This lecture covers some nice stories about the origins of the words "genome" and the derived word "genomics". the lecture also introduces viral, bacterial, and eukaryotic genomes.
This lecture covers key findings to the development of genomics as a field. This first part covers briefly Mendel to knowing that DNA is the genetic material by Hershey and Chase
The genetic material of a cell or an organism refers to those materials found in the nucleus, mitochondria and cytoplasm, which play a fundamental role in determining the structure and nature of cell substances, and capable of self-propagating and variation.
This lecture covers some nice stories about the origins of the words "genome" and the derived word "genomics". the lecture also introduces viral, bacterial, and eukaryotic genomes.
This lecture covers key findings to the development of genomics as a field. This first part covers briefly Mendel to knowing that DNA is the genetic material by Hershey and Chase
The genetic material of a cell or an organism refers to those materials found in the nucleus, mitochondria and cytoplasm, which play a fundamental role in determining the structure and nature of cell substances, and capable of self-propagating and variation.
DNA is the largest molecule known. A single, unbroken strand of it can contain many millions of atoms. When released from a cell, DNA typically breaks up into countless fragments. In solutions, these strands have a slight negative electric charge, a fact that makes for some fascinating chemistry.
DNA is the largest molecule known. A single, unbroken strand of it can contain many millions of atoms. When released from a cell, DNA typically breaks up into countless fragments. In solutions, these strands have a slight negative electric charge, a fact that makes for some fascinating chemistry.
The material of a talk that I prepared to give in the online camel conference of Oman. Unfortunately, I had a death in the family the day before the conference and the material was presented by my friend Dr. Mohammed Alabri from Oman. The material is in Arabic and focused for camel breeders.
The material of a two days workshop that I gave at Sultan Qaboos University in Oman about the importance of livestock biobanks and how to establish an organized one. The workshop was given in Arabic.
A presentation as a webinar for the Winn Feline Foundation that focuses on recent findings related to the signatures of selection in the domestic cat genome
This was my presentation at the Plant and Animal Genome Conference 2019 in San Diego. My talk was a presentation of the thesis project of my student Mona Abdi. The focus of the presentation and project was the genomic signatures of selection in the domestic cat breeds.
This is a my lecture about camels title "Journey around the camel". The lecture was in Arabic and is related to a book under preparation with the same title. This part of the journey around the camel introduces the major camel breeds in the Arabian Peninsula and their external phenotypes and groupings.
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...Travis Hills MN
Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.
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/
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.
ESR spectroscopy in liquid food and beverages.pptxPRIYANKA PATEL
With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
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.
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.
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
3. Aims
• Introduce the experiments that led to
discovering the identity of the genetic code.
• Explain the progression of scientific
thought and evidence associated with DNA
discovery.
• Explain when the lines of evidence were
sufficient to conclude DNA is the genetic
code.
8. Nuclein
Fredrick Miescher
bloody bandages
(1869)
• Bloody bandages as a source of cells.
• When added HCl, got pure nuclei (singular =
nucleus).
• When adding a base then an acid to the nuclei,
got a gray precipitate.
9. Nuclein
• The molecule is different than other molecules
(contain C, O, N, H, and P – not known to be in
proteins).
• Since the molecule came from nucleus, he called
it Nuclein (today called DNA).
10. Chromatin
Walther Flemming
band structure in
dividing cells (1879)
• Used cells of salamanders and staining
techniques to study cell division (he called it
mitosis).
• The intensely stained parts of the nucleus he
called chromatin (chroma is Greek for color).
12. Chromatin
Walther Flemming
band structure in
dividing cells (1879)
• When a base then an acid added to chromatin,
the same gray precipitate is found.
• Conclusion: Miescher’s nuclien and chromatin
are the same.
13. Chromosomes
Hermann Fol and Oscar
Hertwig (1870-1880)
• Observed fertilization and fusion of the eggs
and sperms nuclei.
• Chromatin is called chromosomes.
14. Chromosomes
• The study of fertilization using light
microscopy led to:
• Eggs and sperms have equal number of
chromosomes.
• Chromosomes get passed to future
generations.
• By 1890 almost everybody agreed that
nuclien = chromatin = chromosomes are
the basis of heredity.
15. Chromosomes and heredity
• Chromosomes are proteins and nucleic acid.
Which one is the genetic molecule?
• Many suspected proteins to be the hereditary
molecule because of the high capacity to store info
(20 amino acids – now 22) compared to 4
nucleotides in DNA.
16. Characteristics of genetic material
• What should the hereditary molecule have?
• Contain the information in a stable form.
• Able to self replicate and pass to future
generations.
• Can be changed (allowing for adaptation
and evolution).
18. Griffith’s transformation experiment
• Fredrick Griffith used Streptococus pneumonia
(causes lung disease – pneumonia).
S strain
Smooth colonies
(highly infectious)
Streptococus pneumonia
R strain
Rough colonies
(Not infectious)
Mice die
Inject mice Inject mice
H
eated/killed
Alive
Mice die
So R living cells were transformed by interacting with
molecules of dead S starin
Mice live
19. Griffith’s transformation experiment
• He called the molecule (the transforming
principle).
• So some thing is genetic?
• Protein ?
• DNA ?
• Don’t know.
20. Griffith’s transformation experiment
• He called the molecule (the transforming
principle).
• So something is genetic?
• Is it Protein ?
• Is it DNA ?
• Don’t know.
What is the chemical identity of the genetic
material?
21. Avery’s transformation experiment
• Avery is asking the question: which component of
the S cells is the transforming principle (genetic
code)?
• Rerun Griffith’s experiment with some
modifications.
• lysed cells contain:
• Proteins
• Polysaccharides
• RNA
• DNA
One of these molecules
must be the genetic
material
22. Avery’s
transformation
experiment
• He used enzymes to degrade a specific class of
molecules at a time then study the transformed
cells.
• When DNA was degraded with DNase, no
transformation occurred.
• Thus, DNA is the transformation principle!
• Clever right?
• Not good enough and convincing for some
scientists. Why?
• Because the degrading enzymes were not pure!
24. • Need more evidence that DNA is the genetic
code.
• Hershey and Chase used a bacterial parasite
(virus) to study the genetic code.
• Bacteriophage (phage):
• Protein body.
• DNA inside.
• Use the knowledge about the life
cycle to study the genetic code.
• What is phage’s life cycle?
Hershey and Chase experiment
26. Hershey and Chase experiment
Track where the radioactive material go!
• Labeled proteins with radioactive S35.
• Labeled DNA with radioactive P32.
• The molecule that would enter the cell is the
hereditary molecule.
• Study where the molecule go (in pellet or in
supernatant)?
27. Hershey and Chase experiment
Track where the radioactive material go!
DNA is the genetic material!!!
28. Hershey and Chase experiment
Track where the radioactive material go!
29. To study
Transforming principle
Griffith’s transformation experiment
Avery’s transformation experiment
Hershey and Chase experiment
S Strain
R Strain
Bacteriophage
Phage
Nuclien
Phage life cycle
Radioactive P
Radioactive S
Dominant
30. Expectations
• Know the experiments that lead to the
conclusion that DNA is the genetic material.
• Know what each experiment added to the
previous knowledge.
• You know a bit of the story to tell your
friends and family.