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Publisher: Ke Ai   (Total: 15 journals)   [Sort by number of followers]

Showing 1 - 15 of 15 Journals sorted alphabetically
Advances in Climate Change Research     Open Access   (Followers: 14, SJR: 0.485, CiteScore: 1)
Animal Nutrition     Open Access   (Followers: 18, SJR: 0.442, CiteScore: 1)
Bioactive Materials     Open Access   (Followers: 1)
Chronic Diseases and Translational Medicine     Open Access  
Emerging Contaminants     Open Access   (SJR: 1.233, CiteScore: 3)
Geodesy and Geodynamics     Open Access   (SJR: 0.469, CiteScore: 1)
Green Energy & Environment     Open Access   (Followers: 2)
Infectious Disease Modelling     Open Access   (Followers: 2)
J. of Finance and Data Science     Open Access   (Followers: 3)
J. of Natural Gas Geoscience     Open Access   (SJR: 0.783, CiteScore: 1)
Non-coding RNA Research     Open Access  
Petroleum     Open Access  
Plant Diversity     Open Access  
Synthetic and Systems Biotechnology     Open Access   (Followers: 1, SJR: 0.841, CiteScore: 0)
World J. of Otorhinolaryngology - Head and Neck Surgery     Open Access  
Journal Cover
Synthetic and Systems Biotechnology
Journal Prestige (SJR): 0.841
Number of Followers: 1  

  This is an Open Access Journal Open Access journal
ISSN (Print) 2405-805X
Published by Ke Ai Homepage  [15 journals]
  • RiPPing apart the rules for peptide natural products

    • Abstract: Publication date: Available online 5 April 2018
      Source:Synthetic and Systems Biotechnology
      Author(s): Aman S. Imani, Michael F. Freeman


      PubDate: 2018-04-13T15:13:24Z
       
  • Prospective study of probiotic supplementation results in immune
           stimulation and improvement of upper respiratory infection rate

    • Abstract: Publication date: Available online 12 March 2018
      Source:Synthetic and Systems Biotechnology
      Author(s): Hong Zhang, Chiajung Yeh, Zonglian Jin, Liwei Ding, Bryan Y. Liu, Li Zhang, H. Kathleen Dannelly
      The human gut microbiota is an important environmental factor for human health with evolutionarily conserved roles in immunity, metabolism, development, and behavior of the host. Probiotic organisms are claimed to offer several functional properties including stimulation of immune system. The purpose of this study is to investigate the effects of a probiotic supplementation on adult volunteers who have contracted the common cold four or more times in the past year. This study is a single center, double-blind, randomized, controlled, prospective trial. Subjects received a probiotic drink containing Lactobacillus paracasei (at least 3 × 107 colony forming units (CFU) ml−1), Lactobacillus casei 431® (at least 3 × 107 CFU ml−1) and Lactobacillus fermentium PCC® (at least 3 × 106 CFU ml−1) or an identical placebo without probiotics for a 12-week study period. The consumption of probiotics significantly reduced the incidence of upper respiratory infection (p < 0.023) and flu-like symptoms with an oral temperature higher than 38 °C (p < 0.034) as compared to the placebo group. Subjects that consumed probiotics demonstrated a significantly higher level of IFN-γ in the serum (p < 0.001) and sIgA in the gut (p < 0.010) as compared to the placebo group and a significant higher level of serum IFN-γ (p < 0.001) and gut sIgA (p < 0.001) as compared to their baseline test results. In contrast, there were no significant differences in the serum IL-4, IL-10, IgA, IgG or IgM between the probiotics and the placebo groups. Results of this study demonstrated that probiotics were safe and effective for fighting the common cold and influenza-like respiratory infections by boosting the immune system.

      PubDate: 2018-03-13T16:33:22Z
       
  • Synergistic and non-specific nucleic acid production by T7 RNA polymerase
           and Bsu DNA polymerase catalyzed by single-stranded polynucleotides

    • Abstract: Publication date: Available online 3 March 2018
      Source:Synthetic and Systems Biotechnology
      Author(s): Nicholas J. Emery, Sagardip Majumder, Allen P. Liu
      Point-of-care molecular diagnostic tests show great promise for providing accurate, timely results in low-infrastructure healthcare settings and at home. The design space for these tests is limited by a variety of possible background reactions, which often originate from relatively weak promiscuous activities of the enzymes used for nucleic acid amplification. When this background signal is amplified alongside the signal of the intended biomarker, the dynamic range of the test can be severely compromised. Therefore, a detailed knowledge of potential side reactions arising from enzyme promiscuity can improve rational design of point-of-care molecular diagnostic tests. Towards this end, we report a previously unknown synergistic reaction between T7 RNA polymerase and Bsu DNA polymerase that produces nucleic acid in the presence of single-stranded DNA or RNA. This reaction occurs in the absence of any previously reported substrates for either polymerases and compromises a theoretical microRNA amplification scheme utilizing these polymerases.

      PubDate: 2018-03-13T16:33:22Z
       
  • Cell-free protein synthesis enabled rapid prototyping for metabolic
           engineering and synthetic biology

    • Abstract: Publication date: Available online 22 February 2018
      Source:Synthetic and Systems Biotechnology
      Author(s): Lihong Jiang, Jiarun Zhao, Jiazhang Lian, Zhinan Xu
      Advances in metabolic engineering and synthetic biology have facilitated the manufacturing of many valuable-added compounds and commodity chemicals using microbial cell factories in the past decade. However, due to complexity of cellular metabolism, the optimization of metabolic pathways for maximal production represents a grand challenge and an unavoidable barrier for metabolic engineering. Recently, cell-free protein synthesis system (CFPS) has been emerging as an enabling alternative to address challenges in biomanufacturing. This review summarizes the recent progresses of CFPS in rapid prototyping of biosynthetic pathways and genetic circuits (biosensors) to speed up design-build-test (DBT) cycles of metabolic engineering and synthetic biology.

      PubDate: 2018-03-01T19:20:22Z
       
  • Cell-free synthesis of stable isotope-labeled internal standards for
           targeted quantitative proteomics

    • Abstract: Publication date: Available online 21 February 2018
      Source:Synthetic and Systems Biotechnology
      Author(s): Ryohei Narumi, Keiko Masuda, Takeshi Tomonaga, Jun Adachi, Hiroki R. Ueda, Yoshihiro Shimizu
      High-sensitivity mass spectrometry approaches using selected reaction monitoring (SRM) or multiple reaction monitoring (MRM) methods are powerful tools for targeted quantitative proteomics-based investigation of dynamics in specific biological systems. Both high-sensitivity detection of low-abundance proteins and their quantification using this technique employ stable isotope-labeled peptide internal standards. Currently, there are various ways for preparing standards, including chemical peptide synthesis, cellular protein expression, and cell-free protein or peptide synthesis. Cell-free protein synthesis (CFPS) or in vitro translation (IVT) systems in particular provide high-throughput and low-cost preparation methods, and various cell types and reconstituted forms are now commercially available. Herein, we review the use of such systems for precise and reliable protein quantification.

      PubDate: 2018-03-01T19:20:22Z
       
  • Cell-free synthetic biology for in vitro biosynthesis of
           pharmaceutical natural products

    • Abstract: Publication date: Available online 17 February 2018
      Source:Synthetic and Systems Biotechnology
      Author(s): Jian Li, Lingkai Zhang, Wanqiu Liu
      Natural products with significant biological activities continuously act as rich sources for drug discovery and development. To harness the potential of these valuable compounds, robust methods need to be developed for their rapid and sustainable production. Cell-free biosynthesis of pharmaceutical natural products by in vitro reconstruction of the entire biosynthetic pathways represents one such solution. In this review, we focus on in vitro biosynthesis of two important classes of natural products, polyketides (PKs) and nonribosomal peptides (NRPs). First, we summarize purified enzyme-based systems for the biosynthesis of PKs, NRPs, and PK/NRP hybrids. Then, we introduce the cell-free protein synthesis (CFPS)-based technology for natural product production. With that, we discuss challenges and opportunities of cell-free synthetic biology for in vitro biosynthesis of natural products.

      PubDate: 2018-02-21T15:20:45Z
       
  • Metabolic pathway engineering

    • Abstract: Publication date: Available online 13 February 2018
      Source:Synthetic and Systems Biotechnology
      Author(s): Hal S. Alper, José L. Avalos


      PubDate: 2018-02-21T15:20:45Z
       
  • Puromycin A, B and C, cryptic nucleosides identified from Streptomyces
           alboniger NRRL B-1832 by PPtase-based activation

    • Abstract: Publication date: Available online 12 February 2018
      Source:Synthetic and Systems Biotechnology
      Author(s): Xiaoli Yan, Benyin Zhang, Wenya Tian, Qi Dai, Xiaoqin Zheng, Ke Hu, Xinxin Liu, Zixin Deng, Xudong Qu
      Natural product discovery is pivot for drug development, however, this endeavor is often challenged by the wide inactivation or silence of natural products biosynthetic pathways. We recently developed a highly efficient approach to activate cryptic/silenced biosynthetic pathways through augmentation of the phosphopantetheinylation of carrier proteins. By applying this approach in the Streptomyces alboniger NRRL B-1832, we herein identified three cryptic nucleosides products, including one known puromycin A and two new derivatives (puromycin B and C). The biosynthesis of these products doesn't require the involvement of carrier protein, indicating the phosphopantetheinyl transferase (PPtase) indeed plays a fundamental regulatory role in metabolites biosynthesis. These results demonstrate that the PPtase-based approach have a much broader effective scope than the previously assumed carrier protein-involving pathways, which will benefit future natural products discovery and biosynthetic studies.

      PubDate: 2018-02-21T15:20:45Z
       
  • Investigating the consequences of asymmetric endoplasmic reticulum
           inheritance in Saccharomyces cerevisiae under stress using a combination
           of single cell measurements and mathematical modelling

    • Abstract: Publication date: Available online 17 January 2018
      Source:Synthetic and Systems Biotechnology
      Author(s): Felix R.H. Jonas, Kate E. Royle, Rochelle Aw, Guy-Bart V. Stan, Karen M. Polizzi
      Adaptation allows organisms to maintain a constant internal environment, which is optimised for growth. The unfolded protein response (UPR) is an example of a feedback loop that maintains endoplasmic reticulum (ER) homeostasis, and is characteristic of how adaptation is often mediated by transcriptional networks. The more recent discovery of asymmetric division in maintaining ER homeostasis, however, is an example of how alternative non-transcriptional pathways can exist, but are overlooked by gold standard transcriptomic or proteomic population-based assays. In this study, we have used a combination of fluorescent reporters, flow cytometry and mathematical modelling to explore the relative roles of asymmetric cell division and the UPR in maintaining ER homeostasis. Under low ER stress, asymmetric division leaves daughter cells with an ER deficiency, necessitating activation of the UPR and prolonged cell cycle during which they can recover ER functionality before growth. Mathematical analysis of and simulation results from our mathematical model reinforce the experimental observations that low ER stress primarily impacts the growth rate of the daughter cells. These results demonstrate the interplay between homeostatic pathways and the importance of exploring sub-population dynamics to understand population adaptation to quantitatively different stresses.
      Graphical abstract image

      PubDate: 2018-01-18T22:24:48Z
       
  • Engineering metabolic pathways in Amycolatopsis japonicum for the
           optimization of the precursor supply for heterologous brasilicardin
           congeners production

    • Abstract: Publication date: Available online 12 January 2018
      Source:Synthetic and Systems Biotechnology
      Author(s): Paul N. Schwarz, Luisa Roller, Andreas Kulik, Wolfgang Wohlleben, Evi Stegmann
      The isoprenoid brasilicardin A is a promising immunosuppressant compound with a unique mode of action, high potency and reduced toxicity compared to today's standard drugs. However, production of brasilicardin has been hampered since the producer strain Nocardia terpenica IFM0406 synthesizes brasilicardin in only low amounts and is a biosafety level 2 organism. Previously, we were able to heterologously express the brasilicardin gene cluster in the nocardioform actinomycete Amycolatopsis japonicum. Four brasilicardin congeners, intermediates of the BraA biosynthesis, were produced. Since chemical synthesis of the brasilicardin core structure has remained elusive we intended to produce high amounts of the brasilicardin backbone for semi synthesis and derivatization. Therefore, we used a metabolic engineering approach to increase heterologous production of brasilicardin in A. japonicum. Simultaneous heterologous expression of genes encoding the MVA pathway and expression of diterpenoid specific prenyltransferases were used to increase the provision of the isoprenoid precursor isopentenyl diphosphate (IPP) and to channel the precursor into the direction of diterpenoid biosynthesis. Both approaches contributed to an elevated heterologous production of the brasilicardin backbone, which can now be used as a starting point for semi synthesis of new brasilicardin congeners with better properties.

      PubDate: 2018-01-18T22:24:48Z
       
  • Introduction to the Special Issue: “Arnold Demain – Industrial
           microbiologist extraodinaire”

    • Abstract: Publication date: March 2017
      Source:Synthetic and Systems Biotechnology, Volume 2, Issue 1
      Author(s): Mattheos Koffas, Qiang Gao, Lixin Zhang


      PubDate: 2018-01-08T16:02:21Z
       
  • Conditional knockout tools: Application of site-specific incorporation of
           unnatural amino acid via genetic code expansion in viral and parasite
           vaccine development

    • Abstract: Publication date: March 2017
      Source:Synthetic and Systems Biotechnology, Volume 2, Issue 1
      Author(s): Pinghua Liu, Lubin Jiang


      PubDate: 2018-01-08T16:02:21Z
       
  • Development of fungal cell factories for the production of secondary
           metabolites: Linking genomics and metabolism

    • Abstract: Publication date: March 2017
      Source:Synthetic and Systems Biotechnology, Volume 2, Issue 1
      Author(s): Jens Christian Nielsen, Jens Nielsen
      The genomic era has revolutionized research on secondary metabolites and bioinformatics methods have in recent years revived the antibiotic discovery process after decades with only few new active molecules being identified. New computational tools are driven by genomics and metabolomics analysis, and enables rapid identification of novel secondary metabolites. To translate this increased discovery rate into industrial exploitation, it is necessary to integrate secondary metabolite pathways in the metabolic engineering process. In this review, we will describe the novel advances in discovery of secondary metabolites produced by filamentous fungi, highlight the utilization of genome-scale metabolic models (GEMs) in the design of fungal cell factories for the production of secondary metabolites and review strategies for optimizing secondary metabolite production through the construction of high yielding platform cell factories.

      PubDate: 2018-01-08T16:02:21Z
       
  • Reactive oxygen species and antioxidant properties from mushrooms

    • Abstract: Publication date: March 2017
      Source:Synthetic and Systems Biotechnology, Volume 2, Issue 1
      Author(s): Carmen Sánchez
      Preventive medicine and food industry have shown an increased interest in the development of natural antioxidants, since those most commonly used synthetic antioxidants may have restricted use in food. This could explain why there is currently much research on the antioxidant properties from natural products such as mushrooms. Many mushrooms have been reported to possess antioxidant properties, which enable them to neutralize free radicals. The oxygen molecule is a free radical, which lead to the generation of the reactive oxygen species and can damage the cells. Cell damage caused by free radicals appears to be a major contributor to aging and degenerative diseases. Mushrooms antioxidant components are found in fruit bodies, mycelium and culture both, which include polysaccharides, tocopherols, phenolics, carotenoids, ergosterol and ascorbic acid among others. Fruit bodies or mycelium can be manipulated to produce active compounds in a relatively short period of time, which represent a significant advantage in antioxidant compounds extraction from mushrooms. Antioxidant compounds may be extracted to be used as functional additives or mushrooms can be incorporated into our food regime, representing an alternative source of food to prevent damage caused by oxidation in the human body.

      PubDate: 2018-01-08T16:02:21Z
       
  • Cell-free synthetic biology: Engineering in an open world

    • Abstract: Publication date: March 2017
      Source:Synthetic and Systems Biotechnology, Volume 2, Issue 1
      Author(s): Yuan Lu
      Cell-free synthetic biology emerges as a powerful and flexible enabling technology that can engineer biological parts and systems for life science applications without using living cells. It provides simpler and faster engineering solutions with an unprecedented freedom of design in an open environment than cell system. This review focuses on recent developments of cell-free synthetic biology on biological engineering fields at molecular and cellular levels, including protein engineering, metabolic engineering, and artificial cell engineering. In cell-free protein engineering, the direct control of reaction conditions in cell-free system allows for easy synthesis of complex proteins, toxic proteins, membrane proteins, and novel proteins with unnatural amino acids. Cell-free systems offer the ability to design metabolic pathways towards the production of desired products. Buildup of artificial cells based on cell-free systems will improve our understanding of life and use them for environmental and biomedical applications.

      PubDate: 2018-01-08T16:02:21Z
       
  • Evaluation of fermentation conditions triggering increased antibacterial
           activity from a near-shore marine intertidal environment-associated
           Streptomyces species

    • Abstract: Publication date: March 2017
      Source:Synthetic and Systems Biotechnology, Volume 2, Issue 1
      Author(s): A.L. English, A. Boufridi, R.J. Quinn, D.I. Kurtböke
      A near-shore marine intertidal environment-associated Streptomyces isolate (USC-633) from the Sunshine Coast Region of Queensland, Australia, cultivated under a range of chemically defined and complex media to determine optimal parameters resulting in the secretion of diverse array of secondary metabolites with antimicrobial properties against various antibiotic resistant bacteria. Following extraction, fractioning and re-testing of active metabolites resulted in persistent antibacterial activity against Escherichia coli (Migula) (ATCC 13706) and subsequent Nuclear Magnetic Resonance (NMR) analysis of the active fractions confirmed the induction of metabolites different than the ones in fractions which did not display activity against the same bacterial species. Overall findings again confirmed the value of One Strain–Many Compounds (OSMAC) approach that tests a wide range of growth parameters to trigger bioactive compound secretion increasing the likelihood of finding novel therapeutic agents. The isolate was found to be adaptable to both marine and terrestrial conditions corresponding to its original near-shore marine intertidal environment. Wide variations in its morphology, sporulation and diffusible pigment production were observed when different growth media were used.

      PubDate: 2018-01-08T16:02:21Z
       
  • Proteome-wide alterations in an industrial clavulanic acid producing
           strain of Streptomyces clavuligerus

    • Abstract: Publication date: March 2017
      Source:Synthetic and Systems Biotechnology, Volume 2, Issue 1
      Author(s): Eser Ünsaldı, Aslıhan Kurt-Kızıldoğan, Birgit Voigt, Dörte Becher, Gülay Özcengiz
      The usefulness of genetic/metabolic engineering for further improvement of industrial strains is subject of discussion because of the general lack of knowledge on genetic alterations introduced by iterative cycles of random mutagenesis in such strains. An industrial clavulanic acid (CA)-overproducer Streptomyces clavuligerus DEPA was assessed to understand proteome-wide changes that have occurred in a local industrial CA overproducer developed through succesive mutagenesis programs. The proteins that could be identified corresponded to 33 distinct ORFs for underrepresented ones and 60 ORFs for overrepresented ones. Three CA biosynthetic enzymes were overrepresented in S. clavuligerus DEPA; carboxyethylarginine synthase (Ceas2), clavaldehyde dehydrogenase (Car) and carboxyethyl-arginine beta-lactam-synthase (Bls2) whereas the enzymes of two other secondary metabolites were underrepresented along with two important global regulators [two-component system (TCS) response regulator (SCLAV_2102) and TetR-family transcriptional regulator (SCLAV_3146)] that might be related with CA production and/or differentiation. γ-butyrolactone biosynthetic protein AvaA2 was 2.6 fold underrepresented in S. clavuligerus DEPA. The levels of two glycolytic enzymes, 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase and phosophoglycerate kinase were found decreased while those of dihydrolipoyl dehydrogenase (E3) and isocitrate dehydrogenase, with two isoforms were found as significantly increased. A decrease of amino acid metabolism, methionine biosynthesis in particular, as well as S-adenosylmethionine synthetase appeared as one of the prominent mechanisms of success of S. clavuligerus DEPA strain as a prolific producer of CA. The levels of two enzymes of shikimate pathway that leads to the production of aromatic amino acids and aromatic secondary metabolites were also underrepresented. Some of the overrepresented stress proteins in S. clavuligerus DEPA included polynucleotide phosphorylase/polyadenylase (PNPase), ATP-dependent DNA helicase, two isoforms of an anti-sigma factor and thioredoxin reductase. Downregulation of important proteins of cell wall synthesis and division was recorded and a protein with β-lactamase domain (SCLAV_p1007) appeared in 12 isoforms, 5 of which were drastically overrepresented in DEPA strain. These results described herein provide useful information for rational engineering to improve CA production in Streptomyces clavuligerus.

      PubDate: 2018-01-08T16:02:21Z
       
  • Novel polysaccharide-protein conjugates provide an immunogenic 13-valent
           pneumococcal conjugate vaccine for S. pneumoniae

    • Abstract: Publication date: March 2017
      Source:Synthetic and Systems Biotechnology, Volume 2, Issue 1
      Author(s): Allison E.B. Turner, Jonas E. Gerson, Helen Y. So, Daniel J. Krasznai, Adrienne J. St. Hilaire, Donald F. Gerson
      Pneumonia remains the single leading cause of childhood death worldwide. Despite the commercial availability of multiple pneumococcal conjugate vaccines (PCVs), high dosage cost and supply shortages prevent PCV delivery to much of the developing world. The current work presents high-yield pneumococcal conjugates that are immunogenic in animals and suitable for use in human vaccine development. The 13-valent pneumococcal conjugate vaccine (PCV-13) investigated in this research incorporated serotypes 1, 3, 4, 5, 6A, 6B, 7F, 9V, 14, 18C, 19A, 19F, and 23F. Pneumococcal polysaccharides (PnPSs) and CRM197 carrier protein were produced and purified in-house, and used to prepare PnPS-CRM conjugates using unique, cyanide-free, in vacuo glycation conjugation methods. In vitro characterization confirmed the generation of higher molecular weight PnPS-CRM conjugates low in free protein. In vivo animal studies were performed to compare PnuVax's PCV-13 to the commercially available PCV-13, Prevnar®13 (Pfizer, USA). A boost dose was provided to all groups post-dose 1 at t = 14 days. Post-dose 2 results at t = 28 days showed that all 13 serotypes in PnuVax's PCV-13 were boostable. Per serotype IgG GMCs demonstrated that PnuVax's PCV-13 is immunogenic for all 13 serotypes, with 10 of the 13 serotypes statistically the same or higher than Prevnar®13 post-dose 2. As a result, the novel polysaccharide-protein conjugates developed in this work are highly promising for use in human PCV development. The in vacuo conjugation technique applied in this work could also be readily adapted to develop many other conjugate vaccines.

      PubDate: 2018-01-08T16:02:21Z
       
 
 
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