The document discusses various aspects of genome organization, including:
1. Chromatin assembly begins with the incorporation of histone proteins to form nucleosomes, which are then folded and organized into higher order structures within the nucleus.
2. Genes can be split, overlapping, or pseudogenes. Split genes contain introns that are spliced out, while overlapping genes share nucleotide sequences. Pseudogenes are non-functional copies of genes.
3. Gene families consist of genes related by common ancestry that may be clustered or dispersed throughout the genome. Members can vary in sequence but often retain similar functions.
This presentation is about the transcription machinery that is required for the transcription in eukaryotes. The comparison between the transcription factors involved in prokaryotes and eukaryotes. The initiation of transcription and how it helps in producing a mRNA.
This presentation is about the transcription machinery that is required for the transcription in eukaryotes. The comparison between the transcription factors involved in prokaryotes and eukaryotes. The initiation of transcription and how it helps in producing a mRNA.
Prokaryotic and eukaryotic gene structurestusharamodugu
Organization of genome in Prokaryotes:
The term prokaryote means “primitive nucleus”. Cell in prokaryotes have no nucleus. The prokaryotic chromosome is dispersed within the cell and is not enclosed by a separate membrane. Much of the information about the structure of DNA comes from studies of prokaryotes, because they are less complex than eukaryotes. Prokaryotes are monoploids they have only one set of genes (one copy of the genome). In most viruses and prokaryotes, the single set of genes is stored in a single chromosome (single molecule either RNA or DNA).
Organization of genome in Prokaryotes:
The term prokaryote means “primitive nucleus”. Cell in prokaryotes have no nucleus. The prokaryotic chromosome is dispersed within the cell and is not enclosed by a separate membrane. Much of the information about the structure of DNA comes from studies of prokaryotes, because they are less complex than eukaryotes. Prokaryotes are monoploids they have only one set of genes (one copy of the genome). In most viruses and prokaryotes, the single set of genes is stored in a single chromosome (single molecule either RNA or DNA). Organization of genome in Prokaryotes:
The term prokaryote means “primitive nucleus”. Cell in prokaryotes have no nucleus. The prokaryotic chromosome is dispersed within the cell and is not enclosed by a separate membrane. Much of the information about the structure of DNA comes from studies of prokaryotes, because they are less complex than eukaryotes. Prokaryotes are monoploids they have only one set of genes (one copy of the genome). In most viruses and prokaryotes, the single set of genes is stored in a single chromosome (single molecule either RNA or DNA).
Metabolites, Secondary metabolites are derived from primary metabolites, Why secondary metabolites, Phenolics, Terpenoids, Alkaloids, Special nitrogen metabolites, Cuticular compounds .The major classes of these found in plants
Prokaryotic and eukaryotic gene structurestusharamodugu
Organization of genome in Prokaryotes:
The term prokaryote means “primitive nucleus”. Cell in prokaryotes have no nucleus. The prokaryotic chromosome is dispersed within the cell and is not enclosed by a separate membrane. Much of the information about the structure of DNA comes from studies of prokaryotes, because they are less complex than eukaryotes. Prokaryotes are monoploids they have only one set of genes (one copy of the genome). In most viruses and prokaryotes, the single set of genes is stored in a single chromosome (single molecule either RNA or DNA).
Organization of genome in Prokaryotes:
The term prokaryote means “primitive nucleus”. Cell in prokaryotes have no nucleus. The prokaryotic chromosome is dispersed within the cell and is not enclosed by a separate membrane. Much of the information about the structure of DNA comes from studies of prokaryotes, because they are less complex than eukaryotes. Prokaryotes are monoploids they have only one set of genes (one copy of the genome). In most viruses and prokaryotes, the single set of genes is stored in a single chromosome (single molecule either RNA or DNA). Organization of genome in Prokaryotes:
The term prokaryote means “primitive nucleus”. Cell in prokaryotes have no nucleus. The prokaryotic chromosome is dispersed within the cell and is not enclosed by a separate membrane. Much of the information about the structure of DNA comes from studies of prokaryotes, because they are less complex than eukaryotes. Prokaryotes are monoploids they have only one set of genes (one copy of the genome). In most viruses and prokaryotes, the single set of genes is stored in a single chromosome (single molecule either RNA or DNA).
Metabolites, Secondary metabolites are derived from primary metabolites, Why secondary metabolites, Phenolics, Terpenoids, Alkaloids, Special nitrogen metabolites, Cuticular compounds .The major classes of these found in plants
Genes, Genomics, and Chromosomes computational biology introduction .pptMohamedHasan816582
The 5 ß-globin genes are derived from an ancestral ß-globin gene via gene duplication. Over time, these genes accumulated adaptive mutations via sequence drift resulting in the specialized species of ß-globin proteins. Genomic DNA also contains nonfunctional DNA sequences called pseudogenes that are derived from gene duplication or reverse transcription and integration of cDNA sequences made from mRNA (covered below). ß-globin pseudogenes contain introns and thus were derived by gene duplication. Over time these genes became nonfunctional also due to sequence drift. Because they are not harmful, pseudogenes remain in the genome, marking a gene duplication event in an earlier ancestor.
The ß-globin gene cluster on chromosome 11 is shown in Fig. 6.4a. The ß-globin genes are expressed in different stages of life. , Ag, and Gg are expressed during different trimesters of fetal development (next slide). ß expression begins around birth & continues throughout adult life. Fetal hemoglobin molecules made with the d and G or A polypeptides have a higher affinity for O2 than maternal hemoglobin, facilitating O2 transfer to the fetus.
Higher eukaryotes contain far more noncoding DNA between genes than bacteria and simple eukaryotes (Fig. 6.4). The region of human genomic DNA containing the ß-globin gene cluster shown in the figure actually is a relatively "gene-rich" region of human DNA. Some regions known as gene-poor "deserts" also occur. Higher eukaryotes also contain a larger amount of intron DNA. Although one-third of human DNA is transcribed into pre-mRNA, 95% ends up being degraded after RNA splicing reactions. On average, the typical exon is 50-200 bp in length, while the median length of introns is 3.3 kb in human genes.
DNA fingerprinting is a method for identifying individuals based on their minisatellite DNA (Fig. 6.7). It was developed in the mid-80s and is widely used in forensics, paternity analysis, and for research purposes. In the method, minisatellite DNA from a genomic DNA specimen is amplified by PCR using primers that bind to unique sequences flanking minisatellite repeat units. Bands corresponding to each minisatellite locus then are separated on gels. Although satellite DNA is highly conserved in sequence, the number of tandem copies at each loci is highly variable between individuals. This results from unequal crossing over during formation of gametes in meiosis. Due to the variation in the number of repeats at each locus, different individuals can be readily distinguished based on banding patterns.
Interspersed repeat DNA comprises the largest fraction of repetitious DNA in eukaryotic genomes. This DNA, which is also called moderately repeated DNA makes up ~45% of human genomic DNA. Interspersed repeat DNA is composed of partial and complete transposon sequences or "mobile DNA". Mobile DNAs were discovered by Barbara McClintock in the 1940s. These sequences move by "transposition". Transpositions in germ line cells are inhe
RNA splicing is a form of RNA processing in which a newly made precursor messenger RNA (mRNA) is transformed into a mature RNA by removing the non-coding sequences termed introns.
The process of RNA splicing involves the removal of non-coding sequences or introns and joining of the coding sequences or exons.
RNA splicing takes place during or immediately after transcription within the nucleus in the case of nucleus-encoded genes.
In eukaryotic cells, RNA splicing is crucial as it ensures that an immature RNA molecule is converted into a mature molecule that can then be translated into proteins. The post-transcriptional modification is not necessary for prokaryotic cells.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
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.
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.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
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/
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.
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).
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Exposé invité Journées Nationales du GDR GPL 2024
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.
2. General steps
in chromatin
assembly
The assembly of DNA into chromatin involves a range of events, beginning with the
formation of the basic unit, the nucleosome, and ultimately giving rise to a complex
organization of specific domains within the nucleus.
The first step is the deposition onto the DNA of a tetramer of newly synthesized (H3-
H4)2 to form a sub-nucleosomal particle, which is followed by the addition of two
H2A-H2B dimers.
This produces a nucleosomal core particle consisting of 146 base pairs of DNA
wound around the histone octamer.
This core particle and the linker DNA together form the nucleosome.
Newly synthesized histones are specifically modified (e.g.the acetylation of histone
H4).
3. General steps
in chromatin
assembly
The next step is the maturation step that requires ATP to establish regular spacing of
the nucleosome cores to form the nucleofilament.
During this step the newly incorporated histones are de-acetylated.
Next the incorporation of linker histones is accompanied by folding of the
nucleofilament into the 30nm fibre, the structure of which remains to be elucidated.
Two principal models exist : the solenoid model and the zig zag.
Finally, further successive folding events lead to a high level of organization and
specific domains in the nucleus.
At each of the steps described above, variation in the composition and activity of
chromatin can be obtained by modifying its basic constituents and the activity of
stimulatory factors implicated in the processes
of its assembly and disassembly.
4. Assembly begins with the incorporation of the H3/H4 tetramer (1),
followed by the addition of two H2A-H2B dimers (2) to form a core particle. The
newly synthesized histones utilized are specifically modified; typically, histone H4 is
acetylated at Lys5 and Lys12 (H3-H4*).
Maturation requires ATP to establish a regular spacing, and histones are de-acetylated
(3).
The incorporation of linker histones is accompanied by folding of the nucleofilament.
Here the model presents a solenoid structure in which there are six nucleosomes per
gyre (4).
Further folding events lead ultimately to a defined domain organization within the
nucleus (5).
5. FUNCTIONOF
CHROMATIN
The function of the chromatin is to carry out the genetic
information from one generation to another, by encoding
the past history and future prospects of the cell.
DNA, being the only permanent component of chromatin,
is the sole genetic material of eukaryotes.
It never leaves the cell, thus maintaining heredity of the
cell
DNA is the permanent component of chromosomes and is
the sole genetic material of eukaryotes
6. Split,
Overlapping &
Pseudogenes
Split genes are the sequences containing actual information
of the gene (exons) are interrupted by other
sequences (introns) which are spliced out after transcription;
Overlapping gene sare same as DNA sequences can become
part of two or more genes expressed at different times and in
different reading frames.
Pseudogenes, which represent DNA sequences derived from
mRNA through reverse transcription; these pseudogenes,
therefore, differ from the split genes to which they belong, due
to the absence of intron sequences.
7. Split genes or
Interrupted
Genes:
The coding regions containing actual information of the genes
(exons) of most eukaryotic genes are interrupted by few to several
noncoding sequences called introns (from intervening sequences)
which are spliced out after transcription
Such genes are called split genes since their coding sequences are
split into several parts due to the introns.
But some genes of eukaryotes are not split, e.g., histone genes of
sea urchin.
The first split gene to be described in 1977 by Pierre Chambon and
his colleagues was the ovalbumin genes of chicken coding for the
386 amino acid long ovalbumin protein of eggs.
9. Important
features of
interrupted
genes:
1. Each interrupted gene begins’ with an exon and ends with an
exon.
2.The exons occur in the same precise order in the mRNA in which
they occur in the gene.
3.The same interrupted gene organisation is consistently present
in all the tissues of organisms.
4. Most introns are blocked in all reading frames i.e., termination
codons occur frequently in their three reading frames.Therefore,
most introns do not seem to have coding functions.
10. Significance
ofSplitGenes:
The significance of split organisation of eukaryotic genes is not
clear.
1. In some cases, different exons of a gene code for different
active regions of the protein molecule, e.g., in the case of
antibodies.Thus, it has been suggested that introns are relics of
evolutionary processes that brought together different ancestral
genes to form new larger genes. It is also possible that some
introns have been introduced within certain exons during
evolution.
2. Introns may also provide for increased recombination rates
between exons of a gene and thus may be of some significance in
genetic variation.
3. Introns are known to code for enzymes involved in the
processing of hn RNA (heterogenous RNA).
11. Overlapping
Genes:
The determination of nucleotide sequences of some viral genomes
such as bacteriophage (ɸx174 has clearly shown that at least some
genes share their nucleotide sequences either partially or fully; such
genes are called overlapping genes.
Overlapping genes have been found in the following viruses; MS2
(single stranded RNA), SV40 (double stranded DNA) and phage k
(double stranded DNA).
It has also been discovered in tryptophan mRNA of E. coli.
In view of wide occurrence of overlapping genes, it seems that this
phenomenon is an economic device to make better use of genetic
material through packing of more genetic information in lets DNA.
It is not known if overlapping genes occur in other prokaryotes and in
eukaryotes, or if they are confined to viruses.
Overlapping genes cannot undergo mutation in’ independent of each
other, i.e., they will mutate together, although degeneracy of code
may permit some degree of independence.
Therefore, a single mutation in the overlapping region of such genes
would often result in the loss of activities of two gene products, thus
generating pleiotropy.
12. Pseudogenes:
In multicellular organisms, a wide variety of DNA sequences are
found, which are of no apparent use.
Some of these sequences are defective copies of functional genes
and are, therefore called pseudogenes.
Their general organisation is similar to those of interrupted genes
as they have sequences corresponding to introns and exons.
They are non-functional due to mutations which prevent one or
more, often more of the following: transcription, RNA splicing and
translation (due to frequent occurrence of termination codons).
The pseudogenes are common features of gene clusters and occur
with their functional counterparts.
These pseudogenes have been reported in human beings, mouse
and Drosophila.
13. The most
popular
examples of
these
pseudogenes
include the
following.
(i) Human α-globin and β-globin pseudogenes (Ψ) found in each of the
two globin clusters.
(ii) In mouse there are few a-globin pseudogenes (Ψ), one of them
(Ψα3) is different from other pseudogenes since it has no introns
which are present in a-globin genes as well as in other pseudogenes.
(iii) UsnRNA series of pseudogenes in human beings includes
U1 U2 and U3sn RNA pseudogenes.
(iv) In Drosophila histone pseudogenes have been discovered.,
Several pseudogenes lack introns and resemble mature mRNA
transcripts of their active counterparts, they are called processed
pseudogenes.
These pseudogenes are believed to be reverse transcripts of mature
mRNAs which become inserted into the genome.
Such genes are flanked by direct repeats of 6-21 bp and are located
anywhere in the genome irrespective of the location of the concerned
functional genes.
For example, the mouseTa 3 globin gene in mouse.
14. Gene
Families:
A gene family consists of all those genes that have related sequences
and are believed to have originated form a common ancestral gene
through gene duplication and subsequent mutational variation.
The members of a gene family may be clustered together or dispersed
on different chromosomes.
Some gene families consists of identical members; such genes always
occur in clusters and have two (on lower extreme) to hundreds of
identical genes in tandem.
Extensive tandem repetition of a gene normally occurs when the gene
product is needed in unusually large amounts, e.g., genes for rRNA,
histone genes etc.
The members of a gene family usually have related functions.
When related genes occur at several locations, they are believed to
have arisen through translocation of members located in a cluster.
The genes usually become divergent after they become dispersed.
Sometimes all the members of a gene family are functional, but often
some members are nonfunctional pseudogenes.