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(Sorry to Announce) Field Trip and Lecture Cancellation: This Wednesday, September 19

Posted: September 23, 2012 at 3:46 pm

A very sad announcement: the field trip to, and lecture at, St. Barts Pathology Museum organized as part of my one month residency at The Last Tuesday Society in London--originally scheduled to take place tomorrow, Wednesday September 19 at 7:00 PM--has been cancelled, due to circumstances beyond my control. Apologies to all! And hope to see you at one of these other wonderful upcoming events:

Source:
http://morbidanatomy.blogspot.com/feeds/posts/default?alt=rss

Recommendation and review posted by G. Smith

Microbial beta-glucosidases from cow rumen metagenome enhance the saccharification of lignocellulose in combination with commercial cellulase cocktail

Posted: September 23, 2012 at 3:46 pm

Background:
A complete saccharification of plant polymers is the critical step in the efficient production of bio-alcohols. Beta-glucosidases acting in the degradation of intermediate gluco-oligosaccharides produced by cellulases limit the yield of the final product.
Results:
In the present work, we have identified and then successfully cloned, expressed, purified and characterised 4 highly active beta-glucosidases from fibre-adherent microbial community from the cow rumen. The enzymes were most active at temperatures 45--55[degree sign]C and pH 4.0-7.0 and exhibited high affinity and activity towards synthetic substrates such as p-nitrophenyl-beta-D-glucopyranoside (pNPbetaG) and pNP-beta-cellobiose, as well as to natural cello-oligosaccharides ranging from cellobiose to cellopentaose. The apparent capability of the most active beta-glucosidase, herein named LAB25g2, was tested for its ability to improve, at low dosage (31.25 units g-1 dry biomass, using pNPbetaG as substrate), the hydrolysis of pre-treated corn stover (dry matter content of 20%; 350 g glucan kg-1 dry biomass) in combination with a beta-glucosidase-deficient commercial Trichoderma reseei cellulase cocktail (5 units g-1 dry biomass in the basis of pNPbetaG). LAB25g2 increased the final hydrolysis yield by a factor of 20% (44.5 +/- 1.7% vs. 34.5 +/- 1.5% in control conditions) after 96--120 h as compared to control reactions in its absence or in the presence of other commercial beta-glucosidase preparations. The high stability (half-life higher than 5 days at 50[degree sign]C and pH 5.2) and 2--38000 fold higher (as compared with reported beta-glucosidases) activity towards cello-oligosaccharides may account for its performance in supplementation assays.
Conclusions:
The results suggest that beta-glucosidases from yet uncultured bacteria from animal digestomes may be of a potential interest for biotechnological processes related to the effective bio-ethanol production in combination with low dosage of commercial cellulases.Source:
http://www.biotechnologyforbiofuels.com/rss/

Recommendation and review posted by G. Smith

A constraint-based model of Scheffersomyces stipitis for improved ethanol production

Posted: September 23, 2012 at 3:46 pm

Background:
As one of the best xylose utilization microorganisms, Scheffersomyces stipitis exhibits great potential for the efficient lignocellulosic biomass fermentation. Therefore, a comprehensive understanding of its unique physiological and metabolic characteristics is required to further improve its performance on cellulosic ethanol production.
Results:
A constraint-based genome-scale metabolic model for S. stipitis CBS 6054 was developed on the basis of its genomic, transcriptomic and literature information. The model iTL885 consists of 885 genes, 870 metabolites, and 1240 reactions. During the reconstruction process, 36 putative sugar transporters were reannotated and the metabolisms of 7 sugars were illuminated. Essentiality study was conducted to predict essential genes on different growth media. Key factors affecting cell growth and ethanol formation were investigated by the use of constraint-based analysis. Furthermore, the uptake systems and metabolic routes of xylose were elucidated, and the optimization strategies for the overproduction of ethanol were proposed from both genetic and environmental perspectives.
Conclusions:
Systems biology modelling has proven to be a powerful tool for targeting metabolic changes. Thus, this systematic investigation of the metabolism of S. stipitis could be used as a starting point for future experiment designs aimed at identifying the metabolic bottlenecks of this important yeast.Source:
http://www.biotechnologyforbiofuels.com/rss/

Recommendation and review posted by G. Smith

Down-regulation of the caffeic acid O-methyltransferase gene in switchgrass reveals a novel monolignol analog

Posted: September 23, 2012 at 3:46 pm

Background:
Down-regulation of the caffeic acid 3-O-methyltransferase EC 2.1.1.68 (COMT) gene in the lignin biosynthetic pathway of switchgrass (Panicum virgatum) resulted in cell walls of transgenic plants releasing more constituent sugars after pretreatment by dilute acid and treatment with glycosyl hydrolases from an added enzyme preparation and from Clostridium thermocellum. Fermentation of both wild-type and transgenic switchgrass after milder hot water pretreatment with no water washing showed that only the transgenic switchgrass inhibited C. thermocellum. Gas chromatography--mass spectrometry (GCMS)-based metabolomics were undertaken on cell wall aqueous extracts to determine the nature of the microbial inhibitors.
Results:
GCMS confirmed the increased concentration of a number of phenolic acids and aldehydes that are known inhibitors of microbial fermentation. Metabolomic analyses of the transgenic biomass additionally revealed the presence of a novel monolignol-like metabolite, identified as trans-3, 4-dimethoxy-5-hydroxycinnamyl alcohol (iso-sinapyl alcohol) in both non-pretreated, as well as hot water pretreated samples. iso-Sinapyl alcohol and its glucoside were subsequently generated by organic synthesis and the identity of natural and synthetic materials were confirmed by mass spectrometric and NMR analyses. The additional novel presence of iso-sinapic acid, iso-sinapyl aldehyde, and iso-syringin suggest the increased activity of a para-methyltransferase, concomitant with the reduced COMT activity, a strict meta-methyltransferase. Quantum chemical calculations were used to predict the most likely homodimeric lignans generated from dehydration reactions, but these products were not evident in plant samples.
Conclusions:
Down-regulation of COMT activity in switchgrass resulted in the accumulation of previously undetected metabolites resembling sinapyl alcohol and its related metabolites, but that are derived from para-methylation of 5-hydroxyconiferyl alcohol, and related precursors and products; the accumulation of which suggests altered metabolism of 5-hydroxyconiferyl alcohol in switchgrass. Given that there was no indication that iso-sinapyl alcohol was integrated in cell walls, it is considered a monolignol analog. Diversion of substrates from sinapyl alcohol to free iso-sinapyl alcohol, its glucoside, and associated upstream lignin pathway changes, including increased phenolic aldehydes and acids, are together associated with more facile cell wall deconstruction, and to the observed inhibitory effect on microbial growth. However, iso-sinapyl alcohol and iso-sinapic acid, added separately to media, were not inhibitory to C. thermocellum cultures.Source:
http://www.biotechnologyforbiofuels.com/rss/

Recommendation and review posted by G. Smith

The flat-plate plant-microbial fuel cell: the effect of a new design on internal resistances

Posted: September 23, 2012 at 3:46 pm

Due to a growing world population and increasing welfare, energy demand worldwide is increasing. To meet the increasing energy demand in a sustainable way, new technologies are needed. The Plant-Microbial Fuel Cell (P-MFC) is a technology that could produce sustainable bio-electricity and help meeting the increasing energy demand. Power output of the P-MFC, however, needs to be increased to make it attractive as a renewable and sustainable energy source. To increase power output of the P-MFC internal resistances need to be reduced. With a flat-plate P-MFC design we tried to minimize internal resistances compared to the previously used tubular P-MFC design. With the flat-plate design current and power density per geometric planting area were increased (from 0.15 A/m2 to 1.6 A/m2 and from 0.22 W/m2 to and 0.44 W/m2)as were current and power output per volume (from 7.5 A/m3 to 122 A/m3 and from 1.3 W/m3 to 5.8 W/m3). Internal resistances times volume were decreased, even though internal resistances times membrane surface area were not. Since the membrane in the flat-plate design is placed vertically, membrane surface area per geometric planting area is increased, which allows for lower internal resistances times volume while not decreasing internal resistances times membrane surface area. Anode was split into three different sections on different depths of the system, allowing to calculate internal resistances on different depths. Most electricity was produced where internal resistances were lowest and where most roots were present; in the top section of the system. By measuring electricity production on different depths in the system, electricity production could be linked to root growth. This link offers opportunities for material-reduction in new designs. Concurrent reduction in material use and increase in power output brings the P-MFC a step closer to usable energy density and economic feasibility.Source:
http://www.biotechnologyforbiofuels.com/rss/

Recommendation and review posted by G. Smith

Reproducing Research Results: Removing a Scientific Roadblock

Posted: September 23, 2012 at 3:46 pm


The California stem cell agency faces
no easy task in trying to translate basic research findings into
something that can be used to treat patients and be sold commercially.

Even clinical trials, which only begin
long after the basic research is done and which involve more ordinary
therapeutic treatments than stem cells, fail at an astonishing rate.
Only one out of five that enter the clinical trial gauntlet
successfully finish the second stage, according to industry data
cited last spring by Pat Olson, executive director of scientific activities at the stem cell agency. And
then come even more challenges.
But at a much earlier stage of
research there is the “problem of irreproducible results,” in the
words of writer Monya Baker of the journal Nature. Baker last month reported on
moves by a firm called Science Exchange in Palo Alto, Ca., to
do something to ease the problem and speed up preclinical research.
The effort is called the Reproducibility Initiative and also involves
PLOS and figshare, an open science Internet project.
Elizabeth Iorns
Science Exchange Photo
Science Exchange is headed by Elizabeth
Iorns
, a scientist and co-founder of the firm. She wrote about  test-tube-to-clinic translation issues in a recent article in New
Scientist
that was headlined, “Is medical science built on shaky
foundations?”
Iorns said,

“One goal of scientific publication
is to share results in enough detail to allow other research teams to
reproduce them and build on them. However, many recent reports have
raised the alarm that a shocking amount of the published literature
in fields ranging from cancer biology to psychology is not
reproducible.”

Iorns cited studies in Nature that
reported that Bayer cannot “replicate about two-thirds of published
studies identifying possible drug targets” and that Amgen failed at
even a higher rate. It could not “replicate 47 of 53 highly
promising results they examined.”
The California Stem Cell Report earlier
this week asked Iorns for her thoughts on the implications for the
California stem cell agency, whose motto is "Turning stem cells into cures." Here is the full text of her response.

“First, I think it is important to
accept that there is a crisis affecting preclinical research. Recent
studies estimate that 70% of preclinical research cannot be
reproduced. This is the research that should form the foundation upon
which new discoveries can be made to enhance health, lengthen life,
and reduce the burdens of illness and disability. The
irreproducibility of preclinical research is a significant impediment
to the achievement of these goals. To solve this problem requires
immediate and concrete action. It is not enough to make
recommendations and issue guidelines to researchers. Funders must act
to ensure they fund researchers to produce high quality reproducible
research. One such way to do so, is to reward, or require,
independent validation of results. The reproducibility initiative
provides a mechanism for independent validation, allowing the
identification of high quality reproducible research. It is vital
that funders act now to address this problem, to prevent the wasted
time and money that is currently spent funding non-reproducible
research and to prevent the erosion of public trust and support for
research.”

Source:
http://californiastemcellreport.blogspot.com/feeds/posts/default?alt=rss

Recommendation and review posted by G. Smith


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