Model organisms are non-human species that are widely studied in laboratories to help scientists understand biological processes. They are usually easy to maintain and breed in a lab setting. The document discusses several important model organisms including mice, fruit flies, yeast, and bacteria. It provides details on their genomes, uses for research, and similarities to humans that make them valuable models. Key model organisms like mice and fruit flies have been widely used to study genetics, development, and disease due to their small genomes and short lifecycles.
Cell cell hybridization or somatic cell hybridizationSubhradeep sarkar
What is Cell-Cell Hybridization?
History
More about Somatic cell Hybridization
Mapping of genes by somatic cell Hybridization
Hybridoma technology
Other Applications of Somatic Cell Hybridization
GENETICS
CYTOGENETICS
Definition of Linkage, Coupling and Repulsion hypothesis, Linkage group- Drosophila, maize and man, Types of linkage-complete linkage and incomplete linkage, Factors affecting linkage- distance between genes, age, temperature, radiation, sex, chemicals and nutrition, Significance of linkage.
The tendency of two or more genes to stay together (i.e., the co-existence of two or more genes) in the same chromosome during inheritance is known as LINKAGE. The linked genes are present on the same chromosome are said to be SYNTENIC. The linked genes do not show independent assortment.
LINKAGE v/s INDEPENDENT ASSORTMENT
The frequency of linkage or the strength recombination is influenced by several factors (agents).
cell lineage , cell fate - diverse class of cell fate, cell fate in plant meristem, mammalian development cell fate, nutritional effects on epigenetics, epigenetics of plants,
control of cell fate.
A complementation test (sometimes called a "cis-trans" test) can be used to test whether the mutations in two strains are in different genes. By taking an example of Benzer's work, complementation has been explained.
This presentation contains basic information about the mouse being used as a model organism, its genome, how the genome of the mouse was sequenced and a comparison between mouse genome and human genome.
Cell cell hybridization or somatic cell hybridizationSubhradeep sarkar
What is Cell-Cell Hybridization?
History
More about Somatic cell Hybridization
Mapping of genes by somatic cell Hybridization
Hybridoma technology
Other Applications of Somatic Cell Hybridization
GENETICS
CYTOGENETICS
Definition of Linkage, Coupling and Repulsion hypothesis, Linkage group- Drosophila, maize and man, Types of linkage-complete linkage and incomplete linkage, Factors affecting linkage- distance between genes, age, temperature, radiation, sex, chemicals and nutrition, Significance of linkage.
The tendency of two or more genes to stay together (i.e., the co-existence of two or more genes) in the same chromosome during inheritance is known as LINKAGE. The linked genes are present on the same chromosome are said to be SYNTENIC. The linked genes do not show independent assortment.
LINKAGE v/s INDEPENDENT ASSORTMENT
The frequency of linkage or the strength recombination is influenced by several factors (agents).
cell lineage , cell fate - diverse class of cell fate, cell fate in plant meristem, mammalian development cell fate, nutritional effects on epigenetics, epigenetics of plants,
control of cell fate.
A complementation test (sometimes called a "cis-trans" test) can be used to test whether the mutations in two strains are in different genes. By taking an example of Benzer's work, complementation has been explained.
This presentation contains basic information about the mouse being used as a model organism, its genome, how the genome of the mouse was sequenced and a comparison between mouse genome and human genome.
Caenorhabditis elegans is a tiny, free-living nematode found worldwide. Newly hatched larvae are 0.25 millimeters long and adults are 1 millimeter long. Their small size means that the animals are usually observed with either dissecting microscopes, which generally allow up to 100X magnification, or compound microscopes, which allow up to 1000X magnification. Because C. elegans is transparent, individual cells and subcellular details are easily visualized using Nomarski (differential interference contrast, DIC) optics.
C. elegans has a rapid life cycle and exists primarily as a self-fertilizing hermaphrodite, although males arise at a frequency of <0.2%. These features have helped to make C. elegans a powerful model of choice for eukaryotic genetic studies. In addition, because the animal has an invariant numbers of somatic cells, researchers have been able to track the fate of every cell between fertilization and adulthood in live animals and to generate a complete cell lineage. Researchers have also reconstructed the shape of all C. elegans cells from electron micrographs, including each of the 302 neurons of the adult hermaphrodite. Moreover, because of the invariant wild-type cell lineage and neuroanatomy of C. elegans, mutations that give rise to developmental and behavioral defects are readily identified in genetic screens. Finally, because C. elegans was the first multicellular organism with a complete genome sequence, forward and reverse genetics have led to the molecular identification of many key genes in developmental and cell biological processes.
The experimental strengths and the similarities between the cellular and molecular processes present in C. elegans and other animals across evolutionary time (metabolism, organelle structure and function, gene regulation, protein biology, etc.) have made C. elegans an excellent organism with which to study general metazoan biology. At least 38% of the C. elegans protein-coding genes have predicted orthologs in the human genome, 60-80% of human genes have an ortholog in the C. elegans genome, and 40% of genes known to be associated with human diseases have clear orthologs in the C. elegans genome. Thus, many discoveries in C. elegans have relevance to the study of human health and disease.
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
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.
Toxic effects of heavy metals : Lead and Arsenicsanjana502982
Heavy metals are naturally occuring metallic chemical elements that have relatively high density, and are toxic at even low concentrations. All toxic metals are termed as heavy metals irrespective of their atomic mass and density, eg. arsenic, lead, mercury, cadmium, thallium, chromium, etc.
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/
(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.
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.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
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.
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
2. What are model organisms?
A model organism is a species that has been widely studied, usually because it is
easy to maintain and breed in a laboratory setting and has particular
experimental advantages.
These are non-human species that are used in the laboratory
to help scientists understand biological processes.
They are usually organisms that are easy to maintain and
breed in a laboratory setting.
They may have particularly robust embryos that are easily
studied and manipulated in the lab, this is useful for
scientists studying development.
Or they may occupy a pivotal position in the evolutionary
tree, this is useful for scientists studying evolution.
3. Genome projects and model organisms
Source (Slide Share): Genome projects and model organisms,
Level 3 Molecular Evolution and Bioinformatics by Jim Provan
4. Genome projects
Completed genomes:
Eubacteria (inc. Escherichia coli, Bacillis subtilis,
Haemophilus influenzae, Synechocystis PCC6803)
Archaea (inc. Methanococcus jannaschii,
Methanobacterium thermoautotrophium)
Eukarya:
Saccharomyces cerevisiae
Caenorhabditis elegans
Homo sapiens
Arabidopsis thaliana
Partially sequenced genomes e.g. Drosophila
melanogaster, Fugu rubripes, Oryza sativa
Source (Slide Share): Genome projects and model organisms,
Level 3 Molecular Evolution and Bioinformatics by Jim Provan
5. Relationships between model organisms
H. sapiens
C. elegans
D. melanogaster
S. cerevisiae
A. thaliana
Methanococcus
Archaeglobus
Synechocystis PCC6803
B. subtilis
M. genitalium
M. pneumoniae
B. burgdorferi
H. influenzae
E. coli
Source (Slide Share): Genome projects and model organisms,
Level 3 Molecular Evolution and Bioinformatics by Jim Provan
6. Eubacterial genomes: E. coli
4288 protein coding genes:
Average ORF 317 amino acids
Very compact: average distance
between genes 118bp
Numerous paralogous gene families:
38 – 45% of genes arisen through
duplication
Homologues:
H. influenzae (1130 of 1703)
Synechocystis (675 of 3168)
M. jannaschii (231 of 1738)
S. cerevisiae (254 of 5885)
Source (Slide Share): Genome projects and model organisms,
Level 3 Molecular Evolution and Bioinformatics by Jim Provan
7. The minimum genome and redundancy
Minimum set of genes required for survival:
Replication and transcription
Translation (rRNA, ribosomal proteins, tRNAs etc.)
Transport proteins to derive nutrients
ATP synthesis
Entire pathways eliminated in Mycoplasma:
Amino acid biosynthesis (1 gene vs. 68 in H. influenzae)
Metabolism (44 genes vs. 228 in H. influenzae)
Comparison of M. genitalium and H. influenzae has
identified a minimum set of 256 genes
Source (Slide Share): Genome projects and model organisms,
Level 3 Molecular Evolution and Bioinformatics by Jim Provan
8. Fungal genomes: S. cerevisiae
First completely sequenced
eukaryote genome
Very compact genome:
Short intergenic regions
Scarcity of introns
Lack of repetitive sequences
Strong evidence of duplication:
Chromosome segments
Single genes
Redundancy: non-essential genes
provide selective advantage
Source (Slide Share): Genome projects and model organisms,
Level 3 Molecular Evolution and Bioinformatics by Jim Provan
9. Invertebrate genomes: C. elegans
Genome even less compact than yeast:
One gene every 7143 bp (2155 bp in
yeast)
Due mainly to introns in protein coding
genes
Much more compact than humans (One
gene every 50,000 bp)
Compactness due mainly to
polycistronic arrangement:
Trans-splicing
Co-expression and co-regulation
Source (Slide Share): Genome projects and model organisms,
Level 3 Molecular Evolution and Bioinformatics by Jim Provan
10. Mice as a Model Organism
The mouse is closely related to humans with a striking similarity to us in
terms of anatomy, physiology and genetics. This makes the mouse an
extremely useful model organism.
The sequence of the mouse genome was published in 2002. When compared
with the human genome it was found that the two genomes were of similar
size and almost every gene in the human genome has a counterpart in the
mouse.
So, the researchers have been able to develop thousands of mouse strains
with mutations that mirror those seen in human genetic disease
11. History of Mice in science
In 1902, French biologist Lucien Cuénot was the first to demonstrate
Mendel’s theories of inheritance by highlighting the genetics of coat colour
characteristics in mice.
In Harvard, William Castle began his research in the same year, buying mice
from a local mouse enthusiast. Together with his student Clarence Little,
Castle produced a series of important papers on the genetics of coat colour
in mice.
It took Clarence four years between 1909 and 1913 to create a healthy and
genetically stable inbred strain.
12. Transgenic Mice
Transgenic mice are mice that contain additional, artificially introduced
genetic material in every cell.
This additional genetic material either results in a gain or loss of function of a
certain gene.
For example, this may mean the mouse starts to produce a new protein.
This allows scientists to investigate what specific genes do in the body.
13. Knockout Mice
Knockout mice are the result of the inactivation of a specific gene. The
resulting change in the appearance, behaviour or biochemical
characteristics of the mouse then gives an indication of the gene’s normal
role in the mouse, and perhaps in humans.
Knockout mice are produced by a technique called ‘gene targeting’. This
involves ‘knocking out’ a gene sequence from the mouse genome and
inserting an artificial gene sequence that has been generated in the lab.
14. Knockout Mice
As with transgenic mice, gene targeting is carried out in mouse embryonic
stem cells (ES cells) derived from a very early (usually male) mouse embryo.
By manipulating the cells at this early stage of development, scientists aim to
get the modified ES cells to contribute to the germ line, and give rise to
sperm.
This way the sperm can then carry the mutation and fertilise a normal egg to
carry on the knocked-out genome on to the next generation.
More than 4,000 genes have been ‘knocked-out’ using this method to help
scientists investigate exactly what each gene’s role is in the body.
15. Sequencing the Mice genome
Before the sequenced genome was available, looking for a gene or a
mutation was like looking for a needle in a haystack.
Sequencing of the mouse genome was completed in 2002, a powerful
scientific tool was made available.
Now, with a huge database of information available online, all that is
needed are a few clicks for researchers to be able to look up specific genes
and their location on the mouse chromosomes.
From this we can then choose one or two areas that look the most
promising to search for a mutation.
16. Significance of Mice genome
Researchers have developed an array of mouse models to help
scientists understand a whole collection of human diseases.
This has been made possible by the ability to create
transgenic and knockout mouse models which give scientists
the means to observe the function of individual genes.
The genetic similarities between mice and men means that
the knowledge derived from experiments with these mice can
provide invaluable insights into human biology.
Being able to go back and forth between the mouse and
human genomes so easily has also made it much simpler and
quicker to target related human genes that could be
candidates for drug development.
Now, discoveries that would once have taken years can now
be done in a matter of months.
17. Drosophila as a Model Organism
The fruit fly (Drosophila melanogaster) has been extensively studied for
over a century as a model organism for genetic investigations.
It also has many characteristics which make it an ideal organism for the
study of animal development and behavior, neurobiology, and human
genetic diseases and conditions
A good model organism needs to share, on the molecular level, many similar
features and pathways with humans.
Approximately 60% of a group of readily identified genes that are mutated,
amplified, or deleted in a diverse set of human diseases have a counterpart
in Drosophila
18. Benefits of Fruit fly
The fruit fly has many practical features that allow scientists to carry out
research with ease:
A short life cycle,
Ease of culture and maintenance, and
Less number of chromosomes
Small genome size (in terms of base pairs), but
Giant salivary gland chromosomes, known as polytene chromosomes.
19. Life Cycle of Drosophila melanogaster
Image Source: Carolina
Biological Supply Company
20. Life Cycle of Drosophila melanogaster
The female fruit fly, about 3 mm in length, will lay between 750 and
1,500 eggs in her lifetime.
The life cycle of the fruit fly only takes about 12 days to complete at
room temperature (25°C).
After the egg (at a mere half a millimeter in length) is fertilized, the
embryo emerges in ~24 hours
21. Genome of Drosophila
As with humans, the chromosomes of Drosophila melanogaster come in pairs --
but unlike humans, which have 23 pairs of chromosomes, the fruit fly has only
four: a pair of sex chromosomes (two X chromosomes for females, one X and
one Y for males), together designated Chromosome 1, along with three pairs of
autosomes (non-sex chromosomes) labeled 2 through 4.
Chromosome 4 is the smallest and is also called the dot chromosome. It
represents just ~2% of the fly genome.
22. The giant polytene chromosomes found in the fly's salivary glands (compared here
with the chromosomes from the fly's ovary) are another characteristic that makes
the fruit fly an important organism for laboratory studies. These easily visualized
chromosomes provided a road map for early geneticists.
Image source: Modified from T. S. Painter, J. Hered. 25, 465-476 (1934)
23. Genome of Drosophila
In terms of base pairs, the fly genome is only around 5% of the size of the
human genome -- that is, 132 million base pairs for the fly, compared with 3.2
billion base pairs for the human.
In terms of the number of genes: The fly has approximately 15,500 genes on its
four chromosomes, whereas humans have about 22,000 genes among their 23
chromosomes. Thus the density of genes per chromosome in Drosophila is higher
than for the human genome.
24. Genome of Drosophila
Humans and flies have retained the same genes from their common ancestor
(known as homologs) over about 60% of their genome.
Based on an initial comparison, approximately 60% of genes associated with
human cancers and other genetic diseases are found in the fly genome.
25. The genome of the
cenancestor
Availability of complete genome sequences from the three domains of
life creates an opportunity for the reconstruction of the complete
genome of the common ancestor:
Of minimal bacterial set (256 genes), 143 have orthologues in yeast
(eukaryote)
Universal translation apparatus suggests that cenancestor had a fully
developed translation system
Extreme differences in DNA replication apparatus
Many fundamental metabolic processes are carried out by similar proteins
in Archaea and eubacteria:
Suggests a universal, autotrophic ancestor
Not all central metabolism is universal (methanogenesis, photosynthesis etc.)