Advanced CFD Simulations in Biotechnology using FLOW-3D
This webinar illustrates the benefits of using computational fluid dynamics as an auxiliary R D tool for simulating processes within pharmaceutical, biomedic...
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Advanced CFD Simulations in Biotechnology using FLOW-3D - Video
NUTRA GREEN BIOTECHNOLOGY CO.,LTD.
Nutra Green, focus on researching, manufacturing and innovating raw materials for dietary supplement, sports nutrition supplement, bodybuilding and fitness, ...
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Taiwan Wonders: Chiayi Herbs Biotechnology Park - Hong Kong Law Uk Folk Museum | Hakka
+ 886-3-425-9790 Taiwan : International Civil Aviation Organization (ICAO) http://mitsubishi-logistics-jetro-japan.tumblr.com/ Danilov Vadim AV-VA CIS SEO: h...
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Taiwan Wonders: Chiayi Herbs Biotechnology Park - Hong Kong Law Uk Folk Museum | Hakka - Video
Background:
Butanol is a chemical with potential uses as biofuel and solvent, which can be produced by microbial fermentation. However, the end product toxicity is one of the main obstacles for developing the production process irrespective of the choice of production organism. The long-term goal of the present project is to produce 2-butanol in Saccharomyces cerevisiae. Therefore, unraveling the toxicity mechanisms of solvents such as butanol and understanding the mechanisms by which tolerant strains of S. cerevisiae adapt to them would be an important contribution to the development of a bio-based butanol production process.
Results:
A butanol tolerant S. cerevisiae was achieved through a series of sequential batch cultures with gradual increase of 2-butanol concentration. The final mutant (JBA-mut) tolerates all different alcohols tested at higher concentrations compared to the wild type (JBA-wt). Proteomics analysis of the two strains grown under mild butanol-stress revealed 46 proteins changing their expression by more than 1.5-fold in JBA-mut, 34 of which were upregulated. Strikingly, 21 out of the 34 upregulated proteins were predicted constituents of mitochondria. Among the non-mitochondrial up-regulated proteins, the minor isoform of Glycerol-3-phosphatase (Gpp2) was the most notable, since it was the only tested protein whose overexpression was found to confer butanol tolerance.
Conclusion:
The study demonstrates several differences between the butanol tolerant mutant and the wild type. Upregulation of proteins involved in the mitochondrial ATP synthesizing machinery constituents and glycerol biosynthesis seem to be beneficial for a successful adaptation of yeast cells to butanol stress.Source:
http://www.biotechnologyforbiofuels.com/content/6/1/101
Background:
Fuel ethanol production from sustainable and largely abundant agro-residues such as sugarcane bagasse (SB) provides long term, geopolitical and strategic benefits. Pretreatment of SB is an inevitable process for improved saccharification of cell wall carbohydrates. Recently, ammonium hydroxide-based pretreatment technologies have gained significance as an effective and economical pretreatment strategy. We hypothesized that soaking in concentrated aqueous ammonia-mediated thermochemical pretreatment (SCAA) would overcome the native recalcitrance of SB by enhancing cellulase accessibility of the embedded holocellulosic microfibrils.
Results:
In this study, we designed an experiment considering response surface methodology (Taguchi method, L8 orthogonal array) to optimize sugar recovery from ammonia pretreated sugarcane bagasse (SB) by using the method of soaking in concentrated aqueous ammonia (SCAA-SB). Three independent variables: ammonia concentration, temperature and time, were selected at two levels with center point. The ammonia pretreated bagasse (SCAA-SB) was enzymatically hydrolysed by commercial enzymes (Celluclast 1.5 L and Novozym 188) using 15 FPU/g dry biomass and 17.5 Units of beta-glucosidase/g dry biomass at 500C, 150 rpm for 96 h. A maximum of 28.43 g/l reducing sugars corresponding to 0.57 g sugars/g pretreated bagasse was obtained from the SCAA-SB derived using a 20% v/v ammonia solution, at 700C for 24 h after enzymatic hydrolysis. Among the tested parameters, pretreatment time showed the maximum influence (p value, 0.053282) while ammonia concentration showed the least influence (p value, 0.612552) on sugar recovery. The changes in the ultra-structure and crystallinity of native SCAA-SB and enzymatically hydrolysed SB were observed by scanning electron microscopy (SEM), x-ray diffraction (XRD) and solid-state 13C nuclear magnetic resonance (NMR) spectroscopy. The enzymatic hydrolysates and solid SCAA-SB were subjected to ethanol fermentation under separate hydrolysis and fermentation (SHF) and simultaneous saccharification and fermentation (SSF) by Scheffersomyces (Pichia) stipitis NRRL Y-7124 respectively. Higher ethanol production (10.31 g/l and yield, 0.387 g/g) was obtained through SSF than SHF (3.83 g/l and yield, 0.289 g/g).
Conclusions:
SCAA treatment showed marked lignin removal from SB thus improving the accessibility of cellulases towards holocellulose substrate as evidenced by efficient sugar release. The ultrastructure of SB after SCAA and enzymatic hydrolysis of holocellulose provided insights of the degradation process at the molecular level.Source:
http://www.biotechnologyforbiofuels.com/content/6/1/102
Biotechnology song
A song composed by Joseph Ndunguru and sang by Fountain of Joy Primary School students in Dar es Salaam, Tanzania on March 2013 during the official opening o...
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Biotechnology song - Video
Psykorpsify - Biotechnology
DAW : FL Studio 11 VST Principal : Nexus 2.
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Psykorpsify - Biotechnology - Video
Moms learn about Biotechnology and Pesticides
Moms and consumers have many questions about GMOs. Farmers Paul and Donna Jeschke welcome Chicago-area moms to their farm to have conversations about what GM...
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Moms learn about Biotechnology and Pesticides - Video
Background:
During the pretreatment of biomass feedstocks and subsequent conditioning prior to saccharification, many toxic compounds are produced or introduced which inhibit microbial growth and in many cases, production of ethanol. An understanding of the toxic effects of compounds found in hydrolysate is critical to improving sugar utilization and ethanol yields in the fermentation process. In this study, we established a useful tool for surveying hydrolysate toxicity by measuring growth rates in the presence of toxic compounds, and examined the effects of selected model inhibitors of aldehydes, organic and inorganic acids (along with various cations), and alcohols on growth of Zymomonas mobilis 8b (a ZM4 derivative) using glucose or xylose as the carbon source.
Results:
Toxicity strongly correlated to hydrophobicity in Z. mobilis, which has been observed in Escherichia coli and Saccharomyces cerevisiae for aldehydes and with some exceptions, organic acids. We observed Z. mobilis 8b to be more tolerant to organic acids than previously reported, although the carbon source and growth conditions play a role in tolerance. Growth in xylose was profoundly inhibited by monocarboxylic organic acids compared to growth in glucose, whereas dicarboxylic acids demonstrated little or no effects on growth rate in either substrate. Furthermore, cations can be ranked in order of their toxicity, Ca++ > > Na+ > NH4+ > K+. HMF (5-hydroxymethylfurfural), furfural and acetate, which were observed to contribute to inhibition of Z. mobilis growth in dilute acid pretreated corn stover hydrolysate, do not interact in a synergistic manner in combination. We provide further evidence that Z. mobilis 8b is capable of converting the aldehydes furfural, vanillin, 4-hydroxybenzaldehyde and to some extent syringaldehyde to their alcohol forms (furfuryl, vanillyl, 4-hydroxybenzyl and syringyl alcohol) during fermentation.
Conclusions:
Several key findings in this report provide a mechanism for predicting toxic contributions of inhibitory components of hydrolysate and provide guidance for potential process development, along with potential future strain improvement and tolerance strategies.Source:
http://www.biotechnologyforbiofuels.com/content/6/1/99
Background:
In comparison with phototrophic growth, heterotrophic conditions can significantly increase growth rates, final cell number and cell mass in microalgae cultures. Neochloris oleoabundans is a microalga of biotechnological interest that accumulates lipids under phototrophic and nitrogen-limited conditions. Heterotrophic flask culture experiments were conducted to identify carbon sources that can be metabolized by N. oleoabundans, and bioreactor batch and fed-batch (nitrate pulse additions) cultures supplemented with glucose were performed to study the cellular composition of the microalgae under balanced and high C/N ratios (glucose/nitrate).
Results:
N. oleoabundans was able to grow using glucose and cellobiose as sole carbon sources under strict heterotrophic conditions. Under a balanced C/N ratio of 17 and using bioreactor batch cultures containing 3 g/L glucose, a maximal cell mass of 1.72 g/L was found, with protein being the major cell component (44% w/w). A maximal cell mass of 9.2 g/L was obtained using batch cultures at a C/N ratio of 278. Under these conditions, lipid accumulation was promoted (up to 52% w/w) through N-limitation, resulting in high lipid productivity (528.5 mg/L/day). Fed-batch cultures were performed at a C/N ratio of 278 and with nitrate pulse additions. This condition allowed a maximal cell mass of 14.2 g/L to be achieved and switched the metabolism to carbohydrate synthesis (up to 54% of dry weight), mainly in the form of starch. It was found that transmembrane transport under these conditions was dependent on a proton-motive force, indicating that glucose is transported by a symporter.
Conclusions:
N. oleoabundans was able to grow under strict heterotrophic culture conditions with glucose or cellobiose as the only carbon source. The glucose used is transported by a symporter system. Batch cultures with a balanced C/N ratio accumulate proteins as the major cellular component; a high C/N ratio significantly increased the dry cell mass and resulted in a high lipid content, and a high cell density was achieved using fed-batch cultures promoting carbohydrate accumulation. These results suggest heterotrophic batch cultures of N. oleoabundans as an alternative for the production of proteins or lipids with simple culture strategies and minimal-mineral media supplemented with glucose.Source:
http://www.biotechnologyforbiofuels.com/content/6/1/100
PKM Managing Partner Phil Moore: BioTechnology Services
Phil explains some of PKM #39;s other niche markets including the biotech industry. Background and Experience: As managing partner of PKM, in addition to maintaining a select group of client...
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PKM Managing Partner Phil Moore: BioTechnology Services - Video
Background:
The inevitable depletion of fossil fuels has resulted in an increasing worldwide interest in exploring alternative and sustainable energy sources. Lignocellulose, which is the most abundant biomass on earth, is widely regarded as a promising raw material to produce fuel ethanol. Pretreatment is an essential step to disrupt the recalcitrance of lignocellulosic matrix for enzymatic saccharification and bioethanol production. This paper established an ATSE (alkaline twin-screw extrusion pretreatment) process using a specially designed twin-screw extruder in the presence of alkaline solution to improve the enzymatic hydrolysis efficiency of corn stover for the production of fermentable sugars.
Results:
The ATSE pretreatment was conducted with a biomass/liquid ratio of 1/2 (w/w) at a temperature of 99[degree sign]C without heating equipment. The results indicated that ATSE pretreatment is effective in improving the enzymatic digestibility of corn stover. Sodium hydroxide loading is more influential factor affecting both sugar yield and lignin degradation than heat preservation time. After ATSE pretreatment under the proper conditions (NaOH loading of 0.06 g/g biomass during ATSE and 1 hour heat preservation after extrusion), 71% lignin removal was achieved and the conversions of glucan and xylan in the pretreated biomass can reach to 83% and 89% respectively via subsequent enzymatic hydrolysis (cellulase loading of 20 FPU/g-biomass and substrate consistency of 2%). About 78% of the original polysaccharides were converted into fermentable sugars.
Conclusions:
With the physicochemical functions in extrusion, the ATSE method can effectively overcome the recalcitrance of lignocellulose for the production of fermentable sugars from corn stover. This process can be considered as a promising pretreatment method due to its relatively low temperature (99[degree sign]C), high biomass/liquid ratio (1/2) and satisfied total sugar yield (78%), despite further study is needed for process optimization and cost reduction.Source:
http://www.biotechnologyforbiofuels.com/content/6/1/97
Background:
Recent studies have demonstrated that microalga has been widely regarded as one of the most promising raw materials of biofuels. However, lack of an economical, efficient and convenient method to harvest microalgae is a bottleneck to boost their full-scale application. Many methods of harvesting microalgae, including mechanical, electrical, biological and chemical based, have been studied to overcome this hurdle.
Results:
A new flocculation method induced by decreasing pH value of growth medium was developed for harvesting freshwater microalgae. The flocculation efficiencies were as high as 90% for Chlorococcum nivale, Chlorococcum ellipsoideum and Scenedesmus sp. with high biomass concentrations (>1g/L). The optimum flocculation efficiency was achieved at pH 4.0. The flocculation mechanism could be that the carboxylate ions of organic matters adhering on microalgal cells accepted protons when pH decreases and the negative charges were neutralized, resulting in disruption of the dispersing stability of cells and subsequent flocculation of cells. A linear correlation between biomass concentration and acid dosage was observed. Furthermore, viability of flocculated cells was determined by Evans Blue assay and few cells were found to be damaged with pH decrease. After neutralizing pH and adding nutrients to the flocculated medium, microalgae were proved to maintain a similar growth yield in the flocculated medium comparing with that in the fresh medium. The recycling of medium could contribute to the economical production from algae to biodiesel.
Conclusions:
The study provided an economical, efficient and convenient method to harvest fresh microalgae. Advantages include capability of treating high cell biomass concentrations (>1g/L), excellent flocculation efficiencies (>= 90%), operational simplicity, low cost and recycling of medium. It has shown the potential to overcome the hurdle of harvesting microalgae to promote full-scale application to biofuels from microalgae.Source:
http://www.biotechnologyforbiofuels.com/content/6/1/98
Cizzle Biotechnology
http://cizzlebiotech.co.uk/ Cizzle is a Biotechnology company that is developing research findings into a blood test for cancer, with lung cancer representing our first target. We do Research...
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Cizzle Biotechnology - Video
Emprendedores 2012 13 Aquatic Biotechnology
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Emprendedores 2012 13 Aquatic Biotechnology - Video
A profusion of biotechnology products is expected over the next five to 10 years, and the number and diversity of new products has the potential to overwhelm the U.S. regulatory system, says a new report from the National Academies of Sciences, Engineering, and Medicine. The U.S. Environmental Protection Agency, the Food and Drug Administration, the U.S. Department of Agriculture, and other agencies involved in regulating biotechnology products should increase their scientific capabilities, tools, and expertise in key areas of expected growth, said the committee that conducted the study and wrote the report.
"The rate at which biotechnology products are introduced -- and the types of products -- are expected to significantly increase in the next five to 10 years, and federal agencies need to prepare for this growth," said committee chair Richard Murray, Thomas E. and Doris Everhart Professor of Control and Dynamical Systems and Bioengineering, California Institute of Technology. "We hope this report will support agency efforts to effectively evaluate these future products in ways that ensure public safety, protect the environment, build public confidence, and support innovation."
The U.S. biotechnology economy is growing rapidly, with the scale, scope, and complexity of products increasing. More types of organisms will likely be engineered, the report notes, and the kinds of traits introduced with biotechnology will also increase. Some future biotechnology products are likely to use genome-editing techniques such as CRISPR for familiar applications, such as modifying agricultural crops. Other future products are expected to be entirely new -- plants that can serve as sentinels of environmental contamination, for example, and collections of microorganisms that can produce chemical compounds efficiently. Engineered microbes, plants, and insects designed to live in the environment with little or no human management are likely to be more common. With few exceptions, products such as these have not yet been evaluated by the current regulatory system.
Current staffing levels, expertise, and resources available at EPA, FDA, USDA and other agencies may not be sufficient to address the expected scope and scale of future biotechnology products, the report says. It is critical that the agencies involved in regulation develop and maintain scientific capabilities, tools, and expertise in key evolving areas. Examples of such areas include understanding relationships between intended genetic changes and an organism's observable traits, the unintended effects of genetic changes on target and non-target organisms, predicting and monitoring ecosystem responses, and quantifying the economic and social costs and benefits of biotechnologies.
To respond to the expected increase and diversity of products, the agencies should develop risk-analysis approaches tailored to the familiarity of products and the complexity of their uses, the report says. For biotechnology products that are similar to products already in use, established risk-analysis methods can be applied or modified, and a more expedited process could be used. For products that have less-familiar characteristics or more complex risk pathways, new risk-analysis methods may need to be developed. Regulatory agencies should build their capacity to rapidly determine the type of risk-analysis approaches most appropriate for new products entering the regulatory system.
EPA, FDA, and USDA should identify products that could serve as pilot projects to develop new approaches to assess risks and benefits and to inform regulatory decisions, the report says. Pilot projects could also be used by the agencies to evaluate future products as they move from laboratory scale, to field- or prototype-scale, to full-scale operation.
One challenge regulators will face is finding jurisdiction under existing statutes to regulate the diverse range of anticipated biotech products, the report says. The current collection of statutes and regulations that provide the basis for agencies' oversight, known as the Coordinated Framework for Regulation of Biotechnology, appears to have considerable flexibility to cover a wide range of biotechnology products, but in some cases the agencies' jurisdiction has been defined in ways that could leave gaps or overlaps in regulatory oversight. At times, FDA, EPA, and USDA may need to make use of the flexibility under their statutes to minimize gaps in jurisdiction.
Even when statutes do allow agencies to regulate products, the current statutes may not adequately equip regulators with the tools to regulate the products effectively, the committee said. For example, the statutes may not empower regulators to require product sponsors to share in the burden of generating information about product safety, and may place the burden of proof on regulators to demonstrate that a product is unsafe before they can take action to protect the public. This implies that adequate federal support for research will be crucial to protect consumer and occupational safety and the environment.
Biotechnology products on the horizon are likely to generate substantial public debate, the report notes. Many members of society have concerns over the safety and ethics of various biotechnologies, while others see prospects for biotechnology addressing social or environmental problems. The U.S. regulatory system will need to achieve a balance among competing interests, risks, and benefits when considering how to manage development and use of new biotech products.
In addition, more research may be needed to develop methods for governance systems that integrate ethical, cultural, and social implications into risk assessments in ways that are meaningful. This may not be feasible or even justified for all new biotechnology products -- such as products with which there is already familiarity or products that will not be released into the environment. For example, genetically engineered organisms used in the research laboratory to develop new chemical synthesis methods are not likely to require the same level of public dialogue as products that have more uncertainty associated with them, such as organisms with gene drives, which enhance organisms' ability to pass certain genetic traits on to their offspring.
Overall, the federal government should develop a strategy that scans the horizon for new biotechnology products, identifying and prioritizing those products that are less familiar or that present a need for more complex risk analysis, the report says. The federal government should also work to establish appropriate federal funding levels for sustained, multiyear research to develop the necessary advances in regulatory science. To this end, the National Science Foundation, the U.S. Department of Defense, the U.S. Department of Energy, the National Institutes of Standards and Technology, and other agencies that fund biotechnology research should increase their investments in regulatory science.
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Federal US agencies need to prepare for greater quantity, range of biotechnology products - Science Daily
COVID-19 continues to spread worldwide. The latest situation report from the World Health Organization (WHO) shows that there are now more than 125,000 confirmed cases of the disease and more than 4,600 deaths. Several biotech companies are racing to find a vaccine or a treatment for the rapidly spreading disease.
One of these companies is Vir Biotechnology (NASDAQ:VIR), which focuses on developing treatments for infectious diseases. Recently, Vir announced it was partnering up with Biogen (NASDAQ:BIIB) to develop and manufacture antibodies that could treat COVID-19. Given the gravity of the situation, the two companies decided to start working on this project while negotiating the terms of the deal.
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On Jan. 22, Vir announced it was screening its library of antibodies to identify one that could be effective against COVID-19. The company had previous experience dealing with other coronaviruses, including Middle East Respiratory Syndrome (MERS) and Severe Acute Respiratory Syndrome (SARS). On Feb. 12, Vir announced it identified two antibodies with the potential to be effective against SARS-CoV-2, the virus that causes COVID-19.
The company partnered with other companies in its quest to beat the potentially deadly disease. Vir entered into an agreement with WuXi Biologics, a China-based biologics technology platform that helps companies develop and manufacture drugs.According to the terms of the deal, WuXi Biologics "will conduct cell-line development, process and formulation development, and initial manufacturing for clinical development." WuXi Biologics will hold the right to market this treatment in China if it is approved, and Vir will market it in the rest of the world.
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Biogen and Vir Biotechnology to Collaborate to Find a Treatment for the Coronavirus - The Motley Fool
Alzheimer’s Disease is a critical health condition that cannot be defined in a specific way.It is a very common form of Dementia. Dementia in itself is not a disease. Rather, it is a group of symptoms that start occurring due to occurrence of some other disease or medical condition.Person suffering from Alzheimer’s Disease can face difficulty in remembering even the most recently happened events. This is the initial stage. The disease can lead to death of a person too! The disease starts to occur in people who have crossed 65 years of age or more. Those who get diagnosed with this difficult disease, a good doctor needs to be consulted at the earliest. There are certain questions that need to be placed before the doctor related to the disease. Some of the most important questions are listed below:
What is the usual course of the Alzheimer’s disease?
Life long.
What type of new treatments are available?
Since it is not a disease, there is no particular treatment available. However, some medicines are available but that too works at the early stages.
Are the drugs used to treat the AD symptoms effective?
Yes, at times and mostly during the early stages.
Does these drugs have any sort of side effects?
At time, yes. It can cause poor eyesight problem, gaining weight, as well itching problems.
Does the AD affects a person for the remaining part of his/her living days?
Yes, definitely.
What is the total time period for a person to act in a very normal way post Alzheimer’s diagnosis?
The first and middle stages are still OK with the patients. Although slight changes start taking place but still the behavior doesn’t get completely out of the mark. But, once the patient reaches advanced stage, scenarios tend to become more complicated.
Can a patient of Alzheimer’s Disease be a threat to other or themselves?
The Patient can be a real threat to him/herself. At advanced stage, the patient can even forget her/his own address, name, etc. Scenarios can get real complicated when the patient fails to identify his/her relatives, family members and friends.
Is home or nursing home the best place to take care of the person suffering from AD?
No, there is no such a thing. A lonely person with no one to take care of can stay best in a nursing home. But a person with good family and friends can easily stay in the home. Alzheimer’s is a not a disease but a syndrome that can be as deadly as any other disease. But, there is no specific treatment for it. So, there is no need to spend unnecessary money booking a bed in the nursing home.
What are the necessary precautions to take in order to make the home surroundings safe for someone who has been diagnosed with Alzheimer’s?
A clean surrounding can definitely help. The person suffering from AD should be kept stress free. The patient should have more interaction with family members and friends. However, by no means the patient should be made excited or furious. It can provide extra stress on the brain. This can cause some negative repercussions.
What are the best available support and services are available in the local area related to Alzheimer’s disease?
This is a very important question to ask the doctor. Remember, if local medicinal help can be availed, then much of worries are eliminated.
Is Alzheimer’s considered a hereditary disease?
Yes, definitely. But it is only a small part of the bigger process. AD can develop due to several factors, most important being strong stress.
Source:
http://www.biotechblog.org/entry/questions-doctor-alzheimer-disease/
Background:
Hydrocarbon alkanes have been recently considered as important next-generation biofuels because microbial production of alkane biofuels was demonstrated. However, the toxicity of alkanes to microbial hosts can possibly be a bottleneck for high productivity of alkane biofuels. To tackle this toxicity issue, it is essential to understand molecular mechanisms of interactions between alkanes and microbial hosts, and to harness these mechanisms to develop microbial host strains with improved tolerance against alkanes. In this study, we aimed to improve the tolerance of Saccharomyces cerevisiae, a model eukaryotic host of industrial significance, to alkane biofuels by exploiting cellular mechanisms underlying alkane response.
Results:
To this end, we first confirmed that nonane (C9), decane (C10), and undecane (C11) were significantly toxic and accumulated in S. cerevisiae. Transcriptome analyses suggested that C9 and C10 induced a range of cellular mechanisms such as efflux pumps, membrane modification, radical detoxification, and energy supply. Since efflux pumps could possibly aid in alkane secretion, thereby reducing the cytotoxicity, we formed the hypothesis that those induced efflux pumps could contribute to alkane export and tolerance. In support of this hypothesis, we demonstrated the roles of the efflux pumps Snq2p and Pdr5p in reducing intracellular levels of C10 and C11, as well as enhancing tolerance levels against C10 and C11. This result provided the evidence that Snq2p and Pdr5p were associated with alkane export and tolerance in S. cerevisiae.
Conclusions:
Here, we investigated the cellular mechanisms of S. cerevisiae response to alkane biofuels at a systems level through transcriptome analyses. Based on these mechanisms, we identified efflux pumps involved in alkane export and tolerance in S. cerevisiae. We believe that the results here provide valuable insights into designing microbial engineering strategies to improve cellular tolerance for highly efficient alkane biofuel production.Source:
http://www.biotechnologyforbiofuels.com/content/6/1/95
Background:
Xylose-based ethanol production by recombinant S. cerevisiae is of great interest to basic and applied bioenergy research. By expressing three different fungal pathways in two S. cerevisiae hosts respectively, we found that the xylose utilization efficiency by recombinant S. cerevisiae depends not only on the choice of xylose pathway but also on the choice of host, exhibiting an obvious host or context dependence. To investigate molecular mechanisms of this context dependence, we applied RNA-seq analysis in this study for a systematic characterization of the xylose utilization via different pathways in different S. cerevisiae hosts.
Results:
Based on the RNA-seq analysis, the transcripts that were regulated during xylose utilization have been identified. Three transcription factors involved in regulation of amino acid metabolism, responses to oxidative stresses, and degradation of aggregated proteins, respectively, were found to participate in xylose metabolism regulation regardless of which pathway was expressed and which host the xylose pathway was expressed in. Nine transcription factors, involved in homeostasis, regulation of amino acid metabolism, and stress responses, were identified as the key modules responsible for the host-specific responses to the same xylose pathway. In addition, the transcriptional regulations of xylose utilization in different yeast hosts were compared to two reference regulation patterns, which indicated that diverse regulation strategies were adopted by different hosts for improved xylose utilization.
Conclusions:
This study provides the first transcriptomic study of the host dependence of xylose utilization in S. cerevisiae. Both the conserved regulatory modules for xylose metabolism and the key modules responsible for host dependence were identified. As indicated by the functions of the conserved transcription factors involved in xylose metabolism regulation, the xylose utilization in recombinant S. cerevisiae may be affected by both carbohydrate metabolism regulation and stress responses. Based on the comparison of transcriptional regulation patterns, the metabolic optimizations of xylose utilization in different hosts went toward different directions, which may explain the host dependence observed in this study. The knowledge revealed by this study could provide valuable insights towards the improvement of metabolic engineering strategies for cellulosic ethanol production.Source:
http://www.biotechnologyforbiofuels.com/content/6/1/96