DNA Nanotechnology: Concept and its Applications
DNA Nanotechnology # Various 2 and 3 dimensional shapes of DNA nanotechnology # DNA Origami # with their application and Future scope
Transfection methods (DNA to host cell) Erin Davis
Transfection of DNA to host cell can be done by various methods in lab scale.Gene gun,electroporation,lipofection .These methods are used to transfer DNA to the host cell.
introduction to Nanobiotechnology
what is nanotechnology
bionanotechnology
classical biotechnology industrial production using biological system
modern biotechnology from industrial processes to noval therapeutics
modern biotechnology immunological enzymatic and neucleic acid based technology
Dna based technology
self assembly and supramolecular chemistry
formation of ordered structure at nano scale
Protein based nanostructures for biomedical applications karoline Enoch
Proteins are kind of natural molecules that show unique
functionalities and properties in biological materials and
manufacturing feld. Tere are numerous nanomaterials
which are derived from protein, albumin, and gelatin. Tese
nanoparticles have promising properties like biodegradability, nonantigenicity, metabolizable, surface modifer, greater
stability during in vivo during storage, and being relatively
easy to prepare and monitor the size of the particles.
These particles have the ability to attach covalently with
drug and ligand
Scale up means increasing the quantity or volume of cell culture. For animal cells, the scale up strategies are dependent upon cell types or i.e. whether the cells requires matrix for attachment and growth ( adherent cell culture) or grows freely in suspended form in aqueous media. The scaling up principle for adherent cells are just to increase surface area for attachment while for suspension culture is to increase culture volume. This presentation enlightens the reader about different methods of scaling up of cells culture. Readers are also provided with sample questions for better understanding
DNA Nanotechnology: Concept and its Applications
DNA Nanotechnology # Various 2 and 3 dimensional shapes of DNA nanotechnology # DNA Origami # with their application and Future scope
Transfection methods (DNA to host cell) Erin Davis
Transfection of DNA to host cell can be done by various methods in lab scale.Gene gun,electroporation,lipofection .These methods are used to transfer DNA to the host cell.
introduction to Nanobiotechnology
what is nanotechnology
bionanotechnology
classical biotechnology industrial production using biological system
modern biotechnology from industrial processes to noval therapeutics
modern biotechnology immunological enzymatic and neucleic acid based technology
Dna based technology
self assembly and supramolecular chemistry
formation of ordered structure at nano scale
Protein based nanostructures for biomedical applications karoline Enoch
Proteins are kind of natural molecules that show unique
functionalities and properties in biological materials and
manufacturing feld. Tere are numerous nanomaterials
which are derived from protein, albumin, and gelatin. Tese
nanoparticles have promising properties like biodegradability, nonantigenicity, metabolizable, surface modifer, greater
stability during in vivo during storage, and being relatively
easy to prepare and monitor the size of the particles.
These particles have the ability to attach covalently with
drug and ligand
Scale up means increasing the quantity or volume of cell culture. For animal cells, the scale up strategies are dependent upon cell types or i.e. whether the cells requires matrix for attachment and growth ( adherent cell culture) or grows freely in suspended form in aqueous media. The scaling up principle for adherent cells are just to increase surface area for attachment while for suspension culture is to increase culture volume. This presentation enlightens the reader about different methods of scaling up of cells culture. Readers are also provided with sample questions for better understanding
Immobilization of enzymes refers to the technique of confining/anchoring the enzymes in or on an inert support for their stability & functional reuse.
this slide is about the two most vastly used reactors i.e., batch and continuous.
Folding depends upon sequence of Amino Acids not the Composition. Folding starts with the secondary structure and ends at quaternary structure.
Denaturation occur at secondary, tertiary & quaternary level but not at primary level.
What are an expression vector? Detailed description of plant gene structure. Plant expression vector systems are generally consists of Ri and Ti plasmids.
The other vectors which are generally used are DNA and RNA viruses.
It is a collection of membrane-embedded proteins and organic molecules, most of them organized into four large complexes labeled I to IV.
The resulting proton gradient is used by the ATP synthase complex for ATP formation.
ATP synthesis is driven by the return of protons to the matrix through an integral membrane protein complex known variously as ATP synthase.
Immobilization of enzymes refers to the technique of confining/anchoring the enzymes in or on an inert support for their stability & functional reuse.
this slide is about the two most vastly used reactors i.e., batch and continuous.
Folding depends upon sequence of Amino Acids not the Composition. Folding starts with the secondary structure and ends at quaternary structure.
Denaturation occur at secondary, tertiary & quaternary level but not at primary level.
What are an expression vector? Detailed description of plant gene structure. Plant expression vector systems are generally consists of Ri and Ti plasmids.
The other vectors which are generally used are DNA and RNA viruses.
It is a collection of membrane-embedded proteins and organic molecules, most of them organized into four large complexes labeled I to IV.
The resulting proton gradient is used by the ATP synthase complex for ATP formation.
ATP synthesis is driven by the return of protons to the matrix through an integral membrane protein complex known variously as ATP synthase.
ATP synthase—also called FoF1 ATPase is the universal protein that terminates oxidative phosphorylation by synthesizing ATP from ADP and phosphate.
ATP Synthase is one of the most important enzymes found in the mitochondria of cells
Protein is a macronutrient that is essential to building muscle mass. It is commonly found in animal products, though is also present in other sources, such as nuts and legumes. There are three macronutrients: protein, fats and carbohydrates. Macronutrients provide calories, or energy.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
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.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
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.
DERIVATION OF MODIFIED BERNOULLI EQUATION WITH VISCOUS EFFECTS AND TERMINAL V...Wasswaderrick3
In this book, we use conservation of energy techniques on a fluid element to derive the Modified Bernoulli equation of flow with viscous or friction effects. We derive the general equation of flow/ velocity and then from this we derive the Pouiselle flow equation, the transition flow equation and the turbulent flow equation. In the situations where there are no viscous effects , the equation reduces to the Bernoulli equation. From experimental results, we are able to include other terms in the Bernoulli equation. We also look at cases where pressure gradients exist. We use the Modified Bernoulli equation to derive equations of flow rate for pipes of different cross sectional areas connected together. We also extend our techniques of energy conservation to a sphere falling in a viscous medium under the effect of gravity. We demonstrate Stokes equation of terminal velocity and turbulent flow equation. We look at a way of calculating the time taken for a body to fall in a viscous medium. We also look at the general equation of terminal velocity.
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/
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
2. 28/04/2017
The typical biomolecular motor is a protein that uses free energy from ATP (Adenosine Tri-
phosphate) or other nucleotide triphosphate (NTP) hydrolysis as its fuel to produce mechanical
force.
ATP is the universal currency of energy in biological systems and, is generated from glucose by
a sequence of reactions called glycolysis.
The hydrolysis of ATP to ADP and inorganic phosphate is energetically favorable and the pool of
ATP in a cell is far higher than that of its hydrolysis products, hence serving as a remarkable
store of chemical energy that is used to perform the various cellular functions.
Motor proteins are involved in several critical cellular processes and have functions ranging
from ATP synthesis and muscle contraction.
Biomolecular motor
3. 28/04/2017
Flagellated bacteria, such as Escherichia coli, swim by rotating thin helical filaments, each driven at its
base by a reversible rotary motor, powered by an ion flux. A motor is about 45 nm in diameter and is
assembled from about 20 different kinds of parts. It develops maximum torque at stall but can spin several
hundred Hz.
Its direction of rotation is controlled by a sensory system that enables cells to accumulate in regions
deemed more favorable.
No more than 50 nm in Diameter It spins clockwise (CW) orcounterclockwise (CCW) at speeds on the order of
100 Hz, driving long thin helical filaments that enable cells to swim Receptors near the surface of the cell count
molecules of interest (sugars, amino acids, dipeptides) and control the direction of flagellar rotation. If a leg of
the search is deemed favorable, it is extended,
Flagellar motor
4. 28/04/2017
Fig; A schematic diagram
of the flagellar motor
CheY-P
It is the chemotaxis
signaling molecule that
binds to FliM, and FlgM
is the anti-sigma factor
pumped out of the cell by
the transport apparatus;
5. 28/04/2017
A cell swims steadily in a direction roughly parallel to its long axis for about a second—it is said to
“run”—and then moves erratically in place for a small fraction of a second—it is said to “tumble”—
and then swims steadily again in a new direction. When a cell runs at top speed, all of its flagellar
filaments spin CCW, the filaments form a bundle that pushes the cell steadily forward. When a cell
tumbles, one or more filaments spin CW; these filaments leave the bundle, and the cell changes
course
Motors switch from CCW to CW and back again approximately at random. The likelihood of
spinning CW is enhanced by a chemotactic signaling protein, CheY.
When phosphorylated, CheY binds to the cytoplasmic face of the flagellar motor. The
phosphorylation of CheY is catalyzed by a kinase, the activity of which is controlled by
chemoreceptors.
The different components of the motor are named after the genes that encode them. genes for which
mutant cells lacked flagellar filaments were called fla (for flagellum), but after more than 26 had been
found.
fla genes are now called flg, flh, fli, or flj, depending upon their location on the genetic map. Genes for
which mutant cells produce paralyzed flagella are called mot (for motility). Four of the all gene
products that are involved in gene regulation (FlgM, FlhC, FlhD, FliA);
6. 28/04/2017
The M-ring (for membrane) has affinity for inner-
membrane fractions,
The S-ring is seen just above the inner membrane,
The P-ring (for peptidoglycan) is at the right place to be
embedded in the peptidoglycan,
and the L-ring (for lipopolysaccharide) has affinity for
outer-membrane fractions.
It was found that both the M- and S-rings (now called the
MS-ring) comprise different domains of the same protein,
FliF. Therefore, they function as a unit.
7. 28/04/2017
FliG, FliM, and FliN are also referred to as the “switch complex,” since many mutations of fliG, fliM,
and fliN lead to defects in switching (in control of the direction of rotation)
Operons encoding the proteins of the chemotaxis system of E.
colia
Class 1 Class 2 Class 3
flhDC flgAMN fliC
flgBCDEFGHIJKL motABcheAW
flhBAE tar tap cheRBYZ
fliAZY aer
fliDST trg
Class 1 contains the master operon, flhDC, the expression of which is required for transcription of class 2 and class 3
operons.
Class 2 contains eight operons that encode components required for construction of the hook-basal body complex,
and class 3 contains six more that encode components required for filament assembly and motor function
8. 28/04/2017
ATP Synthase
ATP synthase is one of the wonders of the molecular world. ATP synthase is an enzyme, a molecular motor, an
ion pump, and another molecular motor all wrapped together in one amazing nanoscale machine. It plays an
indispensable role in our cells, building most of the ATP that powers our cellular processes.
Human mitochondrial (mt) ATP synthase, or complex V consists of two functional domains: F1, situated in the
mitochondrial matrix, and Fo, located in the inner mitochondrial membrane. Complex V uses the energy created
by the proton electrochemical gradient to phosphorylate ADP to ATP.
ATP synthase consists of two well defined protein entities: the F1 sector, a soluble portion situated in the
mitochondrial matrix, and the Fo sector, bound to the inner mitochondrial membrane. F1 is composed of three
copies of each of subunits α and β, and one each of subunits γ, δ and ε. F1 subunits γ, δ and ε constitute the
central stalk of complex V. Fo consists of a subunit c-ring (probably comprising eight copies, as shown in
bovine mitochondria and one copy each of subunits a, b, d, F6 and the oligomycin sensitivity-conferring
protein (OSCP). Subunits b, d, F6 and OSCP form the peripheral stalk which lies to one side of the complex.
10. 28/04/2017
Human mitochondrial ATP synthase, or
complex V, consists of two functional domains,
F1 and Fo. F1 comprises 5 different subunits
(three α, three β, and one γ, δ and ε) and is
situated in the mitochondrial matrix. Fo contains
subunits c, a, b, d, F6, OSCP and the accessory
subunits e, f, g and A6L. F1 subunits γ, δ and ε
constitute the central stalk of complex V.
Subunits b, d, F6 and OSCP form the peripheral
stalk. Protons pass from the intermembrane
space to the matrix through Fo, which transfers
the energy created by the proton
electrochemical gradient to F1, where ADP is
phosphorylated to ATP.
Structure of ATP Synthase
Jonckheere I, Smeitink J A M, and Rodenburg R J; Mitochondrial ATP synthase: architecture, function and
pathology (2011), J Inherit Metab Dis
11. 28/04/2017
Fo Region F1 Region
The F1 portion is soluble and consists of a
hexamer, denoted a3b3. This hexamer is arranged
in an annulus about a central shaft consisting of the
coiled-coil γ subunit.
The Fo portion consists of three transmembrane
subunits: a, b2 and c10-14. The remainder of Fo
consists of the transmembrane subunits a, and
b2; the latter is attached by the d subunit to the
a3b3 hexamer so that it anchors the a subunit
to F1. Thus there are two ‘stalks’ connecting Fo
to F1: ge and b2d.
14. 28/04/2017
The binding change mechanism. Notation for site occupancies: T = ATP bound, DP = ADP • Pi bound, D =
ADP bound. b subunits are numbered clockwise. The length of the arrows indicates the relative binding
affinities (a) The system starts with either (β 1, β 2, β 3) = (E, T D•P, D) (b) Clockwise rotation of g
increases the binding affinity of ADP in b1, traps ATP in b2, and promotes Pi binding on b3. (c) Further
rotation of g traps ADP and allows Pi binding in b1, releases the tightly bound ATP and allows ADP
binding in b2, and traps Pi in b3.
15. 28/04/2017
In steps 1 and 2 a site binds ADP and phosphate (not necessarily in that order). While trapped in the catalytic
site in step 3, reactants (ADP and Pi ) and product (ATP) are in chemical equilibrium. Step 4 requires the
input of mechanical torque from Fo on g to trap the reactants in the ATP state and to pry open the site
releasing the tightly bound ATP. The way in which this works is found in the shape of the a3b3 hexamer and
the g shaft
At the top of the a3b3 hexamer is a hydrophobic ‘sleeve’ in which the g shaft rotates. Further down, however,
the annulus is offset from the center, so that as g rotates clockwise, it sequentially pushes outwards on each
catalytic site. In addition, the e subunit is located eccentrically and attached to the g and c subunits so that, as
g rotates, it comes into contact sequentially with each b subunit in a conserved region called the DELSEED
sequence (named for the single letter abbreviation of its constituent amino acids). Together, this asymmetric
rotation exerts stress on the catalytic site loosening its grip on ATP so that thermal fluctuations can free it into
solution.
17. 28/04/2017
A single molecule of F1-ATPase acts as a rotary motor, the smallest known, by direct observation
of its motion. A central rotor of radius approximately 1 nm, formed by its gamma-subunit, turns
in a stator barrel of radius approximately 5nm formed by three alpha- and three beta-subunits. F1-
ATPase, together with the membrane-embedded proton-conducting unit F0, forms the H+-ATP
synthase that reversibly couples transmembrane proton flow to ATP synthesis/hydrolysis in
respiring and photosynthetic cells. In the presence of ATP, the filament rotated for more than 100
revolutions in an anticlockwise direction when viewed from the 'membrane' side. The rotary
torque produced reached more than 40 pN nm(-1) under high load.
Direct observation of the rotation of F1-ATPase.
Noji H, Yasuda R, Yoshida M, Kinosita K Jr.
18. 28/04/2017
In the realm of ATP-driven linear biomotors, the most prominent examples are dynein, kinesin and
myosin, which is involved in muscle contraction. Muscle contraction is a sophisticated process involving
actin and myosin and is a result of actin filaments sliding on myosin heads. Actin filaments are formed of
375 amino acid long subunits that are associated with ATP. Myosin transport along actin is not limited to
muscle contraction, and is involved in several cellular transport processes.
It is thought that the two heads of the myosin move along in a hand-over-hand mechanism based on the
~74nm displacements observed by fluorescent labeling methods.
Interaction of an actin filament
with myosin-coated surface
19. 28/04/2017
1. Itoh, H., et al., (2004) Mechanically driven ATP synthesis by F1-ATPase. Nature,. 427(6973): p. 465-8.
2. Noji, H., et al., (1997) Direct observation of the rotation of F1-ATPase. Nature,. 386(6622): p. 299-302.
3. Oster G, Wang H; ATP Synthase: Two rotary molecular motors working together; University of
California, Berkeley
4. Antoniel M etal., (2014 May) The Oligomycin-Sensitivity Conferring Protein of Mitochondrial ATP
Synthase ; Int J Mol Sci.; 15(5): 7513–7536.
5. Oster G and Wang H; (April 1999) ATP synthase: two motors, two fuels, Elsevier Science
6. Manuela Antoniel, (2014 May) The Oligomycin-Sensitivity Conferring Protein of Mitochondrial ATP
Synthase: Emerging New Roles in Mitochondrial Pathophysiology, International Journal of Molecular
Sciences
References
Editor's Notes
Forisomes re plant motors that enable long distance transport in a natural microfluidics system. These elongate protein bodies of up to 30 µm length are found in the highly specialized cells in the phloem
Journal of Inherited Metabolic Disease
metabolic processes whereby certain organisms obtain energy from organic molecules
a fluorescent actin filament to the gamma-subunit as a marker