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.
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.
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.
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.
(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.
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/
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 .
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. Section 2.1
The Nature of Matter
Objectives
1. To learn about the composition of matter
2. To learn the difference between elements and
compounds
3. To define the three states of matter
3. Section 2.1
The Nature of Matter
A. The Particulate Nature of Matter
• Matter has mass and occupies space.
• It is composed of tiny particles called atoms.
4. Section 2.1
The Nature of Matter
B. Elements and Compounds
Elements
• Elements contain only one type of atom – elemental
copper contains only copper atoms and elemental gold
contains only gold atoms.
5. Section 2.1
The Nature of Matter
B. Elements and Compounds
Compounds
• Compounds are substances that contain two or more
different types of atoms.
6. Section 2.1
The Nature of Matter
C. The States of Matter
• Matter exists in three states:
– Solid: a rigid substance with a definite shape
– Liquid: has a definite volume but takes the shape of its
container
– Gas: takes the shape and volume of its container
7. Section 2.1
The Nature of Matter
Structure of a Solid
• Particles are held close togother in a regular
arrangement or lattice.
• Not able to move freely,but simply vibrate in
their fixed positions.
• Video Clip
9. Section 2.1
The Nature of Matter
Structure of a Liquid
• Particles are closely packed together in an
irregular arrangment.
• Able to move , flow and slide on each other.
• Video Clip
11. Section 2.1
The Nature of Matter
Structure of a Gas
• Particles are in continual straightline motion
(randomly).
• The kinetic energy of the molecule is greater than the
attractive force between them, thus they are much
farther apart and move freely of each other.
• When the molecules collide with each other, or with the
walls of a container, there is no loss of energy.
• Video Clip
13. Section 2.1
The Nature of Matter
• The Kinetic Molecular Theory explains the forces between
molecules and the energy that they possess. This theory has 3
main points :
– Matter is composed of small particles (atoms or molecules).
•
•
• Particles are moving all the time.(higher Temp. higher of
average energy
– The molecules are in constant motion. This motion is different
for the 3 states of matter.
–
14. Section 2.1
The Nature of Matter
•Solid particles are close together in a regular pattern.
•They cannot move from one place to another place.
•Solid particles are vibrating about their positions all
the time.
15. Section 2.1
The Nature of Matter
•Liquid particles are closer.
•They are moving continuously.
16. Section 2.1
The Nature of Matter
A. Physical and Chemical Properties and Changes
• Properties are used to identify and separate the substance.
• Ex: Substance = metals Properties = conduct electricity
• Matter has both physical and chemical properties.
– Chemical properties describe a substance’s ability to change
to a different substance.
– Physical properties are the characteristics of a substance that
do not involve changing to another substance.
• Examples are: shape, size and color, melting point, boiling
point
17. Section 2.1
The Nature of Matter
A. Physical and Chemical Properties and Changes
• Matter undergoes physical and chemical changes.
– A physical change involves a change in one or
more physical properties but no change in
composition.
– Ex:melting, boiling, freezing
20. Section 2.1
The Nature of Matter
B. Physical and Chemical Properties and Changes
• Matter undergoes physical and chemical changes.
– A chemical change transforms a substance into
one or more new substances.
– Ex: electrolysis
21. Section 2.1
The Nature of Matter
Objectives
1. To learn to distinguish between mixtures and pure
substances
2. To learn methods of separating mixtures
22. Section 2.1
The Nature of Matter
A. Mixtures and Pure Substances
• Matter can be classified as a mixture or a pure
substance.
23. Section 2.1
The Nature of Matter
Classification of Matter:
• Mixtures = a blend of two or more kinds of matter, each of
which retains its own identity and properties.
• - Parts can mixed together physically and usually can be
separated.
• - Contain various amounts of different substances, so the
composition needs to be specified. (% Mass = EX: 5 % NaCl
and 95 % water)
• Homogeneous (solutions): Uniform in composition
(Saltwater, air, milk, alloys)
• Heterogeneous: not uniform throughout (can be separated)
(pizza, concrete, salad)
24. Section 2.1
The Nature of Matter
A. Mixtures and Pure Substances
• A pure substance always has the same composition.
• Pure substances are of two types:
– Elements which cannot
be broken down
chemically into simpler
substances
– Compounds which can
be chemically broken
down into elements
Water is a compound. All the
components are the same—H2O molecules.
28. Section 2.1
The Nature of Matter
Summary: The Organization of Matter
29. Section 2.1
The Nature of Matter
Separation techniques of mixtures:
• Filtration = to filter a solid from a liquid
– Filtrate
– Residue
– Decant = used when the mixture consists of
substances of different densities.
• The less dense substances is carefully poured
off of the more dense one.
• Centrifugation - used when the substances have
very similar densities, or when one of the substances
consists of very fine particles suspended in a liquid.
• Electrolysis – electric current to separate water into
hydrogen gas and oxygen gas
30. Section 2.1
The Nature of Matter
B. Separation of Mixtures
Mixtures can be separated into pure substances by
various means.
• filtration
31. Section 2.1
The Nature of Matter
Chromatography
This technique separates substances (dyes and pigments) on
the basis of differences in solubility in a solvent.
Paper Chromatography = A solvent travels through paper by capillary action
and carries the pigments with it. Different pigments are deposited at different
places on the paper depending on how much they like the solvent compared to
how much they like to stick to the paper.
Solvent
Solute
32. Section 2.1
The Nature of Matter
Separation Techniques
• Distillation = to remove dissolved substances from a
liquid or to separate a mixture of liquids that have
different boiling points.
• The original liquid is heated.
• The temperature is measured.
• The vapor is collected and condensed back into a liquid.
• The new liquid is collected.
33. Section 2.1
The Nature of Matter
B. Separation of Mixtures
Mixtures can be separated into pure substances by
various means.
• distillation