This document summarizes the key outcomes, background, significance, and approach of a study that investigated the effects of glycerol thermal processing (GTP) on lignin structure through NMR analysis. The main outcomes were that GTP effectively breaks bonds within lignin, generating smaller molecular weight lignin fragments that are thermally stable up to temperatures over 290°C. The background discusses utilizing lignin for specialty products. The significance is that GTP generates lignin suitable for use as a thermoplastic co-product. The approach involved comparing the properties of GTP lignin to lignin from other processes through structural analysis.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
1. Alteration of of polyketide stereochemistry from
Anti to Syn by a ketoreductase domain exchange
in a type I modular polyketide synthase subunit
Outcomes
• LipPks1+TE contains an A2-type KR domain and specifically yielded
the (2S,3S) configuration (or Anti) in the acid products (Figure B).
• We exchanged the original A2-type KR domain with three different
types of B-type KR domains (B, B-1, and B-2) but none of these
attempts were successful. The reason is still unclear.
• We exchanged the original A2-type KR domain with an A1-type KR
domain and were able to successfully convert the stereochemistry at
the C2 position to generate the Syn products (Figure B).
Eng et al. (2016) “Alteration of of polyketide stereochemistry from anti to syn by a ketoreductase domain
exchange in a type I modular polyketide synthase subunit” Biochemistry, 55, pp. 1677-1680.
Background
• Polyketides made by type I polyketide synthases (PKSs) are typically
rich in stereocenters.
• Altering the stereochemistry is an important method to increase
chemical diversity.
Significance
• These results demonstrate a novel alteration of polyketide product
stereochemistry from Anti to Syn that may prove useful for biofuels
and renewable chemicals.
Approach
• Exchange ketoreductase (KR) domains in a model PKS system
(LipPks1+TE).
• KR domains are responsible for altering the stereochemistry in both the
b-hydroxy and a-alkyl groups.
• A naming conversion has been established to describe b-hydroxy (A or
B) and a-substituent (1 = nonepimerized, 2 = epimerized) as shown in
Figure A.
A A1
B1
A2
B2
A
B
KR domain exchange
B
A2
A1
Anti
Syn
TEACPKRATKSAT ACP
AT ACP KS AT KR ACP TE
2. Outcomes
• A set of 41 mutated lines has been sequenced.
• Over 2400 mutations were identified and 1284 genes
were mutated in the 41 mutants.
• Established a pipeline for analysis of sequences of
mutated lines.
Li, et al. (2016) “Genome-wide sequencing of 41 rice (Oryza sativa L.)
mutated lines reveals diverse mutations induced by fast-neutron
irradiation” Mol. Plant. doi: 10.1016/j.molp.2016.03.009.
Background
• There is a lack of genomics tools available to
determine the function of genes involved in grass cell
wall biosynthesis and other biological processes.
Significance
• These results reveal that a diversity of mutations are
induced by fast-neutron irradiation.
• We have established a whole-genome sequenced mutant
collection that will significantly facilitate biofuel research in
grasses, including switchgrass and sorghum.
Genome-wide characterization of mutations in 41 FN-induced rice mutant
lines. (A) Strategy for generating and sequencing the rice FN mutagenized population.
(B) Representation of the diversity of mutations induced by FN irradiation. The inner pie
chart indicates the number of each type of mutations in the 41 sequenced M3 lines. The
outer circle shows the number of genes affected by each type of mutation. SBS: single
base substitutions; DEL: deletions; INS: insertions; INV: inversions; TRA: translocations;
and DUP: tandem duplications. (C) Comparisons between FN-induced SBSs and the
SNPs present between X.Kitaake and the reference genome. (D) Size distribution of FN-
induced deletions the 41 rice mutant lines. (E) Representation of the twelve rice
chromosomes on an Mb scale. (F) Representation of repetitive sequences in the
reference genome in non-overlapping windows (window size = 500 kb). (G) The
sequencing depth of the 42 rice lines. (H) Genome-wide distribution of FN-induced
mutations in non-overlapping 500-kb windows. (I) Translocations.
Approach
• Whole-genome sequencing of a model grass mutant
population
• Apply complementary bioinformatics algorithms to
identify genetic mutations
Genome-wide sequencing of 41 rice
(Oryza sativa L.) mutated lines reveals diverse
mutations induced by fast-neutron irradiation
3. Biomass Modification, Characterization, and
Process Monitoring Analytics to Support Biofuel
and Biomaterial Production
Outcomes
• Rapid instrumental techniques have been developed for real-time monitoring of
diverse processes, such as the efficacy of specific pretreatment strategies, or
downstream products, such as biofuels and biomaterials.
• Real-time process monitoring techniques are needed for all stages of the
feedstocks-to-biofuels conversion process to maximize efficiency and lower
costs by monitoring and optimizing performance.
Lupoi, J., Simmons, B., & Henry, R. (2016). ”Biomass Modification, Characterization, and Process Monitoring Analytics to
Support Biofuel and Biomaterial Production". Front Bioeng Biotechnol, 4, 25. doi, 10.3389/fbioe.2016.00025
Background
• This Frontiers Research Topic journeys through various challenges
facing researchers seeking to develop fuels and products derived from
lignocellulosic biomass.
Significance
• This collection of papers demonstrates how advances at multiple levels are likely
to contribute to the successful industrial scale production of biofuels and
biomaterials
Approach
• These challenges include: the rapid quantification of plant cell wall chemistry,
enabling yields of potential monomeric sugars to be assessed, identification of
plants possessing ideal trait that can be brought to the forefront of research
efforts; once the native plant chemistry is known, how can yields be improved
by chemically or genetically altering plant cell walls to reduce recalcitrance;
does genetic modification of plants to increase accessibility to saccharification
enzymes hinder the plant’s growth and/or function; are the innovative methods
identified by researchers cost-effective and scalable to a commercial level?
4. Engineering cellular metabolism
Outcomes
• Most strains used for industrial production require
a large number of genetic modifications, not only
in the pathways of interest, but also in other
pathways in order to efficiently redirect metabolic
flux.
• It is often necessary to combine overexpression
of specific enzymes with deregulation of the
pathway in order to ensure high flux through the
pathway of interest.
Nielsen, J., & Keasling, J. D. (2016). "Engineering Cellular Metabolism". Cell, 164(6), 1185-1197.
Background
• Despite the advanced systems and synthetic
biology technologies now available for detailed
phenotypic characterization of cells and genome
editing, developing new cell factories that meet the
economic requirements for industrial scale
production is still challenging.
• Engineering a cell factory involves several rounds
of the so-called ‘design-build-test’’ cycle.
Significance
• The development of a solid knowledge base for such new platform cell factories will obviously
be time-consuming, but using the scaffold for knowledge integration established through
BioCAD, it will be possible to advance rapidly in the development of bioenergy solutions.
(A) According to the bow-tie structure of metabolism, all carbon sources are
converted to 12 precursor metabolites that are used for biosynthesis of all secreted
metabolites. The precursor metabolites are also used for the biosynthesis of all
building blocks that are needed for synthesizing macromolecules making up the
biomass of the cell. (B) Illustration of how an acetyl-CoA over-producing strain can
be used as a platform strain for production of a range of different molecules.
Approach
• Review paper discusses the principles and current
challenges of metabolic engineering, focusing on
how metabolism can be engineered for industrial
level production of specific chemicals.
5. Structural characterization of enzymes in
the lignin β-aryl ether
cleavage pathway
Outcomes
• Nine X-ray crystal structures and kinetic characterization of β-etherase LigD, LigO, LigL and LigG
from Sphingobium.
• Detailed information on the cofactor and substrate binding sites, and on the catalytic mechanisms
of these enzymes.
Significance
• The structure-function relationships and biochemistry of these enzymes
can inform future efforts in producing advanced biofuels and chemicals from lignin-derived materials.
Pereira et al. (2016). “Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-aryl Ether
Cleavage Pathway from Sphingobium sp SYK-6” Journal of Biological Chemistry doi, 10.1074/jbc.M115.700427
Background
• The production of fuels and chemicals
from lignocellulosic biomass has
created new opportunities for
developing high value products from
lignin, the most abundant aromatic
polymer in nature.
• Sphingobium sp. SYK-6 degrades
aromatic oligomers derived from lignin.
Approach
• Using X-ray crystallography, enzyme
kinetic assays, we have characterized
bacterial enzymes that cleave β-aryl
ether bonds, the most abundant inter-
unit linkage in lignin.
FIGURE 1. a) Cartoon and molecular surface
representations of apo-LigL and the LigL-
NADH-(αS,βR)-GGE complex. b) The active
site of LigL in complex with NADH showing
the interactions involving the co-substrate
NADH. c) The substrate binding site for LigL-
NADH-(αS,βR)-GGE showing residues Asp95,
Ser144, Tyr158, Pro188 and Arg222 that
interact directly with the GGE substrate. d)
Active site of LigL-NADH-(αS,βR)-GGE
showing the catalytic tetrad N115-S144-Y158-
K162, and a water molecule (W75) involved
in the extended proton relay system.
FIGURE 2. a) Overall cartoon representation
of the LigG-GS-AV complex dimer. b)
Superposition of the GSH binding site of
apo-LigG (magenta) and LigG-GSH (PDB ID
4G10) (orange) structures. c) Molecular
surface representation of the LigG
monomer in complex with the GS-AV
substrate analog. d) Active site of the LigG-
GS-AV complex. The glutathionyl moiety of
the GS-AV substrate sits on the top of the
four β-strands of the N-terminal thioredoxin
domain.
6. Evaluation of agave bagasse recalcitrance
using AFEXTM, autohydrolysis, and ionic
liquid pretreatments
Outcomes
• AFEX completely preserves plant carbohydrates.
• AH solubilized 62% of xylan from untreated AGB.
• A 25% delignification occurred after IL pretreatment.
• Intensity of β-aryl ether units in aliphatic, anomeric and aromatic regions
of NMR spectra decreased in all pretreated samples
• IL pretreatment generated highest sugar yields
A) Aromatic region of HSQC-NMR
spectra of untreated and pretreated
agave bagasse samples. 1) First time that
S/G lignin ratio of untreated Agave tequilana is
calculated. 2) Untreated AGB had a S/G ratio
of 4.3, which is higher than others current
biofuel feedstocks. 3) An increased S/G ratio is
observed in AFEX (5.0) and IL (4.7) but AH
decrease up to 4.2, due to lignin distribution
changes in the plant cell wall.
Pérez-Pimienta, et al. (2016) “Evaluation of agave bagasse recalcitrance using AFEXTM,
autohydrolysis and ionic liquid pretreatments” Bioresource Technology, 211, pp. 216-223.
Background
• Agave is a drought-resistant cellulosic
feedstock with high productivities in semiarid
regions and minimal water/nutrients inputs.
• Independent bioconversion studies have been
made on agave bagasse (AGB) to reduce its
recalcitrance for downstream process, but
different experimental conditions were applied.
Significance
• These comparative analyses will contribute to a better understanding of
AGB recalcitrance and enable more rational selection of biorefinery
configurations.
B) Glucan conversion of untreated and pretreated
agave bagasse at final saccharification time (72 h) using
a lower and higher biomass loading.
1) IL-pretreated AGB achieved the highest glucan conversion of all
three pretreatments. 2) Yields of glucose in the major hydrolysate
stream were 28.2, 24.0 and 29.1 kg per 100 kg of untreated AGB
for AFEX, IL and AH, respectively.
Approach
• First direct side-by-side comparative pretreatment
assessment on agave bagasse using ammonia
fiber expansion (AFEX), autohydrolysis (AH) and
ionic liquid (IL).
A
B
7. Rapid and robust optimization of energy
traits in crops
Outcomes
• Progress in plant synthetic biology shows great promises
• Synthetic biology can leverage engineering at the genome; transcription,
translation; protein stability, activity and assembly; and metabolic flux levels
• Plant synthetic biology will support the development of multiple traits that are
needed to reach high product yields in different bioenergy crops
Shih P, Liang Y, Loqué D. (2016) “Biotechnology and synthetic biology approaches for metabolic engineering of
bioenergy crops.” The Plant Journal, doi: 10.1111/tpj.13176
Background
• Novel strategies and technologies are needed
to speed up the development of robust and
diverse energy crops to fulfill sustainably and
cheaply U.S. demand in renewable energy.
Significance
• This article highlights the importance and promises of synthetic biology to support the
development and optimization of energy and agronomical traits in crops
Approach
• Application and development of synthetic
biology tools for plants
• Use of synthetic biology to support rapid and
robust plant engineering
8. Revealing the thermal sensitivity of lignin
during glycerol thermal processing (GTP)
through structural analysis
Outcomes
• NMR results indicate that GTP is very effective at
breaking bonds within lignin.
• GTP generated smaller molecular weights of lignin as
a result of depolymerization.
• GTP generated moieties that were stable up to
temperatures >290 oC
Zhang et al. (2016) "Revealing the thermal sensitivity of lignin during glycerol thermal
processing through structural analysis” RSC Advances, 6(36), 30234-30246
Background
• There is a strong specialties market for
selected lignin polymers (e.g., lignosulfonates),
due to their self-assembling properties.
• Kraft lignin has not penetrated commercial
markets due to poor thermal properties.
• Glycerol thermal processing (GTP) offers a
compelling alternative approach.
Significance
• GTP generates a lignin product that is suitable for use as a
polymeric co-product comparable to other thermoplastics.
HSQC of EMAL and isolated GTP lignin – aliphatic region (SGL6:
recovered sweet gum lignin at GTP severity log(R0) ¼ 4.61; SGL8:
recovered sweet gum lignin at GTP severity log(R0) ¼ 5.03).
Approach
• Comparison of the chemical and thermal
properties of lignin generated by a variety of
processes compared to that generated by GTP.