DNA content refers to the amount of DNA in an organism's haploid chromosomes. It varies greatly between organisms, with eukaryotes generally having more DNA than prokaryotes. The amount of DNA does not always correlate with an organism's complexity, known as the C-value paradox. This is because eukaryotic DNA contains large amounts of non-coding repetitive sequences. Chromatin exists in two forms - euchromatin, which is less condensed and permits gene expression, and heterochromatin, which is highly condensed and usually silences genes. Heterochromatin forms in specific regions like centromeres and telomeres and is important for chromosome function and stability.
despite of the enormous genomic diversity, the phage genome mapping is being done using a plethora of techniques,which includes both genetic mapping and physical mapping
Chromosomes are known as hereditary vehicles
They are formed of strands of DNA molecules which contain information for the development of different characteristics and performance of various metabolic activities of the cells
The coordination of various function is brought about through the formation of enzymes which are complex protein molecules
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.
despite of the enormous genomic diversity, the phage genome mapping is being done using a plethora of techniques,which includes both genetic mapping and physical mapping
Chromosomes are known as hereditary vehicles
They are formed of strands of DNA molecules which contain information for the development of different characteristics and performance of various metabolic activities of the cells
The coordination of various function is brought about through the formation of enzymes which are complex protein molecules
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.
Maternal effects are the influences of a mothers genotype on the phenotype of her offspring. It results from the asymmetric contribution of the female parent to the development of zygotes.
In terms of chromosomal genes, both male and female parents contribute equally to the zygote. The female parent contributes to the zygotes initial cytoplasm and organelles. Sperm rarely contribute anything other than chromosomes. Therefore zygotic development begins within a maternal medium and hence the maternal cytoplasm directly affects zygotic development.
Phloem differentiation
sieve elements
companion cells
The ontogeny of phloem sieve element
differentiation process of sieve elements
Phloem as a hub for systemic communication within the root meristem
Maternal effects are the influences of a mothers genotype on the phenotype of her offspring. It results from the asymmetric contribution of the female parent to the development of zygotes.
In terms of chromosomal genes, both male and female parents contribute equally to the zygote. The female parent contributes to the zygotes initial cytoplasm and organelles. Sperm rarely contribute anything other than chromosomes. Therefore zygotic development begins within a maternal medium and hence the maternal cytoplasm directly affects zygotic development.
Phloem differentiation
sieve elements
companion cells
The ontogeny of phloem sieve element
differentiation process of sieve elements
Phloem as a hub for systemic communication within the root meristem
Dr.S.KARTHIKUMAR
Associate Professor
Department of Biotechnology
Kamaraj College of Engineering and Technology, K.Vellakulam-625701, TN, India
Email: skarthikumar@gmail.com
DNA organization or Genetic makeup in Prokaryotic and Eukaryotic SystemsBir Bahadur Thapa
DNA organization or Genetic makeup in Prokaryotic and Eukaryotic Systems!! It is prepared under the syllabus of Tribhuwan University, Nepal, MSc. 3rd Semester as a lecture class!!
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
Similar to Dna content,c value paradox, euchromatin heterochromatin, banding pattern (20)
Autoimmune disease HEMOLYTIC ANEMIA AND DIABETESArchanaSoni3
An autoimmune disease is a condition in which your immune system mistakenly attacks your body.
The immune system normally guards against germs like bacteria and viruses. When it senses these foreign invaders, it sends out an army of fighter cells to attack them.
Normally, the immune system can tell the difference between foreign cells and your own cells.
In an autoimmune disease, the immune system mistakes part of your body — like your joints or skin — as foreign. It releases proteins called autoantibodies that attack healthy cells.
Some autoimmune diseases target only one organ. Type 1 diabetes damages the pancreas. Other diseases, like lupus, affect the whole body.
endocytosis and exocytosis is a procss of cell eating and drinnking. it is a mazor tool for self defence to an individual cell. there are some molecular mechanism for this process described in given notes.
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 .
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.
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.
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.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
Dna content,c value paradox, euchromatin heterochromatin, banding pattern
1. DNA Content
DNA content is defined as the amount of DNA in one copy or in the haploid chomosomes of an
organism. Haploid DNA content is referred to as the "C-value".
The DNA content of an organism can be measured by weight or number of base pairs in a single
copy of the entire sequence of DNA found within cells of that organism.
DNA content varies greatly among organisms. In general, eukaryotes have more DNA content
than prokaryotes.
Among prokaryotes the variation of DNA content or genome size is small ranging only an order
of magnitude, from 0.5 to 5 Mb. The genome sizes of eukaryotes, on the other hand, vary
>80,000-fold. Even among animals there is a nearly 3000-fold variation, and in plants basal
genomes sizes vary by a factor of >6000.
C- Value Complexity and C- Value paradox
Earlier it was believed that DNA-content is correlated with the complexity of an organism. The
idea was that the more complex the species the more genes it needed and hence has more C-
value.
How ever the total amount of chromosomal DNA in different animals and plants does not vary in
a consistent manner with the apparent complexity of the organisms. As compared to human (C-
value 3.3 pg DNA), Amphibians like salamanders (C-value 120 pg DNA), plants like wheat,
broad beans, and garden onions ( C-value 7.0, 14.6, and 16.8 picograms, respectively) are less
complex in their structure and behavior.Even in closely related species like the broad bean and
kidney bean c-value varies about three to four times .
The failure of C values to correspond to phylogenetic complexity is called the C-value paradox.
This perplexing variation in genome size occurs mainly because eukaryotic chromosomes
contain variable amounts of DNA with no demonstrable function, both between genes and within
genes in introns. This apparently nonfunctional DNA is composed of repetitious DNA
sequences, some of which are never transcribed and most all of which are likely dispensable.
These Repetitious DNA include
• Simple DNA repeats
• Moderately repeated DNA
• Transposons
• Viral retro-transposones
• Long interspersed elements
Short interspersed elements
• Unclassified spacer DNA
In addition to the non coding DNA sequences several protein coding genes are present as
multiple copies.These include
• Soiltary genes
• Duplicated and diverged genes(functional gene families and non-functional
pseudogenes)
• Tandem repeated genes encoding rRNA, tRNA and histones
2. Thus there is no direct corelation between total DNA content (C-Value) and the number of
functional genes, which in turn determines the complexity of an organism’s structure and
functions.
Euchromatin and Heterochromatin
Light-microscope studies in the 1930s distinguished between two types of chromatin in the
interphase nuclei of many higher eukaryotic cells: a highly condensed form, called
heterochromatin, and all the rest, which is less condensed, called euchromatin.
It is now established that euchromatin represent the organization level of 30-nm fiber and looped
domains. The loops are between 40 and 100 kbp in length.
Heterochromatin represents more compact levels of organization. Based on compactness feature
heterochromatin can be constitutive if it exist in the compact form permanently or it can be
facultative if compact packing is not permanent.
In a typical mammalian cell, approximately 10% of the genome is packaged into
heterochromatin which is concentrated in specific regions in the chromosome, including the
centromeres and telomeres.
Genes that become packaged into heterochromatin are usually resistant to being expressed,
because heterochromatin is unusually compact, but some genes require location in
heterochromatin regions if they are to be expressed.
When a gene that is normally expressed in euchromatin is experimentally relocated into a region
of heterochromatin, it ceases to be expressed, and the gene is said to be silenced. These
differences in gene expression are examples of position effects, in which the activity of a gene
depend on its position along a chromosome.
The Ends of Chromosomes Have a Special Form of Heterochromatin
In Yeast cells the chromatin extending inward roughly 5000 nucleotide base pairs from each
chromosome end is resistant to gene expression or in other words genes located in this region are
silenced. This corresponds to the heterochromatin.
Extensive genetic analysis has led to the identification of many of the yeast proteins required for
this type of gene silencing.
These include Silent information regulator (Sir) proteins. Sir proteins recognizes underacetylated
N-terminal tails of selected histones .One of the proteins in this complex is a highly conserved
3. histone deacetylase known as Sir2, which has homologs in diverse organisms, including humans,
and presumably has a major role in creating a pattern of histone underacetylation unique to
heterochromatin. Deacetylation of the histone tails is thought to allow nucleosomes to pack
together into tighter arrays and may also render them less susceptible to some chromatin
remodeling complexes. In addition, heterochromatin-specific patterns of histone tail modification
are likely to attract additional proteins involved in forming and maintaining heterochromatin.
These properties of heterochromatin also resemble properties of higher eukaryotic organisms.
Figure : Model for the heterochromatin at the ends of yeast chromosomes
Covalent modifications of the nucleosome core histones have an important role in the
process of heterochromatin formation.
Of special importance in many organisms are the histone methyl transferases, enzymes that
methylate specific lysines on histones including lysine 9 of histone H3 (see Figure 4-35). This
modification is “read” by heterochromatin components (including HP1 in Drosophila) that
specifically bind this modified form of histone H3 to induce the assembly of heterochromatin. It
is likely that a spectrum of different histone modifications is used by the cell to distinguish
heterochromatin from euchromatin .
Having the ends of chromosomes packaged into heterochromatin provides several advantages to
the cell: it helps to protect the ends of chromosomes from being recognized as broken
chromosomes by the cellular repair machinery, it may help to regulate telomere length, and it
may assist in the accurate pairing and segregation of chromosomes during mitosis.
4. Centromeres Are Also Packaged into Heterochromatin
In many complex organisms, including humans, each centromere seems to be embedded in a
very large stretch of heterochromatin that persists throughout interphase, even though the
centromere-directed movement of DNA occurs only during mitosis.
In addition to the modified histones several other protiens are present that compact the
nucleosomes into particularly dense arrangements. For example in yeast a special histone
H3 variant along with the other core histones, is believed to form a centromere-specific
nucleosome. In humans repeated DNA sequences, known as alpha satellite DNA are
charecteristic of centromere heterochromatin.
Figure : Organization of Alpha satellite DNA at the centromere
Heterochromatin May Provide a Defense Mechanism Against Mobile DNA Elements
DNA packaged in heterochromatin often consists of large tandem arrays of short, repeated
sequences that do not code for protein, as we saw above for the heterochromatin of mammalian
centromeres. In contrast, euchromatic DNA is rich in genes and other single-copy DNA
sequences. Although this correlation is not absolute (some arrays of repeated sequences exist in
euchromatin and some genes are present in heterochromatin), this trend suggests that some types
of repeated DNA may be a signal for heterochromatin formation. Repeated tandem copies of
genes results in silencing of these genes.This feature, called repeat-induced gene silencing, may
be a mechanism that cells have for protecting their genomes from being overtaken by mobile
5. genetic elements. These elements can multiply and insert themselves throughout the genome.
According to this idea, once a cluster of such mobile elements has formed, the DNA that
contains them would be packaged into heterochromatin to prevent their further proliferation. The
same mechanism could be responsible for forming the large regions of heterochromatin that
contain large numbers of tandem repeats of a simple sequence, as occurs around centromeres.
DNA Banding Pattern in Eukaryotic chromosomes
When stained with dyes such as Giemsa, mitotic chromosomes show a striking and reproducible
banding pattern along each chromosome.
By examining human chromosomes very early in mitosis, when they are less condensed than at
metaphase, it has been possible to estimate that the total haploid genome contains about 2000
distinguishable bands. These coalesce progressively as condensation proceeds during mitosis,
producing fewer and thicker bands.
Mitotic chromosome bands are detected in chromosomes from species as diverse as humans and
flies. Moreover, the pattern of bands in a chromosome has remained unchanged over long
periods of evolutionary time. Each human chromosome, for example, has a clearly recognizable
counterpart with a nearly identical banding pattern in the chromosomes of the chimpanzee,
gorilla, and orangutan—although there are also clear differences, such as chromosome fusion,
that give the human 46 chromosomes instead of the ape's 48 . This conservation suggests that
chromosomes are organized into large domains that may be important for chromosomal
function.Each band represent more than a million base-pairs.
Chromosomes have regions of variable GC content, which correponds roughly to the banding
pattern in metaphase stage.Bands that stain darkly with Geimsa stain have low GC Content and
are called G-Bands.Bands that stain lightly with Geimsa stain have high GC Content and are
called R-Bands.The GC-rich R-bands have a higher density of genes, especially of “house-
keeping” genes and these are enriched in components that necessary for regulation of gene
expression.
6. Comparison of the Giemsa pattern of the largest human chromosome (chromosome 1) with
that of chimpanzee, gorilla, and orangutan
Comparisons among the staining patterns of all the chromosomes indicate that human
chromosomes are more closely related to those of chimpanzee than to those of gorilla and that
they are more distantly related to those of orangutan
7. Comparison of the Giemsa pattern of the largest human chromosome (chromosome 1) with
that of chimpanzee, gorilla, and orangutan
Comparisons among the staining patterns of all the chromosomes indicate that human
chromosomes are more closely related to those of chimpanzee than to those of gorilla and that
they are more distantly related to those of orangutan