Water potential is the difference in free energy between water in a plant cell and pure water. It is determined by solute potential, pressure potential, matrix potential, and gravitational potential. Solute potential decreases water potential due to dissolved solutes, while pressure potential increases it due to turgor pressure. Water always moves from areas of high water potential to low. In plant cells, matrix and gravitational potentials are usually negligible, so water potential equals solute plus pressure potentials.
The soil-plant-atmosphere continuum (SPAC) is the pathway for water moving from soil through plants to the atmosphere.
Continuum in the description highlights the continuous nature of water connection through the pathway.
The low water potential of the atmosphere, and relatively higher (i.e. less negative) water potential inside leaves, leads to a diffusion gradient across the stomatal pores of leaves, drawing water out of the leaves as vapour.
The soil-plant-atmosphere continuum (SPAC) is the pathway for water moving from soil through plants to the atmosphere.
Continuum in the description highlights the continuous nature of water connection through the pathway.
The low water potential of the atmosphere, and relatively higher (i.e. less negative) water potential inside leaves, leads to a diffusion gradient across the stomatal pores of leaves, drawing water out of the leaves as vapour.
Everything about photoperiodism from scratch to smart, from the oldest models to the latest models as well as proposed one, exclusive and elusive illustrations and models for proper understanding
intro-hostory and discovery-characteristics of phytochrome-chemical nature of phytochrome-mode of action-mechanism-phytochrome mediated physiological responses-phytochrome is a pigment system:some evidences-role of phytochrome
DPD, Water potential, Plasmolyses & ImbibitionSunita Sangwan
This presentation explains DPD (diffusion pressure deficit), Plasmolyses and Imbibition in details. this also include the numericals related to Water potential. difference between DPD & water potential.
Everything about photoperiodism from scratch to smart, from the oldest models to the latest models as well as proposed one, exclusive and elusive illustrations and models for proper understanding
intro-hostory and discovery-characteristics of phytochrome-chemical nature of phytochrome-mode of action-mechanism-phytochrome mediated physiological responses-phytochrome is a pigment system:some evidences-role of phytochrome
DPD, Water potential, Plasmolyses & ImbibitionSunita Sangwan
This presentation explains DPD (diffusion pressure deficit), Plasmolyses and Imbibition in details. this also include the numericals related to Water potential. difference between DPD & water potential.
An explanation found in introductory texts proposes that osmosis is a diffusion process in which water diffuses from a higher to a lower water concentration. This explanation is not theoretically sound and does not match the experimental data. This workshop explores common misconceptions about osmosis and the osmosis explanations given by physicists.
Download the PowerPoint slideshow from SlideShare. The notes sections contain explanations and references.
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 .
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.
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.
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.
2. • Water potential term was coined by Slatyer and
Taylor (1960). It is modern term which is used in
place of DPD.
• The best way to express spontaneous
movement of water from one region to another
is in terms of the difference of free energy of
water between two regions (from higher free
energy level to lower free energy level).
3. • According to principles of thermodynamics,
every components of system is having definite
amount of free energy which is measure of
potential work which the system can do.
• Water Potential is the difference in the free
energy or chemical potential per unit molar
volume of water in system and that of pure
water at the same temperature and pressure.
4. • It is represented by Greek letter.
• The value is measured in bars, pascals or
atmospheres.
• Water always moves from the area of high water
potential to the area of low water potential.
• Water potential of pure water at normal temperature
and pressure is zero.
• This value is considered to be the highest.
• The presence of solid particles reduces the free
energy of water and decreases the water potential.
Therefore, water potential of a solution is always
less than zero or it has negative value.
5. • Components of Water Potential:
• A typical plant cell consists of a cell wall, a
vacuole filled with an aqueous solution and a
layer of cytoplasm between vacuole and cell
wall. When such a cell is subjected to the
movement of water then many factors begin to
operate which ultimately determine the water
potential of cell sap
6. Components of water potential
(a) Solute potential or osmotic potential (Ψs)
(b) Pressure potential (Ψp)
(c) Matrix potential (Ψm)
(d) Gravitational potential (Ψg)
7. • Water potential in a plant cell or tissue can be written
as the sum of -
matrix potential
the solute potential
pressure potential
And gravitational potential ( due to gravity)
Ψw = Ψs + Ψp + Ψm + Ψg
• In case of plant cell, m and g are usually disregarded
and it is not significant in osmosis because of their
very low values. Hence, the above given equation is
written as follows.
Ψw = Ψs + Ψp
8. Solute Potential (Ψs):
• It is defined as the amount by which the water
potential is reduced as the result of the
presence of the solute.
• due to concentration of dissolve solutes which
by its effect on the entropy components reduces
the water potential
• s are always in negative values.
• it is expressed in bars with a negative sign.
9. Pressure Potential (Ψp):
• Due to hydrostatic pressure, which by its effect on
energy components increases the water potential
• Plant cell wall is elastic and it exerts a pressure on
the cellular contents. As a result the inward wall
pressure, hydrostatic pressure is developed in the
vacuole it is termed as turgor pressure.
• The pressure potential is usually positive
• And operates in plant cells as wall pressure and
turgor pressure.
• Its magnitude varies between +5 bars (during day)
and +15 bars (during night).
10. Matrix potential Ψm
• due to binding of water to cell and cytoplasm)
• Nearly negligible
• Substances tend to have affinity towards water
• Highly significant in seeds.
• It is always a negative value because of
absorption of water by cell
11. Gravitational potential(Ψg)
• The force of gravity acts on soil water as it does
on all other bodies.
• In a soil profile the gravitational potential (Ψg) of
water near the soil surface is always higher
thanΨg in the subsoil. As a result of heavy
precipitation or irrigation, therefore, the
difference inΨg causes downward flow of water
deeper into the soil profile.
• Is always negative.
12. • Important Aspects of Water Potential (Ψw):
• (1) Pure water has the maximum water potential
which by definition is zero.
• (2) Water always moves from a region of higher
Ψw to one of lower Ψw.
• (3) All solutions have lower w than pure water.
• (4) Osmosis in terms of water potential occurs
as a movement of water molecules from the
region of higher water potential to a region of
lower water potential through a semi permeable
membrane.
13. Osmotic Relations of Cells
According to Water Potential:
• In case of fully turgid cell:
• The net movement of water into the cell is
stopped. The cell is in equilibrium with the water
outside.
• Turgor pressure is equal and opposite to wall
pressure.
• Consequently the water potential in this case
becomes zero.
• Ψcell = Ψs +Ψp
14. • In case of flaccid cell:
• The turgor becomes zero.
• A cell at zero turgor has an osmotic potential
equal to its water potential.
• Ψcell =Ψs
15. • In case of plasmolysed cell:
• When the vacuolated parenchymatous cells are
placed in solutions of sufficient strength, the
protoplast decreases in volume to such an
extent that they shrink away from the cell wall
and the cells are plasmolysed.
• Such cells are negative value of pressure
potential (negative turgor pressure).
16. • Numerical Problems:
• 1. Suppose there are two cells A and B, cell A has
osmotic potential = -16 bars, pressure potential = 6
bars and cell B as osmotic potential = – 10 bars and
pressure potential = 2 bars. What is the direction of
movement of water?
Water potential of cell A = Ψs +Ψp = – 16 + 6 = – 10
bars
Ψ of cell B = -10 + 2 = -8 bars.
As movement of water is from higher water potential
(lower DPD) to lower water potential (higher DPD),
hence the movement of water is from cell B to cell
17. • 2. If osmotic potential of a cell is – 14 bars and
its pressure potential is 7 bars. What would be
its water potential?
We know Ψw = Ψs + Ψp
Given, osmotic potential (Ψs) is – 14 bars.
Pressure potentials (Ψp) is 7 bars
Therefore,
Water potential = (-14) + 5 = – 9 bars.
