156 results match your criteria Bioengineered bugs[Journal]


The Saccharomyces cerevisiae SCRaMbLE system and genome minimization.

Bioeng Bugs 2012 May-Jun;3(3):168-71. Epub 2012 May 1.

Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

We have recently reported the first partially synthetic eukaryotic genome. Saccharomyces cerevisiae chromosomes synIXR and semi-synVIL are fully synthetic versions of the right arm of chromosome IX and the telomeric segment of the left arm of chromosome VI, respectively, and represent the beginning of the synthetic yeast genome project, Sc2.0, that progressively replaces native yeast DNA with synthetic sequences. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.19543DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3370935PMC
October 2012

Saccharomyces cerevisiae in directed evolution: An efficient tool to improve enzymes.

Bioeng Bugs 2012 May-Jun;3(3):172-7. Epub 2012 May 1.

Department of Biocatalysis, Institute of Catalysis, CSIC, Madrid, Spain.

Over the past 20 years, directed evolution has been seen to be the most reliable approach to protein engineering. Emulating the natural selection algorithm, ad hoc enzymes with novel features can be tailor-made for practical purposes through iterative rounds of random mutagenesis, DNA recombination and screening. Of the heterologous hosts used in laboratory evolution experiments, the budding yeast Saccharomyces cerevisiae has become the best choice to express eukaryotic proteins with improved properties. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.19544DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3370936PMC
October 2012

Saccharomyces cerevisiae STR3 and yeast cystathionine β-lyase enzymes: The potential for engineering increased flavor release.

Bioeng Bugs 2012 May-Jun;3(3):178-80. Epub 2012 May 1.

The Australian Wine Research Institute, Adelaide, SA, Australia.

Selected Saccharomyces cerevisiae strains are used for wine fermentation. Based on several criteria, winemakers often use a specific yeast to improve the flavor, mouth feel, decrease the alcohol content and desired phenolic content, just to name a few properties. Scientists at the AWRI previously illustrated the potential for increased flavor release from grape must via overexpression of the Escherichia coli Tryptophanase enzyme in wine yeast. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.19566DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3370937PMC
October 2012
2 Reads

The winemaker's bug: From ancient wisdom to opening new vistas with frontier yeast science.

Bioeng Bugs 2012 May-Jun;3(3):147-56. Epub 2012 May 1.

University of South Australia, Adelaide, Australia.

The past three decades have seen a global wine glut. So far, well-intended but wasteful and expensive market-intervention has failed to drag the wine industry out of a chronic annual oversupply of roughly 15%. Can yeast research succeed where these approaches have failed by providing a means of improving wine quality, thereby making wine more appealing to consumers? To molecular biologists Saccharomyces cerevisiae is as intriguing as it is tractable. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.19687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3370933PMC
October 2012
9 Reads

Frex and FrexH: Indicators of metabolic states in living cells.

Bioeng Bugs 2012 May-Jun;3(3):181-8. Epub 2012 May 1.

Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, China.

Reduced nicotinamide adenine dinucleotide (NADH) and its oxidized form play central roles in energy and redox metabolisms. For many years, researchers have relied on the weak NADH endogenous fluorescence signal to determine the NADH level in living cells. We recently reported a series of genetically encoded fluorescent sensors highly specific for NADH. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.19769DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3370938PMC
October 2012

H5N1 moratorium: Missing the point.

Authors:
Pat G Casey

Bioeng Bugs 2012 May-Jun;3(3):144. Epub 2012 May 1.

The recent moratorium on research using engineered H5N1 influenza viruses is a move which cannot achieve its aims as it ignores the prevalence of molecular biology. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.20004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3370931PMC
October 2012
1 Read

Avian H5N1 influenza: In or out flew-enza?

Authors:
John G Morgan

Bioeng Bugs 2012 May-Jun;3(3):145-6. Epub 2012 May 1.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.20190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3370932PMC
October 2012
1 Read

A bi-cistronic baculovirus expression vector for improved recombinant protein production.

Bioeng Bugs 2012 Mar-Apr;3(2):129-32. Epub 2012 Mar 1.

Department of Bioscience Technology, Chung Yuan Christian University, Chungli, Taiwan.

Baculoviruses are one of the most studied insect viruses both in basic virology research and in biotechnology applications. Incorporating an internal ribosome entry site (IRES) into the baculovirus genome generates bi-cistronic baculoviruses expression vectors that produce two genes of interest. The bi-cistronic baculoviruses also facilitate recombinant virus isolation and titer determination when the green fluorescent protein was co-expressed. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.19388DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3357334PMC
October 2012
5 Reads

Development and optimization of an EGFP-based reporter for measuring the general stress response in Listeria monocytogenes.

Bioeng Bugs 2012 Mar-Apr;3(2):93-103. Epub 2012 Mar 1.

Department of Microbiology, School of Natural Sciences, National University of Ireland, Galway, Galway, Ireland.

A characteristic of the food-borne pathogen Listeria monocytogenes is its tolerance to the harsh conditions found both in minimally processed foods and the human gastrointestinal tract. This trait is partly under the control of the alternative sigma factor sigma B (σ(B)). To study the mechanisms that trigger the activation of σ(B) , and hence the development of stress tolerance, we have developed a fluorescent reporter fusion that allows the real-time activity of σ(B) to be monitored. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.19476DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3357339PMC
October 2012
20 Reads

Antifungal activity of Lactobacillus against Microsporum canis, Microsporum gypseum and Epidermophyton floccosum.

Bioeng Bugs 2012 Mar-Apr;3(2):104-13. Epub 2012 Mar 1.

Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland.

A total of 220 lactic acid bacteria isolates were screened for antifungal activity using Aspergillus fumigatus and Aspergillus niger as the target strains. Four Lactobacillus strains exhibited strong inhibitory activity on agar surfaces. All four were also identified as having strong inhibitory activity against the human pathogenic fungi Microsporum canis, Microsporum gypseum and Epidermophyton floccosum. Read More

View Article

Download full-text PDF

Source
http://www.tandfonline.com/doi/abs/10.4161/bbug.19624
Publisher Site
http://dx.doi.org/10.4161/bbug.19624DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3357330PMC
October 2012
13 Reads

Outsider to insider: resetting the natural host niche of commensal E. coli K-12.

Bioeng Bugs 2012 Mar-Apr;3(2):133-7. Epub 2012 Mar 1.

Institute of Molecular Medicine, New Delhi, India.

The status of E. coli K-12 as an exclusively non-invasive, non-pathogenic bacterium has almost been incontrovertible. Our recent finding that a mutation in one of its main architectural protein, HU, converts E. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.19686DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3357335PMC
October 2012

Ferretting out the facts behind the H5N1 controversy.

Authors:
Roy D Sleator

Bioeng Bugs 2012 May-Jun;3(3):139-43. Epub 2012 May 1.

Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland.

Recent recommendations by the National Science Advisory Board for Biosecurity (NSABB) to redact key methodological details of two studies involving mammal-to-mammal transmission of the H5N1 (H5) subtype influenza viruses, has led to a temporary moratorium on all research involving live H5N1 or H5 HA reassortant viruses shown to be transmissible in ferrets. Herein, I review the events which led to this impasse and comment on their impact. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.19943DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3370930PMC
October 2012
2 Reads

Identification of iron-regulated genes of Bifidobacterium breve UCC2003 as a basis for controlled gene expression.

Bioeng Bugs 2012 May-Jun;3(3):157-67. Epub 2012 May 1.

Alimentary Pharmabiotic Centre and Department of Microbiology, University College Cork, Cork, Ireland.

Iron is an essential growth factor for virtually all organisms. However, iron is not readily available in most environments and microorganisms have evolved specialized mechanisms, such as the use of siderophores and high-affinity transport systems, to acquire iron when confronted with iron-limiting conditions. In general these systems are tightly regulated to prevent iron-induced toxicity and because they are quite costly to the microbe. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.18985DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3370934PMC
October 2012
14 Reads

Whole-cell biochips for online water monitoring.

Bioeng Bugs 2012 Mar-Apr;3(2):124-8. Epub 2012 Mar 1.

The Alexander Silberman Institute of Life Sciences, Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.

Chip-integrated luminescent recombinant reporter bacteria were combined with fluidics and light detection systems to form a real-time water biomonitor. The biomonitor was exposed to a continuous water flow for up to ten days, in the course of which it was challenged with spikes of both model toxic compounds and toxic environmental samples. All simulated contamination events were reported within 0. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.18879DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3357333PMC
October 2012

Modification of the avian coronavirus infectious bronchitis virus for vaccine development.

Bioeng Bugs 2012 Mar-Apr;3(2):114-9. Epub 2012 Mar 1.

Avian Viral Diseases, Institute for Animal Health, Compton Laboratory, Compton, Newbury, Berkshire, UK.

Infectious bronchitis virus (IBV) causes an infectious respiratory disease of domestic fowl that affects poultry of all ages causing economic problems for the poultry industry worldwide. Although IBV is controlled using live attenuated and inactivated vaccines it continues to be a major problem due to the existence of many serotypes, determined by the surface spike protein resulting in poor cross-protection, and loss of immunogenicity associated with vaccine production. Live attenuated IBV vaccines are produced by the repeated passage in embryonated eggs resulting in spontaneous mutations. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.18983DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3357331PMC
October 2012
1 Read

Computational studies on a new cationic peroxidase isoenzyme from artichoke leaves.

Bioeng Bugs 2012 Jan 1;3(1):60-6. Epub 2012 Jan 1.

Institute of Sciences of Food Production-CNR, Bari, Italy.

Previously we presented the purification, biochemical characterization, and cloning of a cationic peroxidase isoenzyme (CysPrx) from artichoke (Cynara cardunculus subsp scolymus (L.) Hegi) leaves. The protein was shown to have some interesting properties, suggesting that CysPrx could be a considered as a potential candidate for industrial application. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.3.1.17937DOI Listing
January 2012
1 Read

Bench-top fermentative production of plant benzylisoquinoline alkaloids using a bacterial platform.

Bioeng Bugs 2012 Jan 1;3(1):49-53. Epub 2012 Jan 1.

Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi-machi, Ishikawa, Japan.

The plant secondary metabolites benzylisoquinoline alkaloids (BIAs) have diverse pharmaceutical activities, and some are used medicinally (e.g., morphine, codeine, berberine). Read More

View Article

Download full-text PDF

Source
http://www.tandfonline.com/doi/abs/10.4161/bbug.3.1.18446
Publisher Site
http://dx.doi.org/10.4161/bbug.3.1.18446DOI Listing
January 2012
8 Reads

Recombinant D. radiodurans cells for bioremediation of heavy metals from acidic/neutral aqueous wastes.

Bioeng Bugs 2012 Jan 1;3(1):44-8. Epub 2012 Jan 1.

Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.

The stability and superior metal bioremediation ability of genetically engineered Deinococcus radiodurans cells, expressing a non-specific acid phosphatase, PhoN in high radiation environment has already been established. The lyophilized recombinant DrPhoN cells retained PhoN activity and uranium precipitation ability. Such cells also displayed an extended shelf life of 6 months during storage at room temperature and showed surface associated precipitation of uranium as well as other metals like cadmium. Read More

View Article

Download full-text PDF

Source
http://www.tandfonline.com/doi/abs/10.4161/bbug.3.1.18878
Publisher Site
http://dx.doi.org/10.4161/bbug.3.1.18878DOI Listing
January 2012
5 Reads

Molecular diagnostics: the changing culture of medical microbiology.

Bioeng Bugs 2012 Jan 1;3(1):1-7. Epub 2012 Jan 1.

Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland.

Diagnostic molecular biology is arguably the fastest growing area in current laboratory-based medicine. Growth of the so called 'omics' technologies has, over the last decade, led to a gradual migration away from the 'one test, one pathogen' paradigm, toward multiplex approaches to infectious disease diagnosis, which have led to significant improvements in clinical diagnostics and ultimately improved patient care. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.3.1.19011DOI Listing
January 2012
2 Reads

Biomedicals from a soil bug: expanding scFv production host range.

Authors:
Thorben Dammeyer

Bioeng Bugs 2012 Jan 1;3(1):67-71. Epub 2012 Jan 1.

Physical & Theoretical Chemistry, NanoBioSciences, TU-Braunschweig and Helmholtz Centre for Infection Research, Braunschweig, Germany.

Recombinant antibody fragments have a wide range of applications from research to diagnostics and therapy. Of special interest are small fragments like fragment antigen binding (Fab) or single chain fragment variables (scFv) fragments as they can be produced inexpensively in bacterial expression systems. However, recombinant production efficiencies from established production hosts vary significantly leading to inadequate yields. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.3.1.17739DOI Listing
January 2012

Fast track assembly of multigene constructs using Golden Gate cloning and the MoClo system.

Bioeng Bugs 2012 Jan 1;3(1):38-43. Epub 2012 Jan 1.

Icon Genetics GmbH, Halle, Germany.

Recent progress in the field of synthetic biology has led to the creation of cells containing synthetic genomes. Although these first synthetic organisms contained copies of natural genomes, future work will be directed toward engineering of organisms with modified genomes and novel phenotypes. Much work, however, remains to be done to be able to routinely engineer novel biological functions. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.3.1.18223DOI Listing
January 2012
31 Reads

A color-based stable multi-copy integrant selection system for Pichia pastoris using the attenuated ADE1 and ADE2 genes as auxotrophic markers.

Bioeng Bugs 2012 Jan 1;3(1):32-7. Epub 2012 Jan 1.

GlycoFi, Inc., Lebanon, NH, USA.

The methylotropic yeast Pichia pastoris has been used for more than two decades to successfully produce a large number of recombinant proteins. Currently, a wide variety of auxotrophic and drug based selection markers are employed to screen for clones expressing the protein of interest. For most proteins an increased copy number of the integrated plasmid results in higher levels of expression, but these multi-copy integrants can be unstable due to the propensity of P. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.3.1.17936DOI Listing
January 2012

Evolutionary, ecological and biotechnological perspectives on plasmids resident in the human gut mobile metagenome.

Bioeng Bugs 2012 Jan 1;3(1):13-31. Epub 2012 Jan 1.

Centre for Biomedical and Health Science Research, School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, UK.

Numerous mobile genetic elements (MGE) are associated with the human gut microbiota and collectively referred to as the gut mobile metagenome. The role of this flexible gene pool in development and functioning of the gut microbial community remains largely unexplored, yet recent evidence suggests that at least some MGE comprising this fraction of the gut microbiome reflect the co-evolution of host and microbe in the gastro-intestinal tract. In conjunction, the high level of novel gene content typical of MGE coupled with their predicted high diversity, suggests that the mobile metagenome constitutes an immense and largely unexplored gene-space likely to encode many novel activities with potential biotechnological or pharmaceutical value, as well as being important to the development and functioning of the gut microbiota. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.3.1.17883DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329251PMC
January 2012
3 Reads

Genetic analysis of Down syndrome facilitated by mouse chromosome engineering.

Bioeng Bugs 2012 Jan 1;3(1):8-12. Epub 2012 Jan 1.

Children's Guild Foundation Down Syndrome Research Program, Buffalo, NY, USA.

Human trisomy 21 is the most frequent live-born human aneuploidy and causes a constellation of disease phenotypes classified as Down syndrome, which include heart defects, myeloproliferative disorder, cognitive disabilities and Alzheimer-type neurodegeneration. Because these phenotypes are associated with an extra copy of a human chromosome, the genetic analysis of Down syndrome has been a major challenge. To complement human genetic approaches, mouse models have been generated and analyzed based on evolutionary conservation between the human and mouse genomes. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.3.1.17696DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329253PMC
January 2012
2 Reads

Differentiation of programmed Arabidopsis cells.

Bioeng Bugs 2012 Jan 1;3(1):54-9. Epub 2012 Jan 1.

Department of Plant Biology, North Carolina State University, Raleigh, NC, USA.

Plants express genes that encode enzymes that catalyse reactions to form plant secondary metabolites in specific cell types. However, the mechanisms of how plants decide their cellular metabolic fate and how cells diversify and specialise their specific secondary metabolites remains largely unknown. Additionally, whether and how an established metabolic program impacts genome-wide reprogramming of plant gene expression is unclear. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.3.1.17786DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329252PMC
January 2012
2 Reads

Proteins: form and function.

Authors:
Roy D Sleator

Bioeng Bugs 2012 Mar-Apr;3(2):80-5. Epub 2012 Mar 1.

Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland.

An overwhelming array of structural variants has evolved from a comparatively small number of protein structural domains; which has in turn facilitated an expanse of functional derivatives. Herein, I review the primary mechanisms which have contributed to the vastness of our existing, and expanding, protein repertoires. Protein function prediction strategies, both sequence and structure based, are also discussed and their associated strengths and weaknesses assessed. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.18303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3357337PMC
October 2012
2 Reads

Artificially designed promoters: understanding the role of spatial features and canonical binding sites in transcription.

Bioeng Bugs 2012 Mar-Apr;3(2):120-3. Epub 2012 Mar 1.

Department of Biotechnology; University of Natural Resources and Applied Life Sciences, Vienna, Austria.

The promoter is a key element in gene transcription and regulation. We previously reported that artificial sequences rich in the dinucleotide CpG are sufficient to drive expression in vitro in mammalian cell lines, without requiring canonical binding sites for transcription factor proteins. Here, we report that introducing a promoter organization that alternates in CpGs and regions rich in A and T further increases expression strength, as well as how insertion of specific binding sites makes such sequences respond to induced levels of the transcription factor NFκB. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.18530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3357332PMC
October 2012
16 Reads

Probiogenomics as a tool to obtain genetic insights into adaptation of probiotic bacteria to the human gut.

Bioeng Bugs 2012 Mar-Apr;3(2):73-9. Epub 2012 Mar 1.

Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Parma, Italy.

Bifidobacteria and lactobacilli are widely exploited as health-promoting bacteria in many functional foods. However, the molecular mechanisms as to how these bacteria positively impact on host health are far from completely understood. For this reason these microorganisms represent a growing area of interest with respect to their genomics, molecular biology and genetics. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.18540DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3357336PMC
October 2012
2 Reads

Bacterial delivery of large intact genomic-DNA-containing BACs into mammalian cells.

Bioeng Bugs 2012 Mar-Apr;3(2):86-92. Epub 2012 Mar 1.

Division of Natural Sciences, Imperial College London, London, UK.

Efficient delivery of large intact vectors into mammalian cells remains problematical. Here we evaluate delivery by bacterial invasion of two large BACs of more than 150 kb in size into various cells. First, we determined the effect of several drugs on bacterial delivery of a small plasmid into different cell lines. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.18621DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3357338PMC
October 2012
2 Reads

Attenuated Bordetella pertussis BPZE1 as a live vehicle for heterologous vaccine antigens delivery through the nasal route.

Bioeng Bugs 2011 Nov-Dec;2(6):315-9. Epub 2011 Nov 1.

Department of Microbiology, Immunology programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.

Whereas the great majority of the current vaccines are delivered through the parenteral route, mucosal administration has been increasingly considered for controlling infection and preventing disease. Mucosal vaccination can trigger both humoral and cell-mediated protection, not only at the targeted mucosal surface, but also systemically. In this regard, nasal vaccination has shown great potential. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.2.6.18167DOI Listing

The genetic toolbox for Leishmania parasites.

Authors:
Sigrid C Roberts

Bioeng Bugs 2011 Nov-Dec;2(6):320-6. Epub 2011 Nov 1.

Pacific University School of Pharmacy, Hillsboro, OR, USA.

Leishmania parasites cause a variety of devastating diseases in tropical areas around the world. Due to the lack of vaccines and limited availability of drugs, new therapeutic targets are urgently needed. A variety of genetic tools have been developed to investigate the complex biology of this parasite and its interactions with the host. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.2.6.18205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3242788PMC

Online homology modelling as a means of bridging the sequence-structure gap.

Bioeng Bugs 2011 Nov-Dec;2(6):299-305. Epub 2011 Nov 1.

Proteomics Research Group, Department of Biochemistry, University College Cork, Lee Maltings, Prospect Row, Mardyke, Cork, Ireland.

For even the best-studied species, there is a large gap in their representation in the protein databank (PDB) compared to within sequence databases. Typically, less than 2% of sequences are represented in the PDB. This is partly due to the considerable experimental challenge and manual inputs required to solve three dimensional structures by methods such as X-ray diffraction and multi-dimensional nuclear magnetic resonance (NMR) spectroscopy in comparison to high-throughput sequencing. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.2.6.16116DOI Listing

CDPK-driven changes in the intracellular ROS level and plant secondary metabolism.

Bioeng Bugs 2011 Nov-Dec;2(6):327-30. Epub 2011 Nov 1.

Institute of Biology and Soil Science, Far East Branch of Russian Academy of Sciences, Vladivostok 690022, Russia.

Heterologous expression of a constitutively active calcium-dependent protein kinase (CDPK) gene was previously shown to increase secondary metabolite production in cultured cells of Rubia cordifolia, but the critical question of how CDPK activates secondary metabolism remains to be answered. In this article, we report that the expression of the Arabidopsis CDPK gene, AtCPK1, in R. cordifolia cells caused moderate and stable elevation of intracellular reactive oxygen species (ROS) levels. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.2.6.16803DOI Listing
April 2012
3 Reads

Metabolic regulation of an fnr gene knockout Escherichia coli under oxygen limitation.

Bioeng Bugs 2011 Nov-Dec;2(6):331-7. Epub 2011 Nov 1.

Kyushu Institute of Technology, Department of Bioscience & Bioinformatics, Iizuka, Fukuoka, Japan.

In addition to our previous study on the effect of fnr gene knockout on the metabolism in Escherichia coli under aerobic conditions (Kumar and Shimizu, Microb Cell Fact 2011), here we further investigated the effect of fnr gene knockout on the metabolism under micro-aerobic condition based on gene expressions, enzyme activities and intracellular metabolic fluxes. The objective of the present research is to clarify the metabolic regulation mechanism on how the culture environment, such as oxygen level, affects the cell metabolism in relation to gene expressions, enzyme activities and fluxes via global regulators such as Fnr and ArcA/B systems. Under micro-aerobic condition, the flux through Pfl and Frd were reduced for the mutant, which are due to fnr gene knockout. Read More

View Article

Download full-text PDF

Source
http://www.tandfonline.com/doi/abs/10.4161/bbug.2.6.16350
Publisher Site
http://dx.doi.org/10.4161/bbug.2.6.16350DOI Listing
April 2012
18 Reads

Designing symbiosis.

Bioeng Bugs 2011 Nov-Dec;2(6):338-41. Epub 2011 Nov 1.

Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan.

Organisms rarely live as isolated species and usually show symbiosis in nature. As natural selection is not simple in symbiosis, the establishment and development of symbiosis is still unclear. Insight can be gained by not only retracing the history of well-developed natural symbiotic relationships, but also by observing the development of nascent symbiosis. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.2.6.16801DOI Listing
April 2012
3 Reads

Lysins to kill - a tale of viral weapons of mass destruction.

Bioeng Bugs 2011 Nov-Dec;2(6):306-8. Epub 2011 Nov 1.

Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland.

View Article

Download full-text PDF

Source
http://www.tandfonline.com/doi/abs/10.4161/bbug.2.6.16804
Publisher Site
http://dx.doi.org/10.4161/bbug.2.6.16804DOI Listing
April 2012
18 Reads

Shifting from a gene-centric to metabolite-centric strategy to determine the core gut microbiome.

Bioeng Bugs 2011 Nov-Dec;2(6):309-14. Epub 2011 Nov 1.

School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK.

A key challenge in the area of determining how the microbiome communicates with the host's karyome is deciding which microbial functions should be studied. Ideally we would wish to look at functions which are not only important to the microbial host, but which also play roles in host physiology. Selecting the key microbial functions is essential to developing robust strategies to either promote or demote them, with the aim to enhancing host health. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.2.6.17235DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3242787PMC

Metabolic engineering to improve 5-aminolevulinic acid production.

Bioeng Bugs 2011 Nov-Dec;2(6):342-5. Epub 2011 Nov 1.

State Key Laboratory of Microbial Technology, Shandong University, Jinan, China.

5-Aminolevulinic acid (ALA) has recently attracted significant attentions due to its potential applications in many diverse fields. The majority of engineered ALA producers are based on the whole cell catalysis, supplemented with succinate and glycine as precursors. Recently, we succeeded in producing ALA directly from inexpensive glucose, through re-constructing the native C5 pathway of ALA synthesis in Escherichia coli. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.2.6.17237DOI Listing
April 2012
3 Reads

Current knowledge on isobutanol production with Escherichia coli, Bacillus subtilis and Corynebacterium glutamicum.

Bioeng Bugs 2011 Nov-Dec;2(6):346-50. Epub 2011 Nov 1.

Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany.

Due to steadily rising crude oil prices great efforts have been made to develop designer bugs for the fermentative production of higher alcohols, such as 2-methyl-1-butanol, 3-methyl-1-butanol and 2-Methyl-1-propanol (isobutanol), which all possess quality characteristics comparable to traditional oil based fuels. The common metabolic engineering approach uses the last two steps of the Ehrlich pathway, catalyzed by 2-ketoacid decarboxylase and an alcohol dehydrogenase converting the branched chain 2-ketoacids of L-isoleucine, L-leucine, and L-valine into the respective alcohols. This strategy was successfully used to engineer well suited and industrially employed bacteria, such as Escherichia coli, Bacillus subtilis and Corynebacterium glutamicum for the production of higher alcohols. Read More

View Article

Download full-text PDF

Source
http://www.tandfonline.com/doi/abs/10.4161/bbug.2.6.17845
Publisher Site
http://dx.doi.org/10.4161/bbug.2.6.17845DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3242789PMC
April 2012
3 Reads

MrBac: a web server for draft metabolic network reconstructions for bacteria.

Bioeng Bugs 2011 Sep-Oct;2(5):284-7. Epub 2011 Sep 1.

Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan 350, Taiwan.

Genome-scale metabolic network reconstruction can be used for simulating cellular behaviors by simultaneously monitoring thousands of biochemical reactions, and is therefore important for systems biology studies in microbes. However, the labor-intensive and time-consuming reconstruction process has hindered the progress of this important field. Here we present a web server, MrBac (Metabolic network Reconstructions for Bacteria), to streamline the network reconstruction process for draft genome-scale metabolic networks and to provide annotation information from multiple databases for further curation of the draft reconstructions. Read More

View Article

Download full-text PDF

Source
http://www.tandfonline.com/doi/abs/10.4161/bbug.2.5.16113
Publisher Site
http://dx.doi.org/10.4161/bbug.2.5.16113DOI Listing
February 2012
5 Reads

Developing strategies to enhance and focus humoral immune responses using filamentous phage as a model antigen.

Bioeng Bugs 2011 Sep-Oct;2(5):275-83. Epub 2011 Sep 1.

Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A1S6, Canada.

Filamentous bacteriophage are commonly used as immunogenic carriers for peptides and proteins displayed on the phage surface. Previously, we showed that immunization with phage to which peptides had been chemically conjugated can elicit a focused anti-peptide antibody response compared with traditional carrier molecules bearing the same peptide, perhaps due to the low surface complexity of the phage. The regularity of its surface also gives the phage other advantages as a carrier, including immunological simplicity and thousands of well-defined sites for chemical conjugation. Read More

View Article

Download full-text PDF

Source
http://www.tandfonline.com/doi/abs/10.4161/bbug.2.5.16559
Publisher Site
http://dx.doi.org/10.4161/bbug.2.5.16559DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3225742PMC
February 2012
3 Reads

Impact of a new glucose utilization pathway in amino acid-producing Corynebacterium glutamicum.

Bioeng Bugs 2011 Sep-Oct;2(5):291-5. Epub 2011 Sep 1.

Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, D-33501 Bielefeld, Germany.

Corynebacterium glutamicum imports and phosphorylates glucose, fructose and sucrose by the phosphoenolpyruvate-dependent phosphotransferase carbohydrate uptake system (PTS). Recently, we have discovered how glucose can be utilized by C. glutamicum in a PTS-independent manner. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.2.5.17116DOI Listing
February 2012
10 Reads
4 Citations

Miniaturized bacterial biosensor system for arsenic detection holds great promise for making integrated measurement device.

Bioeng Bugs 2011 Sep-Oct;2(5):296-8. Epub 2011 Sep 1.

Laboratory of Microsystems Engineering LMIS4, Ecole Polytechnique Fédérale Lausanne, EPFL-STI-LMIS, Station 17, CH-1015 Lausanne, Switzerland.

Combining bacterial bioreporters with microfluidics systems holds great promise for in-field detection of chemical or toxicity targets. Recently we showed how Escherichia coli cells engineered to produce a variant of green fluorescent protein after contact to arsenite and arsenate can be encapsulated in agarose beads and incorporated into a microfluidic chip to create a device for in-field detection of arsenic, a contaminant of well known toxicity and carcinogenicity in potable water both in industrialized and developing countries. Cell-beads stored in the microfluidics chip at -20°C retained inducibility up to one month and we were able to reproducibly discriminate concentrations of 10 and 50 μg arsenite per L (the drinking water standards for European countries and the United States, and for the developing countries, respectively) from the blank in less than 200 minutes. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.2.5.17236DOI Listing
February 2012
5 Reads

Tools used to study how protein complexes are assembled in signaling cascades.

Bioeng Bugs 2011 Sep-Oct;2(5):247-59. Epub 2011 Sep 1.

Department of Life Sciences, and Materials and Surface Science Institute, University of Limerick, Limerick, Ireland.

Most proteins do not function on their own but as part of large signaling complexes that are arranged in every living cell in response to specific environmental cues. Proteins interact with each other either constitutively or transiently and do so with different affinity. When identifying the role played by a protein inside a cell, it is essential to define its particular cohort of binding partners so that the researcher can predict what signaling pathways the protein is engaged in. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.2.5.17844DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3225741PMC
February 2012
10 Reads

An in silico analysis of osmotolerance in the emerging gastrointestinal pathogen Cronobacter sakazakii.

Bioeng Bugs 2011 Sep-Oct;2(5):260-70. Epub 2011 Sep 1.

Department of Biological Sciences, Cork Institute of Technology, Rossa Avenue, Bishopstown, Cork, Ireland.

Up to 80% of infants infected with Cronobacter sakazakii die within days of birth, making this emerging gastrointestinal pathogen a serious cause for concern. The mode of transmission most often associated with C. sakazakii infection is powdered infant formula (PIF), which typically has a water activity (aw) of ca 0. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.2.5.17238DOI Listing
February 2012

Heterologous activation of the Porphyra tenera HSP70 promoter in Bangiophycean algal cells.

Bioeng Bugs 2011 Sep-Oct;2(5):271-4. Epub 2011 Sep 1.

Graduate School of Fisheries Sciences, Hokkaido University, Minato, Hakodate, Japan.

Porphyra has attracted great attention for its biological and industrial importance. However, establishment of a stable nuclear transformation has not yet been achieved in these organisms, which impedes the molecular biological study and the development of a molecular breeding method for them. Toward establishing the stable transformation, we have recently developed an efficient transient gene expression system in Bangiophycean algae, in which the HSP70 promoter from P. Read More

View Article

Download full-text PDF

Source
http://eprints.lib.hokudai.ac.jp/dspace/bitstream/2115/48273
Web Search
http://www.tandfonline.com/doi/abs/10.4161/bbug.2.5.16938
Publisher Site
http://dx.doi.org/10.4161/bbug.2.5.16938DOI Listing
February 2012
2 Reads

Anti-mycobacterial peptides: made to order with delivery included.

Bioeng Bugs 2011 Sep-Oct;2(5):241-6. Epub 2011 Sep 1.

Department of Biological Sciences, Cork Institute of Technology, Rossa Avenue, Bishopstown, Cork, Ireland.

"TB is too often a death sentence. It does not have to be this way,"- Nelson Mandela. Despite the success of anti-mycobacterial drugs over the past 70 years, mycobacterial disease, particularly tuberculosis is still responsible for millions of annual deaths worldwide. Read More

View Article

Download full-text PDF

Source
http://www.tandfonline.com/doi/abs/10.4161/bbug.2.5.16229
Publisher Site
http://dx.doi.org/10.4161/bbug.2.5.16229DOI Listing
February 2012
1 Read

A non-specific effect of orally administered Escherichia coli.

Authors:
Roman Gardlik

Bioeng Bugs 2011 Sep-Oct;2(5):288-90. Epub 2011 Sep 1.

Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 81108 Bratislava, Slovakia.

A number of genetically modified bacteria able to deliver a therapeutic gene into target cells has already been tested. Apart from the expected effects of bacterial therapy, the therapeutic bacterial strain also mediates a non-specific effect independent of the gene to be delivered. In this regard, we have recently shown that oral administration of the bacterial strain Escherichia coli XL1-Blue via gastric gavage to rats leads to a non-specific decrease in expression of vascular endothelial growth factor (VEGF) in intestinal wall without corresponding changes in other parameters. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.2.5.16115DOI Listing
February 2012

The toxin and antidote puzzle: new ways to control insect pest populations through manipulating inheritance.

Authors:
John M Marshall

Bioeng Bugs 2011 Sep-Oct;2(5):235-40. Epub 2011 Sep 1.

Division of Biology, California Institute of Technology, Pasadena, California, USA.

Insects carry out essential ecological functions, such as pollination, but also cause extensive damage to agricultural crops, and transmit human diseases such as malaria and dengue fever. Advances in insect transgenesis are making it increasingly feasible to engineer genes conferring desirable phenotypes, and gene drive systems are required to spread these genes into wild populations. Medea provides one solution, being able to spread into a population from very low initial frequencies through the action of a maternally-expressed toxin linked to a zygotically-expressed antidote. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.2.5.15801DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3225740PMC
February 2012

How to break recombinant bacteria: does it matter?

Bioeng Bugs 2011 Jul-Aug;2(4):222-5. Epub 2011 Jul 1.

Institut de Biotecnologia i de Biomedicina and Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain.

Recombinant proteins and other materials of industrial interest produced in Escherichia coli are usually retained within the bacterial cell, in the cytoplasmic space, where they have been produced. Different protocols for cell disruption have been implemented as an initial downstream step, which keeps the biological and mechanical properties of the process products. Being necessarily mild, these approaches often result in 95-99% cell disruption, what is more than acceptable from the yield point of view. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/bbug.2.4.15778DOI Listing
March 2012
2 Reads