Olatz Ruiz‐Larrabeiti- PhD
- PhD at The Czech Academy of Sciences
Olatz Ruiz‐Larrabeiti
- PhD
- PhD at The Czech Academy of Sciences
About
13
Publications
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Introduction
Current institution
Additional affiliations
January 2012 - December 2016
Publications
Publications (13)
5‐(β‐d‐Glucopyranosyloxymethyl)‐2’‐deoxyuridine and ‐cytidine 5’‐O‐triphosphates were prepared and used for polymerase‐mediated (primer extension or PCR) synthesis of DNA containing glucosylated 5‐hydroxymethyluracil (5hmU) or 5‐hydroxymethyluracil (5hmC). The presence of any glucosylated pyrimidines fully protected DNA from cleavage by type II res...
Homologues of natural epigenetic pyrimidine nucleosides and nucleotides were designed and synthesized. They included 5-ethyl-, 5-propyl-, 5-(1-hydroxyethyl)-, 5-(1-hydroxypropyl)- and 5-acetyl- and 5-propionylcytosine and -uracil 2'-deoxyribonucleosides and their corresponding 5'-O-triphosphates (dNXTPs). The epimers of 5-(1-hydroxyethyl)- and 5-(1...
Chemical modifications of RNA affect essential properties of transcripts, such as their translation, localization and stability. 5-end RNA capping with the ubiquitous redox cofactor nicotinamide adenine dinucleotide (NAD+) has been discovered in organisms ranging from bacteria to mammals. However, the hypothesis that NAD+ capping might be universal...
The exponential increase in the number of conducted studies combined with the development of sequencing methods have led to an enormous accumulation of partially processed experimental data in the past two decades. Here, we present an approach using literature-mined data complemented with gene expression kinetic modeling and promoter sequence analy...
5-Hydroxymethylcytosine and uracil are epigenetic nucleobases, but their biological roles are still unclear. We present the synthesis of 2-nitrobenzyl photocaged 5-hydroxymethyl-2′-deoxycytidine and uridine 3′-O-phosphoramidites and their use in automated solid-phase synthesis of oligonucleotides (ONs) modified at specific positions. The ONs were u...
Previous studies revealed important roles of small RNAs (sRNAs) in regulation of bacterial metabolism, stress responses and virulence. However, only a minor fraction of sRNAs is well characterized with respect to the spectra of their targets, conditional expression profiles and actual mechanisms they use to regulate gene expression to control parti...
Previous studies revealed important roles of small RNAs (sRNAs) in regulation of bacterial metabolism, stress responses and virulence. However, only a minor fraction of sRNAs is well characterized with respect to the spectra of their targets, conditional expression profiles and actual mechanisms they use to regulate gene expression to control parti...
Bacterial small RNAs (sRNAs) play essential roles in the post-transcriptional control of gene expression. To improve their detection by conventional microarrays, we designed a custom microarray containing a group of probes targeting known and some putative E. coli sRNAs. To assess its potential in detection of sRNAs, RNA profiling experiments were...
Streptomyces coelicolor is a model for studying bacteria renowned as the foremost source of natural products used clinically. Post-genomic studies have revealed complex patterns of gene expression and links to growth, morphological development and individual genes. However, the underlying regulation remains largely obscure, but undoubtedly involves...
Questions
Questions (3)
I am trying to grow cultures of Sso on Brock medium (see below), I think I am having into account the usual suspects (sucrose is D+, water is pure water, equilibrated the pH with sulfuric acid, shaking is enough I believe), and in the beggining I get some growth (OD600 0.02 to 0.1), but after ~24h they get stuck, the medium becomes more yellow but not more turbid, and they don't smell bad, like a tipical Sso culture. Anybody has had this kind of issue with S. solfataricus? How was that overcome?
Brock medium
CaCl2 1000X is autocleaved, final conc. in working medium is 0.7g/L.
Brock II 100x is filtered, final conc. in working medium is (NH4)2SO4 (1.3 g/L), MgSO4 x 7H2O (0.25 g/L), KH2PO4 (0.28 g/L).
Trace element suspesion 2000X is autocleaved, final conc. in working medium is MnCl2 x 4H2O (1.8 mg/L), Na2B4O7 x 10H2O (4.5 mg/L), ZnSO4 x 7H2O (0.22 mg/L), CuCl2 x 2H2O (0.05 mg/L), NaMoO4 x 2H2O (0.03 mg/L) VOSO4 x 2H2O (0.03 mg/L), CoSO4 x 7H2O (0.01 mg/L).
Fe-solution 1000x is filtered, final conc. in working medium is 0.02 g/L.
Triptone solution 20% w/v autocleaved, final conc. in working medium is 0.1% .
Sucrose solution 20% w/v is filtered, final conc. in working medium is 0.2%.
The components are mixed in pure water, equilibrated to pH 3 with sulfuric acid 50% and filtered, medium is inoculated and incubated at 70-75°C.
Hello,
Has anyone heat inactivated E. coli RNase III? what temperature and how long should I incubate for RNase III heat inactivation?
I know its not recomended, but I'm trying to do a secong cleavage assay with other enzyme after having treated my transcripts with RNase III, and so I'd like it to be inactive without having to add EDTA (it would interfere with next enzyme's activity) or do a phenol-choloform extraction (I risk to lose RNA in the extraction-precipitation steps).
Thanks in advance!
I am trying to produce mutants using the system described by Datsenko and Wanner (http://www.ncbi.nlm.nih.gov/pubmed/10829079). I have followed the instructions given in the paper quite precisely. I don't get any antibiotic resistent colony right after transformation, and when I plate the recovery culture incubated overnight at room temperature I sometimes get a few colonies, but PCR show that, even if they do have the FRT-Antibiotic gene-FRT fragment inserted in their genome, they still have the gene that I intened to substitute. This leads me to the thought that I am having a inespecific recombination, although the homology extensions have been blasted and give good result. I've checked other papers where they use the same system succesfully, and I don't see great diferences with my protocol. Anyone have had similar problems or ideas that shed some light on this?
