CloneAssistant 1.0: a stand-alone software for automated cloning primer design.

Abstract:

:"CloneAssistant 1.0" is a stand-alone software compatible with the current Windows operating systems, which can automatically design cloning primers with full consideration of the sequence information of vectors and genes, cloning strategies, the principles of primer design, reading frames, position effects, and enzymatic reaction conditions for users. Five internal XML (extensible markup language) databases [restriction enzymes, plasmids, universal buffers, PCR (polymerase chain reaction) protection bases, and an MCS (multiple cloning site) double digest interference database] were established to serve as the basic support for "CloneAssistant 1.0". The primer pairs designed are sorted according to the difficulty of the follow-up experiments. Once a primer pair is selected by the user, detailed experimental guidance for this primer pair will be provided. In addition, "CloneAssistant 1.0" can be used for restriction map analysis, ORF (open reading frame) finding, sequence alignment and complementary analysis, translation, restriction enzyme and universal buffer queries, and isocaudamer analysis. "CloneAssistant 1.0" makes gene clone design much easier, and it can be freely downloaded from http://bis.zju.edu.cn/clone.

journal_name

J Biotechnol

journal_title

Journal of biotechnology

authors

Shao C,Meng Y,Lv S,Zhong W,Wang Z,Chen M

doi

10.1016/j.jbiotec.2010.09.952

subject

Has Abstract

pub_date

2010-11-01 00:00:00

pages

294-8

issue

3

eissn

0168-1656

issn

1873-4863

pii

S0168-1656(10)01886-9

journal_volume

150

pub_type

杂志文章
  • Complete genome sequence of novel carbon monoxide oxidizing bacteria Citrobacter amalonaticus Y19, assembled de novo.

    abstract::We report here the complete genome sequence of Citrobacter amalonaticus Y19 isolated from an anaerobic digester. PacBio single-molecule real-time (SMRT) sequencing was employed, resulting in a single scaffold of 5.58Mb. The sequence of a mega plasmid of 291Kb size is also presented. ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2015.07.012

    authors: Ainala SK,Seol E,Park S

    更新日期:2015-10-10 00:00:00

  • Methylation and subsequent glycosylation of 7,8-dihydroxyflavone.

    abstract::An O-methyltransferase SpOMT2884, originating from Streptomyces peucetius ATCC 27952, was cloned, expressed, and applied for the production of target metabolite from Escherichia coli. Biochemical characterization of the 25kDa recombinant protein by in vitro and in vivo experiments showed that SpOMT2884 was an S-adenos...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2014.05.005

    authors: Koirala N,Pandey RP,Parajuli P,Jung HJ,Sohng JK

    更新日期:2014-08-20 00:00:00

  • Complete genome sequence of a novel chlorpyrifos degrading bacterium, Cupriavidus nantongensis X1.

    abstract::Cupriavidus nantongensis X1 is a chlorpyrifos degrading bacterium, which was isolated from sludge collected at the drain outlet of a chlorpyrifos manufacture plant. It is the first time to report the complete genome sequence of C. nantongensis species, which has been reported as a novel species of Cupriavidus genus. I...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2016.04.012

    authors: Fang LC,Chen YF,Zhou YL,Wang DS,Sun LN,Tang XY,Hua RM

    更新日期:2016-06-10 00:00:00

  • Enzymes with new biochemical properties in the pectinolytic complex produced by Aspergillus niger MIUG 16.

    abstract::A comprehensive study on the purification and characterization of pectinolytic enzymes produced by Aspergillus niger MIUG 16 on raw materials solid-state fermentation is reported. Five pectinolytic enzymes were purified using a combination of chromatographic techniques. The properties of these homogenous enzymes were ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2007.06.005

    authors: Dinu D,Nechifor MT,Stoian G,Costache M,Dinischiotu A

    更新日期:2007-08-31 00:00:00

  • Purification and characterization of a recombinant listeriolysin O expressed in Escherichia coli and possible diagnostic applications.

    abstract::The secreted pore-forming toxin listeriolysin O (LLO) is an essential virulence factor that allows the food-borne bacterial pathogen Listeria monocytogenes to escape from the phagocytic vacuole and reach the host cytosol. This protein belongs to the group of cholesterol-binding sulfhydryl-activated toxins, expressed b...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2003.10.023

    authors: Giammarini C,Andreoni F,Amagliani G,Casiere A,Barocci S,Magnani M

    更新日期:2004-04-08 00:00:00

  • Validation of an optical sensor-based high-throughput bioreactor system for mammalian cell culture.

    abstract::Cell culture optimization is a labor-intensive process requiring a large number of experiments to be conducted under varying conditions. Here we describe a high-throughput bioreactor system that allows 12 mini stirred-tank bioreactors to be operated simultaneously. All bioreactors are monitored by low-cost minimally i...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2005.12.009

    authors: Ge X,Hanson M,Shen H,Kostov Y,Brorson KA,Frey DD,Moreira AR,Rao G

    更新日期:2006-04-10 00:00:00

  • Metabolic flux analysis gives an insight on verapamil induced changes in central metabolism of HL-1 cells.

    abstract::Verapamil has been shown to inhibit glucose transport in several cell types. However, the consequences of this inhibition on central metabolism are not well known. In this study we focused on verapamil induced changes in metabolic fluxes in a murine atrial cell line (HL-1 cells). These cells were adapted to serum free...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2011.07.028

    authors: Strigun A,Noor F,Pironti A,Niklas J,Yang TH,Heinzle E

    更新日期:2011-09-20 00:00:00

  • Complete genome sequence of Bacillus thuringiensis YBT-1518, a typical strain with high toxicity to nematodes.

    abstract::Bacillus thuringiensis is a ubiquitous spore-forming bacterium and has been widely used as a biopesticide for controlling agricultural insects by the production of insecticidal crystal proteins (ICPs). B. thuringiensis YBT-1518 displays effective toxicity to nematodes. This strain harbors three nematicidal crystal pro...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2013.11.023

    authors: Wang P,Zhang C,Guo M,Guo S,Zhu Y,Zheng J,Zhu L,Ruan L,Peng D,Sun M

    更新日期:2014-02-10 00:00:00

  • Draft genome sequence of Herbinix hemicellulosilytica T3/55 T, a new thermophilic cellulose degrading bacterium isolated from a thermophilic biogas reactor.

    abstract::A novel bacterial species was isolated from an industrial-scale biogas plant. The isolate Herbinix hemicellulosilytica T3/55(T) is able to degrade crystalline cellulose. Comparative 16S rRNA gene sequencing demonstrated that the isolate is closely related to environmental samples forming a hitherto unknown sub-cluster...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2015.07.022

    authors: Koeck DE,Maus I,Wibberg D,Winkler A,Zverlov VV,Liebl W,Pühler A,Schwarz WH,Schlüter A

    更新日期:2015-11-20 00:00:00

  • Polyhydroxyalkanoate (PHA) synthase genes and PHA-associated gene clusters in Pseudomonas spp. and Janthinobacterium spp. isolated from Antarctica.

    abstract::The polyhydroxyalkanoate (PHA) producing capability of four bacterial strains isolated from Antarctica was reported in a previous study. This study analyzed the PHA synthase genes and the PHA-associated gene clusters from the two antarctic Pseudomonas isolates (UMAB-08 and UMAB-40) and the two antarctic Janthinobacter...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2020.03.006

    authors: Tan IKP,Foong CP,Tan HT,Lim H,Zain NA,Tan YC,Hoh CC,Sudesh K

    更新日期:2020-04-10 00:00:00

  • Development of grapevine somatic embryogenesis using an air-lift bioreactor as an efficient tool in the generation of transgenic plants.

    abstract::The grapevine genetic transformation programs have relayed on the use of solid media-based somatic embryogenesis. To reach a high throughput of candidate gene evaluation in 'Thompson Seedless', a semi-automatic system allowing viable transformation of explants was designed. An intermediate procedure using liquid media...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2008.09.009

    authors: Tapia E,Sequeida A,Castro A,Montes C,Zamora P,López R,Acevedo F,Prieto H

    更新日期:2009-01-01 00:00:00

  • Overexpression of GRAS Rhizomucor miehei lipase in Yarrowia lipolytica via optimizing promoter, gene dosage and fermentation parameters.

    abstract::Rhizomucor miehei lipase (RML), a GRAS catalyst with wide applications, was overexpressed in Yarrowia lipolytica, also a GRAS unconventional yeast, via a combined strategy, optimization for promoter, gene dosage and fermentation process. The lipase activity of the recombinant strain was first increased from 19.5 to 26...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2019.09.004

    authors: Zhou Q,Jiao L,Qiao Y,Wang Y,Xu L,Yan J,Yan Y

    更新日期:2019-12-20 00:00:00

  • Mechanistic understanding of the cysteine capping modifications of antibodies enables selective chemical engineering in live mammalian cells.

    abstract::Protein modifications by intricate cellular machineries often redesign the structure and function of existing proteins to impact biological networks. Disulfide bond formation between cysteine (Cys) pairs is one of the most common modifications found in extracellularly-destined proteins, key to maintaining protein stru...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2017.03.006

    authors: Zhong X,He T,Prashad AS,Wang W,Cohen J,Ferguson D,Tam AS,Sousa E,Lin L,Tchistiakova L,Gatto S,D'Antona A,Luan YT,Ma W,Zollner R,Zhou J,Arve B,Somers W,Kriz R

    更新日期:2017-04-20 00:00:00

  • Expression of recombinant cytoplasmic yeast pyruvate carboxylase for the improvement of the production of human erythropoietin by recombinant BHK-21 cells.

    abstract::Recently, a recombinant yeast pyruvate carboxylase expressed in the cytoplasm of BHK-21 cells was shown to reconstitute the missing link between glycolysis and TCA, thus increasing the flux of glucose into the TCA and resulting in a higher intracellular ATP content. Now, these metabolically engineered cells have been ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/s0168-1656(01)00409-6

    authors: Irani N,Beccaria AJ,Wagner R

    更新日期:2002-02-28 00:00:00

  • Efficient MILP formulations for the optimal synthesis of chromatographic protein purification processes.

    abstract::The use of recombinant proteins has increased greatly in recent years, as well as the techniques used for their purification. The selection of an efficient process to purify proteins is a major bottleneck found when trying to scale up results obtained in the laboratory to a large-scale industrial process. One of the m...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2004.02.009

    authors: Vásquez-Alvarez E,Pinto JM

    更新日期:2004-06-10 00:00:00

  • Heterologous production of different styrene oxide isomerases for the highly efficient synthesis of phenylacetaldehyde.

    abstract::The styrene oxide isomerase (SOI, StyC) represents a key enzyme of the styrene-degrading pathway and has been discussed as promising biocatalyst during recent studies. The enzyme enables the synthesis of pure phenylacetaldehyde from styrene oxide. In this study the native as well as the corresponding codon-optimized g...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2017.04.038

    authors: Oelschlägel M,Richter L,Stuhr A,Hofmann S,Schlömann M

    更新日期:2017-06-20 00:00:00

  • Expression levels of antimicrobial peptide tachyplesin I in transgenic Ornithogalum lines affect the resistance to Pectobacterium infection.

    abstract::The genus Ornithogalum includes several ornamental species that suffer substantial losses from bacterial soft rot caused by Pectobacteria. The absence of effective control measures for use against soft rot bacteria led to the initiation of a project in which a small antimicrobial peptide from an Asian horseshoe crab, ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2016.09.008

    authors: Lipsky A,Joshi JR,Carmi N,Yedidia I

    更新日期:2016-11-20 00:00:00

  • Kinetic model of Chlorella vulgaris growth with and without extremely low frequency-electromagnetic fields (EM-ELF).

    abstract::Chlorella vulgaris was grown in two bench-scale photobioreactors with and without the application of a low intensity, low frequency electromagnetic field (EM-ELF) of about 3mT. Cell concentration and tendency of cells to form aggregates inside the reactor were recorded over a 30 days-time period at 0.5L-constant mediu...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2013.10.035

    authors: Beruto DT,Lagazzo A,Frumento D,Converti A

    更新日期:2014-01-01 00:00:00

  • Development of an intra-molecularly shuffled efficient chimeric plant promoter from plant infecting Mirabilis mosaic virus promoter sequence.

    abstract::We developed an efficient chimeric promoter, MUASMSCP, with enhanced activity and salicylic acid (SA)/abscisic acid (ABA) inducibility, incorporating the upstream activation sequence (UAS) of Mirabilis mosaic virus full-length transcript (MUAS, -297 to -38) to the 5' end of Mirabilis mosaic virus sub-genomic transcrip...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2013.08.022

    authors: Acharya S,Sengupta S,Patro S,Purohit S,Samal SK,Maiti IB,Dey N

    更新日期:2014-01-01 00:00:00

  • Analysis of aging in lager brewing yeast during serial repitching.

    abstract::Serial repitching of brewing yeast inoculates is an important economic factor in the brewing industry, as their propagation is time and resource intensive. Here, we investigated whether replicative aging and/or the population distribution status changed during serial repitching in three different breweries with the sa...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2014.07.002

    authors: Bühligen F,Lindner P,Fetzer I,Stahl F,Scheper T,Harms H,Müller S

    更新日期:2014-10-10 00:00:00

  • Cellulosomic profiling produced by Clostridium cellulovorans during growth on different carbon sources explored by the cohesin marker.

    abstract::Clostridium cellulovorans produces large extracellular enzyme complex, called cellulosomes. The diversity of the cellulosomal enzymes, which are secreted by C. cellulovorans that has been cultured on different carbon sources, such as Avicel, xylan, AXP (Avicel-xylan-pectin, 3:1:1) and cellobiose, was explored by two-d...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2009.11.020

    authors: Cho W,Jeon SD,Shim HJ,Doi RH,Han SO

    更新日期:2010-02-01 00:00:00

  • The construction of bifunctional fusion proteins consisting of MutS and GFP.

    abstract::MutS as a mismatch binding protein is a promising tool for SNP detection. Green fluorescent protein (GFP) is known as an excellent reporter domain. We constructed chimeric proteins consisting of MutS from Thermus thermophilus and GFPuv from Aequorea victoria by cloning the GFPuv gene into the plasmid vectors carrying ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2005.08.009

    authors: Stanisławska-Sachadyn A,Sachadyn P,Ihle K,Sydorczuk C,Wiejacha K,Kur J

    更新日期:2006-01-24 00:00:00

  • Synthesis and purification of a deleted human growth hormone, hGH delta 135-146: sensitivity to plasmin cleavage and in vitro and in vivo bioactivities.

    abstract::Proteolytically cleaved human 22 kDa growth hormone (22K hGH) between the amino acid residues 134 and 150 by plasmin or other proteases in vitro has been reported to be most active in growth promoting activity. In this study a deleted mutant hGH lacking amino acid residues from 135 to 146 and having more sensitivity t...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/s0168-1656(99)00234-5

    authors: Alam KS,Fujikawa T,Yoshizato H,Tanaka M,Nakashima K

    更新日期:2000-02-28 00:00:00

  • Optimization of lactic acid production using immobilized Lactobacillus Rhamnosus and carob pod waste from the Lebanese food industry.

    abstract::The valorization of a solid carob waste from the Lebanese industry was investigated by optimizing the production of lactic acid using immobilized Lactobacillus rhamnosus in alginate beads and response surface methodology. The results showed that pH and alginate concentration had a significant effect on the production ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2019.09.017

    authors: Bahry H,Abdalla R,Pons A,Taha S,Vial C

    更新日期:2019-12-20 00:00:00

  • Diversity analysis of ACC deaminase producing bacteria associated with rhizosphere of coconut tree (Cocos nucifera L.) grown in Lakshadweep islands of India and their ability to promote plant growth under saline conditions.

    abstract::ACC deaminase producing Plant growth promoting rhizobacteria (PGPR) offers a great promise for ameliorating the negative impacts of salinity stress manifested on plants. In this context, 28 rhizospheric bacteria associated with ACC deaminase potential (198-1069 nmol α-ketobutyrate mg protein-1 h-1) were isolated from ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2020.10.024

    authors: Pandey S,Gupta S

    更新日期:2020-12-20 00:00:00

  • Marine actinomycetes as an emerging resource for the drug development pipelines.

    abstract::Many representatives of the order Actinomycetales are prolific producers of thousands of biologically active secondary metabolites. Actinomycetes from terrestrial sources have been studied and screened since the 1950s, yielding many important anti-infective and anti-cancer drugs. However, frequent re-discovery of the ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jbiotec.2011.06.002

    authors: Zotchev SB

    更新日期:2012-04-30 00:00:00

  • Solasodine production from self-immobilised Solanum aviculare cells.

    abstract::Procedures were developed for 'self-immobilisation' of Solanum aviculare cells to eliminate the need for artificial immobilisation supports. Depending on the cytokinin used in liquid medium, compact aggregates 0.4-2.0 cm in diameter were formed without dispersed cells also being present. Histochemical analysis showed ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/0168-1656(91)90077-9

    authors: Tsoulpha P,Doran PM

    更新日期:1991-06-01 00:00:00

  • Degradation of natural and synthetic polyesters under anaerobic conditions.

    abstract::Often, degradability under anaerobic conditions is desirable for plastics claimed to be biodegradable, e.g. in anaerobic biowaste treatment plants, landfills and in natural anaerobic sediments. The biodegradation of the natural polyesters poly(beta-hydroxybutyrate) (PHB), poly(beta-hydroxybutyrate-co-11.6%-beta-hydrox...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/s0168-1656(00)00406-5

    authors: Abou-Zeid DM,Müller RJ,Deckwer WD

    更新日期:2001-03-30 00:00:00

  • An improved fluorescence polarization assay in 5'-nuclease reaction for gene promoter methylation detection.

    abstract::The detection of gene promoter methylation plays increasing roles in personalized medicine. In this study, an improved gene promoter methylation assay based on fluorescence polarization in 5'-nuclease reaction was developed. The novel assay offered a homogeneous annealing and cleavage reaction fully integrated with PC...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2015.07.003

    authors: Su H,Wu Z,Wang Y,Jiang Y,Qiang S,Cheng H,Liu W,Zhang J

    更新日期:2015-10-10 00:00:00

  • Complete genome sequence of the actinobacterium Amycolatopsis japonica MG417-CF17(T) (=DSM 44213T) producing (S,S)-N,N'-ethylenediaminedisuccinic acid.

    abstract::We report the complete genome sequence of Amycolatopsis japonica MG417-CF17(T) (=DSM 44213(T)) which was identified as the producer of (S,S)-N,N'-ethylenediaminedisuccinic acid during a screening for phospholipase C inhibitors. The genome of A. japonica MG417-CF17(T) consists of two replicons: the chromosome (8,961,31...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2014.08.034

    authors: Stegmann E,Albersmeier A,Spohn M,Gert H,Weber T,Wohlleben W,Kalinowski J,Rückert C

    更新日期:2014-11-10 00:00:00