Welcome and thank you again for being part of this effort.

Transcripción

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2 INTRODUCTION The Faculty of Science of the Morelos State Autonomous University (Universidad Autónoma del Estado de Morelos, UAEM) is recognized as a successful participant in scientific frontier research and training of highly qualified undergraduate and graduate students for the past 22 years. To respond to the national and global scientific challenges and policies that lie ahead, the Faculty of Science was restructured to give way on the 12 th of December 2014 to the creation of the Cellular Dynamics Research Center (Centro de Investigación en Dinámica Celular, CIDC). The CIDC is developing various strategic scientific programs including its Program in Omics technologies. As a sign of our commitment to scientific collaboration and team effort, the starting line of this program embodies itself in this 1st National Symposium of Structural, Comparative and Functional Genomics to be held on the 6 th and 7 th of August 2015 in Cuernavaca, Morelos, Mexico. The Omics technologies are a reality, and although still developing, they are giving way to an unprecedented boost to current life science research. These technologies epitomize the holistic view of life, allowing us to better understand how cells, tissues and organisms function as a whole. In this symposium we are bringing together cutting-edge research in omics technologies that is being done in Mexico, particularly in the central region. You will hear expert speakers that have implemented omics technologies in Mexico and that want to share their progress on current research projects that include: genome assembly, comparison and study of their evolution, global gene expression based on transcriptomes and how it influences the production of proteins with proteomic methods and the analysis of metagenomic data of non-culturable organisms, but with a great potential to discover new genes of biotechnological significance, to mention a few. All these advances, referred to as high-dimensional biology, are further integrated to study the cell as a complex system and obtain overall responses of cellular functions in what is known as systems biology. Additionally, some services offered by massive sequencing units will be presented.

3 We hope that you enjoy this symposium and that it gives you an opportunity to explore or further strengthen areas of multidisciplinary research and thematic networks, consistent with the vision of the researchers involved in this field of study. Also, it is very important for the CIDC that these technologies be part of the skills that undergraduate and graduate students handle with expertise in their research in view that omics technologies are essential to understand the great challenges facing the life sciences, particularly in solving significant biotechnological and health problems. Welcome and thank you again for being part of this effort.

4 PROGRAM Thursday, August 6th 8:00-8:30 Registration 8:30-9:00 Inauguration of the 1st National Symposium of Structural, Comparative and Functional Genomics 9:00-9:40 Ecological genomics, from genes to ecosystems Edgar Dantán González, PhD Centro de Investigación en Biotecnología - UAEM 9:40-10:20 Benefits of Complete Genome Assemblies for Prokaryotic Genomic Studies Luis Lozano Aguirre, PhD Centro de Ciencias Genómicas - UNAM 10:20-11:00 A probable European origin and trans-atlantic exchanges of the Lyme disease agent Borrelia burgdorferi sensu stricto Santiago Castillo Ramírez, PhD Centro de Ciencias Genómicas - UNAM 11:00-11:40 Proteome and transcriptome analysis associated to a subnuclear fraction of adenovirus infected cells Ramón González García-Conde, PhD Centro de Investigación en Dinámica Celular- UAEM 11:40:12:10 Coffee break 12:10-12:50 Conserved gene expression responses in glucose depleted media: an evolutionary glimpse Armando Hernández Mendoza, PhD Centro de Investigación en Dinámica Celular - UAEM

5 12:50-13:30 The modular structure of bacillus subtilis regulatory network, shows basic principles of their evolution and organization Rosa María Gutiérrez Ríos, PhD Instituto de Biotecnología- UNAM 13:30-14:30 Lunch 14:30-15:30 Poster session 15:30-16:00 Ricardo Sánchez Pérez, PhD ELSEVIER 16:00-16:15 Aedes aegypti blood fed midgut cistrome is enriched in sequence motifs for the binding of zinc finger type transcription factors Verónica Valverde Garduño, PhD Instituto Nacional de Salud Pública 16:15-16:30 RNA-seq insights into the root apical meristem exhaustion of the primary root of Pachycereus pringeli, a sonoran desert cactus Gustavo Rodríguez Alonso, MSc Instituto de Biotecnología -UNAM 16:30-17:00 Next generation sequencing platforms and analysis of vaginal microbiome Alfredo Mendoza Vargas, MSc Instituto Nacional de Medicina Genómica 17:00-17:40 The massive sequencing unit and bioinformatics at the UNAM Ricardo Alfredo Grande Cano, PhD Instituto de Biotecnología UNAM

6 Friday, August 7th 9:00-9:40 A Proteomics perspective on cervical cancer research Sergio Encarnación Guevara, PhD Centro de Ciencias Genómicas - UNAM 9:40-10:20 Proteome response to dengue virus infection in human cell lines Rosa Victoria Pando Robles, PhD Instituto Nacional de Salud Pública 10:20-11:00 Exploring human and animal microbiomes using metagenomics and metatranscriptomics Adrián Ochoa Leyva, PhD Instituto de Biotecnología - UNAM 11:00-11:40 From lignocellulosic genomes (metagenomes) to lignocellulosic genes: trends, challenges and prospects Ramón Batista García, BSc Centro de Investigación en Biotecnología- UAEM 11:40-12:10 Coffee break 12:10-12:40 Specialization through evolutionary trade-offs: a case of thermotolerant yeasts Luis Caspeta Guadarrama, PhD Centro de Investigación en Biotecnología- UAEM 13:00-13:40 Systems biology: a paradigm in the metabolic study of cancer Osbaldo Resendis Antonio, PhD Instituto Nacional de Medicina Genómica 13:40-14:40 Lunch 14:40-15:40 Posters session 15:40-16:20 Transcriptomic and epigenetic analysis on human neonate T cells María Angélica Santana Calderón, PhD and Otoniel Rodríguez Jorge, MSc Centro de Investigación en Dinámica Celular - UAEM

7 16:20-17:00 Starvation-responsive micrornas of Caenorhabditis elegans Juan Miranda Ríos, PhD Instituto de Investigaciones Biomédicas- UNAM 17:00-17:40 Analyzing the pan-genome of environmental multidrugresistant Stenotrophomonas strains using the GET_HOMOLOGUES software package Pablo Vinuesa Fleischmann, PhD Centro de Ciencias Genómicas - UNAM 17:40-18:00 Closing ceremony

8 ACKNOWLEDGEMENTS Academic Staff Edgar Dantán González, PhD. Luis Lozano Aguirre, PhD. Santiago Castillo Ramírez, PhD. Ramón González García-Conde, PhD. Armando Hernández Mendoza, PhD. Rosa María Gutiérrez Ríos, PhD. Verónica Valverde Garduño, PhD. Gustavo Rodríguez Alonso, MSc. Alfredo Mendoza Vargas, MSc. Ricardo Alfredo Grande Cano, PhD. Sergio Encarnación Guevara, PhD. Rosa Victoria Pando Robles, PhD. Adrián Ochoa Leyva, PhD. Ramón Batista García, B. Luis Caspeta Guadarrama, PhD. Osbaldo Resendis Antonio, PhD. María Angélica Santana Calderón, PhD. Otoniel Rodríguez Jorge, MSc. Juan Miranda Ríos, PhD. Pablo Vinuesa Fleischmann, PhD.

9 Administrative and logistical support Roberto Téllez G., MBA. Dante Pérez Méndez, BSc. Sandra R. Manrique Hernández, BSc. Organization of the 1st. Colloquium of the CIDC Iván Martínez Duncker, MD ScD Director Centro de Investigación en Dinámica Celular Armando Hernández Mendoza, PhD Full-time research professor Centro de Investigación en Dinámica Celular Sonia Dávila Ramos, PhD Full-time research professor Centro de Investigación en Dinámica Celular

10 ABSTRACTS OF PRESENTATIONS Edgar Dantán González, PhD Centro de Investigación en Biotecnología - UAEM edantan@uaem.mx Ecological genomics, from genes to ecosystems The power of genetics -- which has been bolstered in the past decade by a broad range of genomic tools -- in dissecting basic cellular and developmental processes is undisputed. It has also been increasingly exploited to understand the interaction between different organisms, particularly between pathogens and their hosts. Because of the technological investments required, genetic and genomic approaches have, however, traditionally been applied only to a small set of carefully chosen model species. These species, such as nematode worms, fruit flies, or the small cabbage relative Arabidopsis, are typically adapted to the laboratory environment and are usually genetically inbred. They necessarily represent abstractions of biological systems, and it is difficult, if not impossible, to infer from these studies how species adapt to their natural environment. But this situation is now changing. A multitude of new approaches are becoming available to begin to address the genetics of adaptations and ecological interactions in natural populations. It is today much easier to develop genetic approaches for ecological model systems than trying to understand the ecology of established genetic model organisms. The research options in ecological genomics have been dramatically increased with the explosive development of DNA sequencing power and genomic approaches in the past years. The major challenge of the next five to ten years will clearly be to find a balance between the awesome power of data generation technologies and the depth of scientific questions that can be addressed with these data. At the same time, it will be necessary to keep in mind that genomic data on their own do not provide much biological meaning. Hence, biological concepts for comparative analysis and experimental strategies for functional analysis that optimally exploit the advances in data collection will have to be developed.

11 Luis Lozano and Gabriela Guerrero, PhD Centro de Ciencias Genómicas UNAM Benefits of Complete Genome Assemblies for Prokaryotic Genomic Studies The sequencing and assembly of prokaryotic genomes is nowadays a necessary issue of most genomic projects. Sequence technologies and assembly software offer the possibility to obtain, with higher quality and in less computational time, complete prokaryotic genomes. However, large-scale genomic studies analyze the biological complexity of bacteria genomic evolution with fragmented genome structure information. The lack of complete prokaryotic genomes impacts the analyses and the generation of important questions about genomic differences between strains or populations that could have a better understanding with the assembly of a complete genome. Several assembly software and pipelines have been designed to help in the analysis of genome projects. The next generation technologies advances have open the possibility of obtaining, in an easier way, complete prokaryotic genomes even for large-scale genomic studies. Nowadays there are no studies that incorporate the last sequencing technology, which can generate single DNA sequences bigger than 20 Kbs, with the aim of obtaining finished high quality genomes in prokaryotic analyses. The use of the new technologies and software will soon aloud research groups to get better complete genomes even in projects where hundreds of bacteria genomes need to be assembled. We show examples of how this kind of assemblies can be achieved and demonstrate the benefits of obtaining finished complete genomes for genomic projects.

12 Santiago Castillo Ramírez, PhD Centro de Ciencias Genómicas UNAM A probable European origin and trans-atlantic exchanges of the Lyme disease agent Borrelia burgdorferi sensu stricto The origin and population structure of Borrelia burgdorferi sensu stricto (s.s.), the causative agent of Lyme disease, remain obscure. This tick-transmitted bacterial species occurs in both North America and Europe, but only a few isolates, mainly from the USA, have been sequenced. We sequenced 17 European isolates and compared these with North American strains. We show that these data suggest a scenario in which a European origin of B. burgdorferi s.s. is likely and that trans-atlantic exchange has occurred in the evolutionary history of this species. We found three distinct genetically differentiated groups; one was the outgroup species Borrelia bissettii, another consisted of two divergent strains from Europe. The last group was composed of strains from both the USA and Europe and phylogenetic analysis indicates that different genotypes were likely to have been introduced several times into the same area. Since core polymorphisms showed signatures of recombination, horizontal gene transfer evidently occurs in this species. Importantly, strains associated with different disease symptoms did not form monophyletic clusters. Our results demonstrate that whether B. burgdorferi s.s. originated in Europe or the USA, later trans-atlantic exchange(s) have occurred. This study clearly shows the utility of next generation sequencing for studying the evolutionary history of bacterial species with low genetic variation.

13 Ramón González García-Conde, PhD Centro de Investigación en Dinámica Celular - UAEM rgonzalez@uaem.mx Gonzalez R.A 1., Anzures M.L 1,2., Hidalgo P 1.2., Valdés M 3., Dobner T 3., Hernández A 1. 1Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca, Morelos. 2Instituto de Biotecnología, UNAM, Av. Universidad 1001, Cuernavaca, Morelos. 3Heinrich-Pette Institute, Leibniz Institute for Experimental Virology, Hamburgo, Alemania. Analysis of the proteome and transcriptome associated to a subnuclear fraction of adenovirus-infected cells. The adenoviral genome encodes three groups of oncogenes that are responsible for establishing conditions in the infected cell that are conducive to efficient viral replication and progeny production. The products of these oncogenes are multifunctional proteins that inhibit anti-viral cellular defenses and simultaneously induce the almost exclusive expression of viral genes. Together, these viral early proteins cooperate to induce cell transformation or the efficient production of viral macromolecules and progeny. The study of adenoviral oncogenes has shown that their products are implicated in the reorganization of the infected-cell nucleus as they participate in the formation of virusinduced structures that constitute nuclear microenvironments that colonize the cell nucleus. These so called viral replication compartments (RC) are the sites where viral DNA is replicated and transcribed, and where posttranscriptional processing of viral mrnas initiates. During their formation viral RC recruit and co-opt proteins that constitute the main cellular defense mechanisms to infection. Some of these include components of the DNA damage response (MRN, BRCA1, ATR); tumor supressors (PML, p53); innate immune response (STAT1); and a growing list of cellular proteins that would normally interfere with viral replication. Hence, viral RCmay serve as hubs to direct viral replication and simultaneously control cellular defense mechanisms. Using a technique that we recently established to obtain isolated RC in a subnuclear fraction of adenovirus-infected cells, we have initiated the analysis of thernas and proteins that are associated to these virus-induced structures. These studies have shown that the isolated RC are highly complex macromolecular assemblies and that the detailed analysis of their RNA and protein composition will reveal important insights into numerous aspects of the interactions between adenovirus and the infected host cell.

14 Armando Hernández Mendoza, PhD Centro de Investigación en Dinámica Celular - UAEM ahm@uaem.mx Vichi-Lozada J. 1, Salazar-Bustamante E. 1, Gonzalez-Martinez R. 1, Anzures Cortés L. 1, and Hernández-Mendoza A. 1 * 1 Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos Conserved gene expression responses in glucose depleted media: an evolutionary glimpse The physiologic response associated to the use of glucose as a carbon and energy source is a conserved cell process in living beings independently of their cell pattern and the process and regulatory mechanisms involved are well studied. Nevertheless, it is unclear whether there is a common response to diminish or depleted glucose growth conditions between organisms unrelated phylogenetically. The aim of this study is to reveal underlying knowledge about evolution of gene expression response in reduced concentration or absence of glucose as carbon source. We perform two approaches using bioinformatic tools and experimental evidence. On one hand, we generate orthologous groups based on 277 human genes set reported in the Kyoto Encycopledia of gene and genomes (KEGG) in four model organisms: Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and Mus musculus. Expression data from 13 studies of caloric restriction (reduced glucose condition) from GEO database were used, normalized with RMA algorithm and analyzed with Gene set enrichment analysis (GSEA) software to determinate enrichment set gene that were compared between different species. We found a conserved expression responses associated to phosphorilation oxidative reaction in the four model organisms and impressively orthologous genes related to neurodegenerative Alzheimer's, Huntington's and Parkinson's diseases with a similar expression pattern, suggesting a conserved expression pattern in all organisms. On the other hand, we isolated and sequenced RNA from Escherichia coli (prokaryotic) and Schizosacharomyces pombe (eukaryotic) growth in glucose (2%) and in a mix of glycerol (2%) /acetate (0.2%) (glucose depleted) and carried out the differential expression gene and gene ontology analysis for comparative features. We detected that a set of gene associated to foraging behavior were differential expressed in glucose absence in both organisms but interestingly, we highlights that genes ontology associated to respiration and neurodegenerative diseases in human were found in this condition as well.

15 Rosa María Gutiérrez Ríos, PhD Instituto de Biotecnología UNAM Gutiérrez-Ríos RM., Majarrez-Casas A. and Freyre-González J. Departamento de Microbiología Molecular Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Morelos 62250, México. The modular structure of Bacillus Subtilis regulatory network, shows basic principles of their evolution and organization. Background Regulation of gene expression at the transcriptional level is a fundamental issue in all life forms. Among the different kind of mechanisms modulating gene transcription, the one based on DNA binding transcription factors (TF), is the most extensively studied and the results, for a great number of model organisms, have been compiled making it possible the in silico construction of their corresponding transcriptional regulatory networks. This information combined with the development of mathematical and computational tools, open the possibility to identify the general properties of these networks and elucidate main issues of their organization and evolution. Results In this paper, we present a deep review of the regulatory elements that constitute the transcriptional regulatory network of Bacillus subtilis in terms of its modular organization and structural properties. In our study we found that some particular functions could be distributed in more than one module whilst some modules might contain more than one related function. The results also highlight the importance of sigma factors as elements that characterize modules, inter or intra-connect them and are key element of the cascades that define relevant cellular processes in this organism. We also suggest that the presence of paralogous proteins confers Bacillus subtilis advantages to adapt and select strategies to successfully face the extreme environmental conditions where it lives. Conclusions We propose that this intricate organization is the product of a non-random network evolution that primarily follows a hierarchical organization reflected in the connections that exist inter and intra-module.

16 Ricardo Sánchez Pérez, PhD ELSEVIER Sánchez R 1. and Prud Homme MA 2. 1 Elsevier de México. Insurgentes Sur 1898 Piso 12 Col. Florida, Distrito Federal México C.P t m Universidad Latinoamericana, Av. Teopanzolco 107 Col. Vista Hermosa, Cuernavaca, Morelos, México C.P monicaprudhomme@hotmail.com. Obesity & chile Introduction. Obesity is the number one national health problem in México. The actual percentage of Mexican adults with this condition is 70 % compared to 56 % and 34 % in Latin America and Worldwide respectively. Despite a great government expending in this health problem, local Obesity genetic studies reported are minimum. This study presents a theoretical genetic approach to improve the molecular understanding of the disease and the pathways modified by the natural occurring compound Capsaicin, the principal component of the Chile. Methodology. Pathways were analyzed and constructed using Pathway Studio. Transcriptome profiling datasets were obtained from the public domain and were analyzed using Pathway Studio. These datasets contain triplicates of non-obese and morbidly-obese individuals. We examined candidate genes that could be up- and down-regulated by Capsaicin. Results. Major Obesity regulator genes (that inhibit the disease) identified using Pathway Studio were LIPE, ESR1, GSK3B, PTGS2, IRS2 and DRD2. Transcriptome profiling results showed that these genes were down-regulated in morbidly-obese individuals compared to non-obese individuals. Conclusions. This study contributes to a better understanding of how Capsaicin susceptibility genes may modify the Obesity pathways. With this information, more targeted functional analysis of Capsaicin-Obesity susceptibility genes can be performed to examine the Capsaicin possible contribution to the Obesity treatment. With this study it can be concluded that a theoretical approach using Pathway Studio represents a valuable alternative to define and construct pathways for the further understanding of diseases.

17 Alfredo Mendoza Vargas, MSc Instituto Nacional de Medicina Genómica Mendoza-Vargas A., Palacios González B., Vadillo Ortega F. Instituto Nacional de Medicina Genómica. Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F. C.P Tel. +52 (55) Next generation sequencing platforms and analysis of vaginal microbiome. Next generation sequencing (NGS) technology has revolutionized genomic and genetic research and has dramatically reduced the cost of DNA sequencing. New types of sequencing instruments that permit amazing acceleration of datacollection rates for DNA sequencing have been developed. Here, I provide an brief perspective of the field, focusing in the newest types of sequencers including single molecule sequencers and an example using these technologies for analysis of cervicovaginal microbiota. The presence of cervicovaginal infections during pregnancy has been associated to preterm labor and it is accepted that directly or indirectly, the presence of an infection can explain preterm labor. The recently accumulated information about the pathophysiology of preterm birth let us propose that this condition may be linked to complex interactions between the cervicovaginal microbiome and environmental factors. An clinical research approach using NGS is characterize changes throughout pregnancy in the cervicovaginal microbiota of women who developed preterm birth. Women included in the Mexico City's Perinatal Cohort were selected according outcome and two groups were analyzed: 1. Term outcome (n=10) (T) and 2. Preterm outcome (n=5) (P). Cervicovaginal swabs were collected and whole genomic DNA was extracted and the V3-V4 hypervariable regions of bacterial 16S rrna genes amplified and sequenced by Illumina MiSeq. Analysis of the data was performed by QIIME. A PCA was performed using taxa. Women who delivered at preterm had a characteristic cervicovaginal microbiome with the presence of Shuttlerworthia, Megaspahera, Gardnerella and Prevotella, in addition we observed a decrease in L. ssp y L. inners in the second trimester of women who developed preterm labor. Our data revealed that the composition of the vaginal microbiota is a dynamic process, which means that the microbiota is modified in several points across the pregnancy. The pathological consequences of these changes must be analyzed in the context of preterm birth.

18 Ricardo Alfredo Grande Cano, PhD Instituto de Biotecnología UNAM Grande R. And Vazquez G. Massive Sequencing and Bioinformatics Unit (MSBU). Instituto de Biotecnología UNAM. Av. Universidad Colonia Chamilpa, Cuernavaca, Morelos México. CP Tel The massive sequencing and bioinformatics unit (USMB) at the UNAM. The MSBU is a service provider unit that offer services of construction and sequencing of DNA and RNA libraries to the scientific community of the country. Born in 2009 as Universitary DNA Massive Sequencing Unit (UDMSU) on the initiative of a consortium of five academic institutions and the Coordination of Scientific Research, all of them from UNAM. That year, the UDMSU acquired to Illumina, Inc the first massive sequencer in Mexico and Latin America, the Illumina s Genome Analyzer IIx (GAIIx). Two years later and with the support of the Technical Council of Scientific Research (TCSR) the UDMSU acquires its second next generation sequencer an Ion Torrent PM to the Life Technologies Company for complemention of services. In 2012 and in response to the growing need for support in handling and data analysis of massive sequencing information, the Universitary Bioinformatics Support Unit (UBSU) is created to provide bioinformatic services to users of UDMSU. Given the relationship of the two units, in 2014 an operational merger gives rise to the Massive Sequencing and Bioinformatics Unit (MSBU), which provides a comprehensive consultancy service, experimental design, construction, sequence and analysis of massive sequencing data to the scientific community and the productive sector of the country. The latest aquisition of the MSBU, was its third sequencing device, this time an Illumina NextSeq 500 sequencer whose operation began in early Currently, in addition to the above services, the MSBU offers the services of nucleic acid purification for library construction and sequencing. To our knowledge, the MSBU is the only entity in the country that provides all of these services with a high quality. The USMB is part of the National Laboratory of Technological Support for Genomic Sciences (LNATGC).

19 Sergio Encarnación Guevara, PhD Centro de Ciencias Genómicas UNAM Encarnación Guevara S., Checa Rojas A., Ramirez-Torres A.C., Gil Valdés J., Delgadillo Silva L. F., Contreras Martínez S., Higareda Almaraz J.C. Laboratorio de Proteómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México. Av.Universidad s/n C.P Cuernavaca Mor., México. Phone, , Fax A proteomics perspective on cervical cancer research. Cervical-uterine cancer (CuCa) is the second most common malignancy affecting women worldwide and is the major cause of morbidity and mortality in developing countries. It has recently begun to be considered that cancer is a systemic disease and that it must be studied at every level of complexity using many of the currently available approaches, including high-throughput technologies and bioinformatics. To achieve such understanding in cervical cancer, we collected information on gene, protein and phosphoprotein expression of the HeLa cell line and performed a comprehensive analysis of the different signaling pathways, transcription networks and metabolic events in which they participate. We observed that the different over- and underregulated pathways in cervical cancer could be interrelated through elements that participate in crosstalks, therefore belong to what we term meta-pathways. These features could be maintained in many other types of cancer, regardless of mutations or genomic rearrangements, and favor their robustness, adaptations and the evasion of tissue control. Probably, this could explain why cancer cells are not eliminated by selective pressure and why therapy trials directed against molecular targets are not as effective as expected. On the other hand, using quantitative proteomics we assessed highly overexpressed proteins in 5 different groups of cervical tissues types compared with normal tissue samples by liquid chromatography tandem mass spectrometry (LC/MS/MS) coupled with isobaric tags for relative and absolute quantitation (itraq) technology. More than five hundred unique proteins were identified (FDR 1%). Analyses were performed to select candidate markers which were validated by immunohistochemistry. From these differentially expressed proteins, some of them appeared to be potential therapeutic targets. Moreover, using 2D PAGE followed by MALDI-TOF-MS we have identified differentially expressed proteins over three different times of tumor development of CuCa tumors, from inoculated female nude mice with the cancer cell lines HeLa and SiHa. Once we established the proteomic dynamics over this period of time, we select

20 the GSTP1 and GSTM3 proteins because of their strong expression and biological function. We made the knockdown of these proteins in different tumor cell lines (HeLa, CaLo, SiHa, Caski, Colo-205 and MDA-231) and we found that the tumor development decreased in four tumors cell lines with the GSTP1 knockdown and in three tumor cell lines with the GSTM3 knockdown. Our results indicate that GSTs play an important role in cell maintenance and survival during tumor development in cervical cancer. Part of this work was supported by PAPIIT-UNAM grant IN and CONACYT grant

21 Rosa Victoria Pando Robles, PhD Instituto Nacional de Salud Pública Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, México. Proteome response to dengue virus infection in human cell lines. Dengue is the most prevalent arthropod-borne viral disease, with a 30-fold increase in global incidence in the past 50 years. Despite its importance as human illness, the pathogenic mechanisms during dengue virus (DENV) infection remain poorly understood and the factors that trigger severe illness are still unclear. Currently, there are no effective vaccines or antiviral therapy for prevention or treatment of the disease. Viruses as obligate intracellular parasites depend on the host cell machinery for replication. As a result of a co-evolution, DENV have developed sophisticated strategies to hijack and use cellular process for its propagation; where a piece of the puzzle to understand dengue virus-host cell interactions involve the identification of proteins expressed in the infected cells as well as their posttranslational modifications and the dynamics of the biological processes implicated during infection. In the last years, DENV-host studies have identified many host changes that occur upon infection; however, the molecular orchestration of these altered pathways remain unclear and substantial gaps continue in the understanding the pathogenesis of dengue disease. In part, this limitation is related to the lack of a suitable animal model and the wide range of cell types infected by DENV. In humans, myeloid lineage cells (dendritic cells, monocytes and macrophages) and hepatocytes are the major sites of DENV replication. In this work, we used proteomics approaches to elucidate the crosstalk between DENV and host cell. We analyzed the proteome response to DENV infection in the monocytic cell line THP-1, and in the hepatic cell line Huh-7; using ITRAQ and label free LC-MS methodology, respectively. In total, we were able to identify and quantify approximately 2,000 unique proteins in each cell type and our results suggest that the response to DENV infection is cell type specific. This Project was supported by UCMexus 2010 and Conacyt-Ciencia Básica

22 Adrián Ochoa Leyva, PhD Instituto de Biotecnología UNAM Instituto de Biotecnología, UNAM. Av. Universidad #2001, Col. Chamilpa C.P Cuernavaca, Morelos. Instituto Nacional de Medicina Genómica (INMEGEN). Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F. C.P Exploring human and animal microbiomes using metagenomics and metatranscriptomics. The advances in experimental methods and the development of high performance bioinformatic tools have substantially improved our understanding of microbial communities associated with human and environmental niches. Many studies have documented that changes in microbial abundance and composition of the microbiome is associated with health and disease. The amount of host DNA varies greatly by sample type, for example samples of sputum tissue contain a large amount of human DNA, sometimes representing even more than 99% of the total DNA. As a result, only a small percentage of the sequence reads from such samples correspond to microbial genomes and consequently a large percentage of sequences are eliminated. Therefore, obtaining sufficient sequence coverage of the metagenomes and metatranscriptomes can become cost prohibitive. Contrarily, the 16S rrna profiling only requires a little amount of sequence to get a reasonable taxonomical census of the microorganisms present in the sample; however, it misses out the determination of gene content. In this talk, we present our recent experimental advances to eliminate human DNA from microbiome samples, obtaining a high deep sequencing coverage of microbial genomes that are present in the sample. We also present our results of 16S rrna gene profiling and DNA/RNA shotgun sequencing data of human and shrimp microbiomes associated to different diseases.

23 Ramón Batista García, BSc Centro de Investigación en Biotecnología UAEM Batista-García R.A. 1,2, Sánchez-Reyes A. 1,2, Casasanero R. 2, Tovar-Herrera O. 3, Sánchez-Carbente M.R. 2, Jackson S. 4, Dobson A. 4, Folch-Mallol J.L. 2 1 Centro de Investigación Dinámica Celular, Univ. Auton. Estado Morelos. 2 Centro de Investigación en Bitecnología, Univ. Auton. Estado Morelos. 3 Centro de Investigación en Biotecnológia, Univ. Auton. Nueva León. 4 Environmental University College Cork, Cork, Ireland. From lignocellulosic genomes (metagenomes) to lignocellulosic genes: trends, challenges and prospects. Lignocellulose is the most abundant biomass on earth and its possibilities to be used for obtaining vast amounts of compounds that are currently obtained from petrol or other fossil sources (natural gas, mineral carbon) have been scarcely exploited. The main reason being that lignocellulose is a complex mixture of polymers whose structural features hinder the access to the monosaccharides, phenolic compounds and acids that compose these polymers. Although microorganisms such as fungi and bacteria can decompose lignocellulose to its monomeric compounds and use them as carbon sources; and even that some of their enzymes and proteins involved in lignocellulose degradation are quite well studied, we are still lacking a comprehensive landscape of how the whole process occurs. It is also true that due to the limitations of culture-based methods to study lignocellulolytic organisms we may be missing some of the key elements that contribute to lignocellulose degradation. In this review we focus on metagenomics approaches to study lignocellulose degradation from structural and functional points of view, which may provide novel insights on this process and help to understand key elements in order to rationally design methods for the extraction of compounds in biomass that could make biorefineries more efficient.

24 Luis Caspeta Guadarrama, PhD Centro de Investigación en Biotecnología UAEM Caspeta L. 1, 2, *, Chen Y. 2, and Nielsen J. 2 Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, MX-62209, Cuernavaca, Morelos, México. Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296, Gothenburg, Sweden. Efficiency in evolutionary trade-offs: a case of thermotolerance in yeasts. An important principle in biological systems that perform multiple tasks is that they always face a fundamental trade-off loss of fitness in non-selective environments, and hence a given phenotype cannot be optimal in all tasks. Here, we show that evolutionary adaptation of Saccharomyces cerevisiae at high temperature improved its fitness within the selective thermal environment and to other stressors, but was accompanied by loss of fitness over cold temperatures of the ancient thermal niche. Seven thermotolerant yeast strains (TTSs) selected from adaptive laboratory evolution experiments displaced their thermal niche to higher temperatures. Consequently, their optimal and maximum growth temperatures were increased by about 3 C, However, they showed a growth trade-off at temperatures below 34 C. Our computational analysis of physical properties of proteins from the entire S. cerevisiae s proteome suggested that the lethal temperature for yeast is around 49 C, since a large fraction of them denature above this temperature. This analysis complemented with a cdnamicroarray analysis suggested that the number of gene functions required for replication diminished in the TTSs compared with the ancestral strain. This seems to be an essential attribute for acquiring thermotolerance and also explains the reduction of yeast functions associated with loss of respiration capacity, which caused the growth trade-off. This was due to the fact that glycerol was overproduced in TTSs reducing biomass yields. Glycerol overproduction and changes in sterol metabolism were associated with improved tolerance of the TTSs to high concentrations of ethanol and glucose, and elevated osmolarity. Our study shows that thermal adaptation of yeast improve tolerance to high temperature and other stressful conditions whereas caused growth trade-offs at ancestral cold temperatures.

25 Osbaldo Resendis Antonio, PhD Instituto Nacional de Medicina Genómica Head of the Human Systems Biology Lab. RAI-UNAM & Instituto Nacional de Medicina Genomica (INMEGEN). México. Systems Biology and the challenges for elucidating the role of biological networks in cancer. Systems Biology is an emergent science whose main objective is to understand and predict the phenotype of a microorganism through the parallel analysis of high throughput data and computational modeling. This systemic, integrative and quantitative description is a new paradigm in genome sciences that contribute to understand the metabolic profile supporting the phenotype in a variety of organism, ranging from the bacteria to the study of metabolic alterations in human diseases. Given the multi-factorial nature of cancer, uncovering its metabolic alterations and evaluating their implications is a major challenge in biomedical sciences that will help in the optimal design of personalized treatments. The advance of high-throughput technologies opens an invaluable opportunity to monitor the activity at diverse biological levels and elucidate how cancer originates, evolves and responds under drug treatments. To this end, researchers are confronted with two fundamental questions: how to interpret high-throughput data and how this information can contribute to the development of personalized treatment in patients. A variety of schemes in systems biology have been suggested to characterize the phenotype states associated with cancer by utilizing computational modeling and high-throughput data. These theoretical schemes are distinguished by the level of complexity of the biological mechanisms that they represent and by the computational approaches used to simulate them. Notably, these theoretical approaches in combination with genome scale metabolic reconstructions have provided a proper framework to explore some distinctive metabolic mechanisms observed in cancer cells, such as the Warburg effect. In this talk I will present some formalisms that can serve as a platform to: 1) integrate and interpret high-throughput data; 2) generate biological hypothesis about their metabolic activity; and 3) design experiments to assess the genotype-phenotype relationship. Given the overwhelming complexity in cancer, multidisciplinary approaches are required to construct the bases of a systemic and personalized medicine, which remains as a fundamental task in the medicine of this century.

26 María Angélica Santana Calderón, PhD Otoniel Rodríguez Jorge, MSc Centro de Investigación en Dinámica Celular UAEM Transcriptomic and epigenetic analysis on human neonate t cells. Neonates are highly susceptible to infections by intracellular pathogens, which are a major cause of infant morbidity and mortality. T cells are responsible for the adequacy of adaptive immunity and immunological memory. We evaluated the global gene expression in adult and neonatal CD8 T cells by means of microarray technology. We found that human neonatal CD8 T cells, as compared to adult lymphocytes, had a distinctive pattern of gene transcription, characterized by a lower expression of genes involved in TCR signalling and cytotoxicity and a high expression of genes involved in cell cycle and innate immunity. Functional studies corroborated that neonatal CD8 T cells are less cytotoxic, transcribe antimicrobial peptides and produce reactive oxygen species. These properties could explain the high sensitivity of neonates to intracellular pathogen infections and outline novel functions of neonatal CD8 T cells. Taking advantage of the data from the BLUEPRINT and ROADMAP consortiums for adult and neonatal CD4 T cells, we analyzed ChIP-seq data from epigenetic marks and generated a model of the chromatin states to substract and annotate the regions corresponding to active promoters and enhancers. We also analyzed microarray and RNA-seq data to find the differentially expressed genes. Together, these analyses revealed that neonatal CD4 T cells too have a low expression of genes involved in TCR and cytokine signaling and a high expression of genes involved in cell cycle, glycolysis and genes encoding antimicrobial peptides. Our current investigations combine advanced experimental and computational approaches to extend current neonatal and adult CD4 and CD8 T cell transcriptomic and epigenomic maps to generate a comprehensive and predictive computational model for T cell receptor signalling in neonatal CD4+ and CD8+ T cells.

27 Juan Miranda Ríos, PhD Instituto de Investigaciones Biomédicas UNAM Miranda-Ríos J, García-Segura L, Abreu-Goodger C, Hernández-Mendoza A, Dimitrova Dinkova TD, Padilla-Noriega L, Pérez-Andrade ME. Unidad de Genética de la Nutrición, Depto. Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, UNAM e Instituto Nacional de Pediatría. Av IMAN #1, Torre de Investigación INP, 4to piso. Coyoacán, CP , tel: , fax: Starvation-responsive micrornas of Caenorhabditis elegans. Introduction. MicroRNAs are non-coding RNAs of ~22 nucleotides in length that regulate gene expression by binding to the 3 UTR of their target mrnas, inhibiting their translation and affecting their stability. mirna s expression is highly regulated during development and a variety of stress conditions. In nature, animals normally experience feast or famine conditions. Our objective was to identify, by deep sequencing, which of the known 302 mirnas of C. elegans was involved in the response to starvation. Methodology. C. elegans early L4 larvae were subjected to fasting for a period of 12-hr. mirna s expression was evaluated by RNA-seq using an Illumina platform. Some of the mirna s and their targets expression was validated by qrt-pcr. Results and conclusions. We showed that by subjecting C. elegans early L4 larvae to a 12-hr starvation period produced worms that are shorter and thinner than well-fed worms, with a decline in lipid accumulation, reduced progeny, diminished gonad size, and an increased life span. Our results showed that 14 mirnas were upregulated, while 2 mirnas were downregulated in 12-hr starved vs well-fed early L4 larvae. A prediction of the targets that were up(down)regulated showed that they are implicated in metabolic and developmental processes. MiRNAs of the family mir-35-3p/mir-41-3p were upregulated 6-20 fold under starvation conditions. Additionally, we showed that the expression of gld-1, whose product is important in oogenesis, and a validated target of the mir-35 family, was down regulated in starvation. The mrna abundance of another target of the mir-35 family, the cell cycle regulator lin-23, was found to be unchanged

28 during starvation. In conclusion, fasting produced changes in the genetic and developmental programs of the worm that are in part mediated by mirnas. Funding was provided by Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica (PAPIIT), Dirección General de Asuntos del Personal Académico (DGAPA), Universidad Nacional Autónoma de México, grants IN and IN203514, and Fondos Federales Instituto Nacional de Pediatría, grant 036/2015.

29 Pablo Vinuesa Fleischmann, PhD Centro de Ciencias Genómicas UNAM Pablo Vinuesa 1 and Bruno Contreras-Moreira 2 1 Centro de Ciencias Genómicas-UNAM, Cuernavaca, Mor. Mexico. 2 Estación Experimental Aula Dei, CSIC, Zaragoza, Spain Analyzing the pan-genome of environmental multidrug- resistant Stenotrophomonas strains using the GET_HOMOLOGUES software package. Background: In recent years we have developed the open-source GET- HOMOLOGUES software package to define robust core- and pan-genomes using any combination of three clustering algorithms. The granularity of the clusters can be finetuned by a user-configurable filtering strategy based on a combination of blastp pairwise alignment parameters, hmmscan-based scanning of Pfam domain composition of the proteins in each cluster, and a partial synteny criterion. The package contains a number of auxiliary scripts that can be used to fit exponential and binomial mixture models to estimate core-and pan-genome sizes, compute pan-genome trees from the pan-genome matrix using a parsimony criterion, analyze and graphically represent the pan- genome structure, identify lineage-specific gene families and compute Average Nucleotide Identity (ANI) values between pairs of genomes using the results from blastn searches on CDSs. The software package, license, and detailed user manual can be downloaded for free for academic use from two mirrors: and Methods: WGS genome was performed on a MiSeq run with v3 chemistry (PE, 2x300). De-novo assembly, gene-calling and annotation were performed with in-house pipelines and comparative pan-genomics performed with GET_HOMOLOGUES. Results: In this work we do a pan-genome analysis of 27 newly sequenced Stentrophomonas spp. genomes (24 S. maltophilia, 2 S. acidaminiphila and 1 S. humilike strains), focusing on the roles of antibiotic resistance genes (ARGs) and efflux pumps (EPs) in multidrug resistance (MDR). We isolated the strains from different environmental sources in Morelos, Mexico. Strains from clean rivers had a mean of ARGs/genome (median 1, range: 1-2), while those from contaminated ones had a mean of ARGs/genome (median 3, range 2-9,). A consensus core genome of 1225 clusters was computed, which contains 9 proteins involved in MDR and EPs. The

30 consensus pan-genome contained clusters, which included 29 EP proteins as part of the large accessory genome. We identified potentially novel MFS, MATE and RND efflux systems, as suggested by phylogenomic and structure modeling analyses. Conclusion: We have more than tripled the number of high quality genomes available for Stenotrophomonas, including 2 species not previously sequenced. We found a plethora of ARGs and EPs not previously reported for the genus and show that the MDR phenotype depends on both types of genes, in a species-specific manner. Acknowledgements: We gratefully thank PAPIIT UNAM IN and CONACyT México for financial support.

31 POSTERS ABSTRACTS EVALUATION OF METHODS FOR QUANTITATIVE ANALYSIS OF MICRORNAs IN Brachypodium distachyon UNDER WATER STRESS Flores-Herrerías A 1., Ríos-Villanueva R.A 1., Peña-Castro J.M 1., Barrera-Figueroa B.E. 1 1 Laboratorio de Biotecnología Vegetal, Instituto de Biotecnología, Universidad del Papaloapan, campus Tuxtepec. Av. Circuito Central No. 200, Col. Parque Industrial. Tuxtepec, Oax. C.P Tel. 287(87) alynherrerias@gmail.com Introduction Next-generation sequencing and genome-wide analysis is a powerful tool for the discovery of microrna expression in plants. Still, additional expression assays of individual micrornas are needed in order validate and confirm the results obtained from next-generation sequencing. There exist at least three techniques for quantitative analysis of micrornas: Stem-Loop, Poly (A) tailing-based, and adaptor-mediated qpcr. Methodology In this work we designed a TaqMan assay to compare the classic Stem-Loop (SL), Spoly(T) (SPT) strategy and adaptor-mediated (AL) quantitative PCR methods. First, the methods were tested using a synthetic RNA oligonucleotide at concentrations ranging from 10 to μm. In a second assay, mir159 and mir156 were directly tested in dilutions of total RNA from B. distachyon. Results In the first assay, SL and SPT showed the best performance with a wide dynamic range along the concentrations tested. The AL method displayed profiles that did not correlated with synthetic RNA oligonucleotide concentration. Nonetheless, all methods produced a single product when analyzed by electrophoresis. In the second assay, AL method failed to detect mir156 and mir159. Consistent with results of the first assay, SL and SPT detected both mirnas efficiently, but SL showed higher sensitivity compared to SPT. These methods are being applied for quantitative analysis of four micrornas in B. distachyon under water stress.