WHAT IS BIOINFORMATICS?
Computational Biology/Bioinformatics is the application of computer sciences and allied technologies to answer the questions of Biologists, about the mysteries of life. It has evolved to serve as the bridge between:
Observations (data) in diverse biologically-related disciplines and
The derivations of understanding (information)
APPLICATIONS OF BIOINFORMATICS
Computer Aided Drug Design
Microarray Bioinformatics
Proteomics
Genomics
Biological Databases
Phylogenetics
Systems Biology
INTRODUCTION
WHAT IS DATA AND DATABASE?
WHAT IS BIOLOGICAL DATABASE?
TYPES OF BIOLOGICAL DATABASE
PRIMARY DATABASE
Nucleic acid sequence database
Protein sequence database
SECONDARY DATABASE
COMPOSITE DATABASE
TERTIARY DATABASE
WHY NEED?
CONCLUSION
REFRENCES
Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble and analyze the function and structure of genomes
INTRODUCTION
WHAT IS DATA AND DATABASE?
WHAT IS BIOLOGICAL DATABASE?
TYPES OF BIOLOGICAL DATABASE
PRIMARY DATABASE
Nucleic acid sequence database
Protein sequence database
SECONDARY DATABASE
COMPOSITE DATABASE
TERTIARY DATABASE
WHY NEED?
CONCLUSION
REFRENCES
Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble and analyze the function and structure of genomes
this presentation is about bioinformatics. the contents of bioinformatics are as under:
1.Introduction to bioinformatics.
2.Why bioinformatics is necessary?
3.Goals of bioinformatics
4.Field of bioinformatics
5.Where bioinformatics help?
6.Applications of bioinformatics
7.Software and tools of bioinformatics
8.References
As an interdisciplinary field of science, bioinformatics combines biology, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data.
Clustal X help to the Bioinformatics candidate to predicts the Multiple Sequence Alignment and Phylogenetic Analysis for given a nuber of Gene Sequences of varrious organism,and find the evolutionary relationship.
Module 2 Sequence similarity.
Part of bioinformatics training session "Basic Bioinformatics concepts, databases and tools" - http://www.bits.vib.be/training
Protein Sequence, Structure, and Functional Databases: UniProtKB, Swiss-Prot, TrEMBL, PIR, MIPS, PROSITE, PRINTS, BLOCKS, Pfam, NDRB, OWL, PDB, SCOP, CATH, NDB, PQS, SYSTERS, and Motif. Presented at UGC Sponsored National Workshop on Bioinformatics and Sequence Analysis conducted by Nesamony Memorial Christian College, Marthandam on 9th and 10th October, 2017 by Prof. T. Ashok Kumar
SWISS-PROT- Protein Database- The Universal Protein Resource Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins.
An integrated publicly accessible bioinformatics resource to support genomic/proteomic research and scientific discovery.
Established in 1984, by the National Biomedical Research Foundation (NBRF) Georgetown University Medial Center, Washington D.C., USA.
It is the source of annotated protein databases and analysis tools for the researchers.
Serve as primary resource for the exploration of protein information.
Accessible by text search for entry and list retrieval, and also BLAST search and peptide match.
this presentation is about bioinformatics. the contents of bioinformatics are as under:
1.Introduction to bioinformatics.
2.Why bioinformatics is necessary?
3.Goals of bioinformatics
4.Field of bioinformatics
5.Where bioinformatics help?
6.Applications of bioinformatics
7.Software and tools of bioinformatics
8.References
As an interdisciplinary field of science, bioinformatics combines biology, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data.
Clustal X help to the Bioinformatics candidate to predicts the Multiple Sequence Alignment and Phylogenetic Analysis for given a nuber of Gene Sequences of varrious organism,and find the evolutionary relationship.
Module 2 Sequence similarity.
Part of bioinformatics training session "Basic Bioinformatics concepts, databases and tools" - http://www.bits.vib.be/training
Protein Sequence, Structure, and Functional Databases: UniProtKB, Swiss-Prot, TrEMBL, PIR, MIPS, PROSITE, PRINTS, BLOCKS, Pfam, NDRB, OWL, PDB, SCOP, CATH, NDB, PQS, SYSTERS, and Motif. Presented at UGC Sponsored National Workshop on Bioinformatics and Sequence Analysis conducted by Nesamony Memorial Christian College, Marthandam on 9th and 10th October, 2017 by Prof. T. Ashok Kumar
SWISS-PROT- Protein Database- The Universal Protein Resource Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins.
An integrated publicly accessible bioinformatics resource to support genomic/proteomic research and scientific discovery.
Established in 1984, by the National Biomedical Research Foundation (NBRF) Georgetown University Medial Center, Washington D.C., USA.
It is the source of annotated protein databases and analysis tools for the researchers.
Serve as primary resource for the exploration of protein information.
Accessible by text search for entry and list retrieval, and also BLAST search and peptide match.
Bioinformatics is defined as the application of tools of computation and analysis to the capture and interpretation of biological data. It is an interdisciplinary field, which harnesses computer science, mathematics, physics, and biology
INTRODUCTION
DEFINITION OF BIOINFORMATICS
HISTORY
OBJECTIVE OF BIOINFORMATIC
TOOLS OF BIOINFORMATICS
PROCEDURE AND TOOLS OF BIOINFORMATIC
BIOLOGICAL DATABASES
HOMOLOGY AND SIMILARITY TOOLS (SEQUENCE ALIGNMENT)
PROTEIN FUNCTION ANALYSIS TOOLS
STRUCTURAL ANALYSIS TOOLS
SEQUENCE MANIPULATION TOOLS
SEQUENCE ANALYSIS TOOLS
APPLICATION
CONCLUSION
REFERENCES
Microbial biotechnology is the use of microorganisms to obtain an economically valuable product or activity at a commercial or large scale.
Like any other man-made technology, microbial biotechnology has both positive and negative effects on the environment.
Biotechnology may carry more risk than other scientific fields: microbes are tiny and difficult to detect, but the dangers are potentially vast.
The use of biotechnical methods—including genetically-engineered microorganisms—is indispensable for the manufacture of many products essential to mankind.
For better or for worse, it is the mankind's task to tackle the problems that are associated with the use of this technology, and which to a high degree are located in the field of unwanted environmental impacts.
The use of biotechnology should be restricted to enhancing the quality of life for plants, animals and human beings only. Anything beyond that is unnatural and highly disastrous to us.
AMR & Alternative Stratergies - MicrobiologySijo A
Antibiotic resistance poses one of the most important health challenges of the 21st century.
The rise of multidrug-resistant bacteria has already led to a significant increase in human disease and death.
The U.S. Centers for Disease Control and Prevention estimates that approximately 2.8 million people worldwide are infected with antibiotic-resistant bacteria, accounting for 35,000 deaths each year in the U.S. and 700,000 deaths around the globe.
When a pathogen enters the body, it’s confronted by elements of the innate immune system, which constitute the first line of defense.
Once breached, the adaptive response takes over, but it typically takes few days to be effective.
Immunity is the processes that occur to defend the body against foreign organisms or molecules.
Immunity includes:
Inflammation.
Complement activation.
Phagocytosis.
Antibody synthesis.
Effector T lymphocytes.
Obligate intracellular, unable to self-replicate.
Once inside living cells, viruses induce the host cell to synthesize virus particles.
The genome is either DNA or RNA (single or double stranded).
Viruses do not have a system to produce ATP.
Viruses range in size from 25 to 270 nm.
Viral tropism!!
The classification of viruses is based on nucleic acid type, size and shape of virion, and presence or absence of an envelope.
Viral Structure
I . Virion is the entire viral particle.
2. Capsid is the protein coat that encloses the genetic material.
3. Capsomer is the protein subunit that makes up the capsid.
4. Nucleocapsid is composed of the capsid and genetic material.
5. The envelope is the outer coating composed of a phospholipid bilayer, which is composed of viral-encoded glycoproteins and sometimes viral encoded matrix proteins. The envelope is derived from a host cell's membrane.
Some viruses use the plasma membrane, whereas others use endoplasmic reticulum, Golgi, or nuclear membranes. Naked nucleocapsids are viruses with no envelopes.
Gram reaction & characteristics:
Gram +ve cocci arrange in clusters (grape-like), non-motile.
Habitat:
Flora in the anterior nares (10-60% of population), nasopharynx, perineal area, skin & mucosa.
Virulence factor:
Protein A (binds Fc portion of IgG), coagulase (forms fibrin coat around organism) hemolysins, leukocidins (destroy RBCs and WBCs), hyaluronidase (breaks down connective tissue), staphylokinase (lyses formed clots), lipase (breaks down fat), Toxic shock syndrome toxin.
Disease:
Causes food poisoning (via enterotoxin), pneumonia, meningitis, osteomyelitis, septic arthritis bacteremia, endocarditis, wounds, abscesses, suppurative cutaneous infections, staphylococcal scalded skin syndrome, boils (carbuncles), furuncles, sinusitis, otitis media, folliculitis, impetigo, scalded skin syndrome (SSS), Tricuspid valve endocarditis (TVIE)> affects IV drug users.
Produces six types of enterotoxin and toxic shock syndrome toxin-1 (TSST-1)> TSS (fever, diarrhea, kidney failure, fever, headache). Ritter’s disease in newborn (severe form of scalded skin syndrome in neonates).
S. aureus is a leading cause of osteomyelitis in children and adults.
Habitat:
large intestine.
Disease:
Amoebic dysentery, Amebic colitis, ulcers (flask shape), amoebic liver abscess (ALA)> Extraintestinal amebiasis. Abdominal cramping, anorexia, fatigue, and diarrhea. Additional conditions include infections of the spleen, brain, and lungs.
Host:
Human is the definitive host.
Infective stage:
Mature cyst: 8 to 22 μm, spherical, One to four nuclei. Chromatoid body.
Diagnostic stage:
1. Cyst.
2. Trophozoite: 5 to 70 μm, Pseudopods, directional motility, One nucleus. Cytoplasm may contain red blood cell (diagnostic).
Mode of transmission:
Cysts are ingested via contaminated food or water.
“mykos” meaning mushroom.
Mycology is the study of fungi.
The fungi possess rigid cell walls:
Chitin and ergosterol, mannan and other polysaccharides.
Beta-glucan is most important, because it is the target of antifungal drug caspofungin.
Fungi are eukaryotic organisms VS bacteria (prokaryotic).
The cell membrane of fungus contains ergosterol, unlike human cell membrane which contains cholesterol.
Most fungi are obligate aerobes or facultative anaerobes, but none are obligate anaerobes.
The natural habitat of most fungi is environment, require a preformed organic source of carbon, association with decaying matter.
C. albicans is an exception!!!
Since antigen and antibody reactions are specific, they can be used to identify each other.
These diagnostic tests are particularly useful in diagnosing for examples: infectious diseases, autoimmune diseases, and in typing of blood and tissues prior to transplantation.
Specimens for bacteriology investigation should be forwarded as soon as possible to the laboratory in leak-proof, sterile containers.
Neutral glycerol saline should be added to stool sample if there is any delay before laboratory examination.
Complete early morning urine specimen (250 ml), for diagnosis of renal tuberculosis.
Plain tube (blood) for serology.
Blood clot may be cultured by adding a selective culture medium, e.g., for enteric organisms.
Blood for blood culture (blood culture bottle, liquid, 5 to 19ml, 50 ml). The blood is injected by insertion of syringe needle through a hole in the cap and through the central rubber or plastic liner. Don’t remove the cap. Blood culture at RT, not more than 12 hrs.
For serous fluids collection (pleural fluid), universal container is used.
Sputum collected in wide-mouthed disposable container.
Anaerobic Gram-Positive Spore-Forming BacilliSijo A
Gram reaction & characteristics:
Gram positive or gram variable bacilli, sore forming, obligate anaerobe, non-motile. brick-shaped rods/box car. Spores rarely seen. Spores are subterminal but difficult to induce.
Habitat:
Common inhabitant of the colon.
Virulence factor:
Produces several exotoxins; alphatoxin, the most important, mediates destruction of host cell membranes; enterotoxin inserts and disrupts membranes of mucosal cells; beta-toxin is a cytotoxin. Hemolysin, necrotizing toxin.
Disease:
Cellulitis, gas gangrene.
Alpha toxin (lecithinase) → muscle cell necrosis, degradative enzymes → subcutaneous gas bubbles → crepitus myonecrosis with crepitus (crackles), gangrenous muscles → black fluid exudate leaking from skin.
Post-abortion sepsis, abdominal infections, and enterocolitis, septicemia.
Most medically important family of non–spore-forming gram-negative rods.
Most species are normal flora of the GI tract. Salmonella, Shigella, and Yersinia are not normal GI flora.
Major cause of nosocomial infections
Diseases include UTIs, gastroenteritis, septicemia, food poisoning, wound infections, peritonitis, pneumonia, and meningitis
The family exhibits four serological characteristics:
O (somatic) antigen-A cell wall antigen-LPS (heat stable), Used for serological grouping of Salmonella & Shigella.
K (envelope) antigen-Capsular antigen (heat labile)
H (flagellar) antigen-Flagellar antigen-protein (heat labile), Used to serotype Salmonella.
Vi antigen-Capsular antigen of Salmonella Typhi-polysaccharide (heat labile), Role in preventing phagocytosis, may mask O Ag, removed by heating.
Enterobacteriaceae are facultative anaerobes, ferment glucose. Positive nitrate and catalase, non-hemolytic. Except for Plesiomonas, they are oxidase negative.
Adenoviruses:
Transmission:
Respiratory, fecal-oral, and direct contact (eye).
Site of latency:
Replication in oropharynx.
Disease:
Acute respiratory disease, Pharyngitis, pharyngoconjunctival fever, keratoconjunctivitis, pneumonia, hemorrhagic cystitis, disseminated disease, and gastroenteritis in children.
Diagnosis:
Cell culture (HEp-2 and other continuous human epithelial lines), enzyme immunoassay (EIA) for gastroenteritis serotypes 40-41.
Prevention:
Vaccine (adenovirus serotypes 4 and 7) for military recruits.
Note:
Adenoviruses has a role as vectors in gene therapy, deliver DNA for gene replacement therapy in few genetic disorders, such as cystic fibrosis.
Non-enveloped. All DNA viruses replicate in the nucleus, except Poxvirus which replicate in the cytoplasm.
The only viruses having a fiber protruding from each of the 12 vertices of the capsid.
Aerobic Non-Spore-Forming Gram-Positive BacilliSijo A
Disease: listeriosis.
L. monocytogenes causes a variety of infections in neonates, pregnant women, and immunosuppressed patients.
CNS infections: meningitis, encephalitis, brain abscess, spinal cord infections.
Neonatal:
Early onset: Granulomatosis infantisepticum—in utero infection disseminated systemically that causes stillbirth.
Late onset: Bacterial meningitis.
Food poisoning, bacteremia.
Mode of transmission:
Direct contact: Human gastrointestinal tract, ingestion of contaminated food, such as meat and dairy products.
Endogenous strain: Colonized mothers may pass organism to fetus. Portal of entry is probably from gastrointestinal tract to blood and in some instances from blood to meninges.
Biofilms are common in the natural world.
Biofilms are a collective of one or more types of microorganisms that can grow on many different surfaces.
The vast majority of the earth’s microorganisms (99 %) live in biofilms.
Microorganisms that form biofilms include bacteria, fungi, algae and some enteric viruses.
The biofilm matrix is an important part of the biofilm containing the microbial cells, exopolysaccharides, and water.
Usually, the microbial cells in a biofilm are embedded in the extracellular polymeric substances (EPS) Produced by themselves which is also called Slime.
EPS contains extracellular DNA, proteins, and polysaccharides which form slime.
Microbial cells in the biofilm are different from the planktonic cells that are single cells and can float on a liquid medium.
Introduction to the science of plant pathology, its objectives, scope and historical background. Classification of plant diseases, symptoms, signs, and related terminology. Parasitic causes of plant diseases (fungi, bacteria, viruses, phytoplasma, protozoa, algae and flowering parasitic plants), their characteristics and classification. Non-parasitic causes of plant diseases. Infection process. Survival and dispersal of plant pathogens. Plant disease epidemiology, forecasting and disease assessment. Principles and methods of plant disease management. Integrated plant disease management.
Pathogen related proteins of inequality are proteins are structurally diverse group of plant proteins that are toxic to invading fungal pathogen
They are widely distributed in plants in trace amounts, but are produced in much greater concentration in pathogen attack on stress full.
PR proteins are either extremely acidic or extremely basic and therefore a highly soluble and reactive.
these are low molecular weight proteins which accumulate 2 significant level in infected plant tissues.
Fungi (singular: fungus) are a kingdom of usually multicellular eukaryotic organisms that are heterotrophs (cannot make their own food) and have important roles in nutrient cycling in an ecosystem. Fungi reproduce both sexually and asexually, and they also have symbiotic associations with plants and bacteria.
Entamoeba histolytica was first discovered by Losch in 1875.
It is worldwide distribution.
It is prevalent in tropical and subtropical countries where sanitary conditions are poor.
In india, it is prevalent in Chandigarh, Tamil Nadu & Maharashtra.
It is found in the colon of man.
It is monogenetic because the whole life cycle completed within a single host, i.e. man.
Botany is the science and art of studying plants, that carry
out photosynthesis. Botany includes a wide range of scientific sub disciplines
t h a t s t u d y t h e s t r u c t u r e , g r o w t h , r e p r o d u c t i o n ,
metabolism, development, diseases, ecology and
evolution of plants. The study of plants is important because they are a
fundamental part of life on Earth, generating food, oxygen, fuel,
medicine and fibers that allow other life forms to exist. Through
photosynthesis they absorb carbon dioxide, a waste
product generated by most animals and a greenhouse gas that
contributes to global warming.
Infectious diseases are mainly caused by
microbes.
These are small microorganisms which are
invisible with the naked eye.
They mainly include bacteria, virus, fungi
and parasites.
The symptoms caused by infection depends
on
the location.
Nature of the infection
Type of the microbe
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
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.
(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.
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 .
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.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
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/
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.
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.
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.
6. 6
WHAT IS BIOINFORMATICS?
Computational Biology/Bioinformatics is the application of computer
sciences and allied technologies to answer the questions of Biologists,
about the mysteries of life.
It has evolved to serve as the bridge between:
Observations (data) in diverse biologically-related disciplines and
The derivations of understanding (information)
APPLICATIONS OF BIOINFORMATICS
Computer Aided Drug Design
Microarray Bioinformatics
Proteomics
Genomics
Biological Databases
Phylogenetics
Systems Biology
Dept. of Computational Biology & Bioinformatics
7. 7
WHAT IS A BIO-SEQUENCE?
WHAT IS SEQUENCE ALIGNMENT?
Arranging DNA/protein sequences side by side to study the extent of their similarity
AGTCTTGATTCTTCTAGTTCTGC
GTCCTGATAAGTCAGTGTCTCC
TGAGTCTAGCTTCTGTCCATGCT
GATCATGTCCATGTTCTAGTCAT
GATAGTTGATTCTAGTGTCCTG
ATTAGCCTTGAATCTTCTAGTTC
TGTCCATTATCCATCTGATGGA
GTAGTTATGCGATCTCATG GT
CCGATACTATCCTGATATAGCTT
AATCTTCTAGTTCTGTCCATTAT
CCATCTGTC
ARNDCQEGHILKMFPUSTWYZEGNDTWRDC
FPUQEGHILDCLKSTMFEWCUWESTHCFPW
RDTCEDUSTTWEGHILDNDTEGHTWUWWE
SPUSTPPUQWRDCCLKSWCUWMFCQEDT
WRWESPWYZWEGHILDDFPTCTWRDSTTFP
UEEDCCDTWCUWGHISTDTKKSUNENDCFE
GWCRGHPPHHLDTWQESRNDCQEGHILKM
FPUSTWYZEGNDTWRDCFPUQEGHILDCLK
STMFEWCUWESTHCFPWRDTCEDUSTTWE
GHILDNDTEGHTWUWWESPUSTPPUQWRD
CCLKSWCUWMFCQEDTWRWESPWYZWEG
HILDDFPTCTWRDSTTFPUEEDCCDTWCUW
DNA, RNA or protein information represented as a series of bases (or
amino acids) that appear in bio-molecules. The method by which a bio-
sequence is obtained is called Bio-sequencing.
DNA/ RNA
SEQUENCE
PROTEIN
SEQUENCE
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CRISIS AFTER DATA EXPLOSION!!
sequencing
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A structured set of data held in a computer, esp. one
that is accessible in various ways.
WHAT IS A DATABASE?
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CLASSIFICATION OF BIOLOGICAL DATABASES
Based on data source
Based on data type
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BASED ON DATA SOURCE
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BIOLOGICAL
DATABASES
PRIMARY DATABASES SECONDARY DATABASES
• First-hand information of
experimental data from
scientists and researchers
• Data not edited or validated
• Raw and original
submission of data
• Made available to public for
annotation
• Derived from information
gathered in primary
database
• Data is manually curated
and annotated
• Data of highest quality as it
is double checked
Dept. of Computational Biology & Bioinformatics
17. Database Website
1. NCBI (National Centre for Biotechnology
Information)
www.ncbi.nlm.nih.gov
2. DDBJ (DNA Data Bank of Japan) www.ddbj.nig.ac.jp
3. EMBL(European Molecular Biology Laboratory) www.ebi.ac.uk/embl
4. PIR (Protein Information Resource) www.pir.georgetown.edu
5. PDB (Protein Data Bank) www.rcsb.org/pdb
6. NDB( Nucleotide Data Bank) www.ndbserver.rutgers.edu
7. SwissProt (Protein- only sequence database) www.expasy.ch
PRIMARY DATABASES
18. SECONDARY DATABASES
Database Website
1. PROSITE (Protein domains, families, functional
sites)
www.expasy.org/prosite
2. Pfam (Protein families) www.sanger.ac.uk/pfam
3. SCOP (Structural Classification Of Proteins) www.scop.mrc-lmb.cam.ac.uk/scop
4. CATH (Class, Architecture, Topology, Homologous
Super Family of Proteins)
www.cathdb.info
5. OMIM (Online Mendelian Inheritance in Man) www.ncbi.nlm.nih/omim
6. KEGG (Kyoto Encyclopedia of Genes and
Genome)
www.genome.jp/kegg/pathway.html
7. MetaCyc (Enzyme Metabolic Pathways) www.metacyc.org
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19. Based on type of data
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BIOLOGICAL
DATABASES
NUCLEOTIDE SEQUENCE DATABASE
PROTEIN SEQUENCE DATABASE
GENOME DATABASE
GENE EXPRESSION DATABASE
ENZYME DATABASE
STRUCTURE DATABASE
PROTEIN INTERACTION DATABASE
PATHWAY DATABASE
LITERATURE DATABASE
BASED ON THE TYPE OF DATA
Dept. of Computational Biology & Bioinformatics
42. Use of Databases in Biology-
Sequence Analysis
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43. Where do we get these sequences from?
Through genome sequencing projects
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44. • Submit sequences to biological databases
• Biological databases helps in efficient manipulation of
large data sets
• Provides improved search sensitivity, search efficiency
• Joining of multiple data sets
• Databases allows the users to analyse the biological
data sets
DNA
RNA
Proteins
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45. Analysis of Nucleic acids & Protein Sequences
• Sequence Analysis
Process of subjecting a DNA, RNA or peptide sequence to any
of a wide range of analytical methods
To understand its features, function, structure, or evolution
To assign function to genes & proteins by the studying the
similarities between the compared sequences
Methodologies include:
Sequence alignment
Searches against biological databases
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Bioinformatics
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46. • Sequence analysis in molecular biology includes a
very wide range of relevant topics:
The comparison of sequences in order to find similarity,
infer if they are related (homologous)
Identification of active sites, gene structures, reading
frames etc.
Identification of sequence differences and variations –
SNP, Point mutations, identify genetic markers
Revealing the evolution and genetic diversity of
sequences and organisms
Identification of molecular structure from sequence
alone
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47. Sequence Alignment
Relationships between these sequences are usually
discovered by
aligning them together
assigning a score to the alignments
Two main types of sequence alignment:
Pair-wise sequence alignment - compares only two
sequences at a time
Multiple sequence alignment- compares many sequences
Two important algorithms for aligning pairs of sequences :
Needleman-Wunsch algorithm
Smith-Waterman algorithm
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Bioinformatics
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48. • Popular tools for sequence alignment include:
Pair-wise alignment - BLAST
Multiple alignment - ClustalW, MUSCLE, MAFFT, T-Coffee etc.
• Alignment methods:
Local alignments - Needleman–Wunsch algorithm
Global alignments - Smith-Waterman algorithm
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Bioinformatics
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49. Pair-wise alignment
• Used to find the best-matching piecewise (local or
global) alignments of two query sequences
• Can only be used between two sequences at a time
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50. Multiple Sequence Alignment
• Is an extension of pairwise alignment to incorporate more than two
sequences at a time
• Align all of the sequences in a given query set
• Often used in identifying conserved sequence regions across a group of
sequences hypothesized to be evolutionarily related
• Alignments helps to establish evolutionary relationships by
constructing phylogenetic trees
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51. Sequence Analaysis Tools
Pair-wise alignment - BLAST
• Basic Local Alignment Search Tool (BLAST)
• Developed by Research staff at NCBI/GenBank as a new
way to perform seq. similarity search
• Available as free service over internet
• Very fast ,Accurate and sensitive database searching
• Server-NCBI
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52. Types of BLAST Programs:
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56. FASTA
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• DNA & Protein sequence alignment software
package
• Fast A “Fast –ALL”
• Works on any Alphabets
- FAST P Protein
- FAST N Nucleotide
58. Sequence Analaysis Tools
Multiple alignment - ClustalW
• Study the identities, Similarities & Differences
• Study evolutionary relationship
• Identification of conserved sequence regions
• Useful in predicting –
Function & structure of proteins
Identifying new members of protein families
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62. Includes all methods, theoretical & computational, used
to model or mimic the behaviour of molecules
Helps to study molecular systems ranging from small
chemical systems to large biological molecules
The methods are used in the fields of :
Computational chemistry
Drug design
Computational biology
Materials science
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Bioinformatics
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63. Structure Analysis of Proteins
• Researchers predict the 3D structure using protein
or molecular modeling
• Experimentally determined protein structures
(templates) are used
• To predict the structure of another protein that
has a similar amino acid sequence (target)
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Bioinformatics
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64. Advantages in Protein Modeling
• Examining a protein in 3D allows for :
greater understanding of protein functions
providing a visual understanding that cannot
always be conveyed through still photographs or
descriptions
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66. Impact of Bioinformatics in
Biology/Biotechnology
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67. • Biological research is the most fundamental research to
understand complete mechanism of living system
• The advancements in technologies helps in providing
regular updates and contribution to make human life
better and better.
Reduced the time consuming experimental procedure
Software development – Bioinformatians & Computational Biologists
Submitting biological sequences to databases
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68. Role of Bioinformatics in
Biotechnology
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69. • Genomics
The study of genes and their expression
Generates vast amount of data from gene
sequences, their interrelations & functions
Understand structural genomics, functional
genomics and nutritional genomics
• Proteomics
Study of protein structure, function &interactions
produced by a particular cell, tissue, or organism
Deals with techniques of genetics, biochemistry and
molecular biology
Study protein-protein interactions, protein profiles,
protein activity pattern and organelles compositions
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70. • Transcriptomics
Study of sets of all messenger RNA molecules in the cell
Also be called as Expression Profiling- DNA Micro array
RNA sequencing –NGS
Used to analyse the continuously changing cellular
transcriptome
• Cheminformatics
Deals with focuses on storing, indexing, searching,
retrieving, and applying information about chemical
compounds
involves organization of chemical data in a logical form - to
facilitate the retrieval of chemical properties, structures &
their relationships
Helps to identify and structurally modify a natural product
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71. • Drug Discovery
Increasingly important role in drug discovery, drug
assessment & drug development
Computer-aided drug design (CADD)- generate more
& more drugs in a short period of time with low risk
wide range of drug-related databases & softwares -
for various purposes related to drug designing &
development process
• Evolutionary Studies
Phylogenetics - evolutionary relationship among
individuals or group of organisms
phylogenetic trees are constructed based on the
sequence alignment using various methods
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72. • Crop Improvement
Innovations in omics based research improve the plant based
research
Understand molecular system of the plant which are used to
improve the plant productivity
comparative genomics helps in understanding the genes &
their functions, biological properties of each species
• Biodefense
Biosecurity of organisms - subjected to biological threats or
infectious diseases (Biowar)
Bioinformatics- limited impact on forensic & intelligence
operations
Need of more algorithms in bioinformatics for biodefense
• Bioenergy/Biofuels
contributing to the growing global demand for alternative
sources of renewable energy
progress in algal genomics + ‘omics’ approach - Metabolic
pathway & genes – genetically engineered micro algal strains
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