Bioengineered bugs最新文献

{"title":"Exploiting recombinant antibodies in point-of-care (POC) diagnostics: the combinatorial advantage.","authors":"Stephen Hearty,&nbsp;Richard O'Kennedy","doi":"10.4161/bbug.2.3.15656","DOIUrl":"https://doi.org/10.4161/bbug.2.3.15656","url":null,"abstract":"<p><p>Antibodies are ubiquitously deployed on in vitro diagnostic (IVD) platforms for detecting a panoply of analytes indicative of environmental and food contamination, residue adulteration and both veterinary and medical diagnostics. In the clinical realm, rapid and accurate determination of disease status is paramount. The significance of immunodiagnostic performance cannot be overemphasized and in many cases reliable diagnosis informs medical intervention which can mean the difference between patient recovery and demise. Cardiovascular disease (CVD) is the single biggest cause of adult mortality in the western world and principal burden on the healthcare services. Although the troponin (Tn) family, in particular troponin I (TnI), are regarded as the gold standard for diagnosis of myocardial damage, over the last decade much research has focused on the identification of alternative cardiac biomarker molecules that can either supplant or complement TnI metrics to add value to cardiac risk stratification criteria. In particular, markers that appear earlier than TnI in the pathophyisiology of cardiac disease are highly sought after. The subject of this addendum represents part of a broader challenge to deliver novel rapid point-of-care (POC) diagnostics to provide a chip-based multi-plexed platform for more comprehensive profiling of cardiac status with additive diagnostic and prognostic value. Specifically, it outlines proof-of-concept direct myeloperoxidase (MPO) detection, demonstrates the benefits of using recombinant antibodies in POC diagnostics and describes optimized strategies for generation of superior candidate antibody panels. </p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"2 3","pages":"182-6"},"PeriodicalIF":0.0,"publicationDate":"2011-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.2.3.15656","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29910497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Engineering lactic acid bacteria for increased industrial functionality.","authors":"Peter A Bron,&nbsp;Michiel Kleerebezem","doi":"10.4161/bbug.2.2.13910","DOIUrl":"https://doi.org/10.4161/bbug.2.2.13910","url":null,"abstract":"<p><p>Based on their spoilage-preventing and flavor-contributing characteristics, lactic acid bacteria (LAB) are employed as starter cultures for the fermentation of foods and feeds. In addition, several specific LAB strains are marketed on basis of their beneficial effects on the consumer's health, representing an explosively growing market for the products containing these so-called probiotics. Due to this extensive industrial use there is a strong interest in unraveling the molecular mechanisms involved in industrial robustness, cognate stress resistance, and health-promoting phenotypes of these LAB that may vary drastically between different starter and probiotic strains currently marketed. This review describes some of the post-genomic tools developed, as well as their employment for the identification of bacterial effector molecules involved in the aforementioned industrially relevant phenotypes. Furthermore, it addresses possible strategies to exploit such knowledge into the rational design of LAB strains with increased industrial functionality.</p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"2 2","pages":"80-7"},"PeriodicalIF":0.0,"publicationDate":"2011-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.2.2.13910","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29910040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Is it possible to produce succinic acid at a low pH?","authors":"Tigran V Yuzbashev,&nbsp;Evgeniya Y Yuzbasheva,&nbsp;Ivan A Laptev,&nbsp;Tatiana I Sobolevskaya,&nbsp;Tatiana V Vybornaya,&nbsp;Anna S Larina,&nbsp;Ilia T Gvilava,&nbsp;Svetlana V Antonova,&nbsp;Sergey P Sineoky","doi":"10.4161/bbug.2.2.14433","DOIUrl":"https://doi.org/10.4161/bbug.2.2.14433","url":null,"abstract":"<p><p>Bio-based succinate is still a matter of special emphasis in biotechnology and adjacent research areas. The vast majority of natural and engineered producers are bacterial strains that accumulate succinate under anaerobic conditions. Recently, we succeeded in obtaining an aerobic yeast strain capable of producing succinic acid at low pH. Herein, we discuss some difficulties and advantages of microbial pathways producing \"succinic acid\" rather than \"succinate.\" It was concluded that the peculiar properties of the constructed yeast strain could be clarified in view of a distorted energy balance. There is evidence that in an acidic environment, the majority of the cellular energy available as ATP will be spent for proton and anion efflux. The decreased ATP:ADP ratio could essentially reduce the growth rate or even completely inhibit growth. In the same way, the preference of this elaborated strain for certain carbon sources could be explained in terms of energy balance. Nevertheless, the opportunity to exclude alkali and mineral acid waste from microbial succinate production seems environmentally friendly and cost-effective.</p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"2 2","pages":"115-9"},"PeriodicalIF":0.0,"publicationDate":"2011-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.2.2.14433","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29910046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stem cell research in the Emerald Isle.","authors":"Stephen Sullivan","doi":"10.4161/bbug.2.2.13576","DOIUrl":"https://doi.org/10.4161/bbug.2.2.13576","url":null,"abstract":"<p><p>Fiscal policy, governance, education and a more internationally integrative strategic policy significantly assists Ireland's competitiveness in stem cell R&D sector.</p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"2 2","pages":"69-70"},"PeriodicalIF":0.0,"publicationDate":"2011-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.2.2.13576","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29910147","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":"LysGH15 reduces the inflammation caused by lethal methicillin-resistant Staphylococcus aureus infection in mice.","authors":"Jingmin Gu,&nbsp;Jing Zuo,&nbsp;Liancheng Lei,&nbsp;Honglei Zhao,&nbsp;Changjiang Sun,&nbsp;Xin Feng,&nbsp;Chongtao Du,&nbsp;Xinwei Li,&nbsp;Yongjun Yang,&nbsp;Wenyu Han","doi":"10.4161/bbug.2.2.14883","DOIUrl":"https://doi.org/10.4161/bbug.2.2.14883","url":null,"abstract":"<p><p>The endolysin LysGH15, derived from staphylococcal phage GH15, has a wide lytic spectrum and strong lytic activity against Staphylococcus aureus, especially methicillin-resistant S. aureus (MRSA), in vitro and in vivo. Here, the ability of lethal MRSA to induce mRNA levels of interleukin-6 (IL-6), interleukin-4 (IL-4), and interferon-γ (IFN-γ) in spleen tissues of mice was studied. A large number of bacteria were detected in spleens. The bacteria caused elevated expression levels of these three cytokines. Administration of LysGH15 significantly reduced the number of bacteria and the levels of IL-6, IL-4, and IFN-γ mRNA in spleen cells compared with those in untreated mice at 24 h (P < 0.05). LysGH15 can eliminate a large number of bacteria and effectively alleviate inflammation induced by infection with lethal MRSA. </p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"2 2","pages":"96-9"},"PeriodicalIF":0.0,"publicationDate":"2011-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.2.2.14883","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29910043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Filamentous fungi in good shape: microparticles for tailor-made fungal morphology and enhanced enzyme production.","authors":"Habib Driouch,&nbsp;Andreas Roth,&nbsp;Petra Dersch,&nbsp;Christoph Wittmann","doi":"10.4161/bbug.2.2.13757","DOIUrl":"https://doi.org/10.4161/bbug.2.2.13757","url":null,"abstract":"<p><p>Filamentous fungi such as Aspergillus niger are important biocatalysts for industrial production of various enzymes as well as organic acids or antibiotics. In suspended culture these microorganisms exhibit a complex morphology which typically has a strong influence on their production properties. In this regard, we have recently shown that the addition of inorganic micro particles to the culture medium is a straightforward and elegant approach to precisely tame fungal morphology. For A. niger a full range of morphological forms from pellets with different diameters to free mycelium could be adjusted by supplementation with talc powder. Aluminium oxide particles similarly affected morphology, showing that this effect is largely independent of the chemical particle composition. Exemplified for different recombinant A. niger strains enzyme production could be strongly enhanced by the addition of microparticles. This was demonstrated for the production of fructofuranosidase, an important high-value biocatalyst for pre-biotic fructo-oligosaccharides, by recombinant A. niger. In a microparticle enhanced fed-batch process, a highly productive mycelium could be achieved. The enzyme titre of 2800 U/mL finally reached was more then tenfold higher then that of any other process reported so far. Here we provide additional insights into the novel production process. This includes the confirmation of the highly selective production of the target enzyme fructofuranosidase using MALDI-TOF MS analysis. Moreover, we show that the obtained enzyme suspension can be efficiently used with minimal pre-treatment for the biosynthesis of short chain fructooligosaccharides of the inulin type, such as 1-kestose and 1-nystose, prebiotics with substantial commercial interest. In particular, these compounds are highly attractive for human consumption, since they have been shown to reduce the risk of colon cancer. In summary, the use of microparticles opens a new avenue of engineering fungal morphology into the desired form for specific production processes.</p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"2 2","pages":"100-4"},"PeriodicalIF":0.0,"publicationDate":"2011-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.2.2.13757","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29910045","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative modelling of LysB from the mycobacterial bacteriophage Ardmore.","authors":"Marine Henry,&nbsp;Aidan Coffey,&nbsp;Jim O' Mahony,&nbsp;Roy D Sleator","doi":"10.4161/bbug.2.2.14138","DOIUrl":"https://doi.org/10.4161/bbug.2.2.14138","url":null,"abstract":"<p><p>Given their potential as specific and natural biocontrol agents, bacteriophages and their associated proteins have become the focus of renewed attention over the last decade. The aim of this study was to use a comparative modelling approach to generate a predicted 3D structure for LysB; a 332 amino acid lipolytic enzyme encoded by the mycobacteriophage Ardmore. The GXSXG pentapeptide, characteristic of lipolytic enzymes, was located at amino acid position 166-170. The three absolutely conserved residues among mycobacteriophage LysB proteins were also identified in Ardmore LysB as Ser-168, Gly-203 and Pro-205. CATH analysis of Ardmore LysB revealed a mainly Beta classification, Beta Barrel architecture and a topology similar to maltoporin. This is unlike the α/β hydrolase structure reported for the D29 LysB protein and, in fact appears in only 3 other sequenced LysB homologues to date. A search for conserved motifs within the amino acid sequence of LysB revealed the presence of both a cutinase motif and a PE-PPE motif. This study presents an in silico 3D predictive model of Ardmore lysin and confirms the high diversity of mycobacteriophages LysB proteins both at the sequence (2D) and structural (predicted 3D) levels.</p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"2 2","pages":"88-95"},"PeriodicalIF":0.0,"publicationDate":"2011-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.2.2.14138","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29910041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Oxidative versus reductive succinic acid production in the yeast Saccharomyces cerevisiae.","authors":"Andreas M Raab,&nbsp;Christine Lang","doi":"10.4161/bbug.2.2.14549","DOIUrl":"https://doi.org/10.4161/bbug.2.2.14549","url":null,"abstract":"<p><p>Bio-based succinic acid is receiving increasing attention, as it could provide a cost-effective, ecologically sustainable alternative to the current petrochemical production process, thus promising a significantly higher market potential. The yeast Saccharomyces cerevisiae is a robust and well-established industrial production organism exhibiting an extraordinarily high acid- and osmotolerance. These features in conjunction with the sophisticated toolbox for genetic engineering make it particularly suitable for succinic acid production. The high tolerance towards acidity is a major advantage over previously established bacterial succinic acid production hosts, since it makes the use of neutralisation salts dispensable and thus enormously facilitates the downstream process. By constructing yeast strains capable of producing significant amounts of succinic acid, we have recently established S. cerevisiae as a promising host for succinic acid production. Our metabolic engineering strategy relied on the implementation of an oxidative production route using the glyoxylate cycle. We here discuss theoretical and practical aspects of oxidative and reductive succinic acid production routes in S. cerevisiae.</p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"2 2","pages":"120-3"},"PeriodicalIF":0.0,"publicationDate":"2011-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.2.2.14549","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29909997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Introducing a new bioengineered bug: Methylobacterium extorquens tuned as a microbial bioplastic factory.","authors":"Philipp Höfer,&nbsp;Patrick Vermette,&nbsp;Denis Groleau","doi":"10.4161/bbug.2.2.15009","DOIUrl":"https://doi.org/10.4161/bbug.2.2.15009","url":null,"abstract":"<p><p>Discussion on and use of methanol as chemical feedstock and as alternative fuel has gained momentum during the past years. Consequently, microorganism and product design based on ''methylotrophism'' is in vogue as reflected by increasing research and development activities in methanol-related areas. A recent example of microorganism and product development is the use of recombinant Methylobacterium extorquens ATCC 55366 strains in the production of second generation biopolyesters. Feeding n-alkenoic acids in addition to methanol yielded functionalized polyhydroxyalkanoates (PHAs) and uncovered how M. extorquens copes with fatty acids. While some parts of the degradation pathway remain unclear, possible metabolic routes are suggested that may explain the significant loss of double bonds prior to polymerization of PHA precursors and occurrence of odd-numbered monomers derived from even-numbered n-alkenoic acids. In addition, microbial discoloration upon fatty acid feeding is discussed and future directions for further genetic modification of M. extorquens are provided. </p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"2 2","pages":"71-9"},"PeriodicalIF":0.0,"publicationDate":"2011-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.2.2.15009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29910042","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characteristics of artificial forisomes from plants and yeast.","authors":"Gundula A Noll,&nbsp;Boje Müller,&nbsp;Antonia M Ernst,&nbsp;Boris Rüping,&nbsp;Sira Groscurth,&nbsp;Richard M Twyman,&nbsp;Lawrence M Kawchuk,&nbsp;Dirk Prüfer","doi":"10.4161/bbug.2.2.14368","DOIUrl":"https://doi.org/10.4161/bbug.2.2.14368","url":null,"abstract":"<p><p>Forisomes are protein bodies found exclusively in the phloem of the Fabaceae (legumes). In response to wounding, the influx of Ca ( 2+) induces a conformational change from a condensed to a dispersed state which plugs the sieve tubes and prevents the loss of photoassimilates. This reversible, ATP-independent reaction can be replicated with purified forisomes in vitro by adding divalent cations or electrically inducing changes in pH, making forisomes ideal components of technical devices. Although native forisomes comprise several subunits, we recently showed that functional homomeric forisomes with distinct properties can be expressed in plants and yeast, providing an abundant supply of forisomes with tailored properties. Forisome subunits MtSEO-F1 and MtSEO-F4 can each assemble into homomeric artificial forisomes, which indicates functional redundancy. However, we provide further evidence that both proteins are subunits of the native heteromeric forisome body in planta. We also show that the properties of artificial forisomes can be modified by immobilization, which is a prerequisite for their incorporation into technical devices.</p>","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"2 2","pages":"111-4"},"PeriodicalIF":0.0,"publicationDate":"2011-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.2.2.14368","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29909996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}