Abstract:
:RNA molecules play vital informational, structural, and functional roles in molecular biology, making them ideal targets for synthetic biology. However, several challenges remain for engineering novel allosteric RNA molecules, and the development of efficient computational design techniques is vitally needed. Here we describe the development of Allosteric RNA Designer (ARDesigner), a user-friendly and freely available web-based system for allosteric RNA design that incorporates mutational robustness in the design process. The system output includes detailed design information in a graphical HTML format. We used ARDesigner to engineer a temperature-sensitive AR, and found that the resulting design satisfied the prescribed properties/input. ARDesigner provides a simple means for researchers to design allosteric RNAs with specific properties. With its versatile framework and possibilities for further enhancement, ARDesigner may serve as a useful tool for synthetic biologists and therapeutic design. ARDesigner and its executable version are freely available at http://biotech.bmi.ac.cn/ARDesigner.
journal_name
J Biotechnoljournal_title
Journal of biotechnologyauthors
Shu W,Liu M,Chen H,Bo X,Wang Sdoi
10.1016/j.jbiotec.2010.10.067subject
Has Abstractpub_date
2010-12-01 00:00:00pages
466-73issue
4eissn
0168-1656issn
1873-4863pii
S0168-1656(10)01981-4journal_volume
150pub_type
杂志文章abstract::The combination of anaerobic and aerobic periods in the operation cycle of a Sequencing Batch Reactor (SBR) was chosen to study biological color removal from simulated textile effluents containing reactive, sulfonated, monoazo and diazo dyes, respectively, Remazol Brilliant Violet 5R and Remazol Black B. 90% color rem...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/s0168-1656(01)00313-3
更新日期:2001-08-23 00:00:00
abstract::Sugarcane bagasse (SCB) is an abundant, renewable and inexpensive agricultural byproduct for the production of biofuel and other biobased products. To effectively saccharify SCB with cellulases, combination with dilute alkali salts Na2SO3/Na3PO4 (0.4% Na3PO4, 0.03% Na2SO3) at 7.5% sulfidity and hot water (DASHW) in "o...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/j.jbiotec.2017.08.004
更新日期:2017-10-10 00:00:00
abstract::The Gram-positive Corynebacterium glutamicum is auxotrophic for biotin. Besides the biotin uptake system BioYMN and the transcriptional regulator BioQ, this bacterium possesses functional enzymes for the last three reactions of biotin synthesis starting from pimeloyl-CoA. Heterologous expression of bioF from the Gram-...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/j.jbiotec.2014.01.023
更新日期:2014-12-20 00:00:00
abstract::Corynebacterium glutamicum possesses export systems for various amino acids including BrnFE, a two-component export system for L-methionine and the branched-chain amino acids L-valine, L-isoleucine and L-leucine. A gene for a putative transcriptional regulator of the Lrp family is transcribed divergently to the brnFE ...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/j.jbiotec.2011.06.003
更新日期:2012-04-30 00:00:00
abstract::A model for transport of ammonia and ammonium ions across cell membranes is presented. The model suggests that ammonium ions compete with potassium ions for inward transport, over the cytoplasmic membrane, via potassium transport proteins like the Na+/K(+)-ATPase and the Na+K+2Cl(-)-cotransporter. It also explains the...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/0168-1656(93)90148-g
更新日期:1993-09-01 00:00:00
abstract::A system has been developed for the release of heterologous proteins from Saccharomyces cerevisiae, based on the use of thermosensitive osmotic-remedial mutants, deficient in cell integrity, that lyse at the non-permissive temperature, thus releasing the bulk of intracellular proteins and leaving behind cell ghosts an...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/0168-1656(94)90149-x
更新日期:1994-11-30 00:00:00
abstract::Transgenic hairy root (HR) systems constitute an interesting alternative to improve the efficiency of phytoremediation process. Since peroxidases (Px) have been associated with phenolic compounds removal, in the present work, transgenic tobacco HR, which expressed basic Px genes from tomato (tpx1 and tpx2), were estab...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/j.jbiotec.2008.11.008
更新日期:2009-02-23 00:00:00
abstract::Bacterial pigments are potential substitute of chemical photosensitizer for dye-sensitized solar cell (DSSC) due to its non-toxic property and cost-effective production from microbial fermentation. Serratia nematodiphila YO1 was isolated from waterfall in Malaysia and identified using 16S ribosomal RNA. Characterizati...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/j.jbiotec.2020.04.011
更新日期:2020-06-20 00:00:00
abstract::Aptamers are single-stranded DNA or RNA oligonucleotides, which have been emerging as recognition elements in disease diagnostics and food control, including the detection of bacterial toxins. In this study, we employed the semi-automated just in time-selection to identify aptamers that bind to cholera toxin (CT) with...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/j.jbiotec.2018.01.012
更新日期:2018-03-10 00:00:00
abstract::Fast and reliable methods to determine biomass concentration are necessary to facilitate the large scale production of microalgae. A method for the rapid estimation of Chlorella sorokiniana biomass concentration was developed. The method translates the suspension particle size spectrum gathered though laser reflectanc...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/j.jbiotec.2016.12.020
更新日期:2017-02-10 00:00:00
abstract::The study describes extraction of extracellular polymeric substances (EPS) from sewage sludge by applying enzymes and enzymes combined with sodium tripolyphosphate (STPP). Additionally, a systematic study of two non-enzymatic extraction agents is described. The assessment of the released products is made by colorimetr...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/j.jbiotec.2007.04.005
更新日期:2007-06-30 00:00:00
abstract::Sulfite dissolving pulp from Eucalyptus grandis contained approximately 3.8% O-acetyl-4-O-methylglucuronoxylan with a molar ratio of xylose:4-O-methylglucuronic acid:acetyl group close to 13.6:1:6.2. The effects produced by purified endo-xylanases from two different glycosyl hydrolase families (family 10 and 11) as we...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/s0168-1656(00)00324-2
更新日期:2000-10-13 00:00:00
abstract::The successful transfer of human embryonic stem cell (hESC) technology and cellular products into clinical and industrial applications needs to address issues of automation, standardization and the generation of relevant cell numbers of high quality. In this study, we combined microcarrier technology and controlled st...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/j.jbiotec.2010.06.015
更新日期:2010-08-02 00:00:00
abstract::Herbinix hemicellulosilytica is a newly isolated, gram-positive, anaerobic bacterium with extensive hemicellulose-degrading capabilities obtained from a thermophilic biogas reactor. In order to exploit its potential as a source for new industrial arabinoxylan-degrading enzymes, six new thermophilic xylanases, four fro...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/j.jbiotec.2017.04.023
更新日期:2017-09-10 00:00:00
abstract::This study examined the kinetics and substrate selectivity of a GH11 Bacillus subtilis XynA xylanase (BsX) sensitive to inhibition by TAXI and an engineered variant, which is much less inhibited by TAXI (BsX(mut)). The main purpose of the work was to elucidate any influence of the structural point mutations on the kin...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/j.jbiotec.2010.02.012
更新日期:2010-04-15 00:00:00
abstract::A newly developed flat panel airlift photobioreactor with a defined circulation path was tested for microalgal culture. The bioreactor exposed the cells to intermittent light to improve the efficiency of light utilization through the flashing-light effect. During batch cultures in the new photobioreactor, the biomass ...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/s0168-1656(01)00350-9
更新日期:2001-12-28 00:00:00
abstract::The construction of expression vectors encoding either the human insulin A- or B-chains fused to a synthetic peptide and the temperature-induced expression of the recombinant genes in Escherichia coli are reported. Using this two-chain approach we also describe the separate isolation of the insulin A- and B-chains fro...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/s0168-1656(98)00189-8
更新日期:1999-02-05 00:00:00
abstract::We previously showed that creation of a double strand DNA break (DSB) by expressing I-SceI in an engineered Trichoderma reesei (Hypocrea jecorina) strain containing a I-SceI recognition site improved transformation and homologous integration efficiencies. In this study, we further improved homologous integration frequ...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/j.jbiotec.2016.02.012
更新日期:2016-03-20 00:00:00
abstract::2'-Fucosyllactose (2-FL) is one of most abundant functional oligosaccharides in human milk, which is involved in many biological functions for human health. To date, most microbial systems for 2-FL production have been limited to use Escherichia coli JM strains since they cannot metabolize lactose. In this study, E. c...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/j.jbiotec.2015.06.431
更新日期:2015-09-20 00:00:00
abstract::It is quite important to understand the basic principle embedded in the main metabolism for the interpretation of the fermentation data. For this, it may be useful to understand the regulation mechanism based on systems biology approach. In the present study, we considered the perturbation analysis together with compu...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/j.jbiotec.2013.06.023
更新日期:2013-10-20 00:00:00
abstract::Rufibacter tibetensis strain 1351, isolated from the soil of the Tibet plateau of China, belongs to the family of Cytophagaceae. It is a red-pigmented, gram-negative, strictly aerobic and rod-shaped bacterium and shows resistance to UV radiation. Here, we report its complete genome sequence, which can help us find the...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/j.jbiotec.2015.10.015
更新日期:2015-12-20 00:00:00
abstract::The methylotropic yeast Pichia pastoris has demonstrated its suitability for large-scale production of recombinant proteins. As an eukaryotic organism P. pastoris presents a series of advantages at expression and processing of heterologous proteins when compared with Escherichia coli. In this work, P. pastoris has bee...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/j.jbiotec.2016.04.024
更新日期:2016-06-10 00:00:00
abstract::The use of the fungus Aspergillus niger for the bioleaching of heavy metals from spent catalyst was investigated, with fluid catalytic cracking (FCC) catalyst as a model. Bioleaching was examined in batch cultures with the spent catalysts at various pulp densities (1-12%). Chemical leaching was also performed using mi...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/j.jbiotec.2004.10.008
更新日期:2005-03-16 00:00:00
abstract::The kinetics of microbial growth and the biodegradation of methanol and toluene in (a) biofilters (BFs), and (b) biotrickling filters (BTFs), packed with inert materials, has been studied and analyzed. The specific growth rate, mu, for the treatment of methanol was 0.037h(-1) for a wide range of operating conditions. ...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/j.jbiotec.2008.08.001
更新日期:2008-11-25 00:00:00
abstract::We report on the isolation and biochemical characterization of a novel, cold-active and metagenome-derived lipase with a high stereo-selectivity for pharmaceutically important substrates. The respective gene was isolated from a cosmid library derived from oil contaminated soil and designated lipCE. The deduced aa sequ...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/j.jbiotec.2007.05.015
更新日期:2007-07-15 00:00:00
abstract::Laccase from the white rot fungus Coriolopsis polyzona was immobilized for the first time through the formation of cross-linked enzyme aggregates (CLEAs). Laccase CLEAs were produced by using 1000g of polyethylene glycol per liter of enzyme solution as precipitant and 200muM of glutaraldehyde as a cross-linking agent....
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/j.jbiotec.2007.07.948
更新日期:2007-10-15 00:00:00
abstract::A cellulase from Trichoderma reesei was immobilized on Eudragit L-100, a reversibly soluble polymer depending on the pH of the medium. The solubility of the modified cellulase was studied at different pH values. By changing the pH, the adsorption equilibrium of the derivatized proteins is switched towards the liquid p...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/s0168-1656(02)00178-5
更新日期:2002-10-23 00:00:00
abstract::Ubiquitination is one of the most significant posttranslational modifications (PTMs). To evaluate the ability of an insect cell-free protein synthesis system to carry out ubiquitin (Ub) conjugation to in vitro translated proteins, poly-Ub chain formation was studied in an insect cell-free protein synthesis system. Pol...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/j.jbiotec.2009.10.009
更新日期:2010-01-01 00:00:00
abstract::Enzyme prodrug therapies hold potential as a targeted treatment option for cancer patients. However, off-target effects can be detrimental to patient health and represent a safety concern. This concern can be alleviated by including a failsafe mechanism that can abort the therapy in healthy cells. This feature can be ...
journal_title:Journal of biotechnology
pub_type: 杂志文章
doi:10.1016/j.jbiotec.2017.09.005
更新日期:2017-10-20 00:00:00
abstract::The genus Listeria comprises a group of non-sporulating, Gram-positive, soil bacteria belonging to the low G+C group of microorganisms. The genus consists of only six species, L. monocytogenes, L. ivanovii, L. seeligeri, L. innocua, L. welshimeri, and L. grayi.L. monocytogenes and L. ivanovii are the only known pathog...
journal_title:Journal of biotechnology
pub_type: 杂志文章,评审
doi:10.1016/j.jbiotec.2006.03.047
更新日期:2006-10-20 00:00:00