Bioengineered bugs最新文献

{"title":"Avian H5N1 influenza: In or out flew-enza?","authors":"John G Morgan","doi":"10.4161/bbug.20190","DOIUrl":"https://doi.org/10.4161/bbug.20190","url":null,"abstract":"The recent controversy about the potential dangers of publishing scientific methodologies on the generation of variants of avian HIN1 influenza capable of infecting ferrets raises some interesting and relevant issues. One of the central issues is does the publication of such scientific data offer the potential for the production of a bioterrorism agent. \u0000 \u0000Influenza A virus is a serious human pathogen. The pandemic influenza outbreak in 1918 (“Spanish flu”) may have killed at least 50 million people worldwide.1 The WHO estimates that up to 50% of the world’s population became infected approximating to a mortality rate of 2–2.5%. In fact, this is almost definitively an underestimation and progressive studies tends to result in an upwards revision of mortality estimates. Poor record keeping, loss of data and probably, in some parts of the world, little documentation of cases account for the difficulty in establishing the total number of cases. Just how lethal the 1918 virus was can be put in context when compared with a death rate of approximately 100,000 cases for the combined 1957 and 1968 influenza pandemics. The 1918 flu pandemic came in three waves, the first wave occurred in the spring of 1918, the second wave in the autumn (September to November) and the third wave in the spring of 1919. The second wave was by far the most virulent and lethal and probably resulted from the virus acquiring mutations that dramatically improved its human to human transmission and pathogenic characteristics. \u0000 \u0000It has not been definitively established that the 1918 influenza pandemic virus was an avian virus that adapted to successfully infect humans or whether it may have originated from gene reassortment (antigenic shift) as was observed in the subsequent emergence of the 1957 (Asian flu) and 1968 (Hong Kong flu) flu pandemics.2 Evidence for the avian origins of the 1918 has been argued based on sequence analysis of amino acid variation in the polymerase proteins consistent with that of avian-derived virus sequences.3 The polymerase PB1 gene and the haemagglutinin gene in both the 1957 and 1968 pandemic viruses are also believed to be of avian origin, acquired by genetic reassortment. Troubling, perhaps, is the observation that many of the present circulating pathogenic H5N1 viruses are accumulating similar amino acid changes in the polymerase protein. \u0000 \u0000H5N1 viruses have been circulating in poultry certainly since 1996 and possibly for decades.4 Highly pathogenic strains of H5N1 virus have spread from Asia to Europe and Africa infecting millions of poultry and wild birds. In 1997 in China, a novel avian influenza virus, H5N1, capable of infecting humans emerged and has continued to cause human infection and death. Perhaps one of the prime concerns relating to the danger of H5N1 transmission and infection of humans is the widely published mortality rate of 50–60% among people infected with H5N1 (352 deaths in 598 cases).5 Many of these cases have occurred in ","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"3 3","pages":"145-6"},"PeriodicalIF":0.0,"publicationDate":"2012-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.20190","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30606721","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"H5N1 moratorium: Missing the point.","authors":"Pat G Casey","doi":"10.4161/bbug.20004","DOIUrl":"https://doi.org/10.4161/bbug.20004","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"3 3","pages":"144"},"PeriodicalIF":0.0,"publicationDate":"2012-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.20004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30606722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of iron-regulated genes of Bifidobacterium breve UCC2003 as a basis for controlled gene expression.","authors":"Michelle Cronin,&nbsp;Aldert Zomer,&nbsp;Gerald F Fitzgerald,&nbsp;Douwe van Sinderen","doi":"10.4161/bbug.18985","DOIUrl":"https://doi.org/10.4161/bbug.18985","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"3 3","pages":"157-67"},"PeriodicalIF":0.0,"publicationDate":"2012-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.18985","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30333801","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Saccharomyces cerevisiae STR3 and yeast cystathionine β-lyase enzymes: The potential for engineering increased flavor release.","authors":"Sylvester Holt,&nbsp;Antonio G Cordente,&nbsp;Chris Curtin","doi":"10.4161/bbug.19566","DOIUrl":"https://doi.org/10.4161/bbug.19566","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"3 3","pages":"178-80"},"PeriodicalIF":0.0,"publicationDate":"2012-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.19566","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30606135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The winemaker's bug: From ancient wisdom to opening new vistas with frontier yeast science.","authors":"Isak S Pretorius,&nbsp;Christopher D Curtin,&nbsp;Paul J Chambers","doi":"10.4161/bbug.19687","DOIUrl":"https://doi.org/10.4161/bbug.19687","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"3 3","pages":"147-56"},"PeriodicalIF":0.0,"publicationDate":"2012-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.19687","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30606136","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Saccharomyces cerevisiae in directed evolution: An efficient tool to improve enzymes.","authors":"David Gonzalez-Perez,&nbsp;Eva Garcia-Ruiz,&nbsp;Miguel Alcalde","doi":"10.4161/bbug.19544","DOIUrl":"https://doi.org/10.4161/bbug.19544","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"3 3","pages":"172-7"},"PeriodicalIF":0.0,"publicationDate":"2012-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.19544","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30606138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Frex and FrexH: Indicators of metabolic states in living cells.","authors":"Yuzheng Zhao,&nbsp;Yi Yang","doi":"10.4161/bbug.19769","DOIUrl":"https://doi.org/10.4161/bbug.19769","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"3 3","pages":"181-8"},"PeriodicalIF":0.0,"publicationDate":"2012-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.19769","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30606723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Saccharomyces cerevisiae SCRaMbLE system and genome minimization.","authors":"Jessica Dymond,&nbsp;Jef Boeke","doi":"10.4161/bbug.19543","DOIUrl":"https://doi.org/10.4161/bbug.19543","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"3 3","pages":"168-71"},"PeriodicalIF":0.0,"publicationDate":"2012-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.19543","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30606139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ferretting out the facts behind the H5N1 controversy.","authors":"Roy D Sleator","doi":"10.4161/bbug.19943","DOIUrl":"https://doi.org/10.4161/bbug.19943","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":" ","pages":"139-43"},"PeriodicalIF":0.0,"publicationDate":"2012-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.19943","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40151251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacterial delivery of large intact genomic-DNA-containing BACs into mammalian cells.","authors":"Wing Cheung,&nbsp;George Kotzamanis,&nbsp;Hassan Abdulrazzak,&nbsp;Sylvie Goussard,&nbsp;Tadashi Kaname,&nbsp;Athanassios Kotsinas,&nbsp;Vassilis G Gorgoulis,&nbsp;Catherine Grillot-Courvalin,&nbsp;Clare Huxley","doi":"10.4161/bbug.18621","DOIUrl":"https://doi.org/10.4161/bbug.18621","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"3 2","pages":"86-92"},"PeriodicalIF":0.0,"publicationDate":"2012-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.18621","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30119087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}