1,214 research outputs found
The Zur regulon of Corynebacterium glutamicum ATCC 13032
No full textSchröder J, Jochmann N, Rodionov DA, Tauch A. The Zur regulon of Corynebacterium glutamicum ATCC 13032. BMC Genomics. 2010;11(1): 12.Background Zinc is considered as an essential element for all living organisms, but it can be toxic at large concentrations. Bacteria therefore tightly regulate zinc metabolism. The Cg2502 protein of Corynebacterium glutamicum was a candidate to control zinc metabolism in this species, since it was classified as metalloregulator of the zinc uptake regulator (Zur) subgroup of the ferric uptake regulator (Fur) family of DNA-binding transcription regulators. Results The cg2502 (zur) gene was deleted in the chromosome of C. glutamicum ATCC 13032 by an allelic exchange procedure to generate the zur-deficient mutant C. glutamicum JS2502. Whole-genome DNA microarray hybridizations and real-time RT-PCR assays comparing the gene expression in C. glutamicum JS2502 with that of the wild-type strain detected 18 genes with enhanced expression in the zur mutant. The expression data were combined with results from cross-genome comparisons of shared regulatory sites, revealing the presence of candidate Zur-binding sites in the mapped promoter regions of five transcription units encoding components of potential zinc ABC-type transporters (cg0041-cg0042/cg0043; cg2911-cg2912-cg2913), a putative secreted protein (cg0040), a putative oxidoreductase (cg0795), and a putative P-loop GTPase of the COG0523 protein family (cg0794). Enhanced transcript levels of the respective genes in C. glutamicum JS2502 were verified by real-time RT-PCR, and complementation of the mutant with a wild-type zur gene reversed the effect of differential gene expression. The zinc-dependent expression of the putative cg0042 and cg2911 operons was detected in vivo with a gfp reporter system. Moreover, the zinc-dependent binding of purified Zur protein to double-stranded 40-mer oligonucleotides containing candidate Zur-binding sites was demonstrated in vitro by DNA band shift assays. Conclusion Whole-genome expression profiling and DNA band shift assays demonstrated that Zur directly represses in a zinc-dependent manner the expression of nine genes organized in five transcription units. Accordingly, the Zur (Cg2502) protein is the key transcription regulator for genes involved in zinc homeostasis in C. glutamicum
Творчість В. Родіонова: проблемний діапазон художнього світогляду (Creativity V. Rodionov: problem diapazon of the artistic swiss)
No full textУ статті акцентується увага на творчості В. Родіонова. Зроблено акцент на проблематиці творів письменника; визначено, що діяльність В. Родіонова характеризується актуальністю та вагомістю проблематики, висвітлення якої прямолінійне, позбавлене завуальовувань і спрямоване на екзистенційний аналіз фактів щоденного буття в усіх його проявах, що реалізується на двох рівнях: загальнолюдському й національному.
(The article focuses on the work of V. Rodionov. The emphasis is placed on the problems of the writer’s works. It is determined that V. Rodionov’s activity is characterized by urgency and weight of problems, the coverage of which is straightforward, deprived of veils, and aimed at an existential analysis of the facts of everyday life in all its manifestations, which is realized on two levels: universal and national. The problem range of the universal is due to the analysis of the values of human life. Research in this direction is not accidental, since the artist seeks to form a peculiar view that will cover such aspects as: the depreciation of life and human relationships, despair and loss of spirituality, the presence of a disharmonious movement of society, the value of artistic paintings, literary works at the present stage of development, the problem of modern interpretation the concept of «love», the importance of the phenomenon of memory as a way to integrate the experience of the past into the present, and hence the ability to compare and contrast, to create a projection into the future, to avoid the occurrence of problem situations in different chronological limits. Acute social and moral issues, highlighted in the literary work of V. Rodionov, are usually distinguished by the author. At the heart of every single piece of poetic or prose nature always lies one actual problem. Violation of the profound problems provoked the emergence of didacticism, the narrative of the most important, verbal-fi gurative thinking, but to moralise and insist on the expediency of his statements. V. Rodionov does not strive, since he has the sole purpose of conveying the acuteness of the problem, the avoidance of which will contribute to the progress of the individual and society as a whole.
The subsystems approach to genome annotation and its use in the Project to Annotate 1000 Genomes
No full textOverbeek R, Begley T, Butler RM, et al. The subsystems approach to genome annotation and its use in the Project to Annotate 1000 Genomes. Nucleic Acids Research. 2005;33(17):5691-5702.The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the Project to Annotate 1000 Genomes. The project is built around the principle that the key to improved accuracy in high-throughput annotation technology is to have experts annotate single subsystems over the complete collection of genomes, rather than having an annotation expert attempt to annotate all of the genes in a single genome. Using the subsystems approach, all of the genes implementing the subsystem are analyzed by an expert in that subsystem. An annotation environment was created where populated subsystems are curated and projected to new genomes. A portable notion of a populated subsystem was defined, and tools developed for exchanging and curating these objects. Tools were also developed to resolve conflicts between populated subsystems. The SEED is the first annotation environment that supports this model of annotation. Here, we describe the subsystem approach, and offer the first release of our growing library of populated subsystems. The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms
Activity in the precuneus gates generalizes spike-and-wave discharges: An example of the interaction of resting state brain activity and epileptiform events
No full textDynamic Causal Modelling of fMRI data suggests a facilitating role of the precuneus on a thalamocortical network during generalized spike-and-wave discharges
No full textDynamic causal modelling of FMRI data suggests a balanced cortico-subcortical loop influenced by the precuneal state during generalized spike-wave discharges
No full textA novel method for the classification of interictal EEG abnormalities in partial epilepsy: an EEG/fMRI validation study
No full textExemplifying Natural (<i>R</i>)‑β-Transamination Potential of Fold Type-IV Transaminase for Kinetic Resolution of <i>rac</i>-β-Amino Acids Synthesized from Aldehydes
No full textSustainable synthesis of chiral β-amino acids from
renewable
feedstocks is of significant importance. The Rodionov reaction is
a popular method to synthesize rac-β-amino
acids from aldehydes, which are abundant byproducts of biomass. rac-β-Amino acids are easily converted into the enantiopure
(R)-form by kinetic resolution using (S)-β-transaminases (TAs). However, the inaccessibility
of natural (R)-β-transaminases
with a broader substrate scope limits the application of the Rodionov
reaction to produce (S)-β-amino acids. Here,
we report the kinetic resolution of rac-β-amino
acids by employing fold type-IV transaminase from Thermobaculum
terrenum (TATT) with natural (R)-β-transaminase activity. Various rac-β-amino acids were successfully resolved by TATT into (S)-form with excellent conversions (∼50%) and enantiomeric
excess (>99%) using pyruvate as an amino acceptor. The directed
evolution
of TATT resulted in a variant M-58 (K112F/F114M) with ∼2-fold
higher activity and was able to perform large-scale kinetic resolution
of 20 mM rac-3-amino-3-(3-fluorophenyl) propanoic
acid (1h) with complete conversion and enantiomeric excess
>99% within 24 h
Supplement 1. Annotated R scripts and sediment core data used to investigate regime shift dynamics in a Galapagos coastal lagoon.
No full textFile List
data.csv (MD5: a6d684a54a17794fa0a79c739d403b63) Diablas lagoon diatom (%), stable carbon isotope (‰) and interpolated Ti influx data (µg.cm-2.yr-1). Four minor data handling errors have been corrected in the stable carbon isotope data from Seddon et al. 2011.
Script.R (MD5: 4b2c776d9ead3f85f9a3bb37af7a77a3) Example R script to apply regime shift detection techniques and non-linear regressions in this study for analysis of data.csv.
STARS.R (MD5: 99bcf013e9a5738843813b7815ce74e9) R script required to implement Sequential T-test Analysis of Regime Shifts Algorithm (Rodionov 2004, 2006) in script.R.
Description
The supplements are designed to provide an example of the framework used to investigate regime shifts in this study. The main file script.R is annotated and split into two parts: STEP 1 investigates whether regime shifts can be identified in diatom assemblages, STEP 2 provides an example of fitting non-linear regressions on the PC1 axis of the diatom data across Regime Shift 1. This can be repeated across other time steps and other datasets (e.g., Ti influx, δ13C) in the way. A number of other packages are required, documented within the script.R file. See R documentation for more information.
To run the script, place all data files into the same directory, open R and set the working directory to that folder. Open up the file script.R and follow the annotations (marked with #) to detect regime shifts in the diatom data and then statistically model the changes in the temporal series.
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