205 research outputs found
Assessing the impact of alternative splicing on the diversity and evolution of the proteome in plants
No full text Splicing is one of the key processing steps during the maturation of a gene’s primary transcript into the mRNA molecule used as a template for protein production. Splicing involves the removal of segments called introns and re-joining of the remaining segments called exons. It is by now well established that not always the same segments are removed from a gene’s primary transcript during the splicing process. The consequence of this splicing variation, termed Alternative Splicing (AS), is that multiple distinct mature mRNA molecules can be produced from a single gene. One of the two biological roles that are ascribed to AS is that of a mechanism which enables an organism to produce multiple functionally distinct proteins from a single gene. Alternatively, AS can serve as a means for controlling gene expression at the post-transcriptional level. Although many clear examples have been reported for both roles, the extent to which AS increases the functional diversity of the proteome, regulates gene expression or simply reflects noise in splicing machinery is not well known. Determining the full functional impact of AS by designing and performing wet-lab experiments for all AS events is unfeasible and bioinformatics approaches have therefore widely been used for studying the impact of AS at a genome-wide scale. In this thesis four bioinformatics studies are presented that were aimed at determining the extent to which AS is used in plants as a mechanism for producing multiple distinct functional proteins from a single gene. Each chapter uses a different method for analyzing specific properties of AS. Under the premise that functional genetic features are more likely to be conserved than non-functional ones, AS events that are present in two or more species are more likely to be biologically relevant than those that are confined to a single species. In chapter 2 we analyzed the conservation of AS by performing a comparative analysis between three divergent plant species. The results of that study indicated that the vast majority of AS events does not persist over long periods of evolution. We concluded, based on this lack of conservation, that AS only has a limited impact on the functional diversity of the proteome in plants. Following this conclusion, it can hypothesized that the variation that AS induces at the transcriptome level is not likely to be manifested at the protein level. In chapter 3 we tested this hypothesis by analyzing two independent proteomics datasets. This type of data can be used to directly identify proteins present in a biological sample. Our results indicated that the variation induced by AS at the transcriptome level is also manifested at the protein level. We concluded that either many AS events have a confined species-specific (not conserved) function or simply produce protein variants that are stable enough to escape rapid turn-over. Another method for determining whether AS increases the functional diversity of the proteome is by determining whether protein sequence variations that are typically induced by AS are common within the plant kingdom. We found (chapter 4) that this is not the case in plants and concluded that novel functions do not frequently arise through AS. We also found that most of the AS-induced variation is lost, similarly as for redundant gene copies, within a very short evolutionary time period. One limitation of genome-wide analyses is that these capture only the more general patterns. However, the functional impact of AS can be very different in different genes or gene-families. In order fully assess the functional impact of AS, it is therefore important to also study the process within the functional context of individual genes or gene families. In chapter 5 we demonstrated this concept by performing a detailed analysis of AS within the MADS-box gene family. We were able to provide clues as to how AS might impact the protein-protein interaction capabilities of individual MADS proteins. Some of our predictions were supported by experimental evidence. We further showed how AS can serve as an evolutionary mechanism for experimenting with novel functions (novel interactions) without the explicit loss of existing functions. The overall conclusion, based on the performed analyses is as follows: AS primarily is a consequence of noise in the splicing machinery and results in an increased diversity of the proteome. However, only a small fraction of the proteins resulting from AS will have beneficial functions and are subsequently selected for during evolution. The large remaining fraction is, similarly as for redundant gene-copies, lost within a very short evolutionary time period after its emergence. </p
Escherichia coli Raw sequence reads: Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution
No full textThe Illumina sequencing data associated with the study: "Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution" by Martijn Schenk, Mark P. Zwart, Sungmin Hwang, Philip Reulens, Edouard Severing, Joachim Krug, and Arjan de Visser, are provided in this project. The different SRAs contain the sequencing data for both clones and metapopulation. Note that there sequencing data for 4 starting clones (clones 1, 2, 3 and 5), as sequencing failed for starting clone 4 and these data could not be used in the analysis
Escherichia coli Raw sequence reads: Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution
No full textThe Illumina sequencing data associated with the study: "Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution" by Martijn Schenk, Mark P. Zwart, Sungmin Hwang, Philip Reulens, Edouard Severing, Joachim Krug, and Arjan de Visser, are provided in this project. The different SRAs contain the sequencing data for both clones and metapopulation. Note that there sequencing data for 4 starting clones (clones 1, 2, 3 and 5), as sequencing failed for starting clone 4 and these data could not be used in the analysis
Are failproof banking systems feasible? Desirable?
No full textIn recent years, instability of the banking system has returned as a major problem in many countries, particularly in the developing world. In many cases, this instability has been so threatening to financial intermediation and the functioning of the payments system that governments have felt compelled to intervene and restructure banks, often at considerable cost to the public budget. One response to these problems has been a proposal to create failproof banking systems - to radically transform the structure, priorities, and operation of the banking and financial system. Banks would be limited to issuing deposits, holding essentially riskless portfolios, and operating the payments system. To minimize the resulting disruptions to the financial system, banks would be authorized (and encouraged) to set up holding companies and then transfer to holding company affiliates all the functions - including lending - that banks would no longer be permitted to perform. So while the failproof banking proposal would severely restrict the activity of banks, it would not restrict the activities of banking organizations that convert to a holding company form of organization. This proposal would produce major public benefits. It would assure a nation of a smoothly functioning banking and payments system, would substantially reduce the resources committed to banking supervision, would prevent bank-type regulation from expanding to the rest of the financial system, and would place banking and nonbanking organizations on a level playing field for the financial activities in which they compete. There are two major problems with the proposal. First, it might be difficult to implement because of too few riskless assets in a nation's financial system. (The author suggests several modifications that would alleviate this problem in some countries.) Second, the proposal might hurt the financial market by: (a) increasing interest rates for higher-risk borrowers, forcing them out of the market; and (b) transfering greater risk to the nonbank sector of the financial system, making it more susceptible to crisis. Although the proposal would benefit developing countries (more prone to banking instability) more than industrial countries, it would also be more difficult to implement in developing countries. And the adverse effects of the proposal would be felt more severely in the financial markets of developing countries than in industrial countries, which have deeper, more responsive financial markets.Banks&Banking Reform,Financial Intermediation,Financial Crisis Management&Restructuring,Banking Law,Settlement of Investment Disputes
Assessing the contribution of alternative splicing to proteome diversity in <it>Arabidopsis thaliana </it>using proteomics data
No full textAbstract Background Large-scale analyses of genomics and transcriptomics data have revealed that alternative splicing (AS) substantially increases the complexity of the transcriptome in higher eukaryotes. However, the extent to which this complexity is reflected at the level of the proteome remains unclear. On the basis of a lack of conservation of AS between species, we previously concluded that AS does not frequently serve as a mechanism that enables the production of multiple functional proteins from a single gene. Following this conclusion, we hypothesized that the extent to which AS events contribute to the proteome diversity in Arabidopsis thaliana would be lower than expected on the basis of transcriptomics data. Here, we test this hypothesis by analyzing two large-scale proteomics datasets from Arabidopsis thaliana. Results A total of only 60 AS events could be confirmed using the proteomics data. However, for about 60% of the loci that, based on transcriptomics data, were predicted to produce multiple protein isoforms through AS, no isoform-specific peptides were found. We therefore performed in silico AS detection experiments to assess how well AS events were represented in the experimental datasets. The results of these in silico experiments indicated that the low number of confirmed AS events was the consequence of a limited sampling depth rather than in vivo under-representation of AS events in these datasets. Conclusion Although the impact of AS on the functional properties of the proteome remains to be uncovered, the results of this study indicate that AS-induced diversity at the transcriptome level is also expressed at the proteome level.</p
Arabidopsis thaliana ambient temperature responsive lncRNAs
No full textBackground: Long non-coding RNAs (lncRNAs) have emerged as new class of regulatory molecules in animals where they regulate gene expression at transcriptional and post-transcriptional level. Recent studies also identified lncRNAs in plant genomes, revealing a new level of transcriptional complexity in plants. Thousands of lncRNAs have been predicted in the Arabidopsis thaliana genome, but only a few have been studied in depth. Results: Here we report the identification of Arabidopsis lncRNAs that are expressed during the vegetative stage of development in either the shoot apical meristem or in leaves. We found that hundreds of lncRNAs are expressed in these tissues, of which 50 show differential expression upon an increase in ambient temperature. One of these lncRNAs, FLINC, is down-regulated at higher ambient temperature and affects ambient temperature-mediated flowering in Arabidopsis. Conclusion: A number of ambient temperature responsive lncRNAs were identified with potential roles in the regulation of temperature-dependent developmental changes, such as the transition from the vegetative to the reproductive (flowering) phase. The challenge for the future is to characterize the biological function and molecular mode of action of the large number of ambient temperature-regulated lncRNAs that have been identified in this study.</p
Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species
No full textGenome-wide landscapes of transcription factor (TF) binding sites (BSs) diverge during evolution, conferring species-specific transcriptional patterns. The rate of divergence varies in different metazoan lineages but has not been widely studied in plants. We identified the BSs and assessed the effects on transcription of FLOWERING LOCUS C (FLC) and PERPETUAL FLOWERING 1 (PEP1), two orthologous MADS-box TFs that repress flowering and confer vernalization requirement in the Brassicaceae species Arabidopsis thaliana and Arabis alpina, respectively. We found that only 14% of their BSs were conserved in both species and that these contained a CArG-box that is recognized by MADS-box TFs. The CArG-box consensus at conserved BSs was extended compared with the core motif. By contrast, species-specific BSs usually lacked the CArG-box in the other species. Flowering-time genes were highly over-represented among conserved targets, and their CArG-boxes were widely conserved among Brassicaceae species. Cold-regulated (COR) genes were also overrepresented among targets, but the cognate BSs and the identity of the regulated genes were usually different in each species. In cold, COR gene transcript levels were increased in flc and pep1-1 mutants compared with WT, and this correlated with reduced growth in pep1-1. Therefore, FLC orthologs regulate a set of conserved target genes mainly involved in reproductive development and were later independently recruited to modulate stress responses in different Brassicaceae lineages. Analysis of TF BSs in these lineages thus distinguishes widely conserved targets representing the core function of the TF from those that were recruited later in evolution.Fil: Mateos, Julieta Lisa. Max Planck Institute Fur Zuchtungsforschung; Alemania. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Tilmes, Vicky. Max Planck Institute Fur Zuchtungsforschung; AlemaniaFil: Madrigal, Pedro. Polish Academy of Sciences; ArgentinaFil: Severing, Edouard. Max Planck Institute Fur Zuchtungsforschung; AlemaniaFil: Richter, René. Max Planck Institute Fur Zuchtungsforschung; AlemaniaFil: Rijkenberg, Colin W.M.. Max Planck Institute Fur Zuchtungsforschung; AlemaniaFil: Krajewski, Pawel. Polish Academy of Sciences; ArgentinaFil: Coupland, George. Max Planck Institute Fur Zuchtungsforschung; Alemani
Gibberellins Act Downstream of Arabis PERPETUAL FLOWERING1 to Accelerate Floral Induction during Vernalization
No full textRegulation of flowering by endogenous and environmental signals ensures that reproduction occurs under optimal conditions to maximize reproductive success. Involvement of the growth regulator gibberellin (GA) in the control of flowering by environmental cues varies among species. Arabis alpina Pajares, a model perennial member of the Brassicaceae, only undergoes floral induction during vernalization, allowing definition of the role of GA specifically in this process. The transcription factor PERPETUAL FLOWERING1 (PEP1) represses flowering until its mRNA levels are reduced during vernalization. Genome-wide analyses of PEP1 targets identified genes involved in GA metabolism and signaling, and many of the binding sites in these genes were specific to the A. alpina lineage. Here, we show that the pep1 mutant exhibits an elongated-stem phenotype, similar to that caused by treatment with exogenous GA, consistent with PEP1 repressing GA responses. Moreover, in comparison with the wild type, the pep1 mutant contains higher GA4 levels and is more sensitive to GA prior to vernalization. Upon exposure to cold temperatures, GA levels fall to low levels in the pep1 mutant and in wild-type plants, but GA still promotes floral induction and the transcription of floral meristem identity genes during vernalization. Reducing GA levels strongly impairs flowering and inflorescence development in response to short vernalization treatments, but longer treatments overcome the requirement for GA. Thus, GA accelerates the floral transition during vernalization in A. alpina, the down-regulation of PEP1 likely increases GA sensitivity, and GA responses contribute to determining the length of vernalization required for flowering and reproduction.Fil: Tilmes, Vicky. Max-planck-institute For Plant Breeding Research; AlemaniaFil: Mateos, Julieta Lisa. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Madrid, Eva. Max-planck-institute For Plant Breeding Research; AlemaniaFil: Vincent, Coral. Max-planck-institute For Plant Breeding Research; AlemaniaFil: Severing, Edouard. Max-planck-institute For Plant Breeding Research; AlemaniaFil: Carrera, Esther. Universidad Politécnica de Valencia; EspañaFil: López Díaz, Isabel. Universidad Politécnica de Valencia; EspañaFil: Coupland, George. Max-planck-institute For Plant Breeding Research; Alemani
Cortical microtubule orientation in Arabidopsis thaliana root meristematic zone depends on cell division and requires severing by katanin
No full textBackground: Transverse cortical microtubule orientation, critical for anisotropic cell expansion, is established in the meristematic root zone. Intending to elucidate the possible prerequisites for this establishment and factors that are involved, microtubule organization was studied in roots of Arabidopsis thaliana, wild‑type and the p60‑katanin mutants fra2, ktn1‑2 and lue1. Transverse cortical microtubule orientation in the meristematic root zone has proven to persist under several regimes inhibiting root elongation. This persistence was attributed to the constant moderate elongation of meristematic cells, prior to mitotic division. Therefore, A. thaliana wild‑type seedlings were treated with aphidicolin, in order to prevent mitosis and inhibit premitotic cell elongation. Results: In roots treated with aphidicolin for 12 h, cell divisions still occurred and microtubules were transverse. After 24 and 48 h of treatment, meristematic cell divisions and the prerequisite elongation ceased, while microtubule orien‑ tation became random. In meristematic cells of the p60‑katanin mutants, apart from a general transverse microtubule pattern, cortical microtubules with random orientation were observed, also converging at several cortical sites, in contrast to the uniform transverse pattern of wild‑type cells. Conclusion: Taken together, these observations reveal that transverse cortical microtubule orientation in the meris‑ tematic zone of A. thaliana root is cell division‑dependent and requires severing by katanin. © The Author(s) 2018. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated
Bank holding companies : a better structure for conducting universal banking?
No full textBanking systems in many countries have become increasingly unstable in recent years. At the same time, market forces have pushed banks to expand into a variety of universal banking activities without impairing the stability of the banking system. The basic bank holding company proposal contains three major elements : first, any bank that wants to operate as a universal bank must first form a holding company and then conduct all riskier activities in holding company units rather than directly in the bank. The bank would continue to engage in traditional banking activities that involve the usual level of risk; second, the government would develop laws and regulations designed as safeguards to insulate the bank from any financial problems that might occur in holding company affiliates of the bank; and lastly bank regulatory authorities would impose little or no supervision on holding company units. The use of the bank holding company device to conduct universal banking activities can promise important public benefits including : 1) a sounder commercial banking system; 2) less banking regulation; and 3) greater competitive equality between banking and nonbanking units.Microfinance,Banks&Banking Reform,Financial Intermediation,Private Participation in Infrastructure,Small Scale Enterprise
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