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1.  Ferretting out the facts behind the H5N1 controversy 
Bioengineered Bugs  2012;3(3):139-143.
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.
PMCID: PMC3370930  PMID: 22402712
2.  H5N1 moratorium 
Bioengineered Bugs  2012;3(3):144.
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.
PMCID: PMC3370931  PMID: 22572784
3.  Avian H5N1 influenza 
Bioengineered Bugs  2012;3(3):145-146.
PMCID: PMC3370932  PMID: 22572782
4.  Identification of iron-regulated genes of Bifidobacterium breve UCC2003 as a basis for controlled gene expression 
Bioengineered Bugs  2012;3(3):157-167.
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. Because of this tight regulation we chose to explore the response of Bifidobacterium breve UCC2003 to iron limitation. Through microarray and complementation analyses we identified and characterized a presumed ferrous iron uptake system, encoded by bfeUOB, from B. breve UCC2003 and exploited its regulated transcription to develop an inducible expression system for use in bifidobacteria.
PMCID: PMC3370934  PMID: 22179149
iron-regulation; plasmid; probiotic
5.  The Saccharomyces cerevisiae SCRaMbLE system and genome minimization 
Bioengineered Bugs  2012;3(3):168-171.
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. We have designed synthetic chromosome sequences according to principles specifying a wild-type phenotype, highly stable genome, and maintenance of genetic flexibility. Although other synthetic genome projects exist, the Sc2.0 approach is unique in that we have implemented design specifications predicted to generate a wild-type phenotype until induction of “SCRaMbLE,” an inducible evolution system that generates significant genetic diversity. Here we further explore the significance of Sc2.0 and show how SCRaMbLE can serve as a genome minimization tool.
PMCID: PMC3370935  PMID: 22572789
genome minimization; Sc2.0; syn VIL; Synthetic genome; yeast
6.  Saccharomyces cerevisiae in directed evolution 
Bioengineered Bugs  2012;3(3):172-177.
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. S. cerevisiae not only allows mutant enzymes to be secreted but also, it permits a wide range of genetic manipulations to be employed, ranging from in vivo cloning to the creation of greater molecular diversity, thanks to its efficient DNA recombination apparatus. Here, we summarize some successful examples of the use of the S. cerevisiae machinery to accelerate artificial evolution, complementing the traditional in vitro methods to generate tailor-made enzymes.
PMCID: PMC3370936  PMID: 22572788
directed evolution; DNA recombination; IvAM; IVOE; random mutagenesis; Saccharomyces cerevisiae
7.  Saccharomyces cerevisiae STR3 and yeast cystathionine β-lyase enzymes 
Bioengineered Bugs  2012;3(3):178-180.
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. To pursue a self-cloning approach for improving the aroma production, we recently characterized the S. cerevisiae cystathionine β-lyase STR3, and investigated its flavor releasing capabilities. Here, we continue with a phylogenetic investigation of STR3 homologs from non-Saccharomyces yeasts to map the potential for using natural variation to engineer new strains.
PMCID: PMC3370937  PMID: 22572787
aromatic thiols; cystathionine β-lyase; flavor; non-Saccharomyces; self-cloning; wine; yeast
8.  Frex and FrexH 
Bioengineered Bugs  2012;3(3):181-188.
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. These sensors allow real-time, quantitative measurement of this significant molecule in different subcellular compartments. In this study, we provide a more detailed discussion of the benefits and limitations of these genetically encoded fluorescent sensors. These sensors are utilized in most laboratories without the need for sophisticated instruments because of their superior sensitivity and specificity. They are also viable alternatives to existing techniques for measuring the endogenous fluorescence of intracellular NAD(P)H.
PMCID: PMC3370938  PMID: 22572785
electron transport chain; genetically encoded sensor; glucose; hypoxia; metabolic state; reduced nicotinamide adenine dinucleotide (NADH); subcellular distribution
9.  Antifungal activity of Lactobacillus against Microsporum canis, Microsporum gypseum and Epidermophyton floccosum 
Bioengineered Bugs  2012;3(2):102-111.
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. One of the four lactobacilli, namely Lb. reuteri ee1p exhibited the most inhibition against dermatophytes. Cell-free culture supernatants of Lb. reuteri ee1p and of the non-antifungal Lb. reuteri M13 were freeze-dried and used to access and compare antifungal activity in agar plate assays and microtiter plate assays. Addition of the Lb. reuteri ee1p freeze-dried cell-free supernatant powder into the agar medium at concentrations greater than 2% inhibited all fungal colony growth. Addition of the powder at 5% to liquid cultures caused complete inhibition of fungal growth on the basis of turbidity. Freeze-dried supernatant of the non-antifungal Lb. reuteri M13 at the same concentrations had a much lesser effect. As Lb. reuteri M13 is very similar to the antifungal strain ee1p in terms of growth rate and final pH in liquid culture, and as it has little antifungal activity, it is clear that other antifungal compounds must be specifically produced (or produced at higher levels) by the anti-dermatophyte strain Lb. reuteri ee1p. Reuterin was undetectable in all four antifungal strains. The cell free supernatant of Lb. reuteri ee1p was analyzed by LC-FTMS using an Accela LC coupled to an LTQ Orbitrap XL mass spectrometer. The high mass accuracy spectrum produced by compounds in the Lb. reuteri ee1p strain was compared with both a multianalyte chromatogram and individual spectra of standard anti-fungal compounds, which are known to be produced by lactic acid bacteria. Ten antifungal metabolites were detected.
PMCID: PMC3357330  PMID: 22539027
Epidermophyton floccosum; antifungal; lactic acid bacteria; Microsporum canis; Microsporum gypseum
10.  Modification of the avian coronavirus infectious bronchitis virus for vaccine development 
Bioengineered Bugs  2012;3(2):112-117.
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. As a consequence attenuated viruses have only a few mutations responsible for the loss of virulence, which will differ between vaccines affecting virulence and/or immunogenicity and can revert to virulence. A new generation of vaccines is called for and one means of controlling IBV involves the development of new and safer vaccines by precisely modifying the IBV genome using reverse genetics for the production of rationally attenuated IBVs in order to obtain an optimum balance between loss of virulence and capacity to induce immunity.
PMCID: PMC3357331  PMID: 22179147
avian; coronavirus; homologous recombination; infectious bronchitis virus; infectious clone; poultry; reverse genetics; spike glycoprotein; vaccine; vaccinia virus
11.  Artificially designed promoters 
Bioengineered Bugs  2012;3(2):118-121.
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. Our findings further contribute to the mechanistic understanding of promoters, as well as how these sequences might be shaped by evolutionary pressure in living organisms.
PMCID: PMC3357332  PMID: 22095054
Artificial promoters; canonical binding sites; CpG content; CpG spacing; NFκB
12.  Whole-cell biochips for online water monitoring 
Bioengineered Bugs  2012;3(2):122-126.
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 0.5–2.5 h. Furthermore, the response pattern of the reporter bacteria was indicative of the nature of the contaminating chemicals. Efforts were aimed at improving signal quality and at the development of an alarm management software. Following further research, a device of the proposed design could be implemented in monitoring networks as an early warning system against water pollution by toxic chemicals.
PMCID: PMC3357333  PMID: 22179148
biochip; bioluminescence; biosensor; reporter bacteria; toxicity bioassays; water monitoring
13.  A bi-cistronic baculovirus expression vector for improved recombinant protein production 
Bioengineered Bugs  2012;3(2):127-130.
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. Furthermore, when the secretion proteins were co-expressed with the cytosolic green fluorescent protein, the cell lysis and cytosolic protein released into the culture medium could be monitored by the green fluorescence, thus facilitating purification of the secreted proteins.
PMCID: PMC3357334  PMID: 22539029
baculovirus; bi-cistronic; EGFP; IRES; secretion proteins
14.  Outsider to insider 
Bioengineered Bugs  2012;3(2):131-135.
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. coli K-12 to an actively invasive form suggests that gaining host cell entry might be an expedient survival tactic for traditional commensals during certain altered host conditions. The mutant E. coli (SK3842) exhibits properties usually associated with pathogenic bacteria: host cell invasion, phagosomal disruption and intracellular replication. However, unlike the situation with some pathogens, internalized SK3842 imparts anti-apoptotic and cyto-protective effects rather than lethality on the host cell, both in vitro and in vivo. Here, we show that SK3842 also provides colonization resistance against other invasive pathogens—a trait not shared by the parental commensal strain. Thus, the altered lifestyle of SK3842 encompasses characteristics both from traditional pathogens as well as beneficial probiotic strains.
PMCID: PMC3357335  PMID: 22539026
E. coli K-12; Apoptosis; histone-like protein HU; intestinal epithelial cells; invasive bacteria
15.  Probiogenomics as a tool to obtain genetic insights into adaptation of probiotic bacteria to the human gut 
Bioengineered Bugs  2012;3(2):73-79.
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. Recent genome sequencing of a large number of strains of bifidobacteria and lactobacilli has allowed access to the complete genetic makeup of representative members of these bacteria. Here, we will discuss how the analysis of genomic data has helped us to understand the mechanisms by which these bacteria adapt to the specific environment of the gastrointestinal tract, while also revealing genetic functions that mediate specific host-microbe interactions.
PMCID: PMC3357336  PMID: 22095053
bifidobacteria; genomics; gut microbiota; lactobacilli; probiotic bacteria
16.  Proteins 
Bioengineered Bugs  2012;3(2):80-85.
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.
PMCID: PMC3357337  PMID: 22095055
circular permutation; combination; divergence; evolution; gene duplication; homology-based transfer; ontologies; protein domains; protein function; sequence and structure motifs
17.  Bacterial delivery of large intact genomic-DNA-containing BACs into mammalian cells 
Bioengineered Bugs  2012;3(2):86-92.
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. Most drugs tested resulted in a marginal increase of the overall efficiency of delivery in only some cell lines, except the lysosomotropic drug chloroquine, which was found to increase the efficiency of delivery by 6-fold in B16F10 cells. Bacterial invasion was found to be significantly advantageous compared with lipofection in delivering large intact BACs into mouse cells, resulting in 100% of clones containing intact DNA. Furthermore, evaluation of expression of the human hypoxanthine phosphoribosyltransferase (HPRT) gene from its genomic locus, which was present in one of the BACs, showed that single copy integrations of the HPRT-containing BAC had occurred in mouse B16F10 cells and that expression of HPRT from each human copy was 0.33 times as much as from each endogenous mouse copy. These data provide new evidence that bacterial delivery is a convenient and efficient method to transfer large intact therapeutic genes into mammalian cells.
PMCID: PMC3357338  PMID: 22095052
BACs; bacterial transfer; lysosomotropic drugs
18.  Development and optimization of an EGFP-based reporter for measuring the general stress response in Listeria monocytogenes 
Bioengineered Bugs  2012;3(2):93-103.
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 (σB). To study the mechanisms that trigger the activation of σB, and hence the development of stress tolerance, we have developed a fluorescent reporter fusion that allows the real-time activity of σB to be monitored. The reporter, designated Plmo2230::egfp, fuses the strong σB-dependent promoter from the lmo2230 gene (which encodes a putative arsenate reductase) to a gene encoding enhanced green fluorescence protein (EGFP). The reporter was integrated into the genomes of the wild-type strain L. monocytogenes EGD-e as well as two mutant derivatives lacking either sigB or rsbV. The resulting strains were used to study σB activation in response to growth phase and hyperosmotic stress. The wild-type was strongly fluorescent in stationary phase or in cultures with added NaCl and this fluorescence was abolished in both the sigB and rsbV backgrounds, consistent with the σB-dependency of the lmo2230 promoter. During sudden osmotic upshock (addition of 0.5 M NaCl during growth) a real-time increase in fluorescence was observed microscopically, reaching maximal activation after 30 min. Flow cytometry was used to study the activation of σB at a population level by hyperosmotic stress during exponential growth. A strong and proportional increase in fluorescence was observed as the salt concentration increased from 0 to 0.9 M NaCl. Interestingly, there was considerable heterogeneity within the population and a significant proportion of cells failed to induce a high level of fluorescence, suggesting that σB activation occurs stochastically in response to hyperosmotic stress. Thus the Plmo2230::egfp is a powerful tool that will allow the stress response to be better studied in this important human pathogen.
PMCID: PMC3357339  PMID: 22539028
Listeria monocytogenes; EGFP; hyperosmotic stress; lmo2230; reporter; RsbV; sigma B
19.  Genetic analysis of Down syndrome facilitated by mouse chromosome engineering 
Bioengineered Bugs  2012;3(1):8-12.
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. These efforts have been greatly facilitated by Cre/loxP-mediated mouse chromosome engineering, which may result in the establishment of minimal critical genomic regions and eventually new dosage-sensitive genes associated with Down syndrome phenotypes. The success in genetic analysis of Down syndrome will further enhance our understanding of this disorder and lead to better strategies in developing effective therapeutic interventions.
PMCID: PMC3329253  PMID: 22126738
chromosome engineering; Down syndrome; genetic dissection; mouse models; trisomy 21
20.  Differentiation of programmed Arabidopsis cells 
Bioengineered Bugs  2012;3(1):54-59.
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. We recently isolated PAP1-programmed anthocyanin-producing (red) and -free (white) cells from Arabidopsis thaliana; our previous studies have indicated that the PAP1 expression level is similar between these two different cell types. Transcriptional analysis showed that the red cells contain the TTG1-GL3/TT8-PAP1 regulatory complex, which controls anthocyanin biosynthesis; in contrast, the white cells and the wild-type cells lack this entire complex. These data indicate that different regulatory programming underlies the different metabolic states of these cells. In addition, our previous transcriptomic comparison indicated that there is a clear difference in the gene expression profiles of the red and wild-type cells, which is probably a consequence of cell-specific reprogramming. Based on these observations, in this report we discuss the potential mechanisms that underlie the programming and reprogramming of gene expression involved in anthocyanin biosynthesis.
PMCID: PMC3329252  PMID: 22126737
Anthocyanin; Arabidopsis thaliana; metabolic engineering; metabolic fate; PAP1; plant secondary metabolism
21.  The winemaker’s bug 
Bioengineered Bugs  2012;3(3):147-156.
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. A simple unicellular eukaryote, it is an ideal model organism, enabling scientists to shed new light on some of the biggest scientific challenges such as the biology of cancer and aging. It is amenable to almost any modification that modern biology can throw at a cell, making it an ideal host for genetic manipulation, whether by the application of traditional or modern genetic techniques. To the winemaker, this yeast is integral to crafting wonderful, complex wines from simple, sugar-rich grape juice. Thus any improvements that we can make to wine, yeast fermentation performance or the sensory properties it imparts to wine will benefit winemakers and consumers. With this in mind, the application of frontier technologies, particularly the burgeoning fields of systems and synthetic biology, have much to offer in their pursuit of “novel” yeast strains to produce high quality wine. This paper discusses the nexus between yeast research and winemaking. It also addresses how winemakers and scientists face up to the challenges of consumer perceptions and opinions regarding the intervention of science and technology; the greater this intervention, the stronger the criticism that wine is no longer “natural.” How can wine researchers respond to the growing number of wine commentators and consumers who feel that scientific endeavors favor wine quantity over quality and “technical sophistication, fermentation reliability and product consistency” over “artisanal variation”? This paper seeks to present yeast research in a new light and a new context, and it raises important questions about the direction of yeast research, its contribution to science and the future of winemaking.
PMCID: PMC3370933  PMID: 22572786
Saccharomyces cerevisiae; wine; yeast
22.  Evolutionary, ecological and biotechnological perspectives on plasmids resident in the human gut mobile metagenome 
Bioengineered Bugs  2012;3(1):13-31.
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. Of the various types of MGE that comprise the gut mobile metagenome, plasmids are of particular importance since these elements are often capable of autonomous transfer between disparate bacterial species, and are known to encode accessory functions that increase bacterial fitness in a given environment facilitating bacterial adaptation. In this article current knowledge regarding plasmids resident in the human gut mobile metagenome is reviewed, and available strategies to access and characterize this portion of the gut microbiome are described. The relative merits of these methods and their present as well as prospective impact on our understanding of the human gut microbiota is discussed.
PMCID: PMC3329251  PMID: 22126801
gut microbiome; horizontal gene transfer; host-microbe interactions; mobile genetic elements; mobile metagenome; plasmid isolation; TRACA

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