seed development is a crucial factor of agricultural production. Thus, a comprehensive understanding of the mechanisms governing it in cultivated plants is pivotal for crop productivity. The unique features of angiosperm life cycle such as continuous development, avoidance of a germline, flexible and reversible cellular differentiation, and the alteration of haploid and diploid generations are characteristics that confer a high level of plasticity upon flowering plants. Intriguingly, angiosperm nucellar cells can either engage in or forgo meiosis, a cell fate “decision” depending on the developmental context. Consequently, in angiosperms, two developmental pathways of reproduction can be followed: sexual or amphimictic, and asexual (apomictic); the latter remaining the holy grail of basic research initiatives due to its elusive nature. When paralleled, the cell fate decision of the initiatory cell being the depository of the information triggering incipient mechanisms eventually leading to embryo formation of a particular nucellar/sexual cell in the angiosperm ovule is in contrast with the conditions required in vitro either for a reconstituted oocyte exploited to produce clones by somatic cell nuclear transfer (SCNT), or for mammalian stem cells induced to undergo meiosis and produce synthetic gametes. Viewed from an evolutionary perspective, the genomes of angiosperm species are more dynamic and labile at both the sequence and chromosome level, whereas mammalian genomes are more stable mainly due to setting the germ line cells apart during an early stage of development. It appears that in attempts to unravel the molecular and cellular events leading to the “derailment” of the normal sexual pathway in the female gametophyte as it unfolds during the alternative developmental pathway during asexual seed formation, considering only gene-regulation networks in terms of the transcriptome may not supply us with a comprehensive picture pertaining to addressing the developmental flexibility of the nucellar tissues since an even greater complexity is conferred upon the angiosperm nucellus by the proteome. Furthermore, the wide range of plant transcription factors could be expounded by a unique feature of plants: their complex secondary metabolism providing a plethora of secondary metabolites; up to 25% of all plant genes are associated with a unique set of secondary metabolites not found in animals (the total number of plant secondary metabolites is close to 50,000, albeit it is estimated to be several hundred thousands) Essentially, transcriptomics studies launched in wheat, being one of the most staple food crops in the world, promise to be of use in disentangling the expression profile of genes that control many agriculturally important traits. However, the use of wheat microarrays for gene expression measurements in hexaploid wheat having an enormous genome may be deemed to be limited, and even when coupled with approaches based on powerful tools such as sequencing-based transcriptomics techniques may not be deemed to enable us to fully decipher the complexity of mechanisms involved in embryonic development ensuing either upon or without fertilisation in female gametes/nuclear cells. Elements of a complex system involving auxin gradient, positional information, maternal control end epigenetic factors will be touched upon in summarising the state of the art of endeavours addressing these issues of utmost importance in developmental biology.
- Track 10: Expression Profiling, Track 13: Genomics, Proteomics and Bioinformatics
Chair
Sang Ming WANG
University of Nebraska Medical Center, USA
Co-Chair
Punit Kaur
Morehouse School of Medicine, USA
Session Introduction
Max H Garzon
The University of Memphis, USA
Title: Genomic Positioning Systems for DNA and the Tree of Life
Time : 14:10-14:30
Biography:
Max H. Garzon is professor of computer science and bioinformatics. He has (co-)authored over 150 books, book chapters, journal and refereed conference publications. The main theme of his research is biomolecule-based computing and applications to areas such as bioinformatics, nanotechnology, self-assembly, semantic indexing and data mining. He is on the editorial board of several journals in these areas, including the International Journal of Genomic Medicine. He has served as TPC and organizer of many scientific conferences and professional meetings in these areas. He has been a visiting professor and guest scientist at a number of research institutions around the world.
Abstract:
Geographic information systems represent the modern version of the scientific revolution ushered in by the introduction of now standard Cartesian coordinates and analytic geometry in the 1600s. They provide a universal means of communication and computation in a unified system that makes possible identification, comparisons and validations of geographic position, previously unattainable on a global scale. In this talk, I propose an analogous coordinate system for the far more complex genomic biosphere based on the concept of “genomic” distance enjoying the geometric properties characteristic of geometric distance. The system has several properties: it is universal (applicable to any genome, known or unknown), feasible (computable for every given genome), zoomable (adaptable precision to various scales of resolution) and, more importantly, capable of revealing important functional and structural features of a given genome relative to other genomes. After a brief sketch of the foundations and contrast with earlier approaches, I illustrate how these two latter features make possible a number of applications in various omics areas, such as molecular phylogenetics, universal genetic marker generation and classification, and comparative whole-genomic analyses on a common framework that may reveal significant commonalities in hitherto disparate taxonomies and procedures. Time permitting, some potential applications will be sketched in some detail, including applications of interest in transcriptomics, such as molecular systematics, the Tree of Life, and Next-Generation Sequencing
Tao Liu
University of New South Wales, Australia
Title: The long noncoding RNA MALAT1 promotes tumour-driven angiogenesis by up-regulating pro-angiogenic gene expression
Time : 14:30-14:50
Biography:
Dr Tao Liu obtained his PhD from The University of New South Wales Australia in 2000. He then worked as a post-doc with Professor Samuel Breit at St. Vincent's Centre for Applied Medical Research Sydney. He is now Head of Histone Modification Group at Children’s Cancer Institute Australia, and an Australian Research Council Future Fellow at The University of New South Wales. In the last 5 years, Dr. Liu has been working on the roles of long noncoding RNAs, histone methyltransferases and histone deacetylases in modulating gene transcription, N-Myc-regulated malignant transformation, neuroblastoma initiation and progression in vitro and in vivo.
Abstract:
Neuroblastoma is the most common solid tumour during early childhood, and accounts for 15% of all childhood cancer death. One of the key features of neuroblastoma is disease progression due to tumour-driven angiogenesis. However, the mechanism through which neuroblastoma cells drive angiogenesis is unclear. Here we showed that the long noncoding RNA MALAT1 was over-expressed in human neuroblastoma cells under hypoxic condition, the condition which triggers pro-angiogenic switch and angiogenesis. In vitro angiogenesis assays demonstrated that conditioned medium from neuroblastoma cells transfected with MALAT1 siRNAs, compared with conditioned medium from neuroblastoma cells transfected with control siRNAs, induced considerably less endothelial cell migration, invasion and vascular sprouting under hypoxic condition. Affymetrix microarray differential gene expression study showed that one of the genes most significantly down-regulated by MALAT1 siRNAs in human neuroblastoma cells under hypoxic condition was fibroblast growth factor (FGF). RT-PCR and immunoblot analyses confirmed that MALAT1 siRNAs reduced FGF mRNA and protein expression, and in vitro angiogenesis assays demonstrated that forced over-expression of FGF in neuroblastoma cells blocked MALAT1-mediated endothelial cell migration, invasion and vascular sprouting. Taken together, our data suggest that over-expression of MALAT1 in human neuroblastoma cells plays an important role in tumour-driven angiogenesis by up-regulating FGF mRNA expression.
Bingsong Zheng
Zhejiang A & F University, China
Title: Studying the expression pattern of auxin-associated genes in Carya cathayensis (Hickory) during the grafting process
Time : 14:50-15:10
Biography:
Bingsong Zheng has completed his PhD in 2003 from Zhejiang University and Postdoctoral studies from INRA. He is the Vice-Dean of School of Forestry & Biotechnology, Zhejiang A & F University. He has published more than 30 papers in reputed journals and has been serving as an Editorial Board Member of repute.
Abstract:
Application of various hormones improves the grafting process and among which auxin plays a vital role for the formation of vascular reconnection. Auxin role in the grafting process was analyzed by studying the differential expression pattern of auxin-associated genes (ARF, GH3) and transporter genes (ABC and Aux: Hyd) under auxin- and NPA- (an auxin inhibitor) applied conditions at 0, 3, 7 and 14 days after grafting (dag). Analysis shows that the expression of GH3, ARF and Aux: Hyd genes were found to be low at the time of grafting but increased at 3 and 7 dag and again get reduced at 14 dag. While the expression of ABC gene was found to be high at 14 dag and got reduced at 3 and 7 dag. Further the application of IAA or NPA to the grafted sample is not influencing the gene expression in a concordant way. With the availability of rough draft unigene library for Hickory tree species to our group, 34 different ARF genes were identified and analyzed for their expression level at 0, 7 and 14 dag. Among the 23 genes analyzed, 15 genes expression level are not affected at various time of analysis and 5 of the genes expression were not detected in the grafted plants. While 3 of the gene expression level got drastically reduced at 7 and 14 dag when compared with 0 dag which shows that these ARF genes have specific role in the grafting process which has to be studied in detail in the future.
Punit Kaur
Morehouse School of Medicine, USA
Title: A Mouse Model for Triple-Negative Breast Cancer Stem Cells (TNBC-CSC) Exhibits an Aggressive Phenotype
Time : 15:10-15:30
Biography:
Punit Kaur finished her B.Sc. in 1999 with Botany, Zoology and Chemistry from Punjab University, Chandigarh, India. Then she went for Postgrad (M.Sc.) (1999-2001) in Microbiology from Guru Nanak Dev University, Amritsar, Punjab, India. Later she pursued for Ph.D (2001-2008) on the topic Experimental Medicine and Biotechnology from the Postgraduate Institute of Medical Education and Research, Chandigarh, India
Abstract:
There has been an increase of 40% in the number of Americans diagnosed with diabetes. Over that same period, the obesity rate has also increased by nearly 20%. Therefore, efforts to identify any biomarker(s) to assist with obesity and diabetes prevention are of paramount importance. This study was designed to address the link between obesity and diabetes using proteomic analysis of drawn blood and collected urine samples. Four of 14 primary care clinics of a large University-affiliated, multi-specialty group practice associated with an 186,000-member HMO in Central Texas. Six volunteer adult female Caucasian patients aged 35 years to 55 were identified with study inclusion criteria via Electronic Medical Record (EMR) search. Patients were divided into four groups on the basis of body mass index (BMI) and fasting blood glucose (FBG): group A presented with BMI>25, FBG<100; group B with BMI>25, FBG 110-125; group C with BMI>25, FBG>125; and group D were controls with BMI<25 and FBG<100. Plasma was separated from drawn blood, aliquoted and kept at -80°C until required. The plasma samples were analyzed using liquid chromatography mass spectrometry to measure changes in the protein profiles. Proteins including angiotensinogen protein, glycoprotein, apolipoproteins, complement proteins, hemopexin and vitronectin were found to be significantly increased in patients with obesity and diabetes. Importantly, angiotensinogen protein was significantly increased in group C considered as obese and diabetic individuals. Our results suggest that angiotensinogen protein, known to be linked to hypertension, might be an important early biomarker that links obesity and diabetes. Further studies using a larger sample size is required before concluding angiotensinogen as a potential biomarker that links obesity and diabetes.
Baris E. Suzek
Mugla Sitki Kocman University, Turkey
Title: Locating disease-associated single amino acid polymorphisms on proteins
Time : 15:30-15:50
Biography:
Baris E. Suzek has completed MS in Computer Science at Johns Hopkins University and PhD in Bioinformatics and Computational Biology at George Mason University. Currently, he is an Assistant Professor in Computer Engineering Department at Mugla Sitki Kocman University in Turkey and an Adjunct Assistant Professor at Georgetown University in USA. Before 2013, he served as a Research Assistant Professor in Department of Biohemistry and Bioinformatics Team Co-lead in Protein Information Resource at Georgetown University. He has published more than 20 papers in reputed journals, holds one patent and is recipient of several national awards in USA.
Abstract:
The next generation sequencing technologies are continuously improving and large sets of human mutations are becoming available within institutions and through public resources. A subset of these mutations lead to single amino acid polymorphisms (SAPs). Identifying SAPs’ disease-causing impact and developing methods to identify SAPs disease-associations are active research areas. In this work, we investigated the link between disease-associated SAPs and their protein sequence context (i.e. sequence features). We have integrated disease-associated SAPs and sequence features from several public bioinformatics resources. The SAPs and sequence features are then mapped to each other using protein resource UniProt Knowledgebase. Based on our initial results, over 39% of disease-associated SAPs are located on functional domains, topological domains and near post translational modifications. Over 19% of them are located on known secondary structures. Our findings will help in better understanding of SAPs’ disease associations. In the future, the protein sequence context for SAPs can be utilized in development of more accurate computational methods to predict disease-associated SAPs.
Babak Behnam
Iran University of Medical Sciences, Iran
Title: SLUG and SOX9 Cooperatively Regulate Tumor Initiating Niche Factors in Breast Cancer
Time : 15:50-16:10
Biography:
Babak Behnam has completed his MD degree at Iran University of Medical Sciences (IUMS), and his PhD degree at the University College London (UCL) in Human Genetics. Then he served as postdoctoral research fellow for 4 years at the University of Michigan School of Medicine and University of Central Florida. Then he has joined IUMS and directed medical genetics laboratory at IUMS-Children hospital in parallel to his translational research focused on molecular metastatic pathway and breast cancer stem cell. He has published more than 25 peer-reviewed papers and is also serving as an Editorial Board Member of scientific journals.
Abstract:
Background Presence of tumor initiating cells and a proper niche is essential for metastatic colonization. SLUG and SOX9 transcription factors play essential roles in induction and maintenance of tumor initiating capacity in breast cancer cells. On the other hand, Tenascin-C and Periostin are crucial factors in metastatic niche that support tumor initiating capability in breast cancer. Method In this study, regulatory effect of SLUG and SOX9 transcription factors on the expression of Tenascin-C and Periostin transcripts was examined. SLUG and SOX9 were overexpressed and knocked-down via lentivirus constructs in MCF7 in MDA-MB-231 cells, as non-invasive and invasive breast cancer-derived cells respectively. Then, Tenascin-C and Periostin expression levels were measured side by side of the SLUG and SOX9 via Real-Time PCR. Results Simultaneous overexpression of SLUG and SOX9 significantly induced Tenascin-C and Periostin Expression. SLUG and SOX9 knock-down also significantly reduced the expression of Tenascin-C and Periostin. In this analysis, Periostin showed the most deviation in both up- and down-regulation levels. Conclusion This regulatory effect might shed light to a crosstalk between factors involved in the tumor initiating capacity and metastatic niche of the breast cancer.
- Young Researchers Forum
Session Introduction
Yu Zhou
Tulane University, USA
Title: Pathway analysis for female osteoporosis
Time : 16:25-16:45
Biography:
Yu Zhou is from Tulane University, USA. His research interests reflect in his wide range of publications in various national and international journals.
Abstract:
Osteoporosis is a prevalent bone metabolic disease characterized by bone fragility. As a key pathophysiological mechanism, the disease is caused by excessive bone resorption (by osteoclasts) over bone formation (by osteoblasts). Peripheral blood monocytes represent a major systemic cell type for bone metabolism by serving as progenitors of osteoclasts and producing cytokines important for osteoclastogenesis. To identify the key dysfunctional pathways in osteoporosis, we performed pathway analysis on microarray data of monocytes from 73 Caucasian females with extremely high or low hip BMD (bone mineral density). In current major approaches, pathways are treated as independent, but the genes overlap among them will cause “crosstalk” phenomenon and interfere the results severely. So, we firstly performed a traditional pathway analysis (Fisher’s exact test using kegg database) on our microarray data. Then we proposed a novel approach which considers the correlation among genes in the same pathway based on the real experiment data to correct the crosstalk effects in the analysis. We also applied a correction technique, MIE (maximum impact estimation) which has been reported, to our study. In traditional analysis, 10 pathways were found to be significantly associated with BMD variation. After correction by our methods, four of them (hsa05010, hsa00601, hsa01212, hsa04622) were still significant. Thus, they were considered as independent and important pathways in bone mechanism. Moreover, one pathway, MAPK signaling pathway (hsa04010) which has been proved to be important for osteoclastogenesis, became significant. Comparing with the available correction technique (MIE), all the findings in our method were biologically meaningful for osteoporosis. Because it was based on the correlation among genes in real experiment data, our method was available to reduce the false positive results and get better understanding of biological networks in the disease. In summary, we described a novel method to correct the crosstalk effect in pathway analysis and found five key independent pathways involved in BMD regulation.
Peter Olah
University of Szeged, Hungary
Title: Characterization of 5-methylcytosine patterns in Pseudorabies virus
Time : 16:45-17:05
Biography:
Peter Olah is a graduate student at the Department of Medical Biology on the University Of Szeged, Hungary. He obtained his MSc in Biotechnology from the University of Debrecen, Hungary, followed by work as a sequencing laboratory assistant. His main area is bioinformatics and sequencing data analysis related to the life cycle and gene expression regulation of herpesviruses.
Abstract:
Introduction: Pseudorabies Virus (PRV or Aujeszky's disease virus) is a neurotrophic herpes virus with a broad host range consisting of mammalian species which causes fatalities in swine populations prenatally and in young animals. It is also a widely used model organism for studies of gene expression, neuronal tracing and the viral life cycle of Alpha herpesviridae. A main characteristic of alphaherpes viruses is the strictly regulated, cascade-like gene expression pattern during lytic infection. In addition, viral genes are arranged in tightly packed functional clusters in various overlapping orientations. In order to assess whether 5-methylcytosine is present and occurs at specific loci in relation to the gene clusters in the PRV genome, wild-type and mutant PRV strains were subjected to bisulfite sequencing (BS-Seq). Materials & Methods: PRV virions of the wild-type PRV strain Kaplan and mutant viruses lacking key trans-activators (US1, UL54, EP0 and IE180 null-mutants) were harvested 12 hours post infection from PK-15 cells by ultracentrifugation followed by DNA isolation. BS-Seq libraries were constructed for paired-end 100 bp sequencing on an Illumina Hiseq 2000. Alignments were generated using Bowtie2 following strict adapter and quality trimming; the resulting alignments were processed in Bismark for methylation calling. Results: In PRV, interpreting CpG methylation is complicated by the extremely high GC-content of the virus. The number of methylated cytosine residues varied slightly (4-7%) between samples at lower amounts than the average methylation density in mammalian CpG islands. The intra-sample distribution of methylated residues was however non-random, indicating preferred sites of base modification and was consistent between samples which suggests that methylation at intergenic boundaries might serve important roles in viral gene expression regulation.
Saurabh Chaudhary
Guru Gobind Singh Indraprastha University, India
Title: De novo transcriptome assembly and identification of cold and freeze responsive genes in sea buckthorn
Time : 17:05-17:25
Biography:
Saurabh Chaudhary is presently pursuing his PhD under the guidance of Prof P C Sharma, Dean, University School of Biotechnology, GGSIPU, New Delhi, India. His research area includes transcriptome analysis of sea buckthorn, a medicinally and ecologically important plant. He has studied digital gene expression profiling under cold and freeze stress using DeepSAGE in sea buckthorn. The major achievements of his work are: comprehensive study of sea buckthorn transcriptome, assembly of 88,297 putative uni-genes of sea buckthorn and identification of 11,922 differentially expressed genes under cold and freeze stress in seabuckthorn. He has three research publications in peer reviewed international journals.
Abstract:
Sea buckthorn (Hippophae rhamnoides L.) is well known for its immense medicinal, nutritional and ecological value, and also for its ability to grow in extreme environments. We used next generation Illumina sequencing to gain a comprehensive view of the seabuckthorn transcriptome. A total of 86,253,874 high quality short reads were assembled using different assembly tools and parameters. The use of short read assembler ABySS with an additive k-mer approach followed by TGICL suite was found most promising for de novo transcriptome assembly. Finally, 88,297 transcripts (>100 bp) were generated representing 53 Mb transcriptome. The average transcript length and N50 length remained 610 bp and 1,193 bp, respectively and 91% of the short reads uniquely mapped back to the seabuckthorn transcriptome. Further, 41,340 (46.8%) transcripts showed significant similarity with the sequences present in nr protein databases of NCBI (E-value <1E-06). Assembled transcripts were also screened for the presence of transcription factors and simple sequence repeats. Next, DeepSAGE, a tag based approach was also followed to identify differentially expressed genes under cold and freeze stress. In all, 11,922 differentially expressed genes (DEGs) were identified including 6,539 up regulated and 5,383 down regulated genes. Gene ontology and KEGG pathway analysis was performed to assign gene ontology term to DEGs and ascertain their biological functions. Expression of selected 22 DEGs was validated using qRT-PCR.A combination of de novo transcriptome assembly and DeepSAGE analysis proved to be a powerful method for transcriptome analysis and identifying abiotic stress responsive genes in seabuckthorn.