1. The document discusses cellular respiration and fermentation in yeast cells. It provides background on how cells harvest energy from food sources and defines aerobic respiration, which uses oxygen to break down glucose, and anaerobic respiration, called fermentation, which occurs without oxygen.
2. The main steps of aerobic respiration and fermentation are described. Aerobic respiration breaks down glucose and oxygen to produce carbon dioxide, water, and ATP. Fermentation produces ethanol or lactic acid instead of using oxygen.
3. Yeast undergoes alcoholic fermentation, converting pyruvic acid to carbon dioxide and ethanol with some ATP also produced. The rate of carbon dioxide production during fermentation would be affected by the availability of
Cellular respiration is a process in which cells produce the energy they need to survive. Cells use oxygen to break down the sugar glucose and store its energy in molecules of adenosine triphosphate (ATP). Cellular respiration is critical for the survival of most organisms because the energy in glucose cannot be used by cells until it is stored in ATP. Two critical ingredients required for cellular respiration are glucose and oxygen. Although most organisms on Earth carry out cellular respiration to generate ATP, a few rely on alternative pathways to make this vital molecule. These pathways are anaerobic
that is, they don't require oxygen. Fermentation is a type of anaerobic pathway used by certain species of bacteria that live in anaerobic environments, such as stagnant ponds or decaying vegetation. Some cells produce ATP using both anaerobic and aerobic pathways ( Lagunzad, 2004).
Cellular respiration is a process in which cells produce the energy they need to survive. Cells use oxygen to break down the sugar glucose and store its energy in molecules of adenosine triphosphate (ATP). Cellular respiration is critical for the survival of most organisms because the energy in glucose cannot be used by cells until it is stored in ATP. Two critical ingredients required for cellular respiration are glucose and oxygen. Although most organisms on Earth carry out cellular respiration to generate ATP, a few rely on alternative pathways to make this vital molecule. These pathways are anaerobic
that is, they don't require oxygen. Fermentation is a type of anaerobic pathway used by certain species of bacteria that live in anaerobic environments, such as stagnant ponds or decaying vegetation. Some cells produce ATP using both anaerobic and aerobic pathways ( Lagunzad, 2004).
laboratory Fermentation of ethyl alcohol from molasses
this shows how fermentation can be carried out in laboratory
a simple flow sheet and precautions to be taken in lab
mentioned in {annexure 1} and about how enzymes carry out catalysis about yeast and industrial fermenntation
Energy for food process: According to estimates, a retail food product requires between 50 and 100 MJ (megajoules) of energy to produce and package each kilograms. Energy is needed in the food processing sector for power, heating, and cooling.
This pdf is about the Schizophrenia.
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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.
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.
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.
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.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
1. December
20, 2015
PRACTICAL CELL BIOLOGY LAB 9
Cellular Respiration and Fermentation in Yeast
BACKGROUND
Living systems require free energy and matter to maintain order, to grow,
and to reproduce. Energy deficiencies are not only detrimental to individual
organisms, but they cause disruptions at the population and ecosystem levels as
well. Organisms employ various strategies that have been conserved through
evolution to capture, use, and store free energy. Autotrophic organisms capture
free energy from the environment through photosynthesis and chemosynthesis,
whereas heterotrophic organisms harvest free energy from carbon compounds
produced by other organisms. In cellular respiration, free energy becomes available
to drive metabolic pathways vital to cellular processes primarily by the conversion
of ADP → ATP.
Cellular respiration is the process that cells use to transfer energy
from the organic molecules in food to ATP. The following equation
summarizes the chemical changes that occur in cellular respiration of the
monosaccharide glucose when oxygen is available.
C6H12O6 + 6O2 → 6CO2 + 6H2O + Energy (as ATP)
The word equation for this is:
Glucose (sugar) + Oxygen → Carbon dioxide + Water + Energy (as ATP)
All living cells, including the cells in your body and unicellular such
as yeast, need energy for cellular processes such as pumping molecules
into or out of the cell, synthesizing needed molecules, their metabolism,
2. December
20, 2015
PRACTICAL CELL BIOLOGY LAB 9
their activity. ATP is a special molecule which provides energy in a form
that cells can use for cellular processes.
There is another important feature of cellular respiration which is
not shown in above equation. Cellular respiration involves many small
steps; these multiple steps allow the cell to use the energy from each
glucose molecule efficiently in order to make as many ATP molecules as
possible. The multiple steps of cellular respiration are described in your
textbook. Our description will focus on some major steps and how these
steps differ, depending on whether oxygen is available or not.
The first major step in cellular respiration is glycolysis
1 glucose converts to2 pyruvate + 2 ATP
What happens next depends on whether or not oxygen is available to the
cells. When oxygen is available, cells can use the Krebs cycle and the
electron transport chain to make up to 36 ATPs (see the right side of the
figure).
2 pyruvate + 6 O2 convert to6 CO2 + 36 ATP
Cellular respiration that uses O2 is called aerobic respiration. Most
of the time, the cells in our bodies use aerobic respiration. When oxygen is
not available, cells use anaerobic processes to produce ATP.
3. December
20, 2015
PRACTICAL CELL BIOLOGY LAB 9
Aerobic respiration
Is the process that takes place in the presence of oxygen and involves
break down of fuel molecule to obtain energy. The process of obtaining
energy in aerobic respiration can be represented in the following equation:
Glucose + Oxygen -------------->Energy + Water + Carbon dioxide
Anaerobic respiration
Is the process of oxidation of molecules in the absence of oxygen to
produce energy in the form ATP. Anaerobic respiration is synonymous with
fermentation. There are two types of fermentation
1. Lactate fermentation (Glucose -------------->energy + Lactic Acid +
Carbon dioxide).
2. Alcoholic fermentation (Glucose -------------->energy + Ethanol +
Carbon dioxide)
4. December
20, 2015
PRACTICAL CELL BIOLOGY LAB 9
Fermentation has two disadvantages compared to aerobic respiration.
Low ATP production.
Produces a toxic byproduct (lactic acid or alcohol).
Yeasts are tiny single-celled (unicellular) fungi. The organisms in
the Kingdom Fungi are not capable of making their own food. Fungi, like
any other organism, need food for energy. They rely on sugar found in
their environment to provide them with this energy so that they can grow
and reproduce.
Yeast will undergo alcoholic fermentation, which converts pyruvic acid into
CO2.as well as alcohol, Overall, the final equation for glycolysis plus fermentation
would be:
C6H12O6 2CO2 + 2C2H5OH, with 2 ATP also produced.
For the yeast cell, this chemical reaction is necessary to produce the energy
for life. The alcohol and the carbon dioxide are waste products produced by the
yeast. Fermentation can be watched and measured by the amount of carbon dioxide
gas that is produced from the breakdown of glucose.
Do you think that the rate of carbon dioxide production during fermentation
would be affectedby the availability of simple sugars?
PROCEDURE1:
1. Get two plastic cups and label them A and B.
2. Put water, sugar and yeast in cup A
3. Put water and yeast in cup B
4. Close the opening both cups with balloon
5. Wait for 1hr
6. Note the result.