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BayGO: Bayesian analysis of ontology term enrichment in microarray data

Ricardo Z N Vêncio, Tie Koide, Suely L Gomes, Carlos A de B Pereira
2006 BMC Bioinformatics  
Koide, R.Z.N. Vêncio and S.L.Gomes, submitted).  ... 
doi:10.1186/1471-2105-7-86 pmid:16504085 pmcid:PMC1440873 fatcat:jqjkhmvinrg3rmikksuucan3u4

SpotWhatR: a user-friendly microarray data analysis system

Tie Koide, Silvia M Salem-Izacc, Suely L Gomes, Ricardo Z N Vêncio
2006 Genetics and Molecular Research  
SpotWhatR provides the user with the HTself method (Vencio and Koide, 2005 ).  ...  We refer the interested reader to the original work (Vencio and Koide, 2005) for a detailed explanation on this method.  ... 
pmid:16755501 fatcat:66fhekjzgrdpnfrcloee7jdory

The role of predictive modelling in rationally re-engineering biological systems

Tie Koide, Wyming Lee Pang, Nitin S. Baliga
2009 Nature Reviews Microbiology  
Technologies to synthesize and transplant a complete genome into a cell have opened limitless potential to redesign organisms for complex, specialized tasks. However, large-scale re-engineering of a biological circuit will require systems-level optimization that will come from a deep understanding of operational relationships among all the constituent parts of a cell. The integrated framework necessary for conducting such complex bioengineering requires the convergence of systems and synthetic
more » ... iology. Here, we review the status of these rapidly developing interdisciplinary fields of biology and provide a perspective on plausible venues for their merger. Multidisciplinary approaches in science have always resulted in new ideas, broader and deeper levels of understanding, and of course, controversies. The inception of many modern transformative products and technologies, including drug synthesis 1 and recombinant microbial enzyme factories 2 can be attributed to the merging of, until then, distinct disciplines. With recent advances to deconstruct biological function at a systems scale 3,4 and design biological subcircuits with defined properties 5 we can begin to envision spectacular solutions that combine unique functions that have evolved in organisms from diverse environments. In other words, the stage is set for yet another revolutionary merger of two powerful interdisciplinary fields with fundamentally different but complementary outlooks -synthetic biology and systems biology (FIG. 1 ). A systems biologist aims to model and understand an entire organism by characterizing dynamic environment-dependent functional interrelationships between its constituent parts (for example, genes, RNAs, proteins and metabolites). A synthetic biologist, however, uses well characterized parts that are shaped by natural evolution to construct artificial systems that perform new tasks. These fields are on trajectories that are bound to cross paths and even merge as they begin to inform one another. We envision that systems biology will provide both the
doi:10.1038/nrmicro2107 pmid:19252506 pmcid:PMC2734281 fatcat:bqo77xkgujhcdk4msqnubsvcie

Global Gene Expression Analysis during Germination in the ChytridiomyceteBlastocladiella emersonii

Silvia M. Salem-Izacc, Tie Koide, Ricardo Z. N. Vêncio, Suely L. Gomes
2008 Eukaryotic Cell  
Blastocladiella emersoniiis an aquatic fungus of the Chytridiomycete class. During germination, the zoospore, a motile nongrowing cell, goes through a cascade of morphological changes that culminates with its differentiation into the germling cell, capable of coenocytic vegetative growth. Transcriptome analyses ofB. emersoniicells were carried out during germination induced under various environmental conditions. Microarray data analyzing 3,563 distinctB. emersoniigenes revealed that 26% of
more » ... are differentially expressed during germination in nutrient medium at at least one of the time points investigated. Over 500 genes are upregulated during the time course of germination under those conditions, most being related to cell growth, including genes involved in protein biosynthesis, DNA transcription, energetic metabolism, carbohydrate and oligopeptide transport, and cell cycle control. On the other hand, several transcripts stored in the zoospores are downregulated during germination in nutrient medium, such as genes involved in signal transduction, amino acid transport, and chromosome organization. In addition, germination induced in the presence of nutrients was compared with that triggered either by adenine or potassium ions in inorganic salt solution. Several genes involved in cell growth, induced during germination in nutrient medium, do not show increased expression whenB. emersoniizoospores germinate in inorganic solution, suggesting that nutrients exert a positive effect on gene transcription. The transcriptome data also revealed that most genes involved in cell signaling show the same expression pattern irrespective of the initial germination stimulus.
doi:10.1128/ec.00330-08 pmid:19098129 pmcid:PMC2643612 fatcat:lmsuk7iwzngojbk4zwxvp4pl5y

Integration and visualization of systems biology data in context of the genome

J Christopher Bare, Tie Koide, David J Reiss, Dan Tenenbaum, Nitin S Baliga
2010 BMC Bioinformatics  
High-density tiling arrays and new sequencing technologies are generating rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization and exploration of this data is critical to understanding the regulatory logic encoded in the genome by which the cell dynamically affects its physiology and interacts with its environment. Results: The Gaggle Genome Browser is a cross-platform desktop program for interactively visualizing highthroughput data in the context of the
more » ... enome. Important features include dynamic panning and zooming, keyword search and open interoperability through the Gaggle framework. Users may bookmark locations on the genome with descriptive annotations and share these bookmarks with other users. The program handles large sets of usergenerated data using an in-process database and leverages the facilities of SQL and the R environment for importing and manipulating data. A key aspect of the Gaggle Genome Browser is interoperability. By connecting to the Gaggle framework, the genome browser joins a suite of interconnected bioinformatics tools for analysis and visualization with connectivity to major public repositories of sequences, interactions and pathways. To this flexible environment for exploring and combining data, the Gaggle Genome Browser adds the ability to visualize diverse types of data in relation to its coordinates on the genome. Conclusions: Genomic coordinates function as a common key by which disparate biological data types can be related to one another. In the Gaggle Genome Browser, heterogeneous data are joined by their location on the genome to create information-rich visualizations yielding insight into genome organization, transcription and its regulation and, ultimately, a better understanding of the mechanisms that enable the cell to dynamically respond to its environment.
doi:10.1186/1471-2105-11-382 pmid:20642854 pmcid:PMC2912892 fatcat:myezg3bnsfbwhkjayhtmgwxqja

The Primary Antisense Transcriptome of Halobacterium salinarum NRC-1

João Paulo Pereira de Almeida, Ricardo Z. N. Vêncio, Alan P. R. Lorenzetti, Felipe ten- Caten, José Vicente Gomes-Filho, Tie Koide
2019 Genes  
Antisense RNAs (asRNAs) are present in diverse organisms and play important roles in gene regulation. In this work, we mapped the primary antisense transcriptome in the halophilic archaeon Halobacterium salinarum NRC-1. By reanalyzing publicly available data, we mapped antisense transcription start sites (aTSSs) and inferred the probable 3′ ends of these transcripts. We analyzed the resulting asRNAs according to the size, location, function of genes on the opposite strand, expression levels and
more » ... conservation. We show that at least 21% of the genes contain asRNAs in H. salinarum. Most of these asRNAs are expressed at low levels. They are located antisense to genes related to distinctive characteristics of H. salinarum, such as bacteriorhodopsin, gas vesicles, transposases and other important biological processes such as translation. We provide evidence to support asRNAs in type II toxin–antitoxin systems in archaea. We also analyzed public Ribosome profiling (Ribo-seq) data and found that ~10% of the asRNAs are ribosome-associated non-coding RNAs (rancRNAs), with asRNAs from transposases overrepresented. Using a comparative transcriptomics approach, we found that ~19% of the asRNAs annotated in H. salinarum belong to genes with an ortholog in Haloferax volcanii, in which an aTSS could be identified with positional equivalence. This shows that most asRNAs are not conserved between these halophilic archaea.
doi:10.3390/genes10040280 fatcat:5puvjd4h2fhvzdg4s6wny5nl5y

Development of New Modular Genetic Tools for Engineering the Halophilic Archaeon Halobacterium salinarum

Rafael Silva-Rocha, Marjorie Cornejo Pontelli, Gilvan Pessoa Furtado, Livia Soares Zaramela, Tie Koide, Peter Hohenstein
2015 PLoS ONE  
Our ability to genetically manipulate living organisms is usually constrained by the efficiency of the genetic tools available for the system of interest. In this report, we present the design, construction and characterization of a set of four new modular vectors, the pHsal series, for engineering Halobacterium salinarum, a model halophilic archaeon widely used in systems biology studies. The pHsal shuttle vectors are organized in four modules: (i) the E. coli's specific part, containing a
more » ... 1 origin of replication and an ampicillin resistance marker, (ii) the resistance marker and (iii) the replication origin, which are specific to H. salinarum and (iv) the cargo, which will carry a sequence of interest cloned in a multiple cloning site, flanked by universal M13 primers. Each module was constructed using only minimal functional elements that were sequence edited to eliminate redundant restriction sites useful for cloning. This optimization process allowed the construction of vectors with reduced sizes compared to currently available platforms and expanded multiple cloning sites. Additionally, the strong constitutive promoter of the fer2 gene was sequence optimized and incorporated into the platform to allow high-level expression of heterologous genes in H. salinarum. The system also includes a new minimal suicide vector for the generation of knockouts and/or the incorporation of chromosomal tags, as well as a vector for promoter probing using a GFP gene as reporter. This new set of optimized vectors should strongly facilitate the engineering of H. salinarum and similar strategies could be implemented for other archaea.
doi:10.1371/journal.pone.0129215 pmid:26061363 pmcid:PMC4465625 fatcat:qqxiyneg7raphck2htq7m5l7em

Global gene expression under nitrogen starvation in Xylella fastidiosa: contribution of the σ54 regulon

José F da Silva Neto, Tie Koide, Suely L Gomes, Marilis V Marques
2010 BMC Microbiology  
Xylella fastidiosa, a Gram-negative fastidious bacterium, grows in the xylem of several plants causing diseases such as citrus variegated chlorosis. As the xylem sap contains low concentrations of amino acids and other compounds, X. fastidiosa needs to cope with nitrogen limitation in its natural habitat. Results: In this work, we performed a whole-genome microarray analysis of the X. fastidiosa nitrogen starvation response. A time course experiment (2, 8 and 12 hours) of cultures grown in
more » ... ed medium under nitrogen starvation revealed many differentially expressed genes, such as those related to transport, nitrogen assimilation, amino acid biosynthesis, transcriptional regulation, and many genes encoding hypothetical proteins. In addition, a decrease in the expression levels of many genes involved in carbon metabolism and energy generation pathways was also observed. Comparison of gene expression profiles between the wild type strain and the rpoN null mutant allowed the identification of genes directly or indirectly induced by nitrogen starvation in a σ 54 -dependent manner. A more complete picture of the σ 54 regulon was achieved by combining the transcriptome data with an in silico search for potential σ 54 -dependent promoters, using a position weight matrix approach. One of these σ 54predicted binding sites, located upstream of the glnA gene (encoding glutamine synthetase), was validated by primer extension assays, confirming that this gene has a σ 54 -dependent promoter. Conclusions: Together, these results show that nitrogen starvation causes intense changes in the X. fastidiosa transcriptome and some of these differentially expressed genes belong to the σ 54 regulon. * Genes were categorized into functional classes according to the categories defined in the original annotation of the X. fastidiosa genome http://www.lbi.ic. unicamp.br/xf/. # The number of upregulated and downregulated genes, respectively, are indicated in parenthesis. § Number of genes upregulated and downregulated, respectively, during time points of the nitrogen starvation temporal series. da Silva Neto et al. BMC Microbiology 2010, 10:231
doi:10.1186/1471-2180-10-231 pmid:20799976 pmcid:PMC3224663 fatcat:zeiugymrszaojchrcy6g23gknm

Transcription Start Site Associated RNAs (TSSaRNAs) Are Ubiquitous in All Domains of Life

Livia S. Zaramela, Ricardo Z. N. Vêncio, Felipe ten-Caten, Nitin S. Baliga, Tie Koide, Szabolcs Semsey
2014 PLoS ONE  
A plethora of non-coding RNAs has been discovered using high-resolution transcriptomics tools, indicating that transcriptional and post-transcriptional regulation is much more complex than previously appreciated. Small RNAs associated with transcription start sites of annotated coding regions (TSSaRNAs) are pervasive in both eukaryotes and bacteria. Here, we provide evidence for existence of TSSaRNAs in several archaeal transcriptomes including: Halobacterium salinarum, Pyrococcus furiosus,
more » ... anococcus maripaludis, and Sulfolobus solfataricus. We validated TSSaRNAs from the model archaeon Halobacterium salinarum NRC-1 by deep sequencing two independent small-RNA enriched (RNA-seq) and a primary-transcript enriched (dRNA-seq) strand-specific libraries. We identified 652 transcripts, of which 179 were shown to be primary transcripts (,7% of the annotated genome). Distinct growth-associated expression patterns between TSSaRNAs and their cognate genes were observed, indicating a possible role in environmental responses that may result from RNA polymerase with varying pausing rhythms. This work shows that TSSaRNAs are ubiquitous across all domains of life.
doi:10.1371/journal.pone.0107680 pmid:25238539 pmcid:PMC4169567 fatcat:jcbkuvlvuvftpmfs2rr62m5kfy

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

Felipe Ten-Caten, Ricardo Z. N. Vêncio, Alan Péricles R. Lorenzetti, Livia Soares Zaramela, Ana Carolina Santana, Tie Koide
2018 RNA Biology  
Prokaryotic genomes show a high level of information compaction often with different molecules transcribed from the same locus. Although antisense RNAs have been relatively well studied, RNAs in the same strand, internal RNAs (intraRNAs), are still poorly understood. The question of how common is the translation of overlapping reading frames remains open. We address this question in the model archaeon Halobacterium salinarum. In the present work we used differential RNA-seq (dRNA-seq) in H.
more » ... narum NRC-1 to locate intraRNA signals in subsets of internal transcription start sites (iTSS) and establish the open reading frames associated to them (intraORFs). Using C-terminally flagged proteins, we experimentally observed isoforms accurately predicted by intraRNA translation for kef1, acs3 and orc4 genes. We also recovered from the literature and mass spectrometry databases several instances of protein isoforms consistent with intraRNA translation such as the gas vesicle protein gene gvpC1. We found evidence for intraRNAs in horizontally transferred genes such as the chaperone dnaK and the aerobic respiration related cydA in both H. salinarum and Escherichia coli. Also, intraRNA translation evidence in H. salinarum, E. coli and yeast of a universal elongation factor (aEF-2, fusA and eEF-2) suggests that this is an ancient phenomenon present in all domains of life. ARTICLE HISTORY
doi:10.1080/15476286.2018.1509661 pmid:30175688 pmcid:PMC6161675 fatcat:47clhihp6ndsrpy2i5piaqu3h4

A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability

Amy K Schmid, David J Reiss, Min Pan, Tie Koide, Nitin S Baliga
2009 Molecular Systems Biology  
f g ND, transcription start site not detected in high-density tiling array experiments (Koide et al, 2009).  ...  e TSS, transcription start site chromosmal coordinate position determined experimentally by high-density tiling array (Koide et al, 2009).  ... 
doi:10.1038/msb.2009.40 pmid:19536205 pmcid:PMC2710871 fatcat:ubecna6wajaf3ioqpqytppt36e

The F-box Protein FBXO25 Promotes the Proteasome-dependent Degradation of ELK-1 Protein

Felipe R. Teixeira, Adriana O. Manfiolli, Cláudia S. Soares, Munira M. A. Baqui, Tie Koide, Marcelo D. Gomes
2013 Journal of Biological Chemistry  
Identification of SCF1(FBXO25) substrates can be done through in chip ubiquitination on protoarrays. Results: FBXO25 interacts and mediates ubiquitination and proteasomal degradation of the ELK-1 protooncogene regulator. Conclusion: The c-Fos regulator ELK-1 is an SCF1(FBXO25) substrate. Significance: FBXO25 is a potential mitogen pathway regulator through ELK-1 degradation. FBXO25 is one of the 69 known human F-box proteins that serve as specificity factors for a family of ubiquitin ligases
more » ... posed of SKP1, Rbx1, Cullin1, and F-box protein (SCF1) that are involved in targeting proteins for degradation across the ubiquitin proteasome system. However, the substrates of most SCF E3 ligases remain unknown. Here, we applied an in chip ubiquitination screen using a human protein microarray to uncover putative substrates for the FBXO25 protein. Among several novel putative targets identified, the c-fos protooncogene regulator ELK-1 was characterized as the first endogenous substrate for SCF1(FBXO25) E3 ligase. FBXO25 interacted with and mediated the ubiquitination and proteasomal degradation of ELK-1 in HEK293T cells. In addition, FBXO25 overexpression suppressed induction of two ELK-1 target genes, c-fos and egr-1, in response to phorbol 12-myristate 13-acetate. Together, our findings show that FBXO25 mediates ELK-1 degradation through the ubiquitin proteasome system and thereby plays a role in regulating the activation of ELK-1 pathway in response to mitogens.
doi:10.1074/jbc.m113.504308 pmid:23940030 pmcid:PMC3784726 fatcat:j2bkljdzlbhynjdl73n5lafwze

Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea

José Vicente Gomes-Filho, Livia Soares Zaramela, Valéria Cristina da Silva Italiani, Nitin S Baliga, Ricardo Z N Vêncio, Tie Koide
2015 RNA Biology  
extremophile thrives in environments with 4.5M NaCl concentration and has been used as a model organism for systems biology studies. ] [8] [9] [10] [11] In the present work, by revisiting the dataset from Koide  ... 
doi:10.1080/15476286.2015.1019998 pmid:25806405 pmcid:PMC4615843 fatcat:pwawuxyk5rgyhlebrmkiennboq

The MarR family regulator OsbR controls oxidative stress response, anaerobic nitrate respiration, and biofilm formation in Chromobacterium violaceum

Júlia A. Alves, Maristela Previato-Mello, Kelly C. M. Barroso, Tie Koide, José F. da Silva Neto
2021 BMC Microbiology  
Background Chromobacterium violaceum is an environmental opportunistic pathogen that causes rare but deadly infections in humans. The transcriptional regulators that C. violaceum uses to sense and respond to environmental cues remain largely unknown. Results Here, we described a novel transcriptional regulator in C. violaceum belonging to the MarR family that we named OsbR (oxidative stress response and biofilm formation regulator). Transcriptome profiling by DNA microarray using strains with
more » ... letion or overexpression of osbR showed that OsbR exerts a global regulatory role in C. violaceum, regulating genes involved in oxidative stress response, nitrate reduction, biofilm formation, and several metabolic pathways. EMSA assays showed that OsbR binds to the promoter regions of several OsbR-regulated genes, and the in vitro DNA binding activity was inhibited by oxidants. We demonstrated that the overexpression of osbR caused activation of ohrA even in the presence of the repressor OhrR, which resulted in improved growth under organic hydroperoxide treatment, as seem by growth curve assays. We showed that the proper regulation of the nar genes by OsbR ensures optimal growth of C. violaceum under anaerobic conditions by tuning the reduction of nitrate to nitrite. Finally, the osbR overexpressing strain showed a reduction in biofilm formation, and this phenotype correlated with the OsbR-mediated repression of two gene clusters encoding putative adhesins. Conclusions Together, our data indicated that OsbR is a MarR-type regulator that controls the expression of a large number of genes in C. violaceum, thereby contributing to oxidative stress defense (ohrA/ohrR), anaerobic respiration (narK1K2 and narGHJI), and biofilm formation (putative RTX adhesins).
doi:10.1186/s12866-021-02369-x pmid:34736409 pmcid:PMC8567585 fatcat:h62i4qniyba63fzizbdnons4im

New Window Resonances in the Potassium 3sPhotoabsorption Spectrum

Michi Koide, Fumihiro Koike, Ralf Wehlitz, Ming-Tie Huang, Tetsuo Nagata, Jon C. Levin, Stephan Fritzsche, Brett D. DePaola, Shunsuke Ohtani, Yoshiro Azuma
2002 Journal of the Physical Society of Japan  
KOIDE et al.  ... 
doi:10.1143/jpsj.71.1676 fatcat:a63m5nbmmbci7nib6yhmmk2424
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