L-Rhamnose Metabolism inClostridium beijerinckiiStrain DSM 6423

ABSTRACTMacroalgae (or seaweeds) are considered potential biomass feedstocks for the production of renewable fuels and chemicals. Their sugar composition is different from that of lignocellulosic biomasses, and in green species, includingUlva lactuca, the major sugars arel-rhamnose andd-glucose.C. beijerinckiiDSM 6423 utilized these sugars in aU. lactucahydrolysate to produce acetic acid, butyric acid, isopropanol, butanol, and ethanol (IBE), and 1,2-propanediol.d-Glucose was almost completely consumed in diluted hydrolysates, whilel-rhamnose ord-xylose was only partially utilized. In this study, the metabolism ofl-rhamnose byC. beijerinckiiDSM 6423 was investigated to improve its utilization from natural resources. Fermentations ond-glucose,l-rhamnose, and a mixture ofd-glucose andl-rhamnose were performed. Onl-rhamnose, the cultures showed low growth and sugar consumption and produced 1,2-propanediol, propionic acid, andn-propanol in addition to acetic and butyric acids, whereas ond-glucose, IBE was the major product. On ad-glucose–l-rhamnose mixture, both sugars were converted simultaneously andl-rhamnose consumption was higher, leading to high levels of 1,2-propanediol (78.4 mM), in addition to 59.4 mM butanol and 31.9 mM isopropanol. Genome and transcriptomics analysis ofd-glucose- andl-rhamnose-grown cells revealed the presence and transcription of genes involved inl-rhamnose utilization and in bacterial microcompartment (BMC) formation. These data provide useful insights into the metabolic pathways involved inl-rhamnose utilization and the effects on the general metabolism (glycolysis, early sporulation, and stress response) induced by growth onl-rhamnose.IMPORTANCEA prerequisite for a successful biobased economy is the efficient conversion of biomass resources into useful products, such as biofuels and bulk and specialty chemicals. In contrast to other industrial microorganisms, natural solvent-producing clostridia utilize a wide range of sugars, including C5, C6, and deoxy-sugars, for production of long-chain alcohols (butanol and 2,3-butanediol), isopropanol, acetone,n-propanol, and organic acids. Butanol production by clostridia from first-generation sugars is already a commercial process, but for the expansion and diversification of the acetone, butanol, and ethanol (ABE)/IBE process to other substrates, more knowledge is needed on the regulation and physiology of fermentation of sugar mixtures. Green macroalgae, produced in aquaculture systems, harvested from the sea or from tides, can be processed into hydrolysates containing mixtures ofd-glucose andl-rhamnose, which can be fermented. The knowledge generated in this study will contribute to the development of more efficient processes for macroalga fermentation and of mixed-sugar fermentation in general.

Download Full-text

Functional Analyses of Multiple Lichenin-Degrading Enzymes from the Rumen Bacterium Ruminococcus albus 8

Applied and Environmental Microbiology ◽

10.1128/aem.06088-11 ◽

2011 ◽

Vol 77 (21) ◽

pp. 7541-7550 ◽

Cited By ~ 30

Author(s):

Michael Iakiviak ◽

Roderick I. Mackie ◽

Isaac K. O. Cann

Keyword(s):

Plant Cell Wall ◽

Bioinformatic Analysis ◽

Major Product ◽

Glycoside Hydrolases ◽

Rumen Bacterium ◽

Cell Wall Polysaccharides ◽

Ruminococcus Albus ◽

Content Type ◽

Wide Range ◽

Functional Analyses

ABSTRACTRuminococcus albus8 is a fibrolytic ruminal bacterium capable of utilization of various plant cell wall polysaccharides. A bioinformatic analysis of a partial genome sequence ofR. albusrevealed several putative enzymes likely to hydrolyze glucans, including lichenin, a mixed-linkage polysaccharide of glucose linked together in β-1,3 and β-1,4 glycosidic bonds. In the present study, we demonstrate the capacity of four glycoside hydrolases (GHs), derived fromR. albus, to hydrolyze lichenin. Two of the genes encoded GH family 5 enzymes (Ra0453 and Ra2830), one gene encoded a GH family 16 enzyme (Ra0505), and the last gene encoded a GH family 3 enzyme (Ra1595). Each gene was expressed inEscherichia coli, and the recombinant protein was purified to near homogeneity. Upon screening on a wide range of substrates, Ra0453, Ra2830, and Ra0505 displayed different hydrolytic properties, as they released unique product profiles. The Ra1595 protein, predicted to function as a β-glucosidase, preferred cleavage of a nonreducing end glucose when linked by a β-1,3 glycosidic bond to the next glucose residue. The major product of Ra0505 hydrolysis of lichenin was predicted to be a glucotriose that was degraded only by Ra0453 to glucose and cellobiose. Most importantly, the four enzymes functioned synergistically to hydrolyze lichenin to glucose, cellobiose, and cellotriose. This lichenin-degrading enzyme mix should be of utility as an additive to feeds administered to monogastric animals, especially those high in fiber.

Download Full-text

Multiplexed CRISPR-Cas9-Based Genome Editing of Rhodosporidium toruloides

mSphere ◽

10.1128/msphere.00099-19 ◽

2019 ◽

Vol 4 (2) ◽

Cited By ~ 17

Author(s):

Peter B. Otoupal ◽

Masakazu Ito ◽

Adam P. Arkin ◽

Jon K. Magnuson ◽

John M. Gladden ◽

...

Keyword(s):

Genome Editing ◽

Gene Disruption ◽

Genome Engineering ◽

Carbon Sources ◽

Rhodosporidium Toruloides ◽

Optimized Design ◽

Content Type ◽

Wide Range ◽

Fuels And Chemicals ◽

Microbial Biofuel

ABSTRACT Microbial production of biofuels and bioproducts offers a sustainable and economic alternative to petroleum-based fuels and chemicals. The basidiomycete yeast Rhodosporidium toruloides is a promising platform organism for generating bioproducts due to its ability to consume a broad spectrum of carbon sources (including those derived from lignocellulosic biomass) and to naturally accumulate high levels of lipids and carotenoids, two biosynthetic pathways that can be leveraged to produce a wide range of bioproducts. While R. toruloides has great potential, it has a more limited set of tools for genetic engineering relative to more advanced yeast platform organisms such as Yarrowia lipolytica and Saccharomyces cerevisiae. Significant advancements in the past few years have bolstered R. toruloides’ engineering capacity. Here we expand this capacity by demonstrating the first use of CRISPR-Cas9-based gene disruption in R. toruloides. Transforming a Cas9 expression cassette harboring nourseothricin resistance and selecting transformants on this antibiotic resulted in strains of R. toruloides exhibiting successful targeted disruption of the native URA3 gene. While editing efficiencies were initially low (0.002%), optimization of the cassette increased efficiencies 364-fold (to 0.6%). Applying these optimized design conditions enabled disruption of another native gene involved in carotenoid biosynthesis, CAR2, with much greater success; editing efficiencies of CAR2 deletion reached roughly 50%. Finally, we demonstrated efficient multiplexed genome editing by disrupting both CAR2 and URA3 in a single transformation. Together, our results provide a framework for applying CRISPR-Cas9 to R. toruloides that will facilitate rapid and high-throughput genome engineering in this industrially relevant organism. IMPORTANCE Microbial biofuel and bioproduct platforms provide access to clean and renewable carbon sources that are more sustainable and environmentally friendly than petroleum-based carbon sources. Furthermore, they can serve as useful conduits for the synthesis of advanced molecules that are difficult to produce through strictly chemical means. R. toruloides has emerged as a promising potential host for converting renewable lignocellulosic material into valuable fuels and chemicals. However, engineering efforts to improve the yeast’s production capabilities have been impeded by a lack of advanced tools for genome engineering. While this is rapidly changing, one key tool remains unexplored in R. toruloides: CRISPR-Cas9. The results outlined here demonstrate for the first time how effective multiplexed CRISPR-Cas9 gene disruption provides a framework for other researchers to utilize this revolutionary genome-editing tool effectively in R. toruloides.

Download Full-text

Introduction

10.1093/oso/9780198807704.003.0001 ◽

2018 ◽

Author(s):

Anna-Maria Hartmann

Keyword(s):

Sixteenth Century ◽

Early Modern ◽

Literary History ◽

First Generation ◽

Early Modern England ◽

Related Material ◽

Wide Range ◽

The World ◽

Early English

Mythographies were books that collected, explained, and interpreted myth-related material. Extremely popular during the Renaissance, these works appealed to a wide range of readers. While the European mythographies of the sixteenth century have been utilized by scholars, the short, early English mythographies, written from 1577 to 1647, have puzzled critics. The first generation of English mythographers did not, as has been suggested, try to compete with their Italian predecessors. Instead, they made mythographies into rhetorical instruments designed to intervene in topical debates outside the world of classical learning. Because English mythographers brought mythology to bear on a variety of contemporary issues, they unfold a lively and historically well-defined picture of the roles myth was made to play in early modern England. Exploring these mythographies can contribute to previous insights into myth in the Renaissance offered by studies of iconography, literary history, allegory, and myth theory.

Download Full-text

Transfer of Plasmid DNA to Clinical Coagulase-Negative Staphylococcal Pathogens by Using a Unique Bacteriophage

Applied and Environmental Microbiology ◽

10.1128/aem.04190-14 ◽

2015 ◽

Vol 81 (7) ◽

pp. 2481-2488 ◽

Cited By ~ 19

Author(s):

Volker Winstel ◽

Petra Kühner ◽

Bernhard Krismer ◽

Andreas Peschel ◽

Holger Rohde

Keyword(s):

Plasmid Dna ◽

Genetic Manipulation ◽

Current Knowledge ◽

Virulence Determinants ◽

Coagulase Negative Staphylococci ◽

Reliable Technique ◽

Content Type ◽

Research Activities ◽

Wide Range ◽

Genetic Barriers

ABSTRACTGenetic manipulation of emerging bacterial pathogens, such as coagulase-negative staphylococci (CoNS), is a major hurdle in clinical and basic microbiological research. Strong genetic barriers, such as restriction modification systems or clustered regularly interspaced short palindromic repeats (CRISPR), usually interfere with available techniques for DNA transformation and therefore complicate manipulation of CoNS or render it impossible. Thus, current knowledge of pathogenicity and virulence determinants of CoNS is very limited. Here, a rapid, efficient, and highly reliable technique is presented to transfer plasmid DNA essential for genetic engineering to important CoNS pathogens from a uniqueStaphylococcus aureusstrain via a specificS. aureusbacteriophage, Φ187. Even strains refractory to electroporation can be transduced by this technique once donor and recipient strains share similar Φ187 receptor properties. As a proof of principle, this technique was used to delete the alternative transcription factor sigma B (SigB) via allelic replacement in nasal and clinicalStaphylococcus epidermidisisolates at high efficiencies. The described approach will allow the genetic manipulation of a wide range of CoNS pathogens and might inspire research activities to manipulate other important pathogens in a similar fashion.

Download Full-text

Use of Proteins Identified through a Functional Genomic Screen To Develop a Protein Subunit Vaccine That Provides Significant Protection against Virulent Streptococcus suis in Pigs

Infection and Immunity ◽

10.1128/iai.00559-17 ◽

2017 ◽

Vol 86 (3) ◽

Cited By ~ 3

Author(s):

Susan L. Brockmeier ◽

Crystal L. Loving ◽

Tracy L. Nicholson ◽

Jinhong Wang ◽

Sarah E. Peters ◽

...

Keyword(s):

Immune Response ◽

Vaccine Trial ◽

Streptococcus Suis ◽

Protein Subunit ◽

Content Type ◽

Degree Of Protection ◽

Wide Range ◽

Associated Proteins ◽

Clinical Protection ◽

Cellular Immune

ABSTRACT Streptococcus suis is a bacterium that is commonly carried in the respiratory tract and that is also one of the most important invasive pathogens of swine, commonly causing meningitis, arthritis, and septicemia. Due to the existence of many serotypes and a wide range of immune evasion capabilities, efficacious vaccines are not readily available. The selection of S. suis protein candidates for inclusion in a vaccine was accomplished by identifying fitness genes through a functional genomics screen and selecting conserved predicted surface-associated proteins. Five candidate proteins were selected for evaluation in a vaccine trial and administered both intranasally and intramuscularly with one of two different adjuvant formulations. Clinical protection was evaluated by subsequent intranasal challenge with virulent S. suis . While subunit vaccination with the S. suis proteins induced IgG antibodies to each individual protein and a cellular immune response to the pool of proteins and provided substantial protection from challenge with virulent S. suis , the immune response elicited and the degree of protection were dependent on the parenteral adjuvant given. Subunit vaccination induced IgG reactive against different S. suis serotypes, indicating a potential for cross protection.

Download Full-text

Recent Advancements in Polymer/Liposome Assembly for Drug Delivery: From Surface Modifications to Hybrid Vesicles

Polymers ◽

10.3390/polym13071027 ◽

2021 ◽

Vol 13 (7) ◽

pp. 1027

Author(s):

Vincenzo De Leo ◽

Francesco Milano ◽

Angela Agostiano ◽

Lucia Catucci

Keyword(s):

Drug Delivery ◽

First Generation ◽

Phospholipid Bilayer ◽

Bioactive Molecules ◽

Systemic Delivery ◽

Molecular Weights ◽

Liposome Preparation ◽

Wide Range ◽

Liposome Surface

Liposomes are consolidated and attractive biomimetic nanocarriers widely used in the field of drug delivery. The structural versatility of liposomes has been exploited for the development of various carriers for the topical or systemic delivery of drugs and bioactive molecules, with the possibility of increasing their bioavailability and stability, and modulating and directing their release, while limiting the side effects at the same time. Nevertheless, first-generation vesicles suffer from some limitations including physical instability, short in vivo circulation lifetime, reduced payload, uncontrolled release properties, and low targeting abilities. Therefore, liposome preparation technology soon took advantage of the possibility of improving vesicle performance using both natural and synthetic polymers. Polymers can easily be synthesized in a controlled manner over a wide range of molecular weights and in a low dispersity range. Their properties are widely tunable and therefore allow the low chemical versatility typical of lipids to be overcome. Moreover, depending on their structure, polymers can be used to create a simple covering on the liposome surface or to intercalate in the phospholipid bilayer to give rise to real hybrid structures. This review illustrates the main strategies implemented in the field of polymer/liposome assembly for drug delivery, with a look at the most recent publications without neglecting basic concepts for a simple and complete understanding by the reader.

Download Full-text

The role of organizational culture in the knowledge management process

Journal of Knowledge Management ◽

10.1108/jkm-08-2014-0353 ◽

2015 ◽

Vol 19 (3) ◽

pp. 433-455 ◽

Cited By ~ 70

Author(s):

Christina Ling-hsing Chang ◽

Tung-Ching Lin

Keyword(s):

Organizational Culture ◽

Knowledge Management ◽

Customer Service ◽

Survey Methodology ◽

Cultural Dimensions ◽

Content Type ◽

Knowledge Resources ◽

Positive Effects ◽

Wide Range ◽

The Individual

Purpose – The purpose of the study is to focus on the enhancement of knowledge management (KM) performance and the relationship between organizational culture and KM process intention of individuals because of the diversity of organizational cultures (which include results-oriented, tightly controlled, job-oriented, closed system and professional-oriented cultures). Knowledge is a primary resource in organizations. If firms are able to effectively manage their knowledge resources, then a wide range of benefits can be reaped such as improved corporate efficiency, effectiveness, innovation and customer service. Design/methodology/approach – The survey methodology, which has the ability to enhance generalization of results (Dooley, 2001), was used to collect the data utilized in the testing of the research hypotheses. Findings – Results- and job-oriented cultures have positive effects on employee intention in the KM process (creation, storage, transfer and application), whereas a tightly controlled culture has negative effects. Research limitations/implications – However, it would have been better to use a longitudinal study to collect useful long-term data to understand how the KM process would be influenced when organizational culture dimensions are changed through/by management. This is the first limitation of this study. According to Mason and Pauleen (2003), KM culture is a powerful predictor of individual knowledge-sharing behavior, which is not included in this study. Thus, this is the second limitation of this paper. Moreover, national culture could be an important issue in the KM process (Jacks et al., 2012), which is the third limitation of this paper for not comprising it. Practical implications – In researchers’ point of view, results- and job-oriented cultures have positive effects, whereas a tightly controlled culture has a negative effect on the KM process intention of the individual. These findings provide evidences that challenge the perspective of Kayworth and Leidner (2003) on this issue. As for practitioners, management has a direction to modify their organizational culture to improve the performance of KM process. Social implications – Both behavioral and value perspectives of the organizational cultural dimensions (results-oriented, tightly control, job-oriented, sociability, solidarity, need for achievement and democracy) should be examined to ascertain their effects firstly on KM culture and then on the KM process intention of the individual. It is hoped that the current study will spawn future investigations that lead to the development of an integrated model which includes organizational culture, KM culture and the KM process intention of the individual. Originality/value – The results-oriented, loosely controlled and job-oriented cultures will improve the effectiveness of the KM process and will also increase employees’ satisfaction and willingness to stay with the organization.

Download Full-text

From digital citizen to digital professional

Kybernetes ◽

10.1108/k-07-2018-0390 ◽

2019 ◽

Vol 48 (7) ◽

pp. 1463-1477

Author(s):

Olga Marino ◽

Jaime Andres Gutierrez ◽

Sandra Aguirre

Keyword(s):

Information And Communication Technologies ◽

Communication Technologies ◽

Cutting Edge ◽

Case Study Methodology ◽

Content Type ◽

Innovative Strategy ◽

Global Issues ◽

Wide Range ◽

Information And Communication ◽

Teaching Learning

Purpose This paper aims to propose and evaluate a pedagogically sound and innovative strategy to teach a higher education course that prepares future professionals to intelligently use information and communication technologies (ICTs) in their personal and professional lives. Design/methodology/approach The conceptual framework used for the design of the course was the socio-constructivism and activity theories. The implementation of the course was evaluated using the intrinsic case study methodology by including several instruments. Findings The pedagogical strategy proposed proved to be sound, as the evaluation showed that students were able to describe, use and propose innovative uses of a wide range of cutting-edge technologies in their both everyday lives and professional settings; they also had the skills to analyse the opportunities and challenges that these presented. Moreover, students liked this innovative way of learning and ended with a positive attitude towards ICT. Originality/value Although several courses prepare students to be digital citizens or use ICT to enhance the teaching-learning process, millennials are ill prepared to use cutting-edge technologies in an innovative, responsible and critical way in their future professions. The course that was designed is original in that it goes beyond preparing digital citizens to prepare professionals in any domain to use ICT in an informed and responsible way. Moreover, it is a documented, successful example of an undergraduate universal course in a highly important current society dimension. The authors believe that its pedagogical proposal could be transferred to courses dealing with other global issues such as the environment, economy and peace.

Download Full-text

Incompressible smoothed particle hydrodynamics for MHD double-diffusive natural convection of a nanofluid in a cavity containing an oscillating pipe

International Journal of Numerical Methods for Heat &amp Fluid Flow ◽

10.1108/hff-06-2019-0461 ◽

2019 ◽

Vol 30 (2) ◽

pp. 882-917 ◽

Cited By ~ 4

Author(s):

Abdelraheem M. Aly

Keyword(s):

Natural Convection ◽

Smoothed Particle Hydrodynamics ◽

Cavity Wall ◽

Lagrangian Description ◽

Content Type ◽

Wide Range ◽

Particle Hydrodynamics ◽

Smoothed Particle ◽

Incompressible Smoothed Particle Hydrodynamics ◽

Double Diffusive

Purpose This paper aims to adopt incompressible smoothed particle hydrodynamics (ISPH) method to simulate MHD double-diffusive natural convection in a cavity containing an oscillating pipe and filled with nanofluid. Design/methodology/approach The Lagrangian description of the governing partial differential equations are solved numerically using improved ISPH method. The inner oscillating pipe is divided into two different pipes as an open and a closed pipe. The sidewalls of the cavity are cooled with a lower concentration C_c and the horizontal walls are adiabatic. The inner pipe is heated with higher concentration C_h. The analysis has been conducted for the two different cases of inner oscillating pipes under the effects of wide range of governing parameters. Findings It is found that a suitable oscillating pipe makes a well convective transport inside a cavity. Presence of the oscillating pipe has effects on the heat and mass transfer and fluid intensity inside a cavity. Hartman parameter suppresses the velocity and weakens the maximum values of the stream function. An increase on Hartman, Lewis and solid volume fraction parameters leads to an increase on average Nusselt number on an oscillating pipe and left cavity wall. Average Sherwood number on an oscillating pipe and left cavity wall decreases as Hartman parameter increases. Originality/value The main objective of this work is to study the MHD double-diffusive natural convection of a nanofluid in a square cavity containing an oscillating pipe using improved ISPH method.

Download Full-text

Numerical investigation of anguilliform locomotion by the SPH method

International Journal of Numerical Methods for Heat &amp Fluid Flow ◽

10.1108/hff-05-2019-0391 ◽

2019 ◽

Vol 30 (1) ◽

pp. 328-346 ◽

Cited By ~ 5

Author(s):

Amin Rahmat ◽

Hossein Nasiri ◽

Marjan Goodarzi ◽

Ehsan Heidaryan

Keyword(s):

Drag Coefficient ◽

Numerical Investigation ◽

Sph Method ◽

Content Type ◽

Aquatic Locomotion ◽

Wide Range ◽

Particle Hydrodynamics ◽

Dummy Particles ◽

Smoothed Particle ◽

Sph Algorithm

Purpose This paper aims to introduce a numerical investigation of aquatic locomotion using the smoothed particle hydrodynamics (SPH) method. Design/methodology/approach To model this problem, a simple improved SPH algorithm is presented that can handle complex geometries using updatable dummy particles. The computational code is validated by solving the flow over a two-dimensional cylinder and comparing its drag coefficient for two different Reynolds numbers with those in the literature. Findings Additionally, the drag coefficient and vortices created behind the aquatic swimmer are quantitatively and qualitatively compared with available credential data. Afterward, the flow over an aquatic swimmer is simulated for a wide range of Reynolds and Strouhal numbers, as well as for the amplitude envelope. Moreover, comprehensive discussions on drag coefficient and vorticity patterns behind the aquatic are made. Originality/value It is found that by increasing both Reynolds and Strouhal numbers separately, the anguilliform motion approaches the self-propulsion condition; however, the vortices show different pattern with these increments.

Download Full-text