- The document discusses four types of forage sorghum (brown-midrib, non-brown-midrib, photoperiod sensitive, and photoperiod insensitive) and their potential impact on the minimum ethanol selling price at a biorefinery using ionic liquid pretreatment.
- Simulation results show that non-photoperiod sensitive sorghum may result in lower cost biofuels compared to high-yielding photoperiod sensitive varieties under certain conditions.
- If lignin value increases, non-brown-midrib varieties become the most attractive option due to their higher biomass yield outweighing the lower lignin content of brown-midrib varieties.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
The increased availability of biomedical data, particularly in the public domain, offers the opportunity to better understand human health and to develop effective therapeutics for a wide range of unmet medical needs. However, data scientists remain stymied by the fact that data remain hard to find and to productively reuse because data and their metadata i) are wholly inaccessible, ii) are in non-standard or incompatible representations, iii) do not conform to community standards, and iv) have unclear or highly restricted terms and conditions that preclude legitimate reuse. These limitations require a rethink on data can be made machine and AI-ready - the key motivation behind the FAIR Guiding Principles. Concurrently, while recent efforts have explored the use of deep learning to fuse disparate data into predictive models for a wide range of biomedical applications, these models often fail even when the correct answer is already known, and fail to explain individual predictions in terms that data scientists can appreciate. These limitations suggest that new methods to produce practical artificial intelligence are still needed.
In this talk, I will discuss our work in (1) building an integrative knowledge infrastructure to prepare FAIR and "AI-ready" data and services along with (2) neurosymbolic AI methods to improve the quality of predictions and to generate plausible explanations. Attention is given to standards, platforms, and methods to wrangle knowledge into simple, but effective semantic and latent representations, and to make these available into standards-compliant and discoverable interfaces that can be used in model building, validation, and explanation. Our work, and those of others in the field, creates a baseline for building trustworthy and easy to deploy AI models in biomedicine.
Bio
Dr. Michel Dumontier is the Distinguished Professor of Data Science at Maastricht University, founder and executive director of the Institute of Data Science, and co-founder of the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. His research explores socio-technological approaches for responsible discovery science, which includes collaborative multi-modal knowledge graphs, privacy-preserving distributed data mining, and AI methods for drug discovery and personalized medicine. His work is supported through the Dutch National Research Agenda, the Netherlands Organisation for Scientific Research, Horizon Europe, the European Open Science Cloud, the US National Institutes of Health, and a Marie-Curie Innovative Training Network. He is the editor-in-chief for the journal Data Science and is internationally recognized for his contributions in bioinformatics, biomedical informatics, and semantic technologies including ontologies and linked data.
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.
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
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.
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.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
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.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
Multi-source connectivity as the driver of solar wind variability in the heli...
June 2021 - JBEI Research Highlights
1. Identifying Forage Sorghum Ideotypes for
Advanced Biorefineries
Background
• Sorghum spans a diverse range of phenotypes, and it is unclear which
are most desirable as bioenergy feedstocks.
• There are tradeoffs between biomass yield, lignin content, and starch
and sugar contents. High biomass-yielding PS varieties have
previously been considered preferable for bioenergy production.
Approach
• We explore four forage sorghum types, including brown-midrib (bmr),
non-bmr, photoperiod sensitive (PS), and photoperiod insensitive
(non-PS), from the perspective of their impact on minimum bioethanol
selling price (MESP) at an ionic liquid pretreatment-based biorefinery.
• We use field trial data, including yield and composition for each
commercial forage sorghum line, in combination with process
simulation and cash flow analysis to compare individual varieties and
the averages across each type based on MESP
Outcomes and Impacts
• If most starch and sugars from the panicle are retained during storage,
use of non-PS sorghum may result in lower-cost biofuels (MESP of
$1.26/L-gasoline equivalent) compared to high-yielding PS varieties.
• If advances in lignin utilization increase its value such that it can be
dried and sold for $0.50/kg, the MESP for each scenario is lowered
and non-bmr varieties become the most attractive option (MESP of
$1.08/L-gasoline equivalent).
• While bmr varieties have lower lignin content, their comparatively
lower biomass yield results in higher transportation costs that negate
its fuel-yield advantage.
Yang et al. (2021) ACS Sustain. Chem. Eng., doi: 10.1021/acssuschemeng.1c01706
Figure 2. Sensitivity analysis based on composition.
Scenario 1: lignin combustion for onsite energy
generation. Scenario 2: lignin utilization as a byproduct.
Results based on 5% land utilization.
Figure 1. Relationship between minimum ethanol selling
price (MESP: $/L-gasoline equivalent) and biomass yield t/ha
(Mg ha–1) using four forage sorghum types (18 hybrids)
2. Background
• Carbohydrate active enzymes (CAZymes) are vital for the
lignocellulose-based biorefinery. The development of
hypersecreting fungal protein production hosts is therefore a major
aim for both academia and industry. .
• However, despite advances in our understanding of their
regulation, the number of promising candidate genes for targeted
strain engineering remains limited.
Approach
• Here, we resequenced the genome of the classical
hypersecreting Neurospora crassa mutant exo-1 and identified the
causative point of mutation to reside in the F-box protein-encoding
gene.
Outcomes and Impacts
• The corresponding deletion strain displayed amylase and invertase
activities exceeding those of the carbon catabolite derepressed
strain Δcre-1, while glucose repression was still mostly functional in
Δexo-1.
• Aiming to elucidate the underlying mechanism of enzyme
hypersecretion, we found the high secretion of amylases and
invertase in Δexo-1 to be completely dependent on the
transcriptional regulator COL-26.
• we successfully transferred the hypersecretion trait of the exo-
1 disruption by reverse engineering into the industrially deployed
fungus Myceliophthora thermophila using CRISPR-Cas9.
• Our identification of an important F-box protein demonstrates the
strength of classical mutants combined with next-generation
sequencing to uncover unanticipated candidates for engineering.
Gabriel et al. (2021) Proc Natl Acad Soc, doi: 10.1073/pnas.2025689118
Figure 1. Hypersecretion activity of exo-1 mutant and
∆exo-1
The F-box protein gene exo- 1 is a target for reverse
engineering enzyme hypersecretion in filamentous fungi
Figure 2. A model for the function of Exo-1
3. A multiplexed nanostructure-initiator mass spectrometry
(NIMS) assay for simultaneously detecting glycosyl
hydrolase and lignin modifying enzyme activities
Outcomes
Using time-series analysis we determined that crude laccase from Ab has
the higher GH activity and that laccase from Mt has the higher activity
against our lignin model compound. Inhibitor studies showed a significant
reduction in Mt GH activity under low oxygen conditions and increased
activities in the presence of vanillin (common GH inhibitor).
1) Concept of a NIMS multiplexed glycoside
hydrolase and lignin modifying enzyme assay
Ing et al. Sci Rep 11, 11803 (2021) doi: 10.1038/s41598-021-91181-8
Background
Analytical tools capable of quickly detecting both glycan and lignin
deconstruction are needed to support the development and characterization
of efficient enzymes/enzyme cocktails to deconstruct lignocellulosic biomass.
Significance
These assays enable simultaneous analyses of both glycoside hydrolase
and lignin modifying enzyme activities which we anticipate will be helpful in
developing enzyme cocktails for lignocellulose deconstruction. Importantly,
we find that our assay is suitable to examine the inhibition of GH activities
by aromatics which is an important consideration in the development of
economically viable biomass to biofuels approaches.
2) Effect of mediators and inhibitory conditions on
cellotetraose degradation by (A) Mt (B) Ab and (C)
CelE CBM3a (n=3). “✽” indicate ANOVA post hoc
significant differences compared to enzyme only.
Approach
Previously we have described nanostructure-initiator mass spectrometry-
based assays for the analysis of glycosyl hydrolase and most recently an
assay for lignin modifying enzymes. Here we integrate these two assays into
a single multiplexed assay against both classes of enzymes and use it to
characterize crude commercial enzyme mixtures. Application of our
multiplexed platform based on nanostructure-initiator mass spectrometry
enabled us to characterize crude mixtures of laccase enzymes from fungi
Agaricus bisporus (Ab) and Myceliopthora thermophila (Mt) revealing activity
on both carbohydrate and aromatic substrates.
4. Microbial production of advanced biofuels
Background
• Concerns over climate change have necessitated a rethinking of
our transportation infrastructure.
• One possible alternative to carbon-polluting fossil fuels are
biofuels produced from a renewable carbon source using
engineered microorganisms.
• Two biofuels, ethanol and biodiesel, have made inroads to
displacing petroleum-based fuels, but their penetration has been
limited by the amounts that can be used in conventional engines
and by cost.
Approach
• Advanced biofuels that mimic petroleum-based fuels are not
limited by the amounts that can be used in existing transportation
infrastructure, but have had limited penetration due to costs.
• In this review, we discussed the advances in engineering
microbial metabolism to produce advanced biofuels and prospects
for reducing their costs.
Outcomes and Impacts
• We reviewed the engineering of microbial metabolic pathways to
produce advanced biofuels.
• We discussed recent advancements in the engineering of
microbial hosts to express these pathways.
• Methods for improving the carbon efficiency of conversion of
carbon-rich substrates to advanced biofuels were discussed. This
included systematic ways to improve titers, rates, and yields.
• Finally, we addressed the challenging in scale-up of biofuel
production, and the recent advances to address these challenges.
Keasling et al. (2021) Nat Rev Microbiol. doi: 10.1038/s41579-021-00577-w
Major sources of toxicity and inhibition of growth and production.
Three possible approaches to improve TRY in a systematic
manner. Growth coupling combined with Adaptive Lab Evolution
(ALE), leveraging Genome-Scale Models and Machine Learning.