The bromeliad family comprises about 3,000 species distributed in 58 genera and 3 subfamilies: Pitcarnioideae, Bromelioideae and Tillandsioideae. The increasing demand of the market has been responsible for increasing the production and sale of bromeliads. However the illegal extraction is still dramatically reducing existing species. This fact, coupled with the devastation of Brazilian ecosystems, has caused irreparable losses in diversity. Considering this fact, have a basis with stored genetic material for future studies is very important. The main reason for the establishment and maintenance of a germplasm bank is to store and make available germplasm and provide information regarding certain accessions. The aim of the work was to perform the molecular characterization of accessions of native bromeliads prospected in Sergipe State, using tools such as RAPD and ISSR molecular markers and flow cytometry. The collections were performed in four counties of the Sergipe state (Itabaiana, Frei Paulo, Simão Dias e Poço Redondo), whose locations were mapped with the use of a GPS and the individuals were kept in a greenhouse, composing a Active Germplasm Bank (AGB). For molecular analyzes young leaves were collected and used for DNA extraction. Eleven ISSR primers and 13 RAPD primers were used to characterize the prospected accessions. Analyses by flow cytometry were performed for the determination of DNA content, using young leaves and extraction of nuclei was performed following the method of Dolezel. ISSR and RAPD markers detected large genetic variability among the accessions of the AGB. The estimation of the DNA content obtained by flow cytometry of the bromeliad accessions collected in four municipalities of Sergipe State allowed the distinction of two groups (group 1 = 1,59 pg and group 2 = 1,057 pg). / A família bromeliácea compreende aproximadamente 3.000 especies, distribuídas em 58 gêneros e 3 subfamílias: Pitcarnioideae, Bromelioideae e Tillandsioideae. A crescente demanda de mercado tem sido responsável pelo aumento da produção e comercialização das bromélias. No entanto o extrativismo ilegal ainda existente está reduzindo drasticamente as espécies. Esse fato, somado à devastação dos ecossistemas brasileiros, tem causado perdas irreparáveis na diversidade. Diante desse fato, ter uma base com material genético guardado para futuros estudos é muito importante. A principal razão para o estabelecimento e a manutenção de um banco de germoplasma é armazenar e disponibilizar germoplasma e prover informações a respeito de determinado acesso. O objetivo do trabalho foi realizar a caracterização molecular dos acessos de bromélias nativas prospectadas no Estado de Sergipe, empregando ferramentas como marcadores moleculares RAPD, ISSR e citometria de fluxo. As coletas foram realizadas em quatro municípios do Estado de Sergipe (Itabaiana, Frei Paulo, Simão Dias e Poço Redondo), cujos locais foram mapeados com o auxílio de GPS e os indivíduos foram conservados em casa de vegetação, compondo um Banco Ativo de Germoplasma (BAG). Para as análises moleculares folhas jovens foram coletadas e utilizadas para a extração do DNA. Onze iniciadores ISSR e 13 iniciadores RAPD foram utilizados para a caracterização dos acessos prospectados. As análises por citometria de fluxo foram realizadas para a determinação do conteúdo de DNA, usando folhas jovens e as extrações dos núcleos foram realizadas seguindo o método de Dolezel. Os marcadores ISSR e RAPD detectaram ampla variabilidade genética entre os acessos do BAG. A estimativa do conteúdo de DNA obtido pela citometria de fluxo dos acessos de bromélias coletados nos quatro municípios de Sergipe possibilitou a distinção de dois grupos (grupo 1 = 1,59 pg e grupo 2 = 1,057 pg).

T. aestivum ssp. spelta Iranian type has long been thought to potentially be the direct non-free threshing hexaploid progenitor. I evaluated a RIL population derived from a cross between CS and Iranian spelta accession P503 to identify loci suppressing free-threshabilty in P503. Identification of QTL associated with threshability in region known to harbor the Tg2A gene, and an inactive tg2D allele supported the hypothesis of Iranian spelta being derived from a more recent hybridization between free-threshing hexaploid and emmer wheat. Parastagonospora nodorum is an important fungal pathogen and secretes necrotrophic effectors that evoke cell death. In this research, a DH population segregating for Snn5 was used to saturate Snn5 region of chromosome 4B with molecular markers. The physical distance between Snn5 flanking markers was narrowed to 1.38 Mb with genetic distance of 2.8 cM. The markers developed in this study will provide a strong foundation for map-based cloning of Snn5.

<p dir="ltr">Uncovering the mechanisms of senescence in maize will give us a deeper understanding needed to drive future yield increases. Previous work on senescence response to sink disruption has identified a set of genes and biochemical mechanisms. Still, little is understood about the impact of this phenotype on yield and other commercially relevant traits. Uncovering the genetic basis of senescence in maize and testing the effect of these alleles on yield will provide a mechanistic framework for considering this trait to drive future yield increases.</p><p dir="ltr">Ear removal experiments demonstrated that senescence timing is insensitive to the presence or absence of an ear outside a critical window from 10 to 45 days after pollination. Nitrogen fertilization did not impact the SSRS response measured in the upper canopy. In further characterizing the SSRS phenotype, we have provided a spatial and temporal map of the B73 senescence response to sink disruption from the top of the plant to the ear leaf and discovered that this phenomenon is dose dependent and proportional to the size of the sink across two genotypes and years. This relationship was successfully used to predict kernel numbers and grain weight from spectral leaf properties as early as 4 weeks after pollination using remote sensing under agronomic conditions.</p><p dir="ltr">A population of 343 exPVP inbred lines was evaluated for source-sink regulated senescence and hybrid testcrosses were made for a subset of 200 inbred lines to testers for measurement of yield and ear photometry phenotypes. Source-sink regulated senescence of inbred parents was correlated with the yield of intra-family hybrids but was not generally correlated with the yield of hybrids made from crosses between two heterotic groups. The presence of multiple significant SNP association at the Bonferroni-corrected threshold at loci that are associated both with kernel traits and SSRS suggests shared genetic regulation of two traits that is likely driving the observed trait correlations of SSRS with kernel size and yield.</p><p dir="ltr">The maize nested association mapping (NAM) parents reveal a previously unknown breadth of SSRS phenotypes in the global diversity of maize germplasm. Mapping genes for SSRS in the NAM populations supports previously reported loci with large, dominant effects as well as evidence for previously unreported modifiers that are capable of suppressing the dominant alleles and producing a quantitative distribution in SSRS phenotypes. There are distinct alleles within sub-populations worth further study such as sweetcorn populations with non-senescence responses to sink disruption. A multi-factor analysis for QTL mapping, GWAS, and mutant variant sequencing identified highly significant loci on chromosomes 1 from 30.4Mbp to 35.8Mbp, chromosome 2 from 183.2Mbp to 190.8Mbp, chromosome 4 from 38.2Mbp to 134.8Mbp (crosses a centromere), chromosome 5 from 140.8Mbp to 233.9Mbp, chromosome 8 from 112.5Mbp to 123.8Mbp, and chromosome 8 from 155.7Mbp to 163.9Mbp. Candidate genes co-located with Bonferroni SNP in these regions may contribute to SSRS phenotypes through regulation of autophagy, accumulation of flavonoids, and sequestration of sugar in cell walls as an alternative sink. It is possible that co-regulation of these genes could cause all of them to be involved in the stress response of B73 to sugar accumulation. To find the causal variants for these traits, fine mapping and comparisons of near-isogenic lines will be required to narrow the list of candidate genes. Uncovering the alleles responsible for SSRS in global maize diversity could provide the building blocks for a physiological approach to increasing yields through optimizing the senescence responses to elevated sugar levels during grain-fill.</p>

It has been suggested that organismal complexity correlates with the complexity of gene regulation. Transcriptional control of gene expression is mediated by binding of regulatory proteins to cis-acting sequences on the genome. Hence, it is crucial to identify the chromosomal targets of transcription factors (TFs) to delineate transcriptional regulatory networks underlying gene expression programs. The development of ChIP-chip technology has enabled high throughput mapping of TF binding sites across the genome. However, there are many limitations to the technology including the availability of whole genome arrays for complex organisms such human or mouse. To circumvent these limitations, we developed the Sequence Tag Analysis of Genomic Enrichment (STAGE) methodology that is based on extracting short DNA sequences or “tags” from ChIP-enriched DNA. With improvements in sequencing technologies, we applied the recently developed ChIP-Seq technique i.e. ChIP followed by ultra high throughput sequencing, to identify binding sites for the TF E2F4 across the human genome. We identified previously uncharacterized E2F4 binding sites in intergenic regions and found that several microRNAs are potential E2F4 targets. Binding of TFs to their respective chromosomal targets requires access of the TF to its regulatory element, which is strongly influenced by nucleosomal remodeling. In order to understand nucleosome remodeling in response to transcriptional perturbation, we used ultra high throughput sequencing to map nucleosome positions in yeast that were subjected to heat shock or were grown normally. We generated nucleosome remodeling profiles across yeast promoters and found that specific remodeling patterns correlate with specific TFs active during the transcriptional reprogramming. Another important aspect of gene regulation operates at the post-transcriptional level. MicroRNAs (miRNAs) are ~22 nucleotide non-coding RNAs that suppress translation or mark mRNAs for degradation. MiRNAs regulate TFs and in turn can be regulated by TFs. We characterized a TF-miRNA network involving the oncofactor Myc and the miRNA miR-22 that suppresses the interferon pathway as primary fibroblasts enter a stage of rapid proliferation. We found that miR-22 suppresses the interferon pathway by inhibiting nuclear translocation of the TF NF-kappaB. Our results show how the oncogenic TF Myc cross-talks with other TF regulatory pathways via a miRNA intermediary. / text

Promoter region is the key regulatory region, which enables the gene to be transcribed or repressed by anchoring RNA polymerase and other transcription factors, but it is difficult to determine experimentally. Hence an in silico identification of promoters is crucial in order to guide experimental work and to pin point the key region that controls the transcription initiation of a gene. Analysis of various genome sequences in the vicinity of experimentally identified transcription start sites (TSSs) in prokaryotic as well as eukaryotic genomes had earlier indicated that they have several structural features in common, such as lower stability, higher curvature and less bendability, when compared with their neighboring regions. In this thesis work, the variation observed for these DNA sequence dependent structural properties have been used to identify and delineate promoter regions from other genomic regions. Since the number of bacterial genomes being sequenced is increasing very rapidly, it is crucial to have procedures for rapid and reliable annotation of their functional elements such as promoter regions, which control the expression of each gene or each transcription unit of the genome. The thesis work addresses this requirement and presents step by step protocols followed to get a generic method for promoter prediction that can be applicable across organisms. The each paragraph below gives an overall idea about the thesis organization into chapters. An overview of prokaryotic transcriptional regulation, structural polymorphism adapted by DNA molecule and its impact on transcriptional regulation has been discussed in introduction chapter of this thesis (chapter 1). Standardization of promoter prediction methodology - Part I Based on the difference in stability between neighboring upstream and downstream regions in the vicinity of experimentally determined transcription start sites, a promoter prediction algorithm has been developed to identify prokaryotic promoter sequences in whole genomes. The average free energy (E) over known promoter sequences and the difference (D) between E and the average free energy over the random sequence generated using the downstream region of known TSS (REav) are used to search for promoters in the genomic sequences. Using these cutoff values to predict promoter regions across entire E. coli genome, a reliability of 70% has been achieved, when the predicted promoters were cross verified against the 960 transcription start sites (TSSs) listed in the Ecocyc database. Reliable promoter prediction is obtained when these genome specific threshold values were used to search for promoters in the whole E. coli genome sequence. Annotation of the whole E. coli genome for promoter region has been carried out with 49% accuracy. Reference Rangannan, V. and Bansal, M. (2007) Identification and annotation of promoter regions inmicrobial genome sequences on the basis of DNA stability. J Biosci, 32, 851-862. Standardization of promoter prediction methodology - Part II In this chapter, it has been demonstrated that while the promoter regions are in general less stable than the flanking regions, their average free energy varies depending on the GC composition of the flanking genomic sequence. Therefore, a set of free energy threshold values (TSS based threshold values), from the genomic DNA with varying GC content in the vicinity of experimentally identified TSSs have been obtained. These threshold values have been used as generic criteria for predicting promoter regions in E. coli and B. subtilis and M. tuberculosis genomes, using an in-house developed tool ‘PromPredict’. On applying it to predict promoter regions corresponding to the 1144 and 612 experimentally validated TSSs in E. coli (genome %GC : 50.8) and B. subtilis (genome %GC : 43.5) sensitivity of 99% and 95% and precision values of 58% and 60%, respectively, were achieved. For the limited data set of 81 TSSs available for M. tuberculosis (65.6% GC) a sensitivity of 100% and precision of 49% was obtained. Reference Rangannan, V. and Bansal, M. (2009) Relative stability of DNA as a generic criterion for promoter prediction: whole genome annotation of microbial genomes with varying nucleotide base composition. Mol Biosyst, 5, 1758 - 1769. Standardization of promoter prediction methodology - Part III In this chapter, the promoter prediction algorithm and the threshold values have been improved to predict promoter regions on a large scale over 913 microbial genome sequences. The average free energy (AFE) values for the promoter regions as well as their downstream regions are found to differ, depending on their GC content even with respect to translation start sites (TLSs) from 913 microbial genomes. The TSS based cut-off values derived in chapter 3 do not have cut-off values for both extremes of GC-bins at 5% interval. Hence, threshold values have been derived from a subset of translation start sites (TLSs) from all microbial genomes which were categorized based on their GC-content. Interestingly the cut-off values derived with respect to TSS data set (chapter 3) and TLS data set are very similar for the in-between GC-bins. Therefore, TSS based cut-off values derived in chapter 2 with the TLS based cut-off values have been combined (denoted as TSS-TLS based cutoff values) to predict promoters over the complete genome sequences. An average recall value of 72% (which indicates the percentage of protein and RNA coding genes with predicted promoter regions assigned to them) and precision of 56% is achieved over the 913 microbial genome dataset. These predicted promoter regions have been given a reliability level (low, medium, high, very high and highest) based on the difference in its relative average free energy, which can help the users design their experiments with more confidence by using the predictions with higher reliability levels. Reference Rangannan, V. and Bansal, M. (2010) High Quality Annotation of Promoter Regions for 913 Bacterial Genomes. Bioinformatics, 26, 3043-3050. Web applications PromBase : The predicted promoter regions for 913 microbial genomes were deposited into a public domain database called, PromBase which can serve as a valuable resource for comparative genomics study for their general genomic features and also help the experimentalist to rapidly access the annotation of the promoter regions in any given genome. This database is freely accessible for the users via the World Wide Web http://nucleix.mbu.iisc.ernet.in/prombase/. EcoProm : EcoProm is a database that can identify and display the potential promoter regions corresponding to EcoCyc annotated TSS and genes. Also displays predictions for whole genomic sequence of E. coli and EcoProm is available at http://nucleix.mbu.iisc.ernet.in/ecoprom/index.htm. PromPredict : The generic promoter prediction methodology described in previous chapters has been implemented in to an algorithm ‘PromPredict’ and available at http://nucleix.mbu.iisc.ernet.in/prompredict/prompredict.html. Analysing the DNA structural characteristic of prokaryotic promoter sequences for their predominance Sequence dependent structural properties and their variation in genomic DNA are important in controlling several crucial processes such as transcription, replication, recombination and chromatin compaction. In this chapter 6, quantitative analysis of sequences motifs as well as sequence dependent structural properties, such as curvature, bendability and stability in the upstream region of TSS and TLS from E. coli, B. subtilis and M. tuberculosis has been carried out in order to assess their predictive power for promoter regions. Also the correlation between these structural properties and GC-content has been investigated. Our results have shown that AFE values (stability) gives finer discrimination rather than %GC in identifying promoter regions and stability have shown to be the better structural property in delineating promoter regions from non-promoter regions. Analysis of these DNA structural properties has been carried out in human promoter sequences and observed to be correlating with the inactivation status of the X-linked genes in human genome. Since, it is deviating from the theme of main thesis; this chapter has been included as appendix A to the main thesis. General conclusion Stability is the ubiquitous DNA structural property seen in promoter regions. Stability shows finer discrimination for promoter prediction rather than directly using %GC-content. Based on relative stability of DNA, a generic promoter prediction algorithm has been developed and implemented to predict promoter regions on a large scale over 913 microbial genome sequences. The analysis of the predicted regions across organisms showed highly reliable predictive performance of the algorithm.

Indiana University-Purdue University Indianapolis (IUPUI) / The development of new methods to carry out gene transfer has many benefits to several fields, such as gene therapy, agriculture and animal health. The newly established lentiviral vector systems further increase the efficiency of gene transfer dramatically. Some studies have shown that lentiviral vector systems enhance efficiency over 10-fold higher than traditional pronuclear injection. However, the timing for lentiviral vector integration to occur remains unclear. Integrating in different stages of embryogenesis might lead to different integration patterns between tissues. Moreover, in our previous study we found that the vector copy number in transgenic sheep varied, some having one or more copies per cells while other animals having less than one copy per cell suggesting mosaicism. Here I hypothesized that injection of a lentiviral vector into a single cell embryo can lead to integration very early in embryogenesis but can also occur after several cell divisions. In this study, we focus on investigating integration sites in tissues developing from different germ layers as well as extraembryonic tissues to determine when integration occurs. In addition, we are also interested in insertional mutagenesis caused by viral sequence integration in or near gene regions. We utilize linear amplification-mediated polymerase chain reaction (LAM-PCR) and next- generation sequencing (NGS) technology to determine possible integration sites. In this study, we found the evidence based on a series of experiments to support my hypothesis, suggesting that integration event also happens after several cell divisions. For insertional mutagenesis analysis, the closest genes can be found according to integration sites, but they are likely too far away from the integration sites to be influenced. A well-annotated sheep genome database is needed for insertional mutagenesis analysis.

Indiana University-Purdue University Indianapolis (IUPUI) / DNA double strand break (DSB) is one of the most threatening of all types of DNA damages as it leads to a complete breakage of the chromosome. The cell has evolved several mechanisms to repair DSBs, one of which is break-induced replication (BIR). BIR repair of DSBs occurs through invasion of one end of the broken chromosome into a homologous template followed by processive replication of DNA from the donor molecule. BIR is a key cellular process and is implicated in the restart of collapsed replication forks and several chromosomal instabilities. Recently, our lab demonstrated that the fidelity of DNA synthesis associated with BIR in yeast Saccharomyces Cerevisiae is extremely low. The level of frameshift mutations associated with BIR is 1000-fold higher as compared to normal DNA replication. This work demonstrates that BIR stimulates base substitution mutations, which comprise 90% of all point mutations, making them 400-1400 times more frequent than during S-phase DNA replication. We show that DNA Polymerase δ proofreading corrects many of the base substitutions in BIR. Further, we demonstrate that Pif1, a 5’-3’ DNA helicase, is responsible for making BIR efficient and also highly mutagenic. Pif1p is responsible for the majority of BIR mutagenesis not only close to the DSB site, where BIR is less stable but also at chromosomal regions far away from the DSB break site, where BIR is fast, processive and stable. This work further reveals that, at positions close to the DSB, BIR mutagenesis in the absence of Pif1 depends on Rev3, the catalytic subunit of translesion DNA Polymerase ζ. We observe that mutations promoted by Pol ζ are often complex and propose that they are generated by a Pol ζ- led template switching mechanism. These complex mutations were also found to be frequently associated with gross chromosomal rearrangements. Finally we demonstrate that BIR is carried out by unusual conservative mode of DNA synthesis. Based on this study, we speculate that the unusual mode of DNA synthesis associated with BIR leads to various kinds of genomic instability including mutations and chromosomal rearrangements.

Indiana University-Purdue University Indianapolis (IUPUI) / Alzheimer's disease (AD) is the most common form of dementia defined by loss in memory and cognitive abilities severe enough to interfere significantly with daily life activities. Amnestic mild cognitive impairment (MCI) is a clinical condition in which an individual has memory deficits not normal for the individual's age, but not severe enough to interfere significantly with daily functioning. Every year, approximately 10-15% of individuals with MCI will progress to dementia. Currently, there is no treatment to slow or halt AD progression, but research studies are being conducted to identify causes that can lead to its earlier diagnosis and treatment. Genetic variation plays a key role in the development of AD, but not all genetic factors associated with the disease have been identified. Copy number variants (CNVs), a form of genetic variation, are DNA regions that have added genetic material (duplications) or loss of genetic material (deletions). The regions may overlap one or more genes possibly affecting their function. CNVs have been shown to play a role in certain diseases. At the start of this work, only one published study had examined CNVs in late-onset AD and none had examined MCI. In order to determine the possible involvement of CNVs in AD and MCI susceptibility, genome-wide CNV analyses were performed in participants from three cohorts: the ADNI cohort, the NIA-LOAD/NCRAD Family Study cohort, and a unique cohort of clinically characterized and neuropathologically verified individuals. Only participants with DNA samples extracted from blood/brain tissue were included in the analyses. CNV calls were generated using genome-wide array data available on these samples. After detailed quality review, case (AD and/or MCI)/control association analyses including candidate gene and genome-wide approaches were performed. Although no excess CNV burden was observed in cases compared to controls in the three cohorts, gene-based association analyses identified a number of genes including the AD candidate genes CHRFAM7A, RELN and DOPEY2. Thus, the present work highlights the possible role of CNVs in AD and MCI susceptibility warranting further investigation. Future work will include replication of the findings in independent samples and confirmation by molecular validation experiments.

<p dir="ltr">The primary purpose of this thesis is to propose and demonstrate BioGRNsemble, a modular and flexible approach for inferencing gene regulatory networks from RNA-Seq data. Integrating the GENIE3 and GRNBoost2 algorithms, this ensembles-of-ensembles method attempts to balance the outputs of both models through averaging, before providing a trimmed-down gene regulatory network consisting of transcription and target genes. Using a Drosophila Eye Dataset, we were able to successfully test this novel methodology, and our validation analysis using an online database determined over 3500 gene links correctly detected, albeit out of almost 530,000 predictions, leaving plenty of room for improvement in the future.</p>

Genome-wide association studies have greatly improved our understanding of the contribution of common variants to the genetic architecture of complex traits. However, two major limitations have been highlighted. First, common variant associations typically do not identify the causal variant and/or the gene that it is exerting its effect on to influence a trait. Second, common variant associations usually consist of variants with small effects. As a consequence, it is more challenging to harness their translational impact. Association studies of rare variants and complex traits may be able to help address these limitations. Empirical population genetic data shows that deleterious variants are rare. More specifically, there is a very strong depletion of common protein truncating variants (PTVs, commonly referred to as loss-of-function variants) in the genome, a group of variants that have been shown to have large effect on gene function, are enriched for severe disease-causing mutations, but in other instances may actually be protective against disease. This thesis is divided into three parts dedicated to the study of protein truncating variants, their medical relevance, and their functional consequences. First, I present statistical, bioinformatic, and computational methods developed for the study of protein truncating variants and their association to complex traits, and their functional consequences. Second, I present application of the methods to a number of case-control and quantitative trait studies discovering new variants and genes associated to breast and ovarian cancer, type 1 diabetes, lipids, and metabolic traits measured with NMR spectroscopy. Third, I present work on improving annotation of protein truncating variants by studying their functional consequences. Taken together, these results highlight the utility of interrogating protein truncating variants in medical and functional genomic studies.