Topic – Advances in Microbiology - PowerPoint Presentation

1. Topic –Advances in MicrobiologyBioinformaticsPresented byDr. P. N. JadhavProfessor & HeadDepartment of MicrobiologyDeogiri College, Aurangabad

2. B. Sc. First Year Semester – IIPaper IV- Cytology and General MicrobiologyUnit 4: Advances in MicrobiologyBioinformatics

3. Bioinformaticssubdiscipline of biology and computer science concerned with the acquisition, storage, analysis, and dissemination of biological data, most often DNA and amino acid sequences.

4. The fast growth of biological researches has produced huge amount of biological data

5. Growth of GenBank:

6. “Genomic research makes it possible to look at biological phenomena on a scale not previously possible: all genes in a genome, all transcripts in a cell, all metabolic processes in a tissue. One feature that all of these approaches share is the production of massive quantities of data. GenBank, for example, now accommodates >1010 nucleotides of nucleic acid sequence data and continues to more than double in size every year. New technologies for assaying gene expression patterns, protein structure, protein-protein interactions, etc., will provide even more data. How to handle these data, make sense of them, and render them accessible to biologists working on a wide variety of problems is the challenge facing bioinformatics—an emerging field that seeks to integrate computer science with applications derived from molecular biology. We are swimming in a rapidly rising sea of data. . . how do we keep from drowning?” —Roos (2001). Science. 291:1260Genomic researches has given rise to a new field of science, BIOINFORMATICS

7. Definition:(Molecular) bio – informatics: bioinformatics is conceptualising biology in terms of molecules (in the sense of Physical chemistry) and applying “informatics techniques” (derived from disciplines such as applied maths, computer science and statistics) to understand and organise the information associated with these molecules, on a large scale. In short, bioinformatics is a management information system for molecular biology and has many practical applications.(*As submitted to the Oxford English Dictionary).

8. Bioinformatics:Bioinformatics Position in relation with other fields of science

9. What we study with Bioinformatics Tools:

10. Bioinformatics:Bioinformatics is the integrated discipline formed from the combination of biology, computer science, and information technology."The mathematical, statistical and computing methods that aim to solve biological problems using DNA and amino acid sequences and related information.“ –Frank Tekaia

11. Bioinformatics is based on the fact that DNA sequencing is cheap, and becoming easier and cheaper very quickly.the Human Genome Project cost roughly $3 billion and took 12 years (1991-2003). Sequencing James Watson’s genome in 2007 cost $2 million and took 2 monthsToday, you could get your genome sequenced for about $100,000 and it would take a month.The Archon X prize: you win $10 million if you can sequence 100 human genomes in 10 days, at a cost of $10,000 per genome.It is realistic to envision $100 per genome within 10 years: everyone’s genome could be sequenced if they wanted or needed it.Bioinformatics:

12. The first biological database - Protein Identification Resource was established in 1972 by Margaret DayhoffDayhoff and co-workers organized the proteins into families and superfamilies based on degree of sequence similarityIdea of sequence alignment was introduced as well as special tables that reflected the frequency of changes observed in the sequences of a group of closely related proteinsCurrently there are several huge Protein Banks : SwissProt, PIR International, etc.The first DNA database was established in 1979. Currently there are several powerful databases: GenBank, EMBL, DDBJ, etc.Brief history of bioinformatics: Databases

13. Brief history of bioinformatics: evolutionary reconstructions

14. Brief history of bioinformatics: other important steps Development of sequence retrieval methods (1970-80s) Development of principles of sequence alignment (1980s) Prediction of RNA secondary structure (1980s) Prediction of protein secondary structure and 3D (1980-90s) The FASTA and BLAST methods for DB search (1980-90s) Prediction of genes (1990s) Studies of complete genome sequences (late 1990s –2000s)

15. APPLICATIONS

16. Pharmaceutical:BiobanksA biobank is a type of biorepository which stores human biological samples (including tissue providers, others include genetic profiling) for use in research.Since the late 1990s: a key resource for supporting many types of contemporary research, e.g. genomics and personalized medicine.Drivers: the need to accelerate the discovery and development of drugs. As that industry shifts to more-personalised medicine, the need for high-quality, well-maintained biospecimens intensifies. Veterinary Science/ Animal HealthDivided into Production animals and companion animals, the animal health market covers diagnostics, medicines and vaccines for farmed animals and pets.Drivers:growing demand for animal proteins, as well as a strong consumer need for companion animal health care.

17. PharmacogenomicsNot all drugs work on all patients, some good drugs cause death in some patientsSo by doing a gene analysis before the treatment the offensive drugs can be avoidedAlso drugs which cause death to most can be used on a minority to whose genes that drug is well suited – volunteers wanted!Customized treatmentGene TherapyReplace or supply the defective or missing geneE.g: Insulin and Factor VIII or HaemophiliaMedical Implications:

18. Diagnosis of diseaseIdentification of genes which cause the disease will help detect disease at early stage e.g. Huntington disease -Symptoms – uncontrollable dance like movements, mental disturbance, personality changes and intellectual impairment Death in 10-15 yearsThe gene responsible for the disease has been identifiedContains excessively repeated sections of CAGSo once analyzed the couple can be counseledDiagnosis of Disease:

19. Can go up to 15yrs and $700million One of the goals of bioinformatics is to reduce the time and cost involved with it.The processDiscoveryComputational methods can improves thisTestingDrug Design:

20. Target identificationIdentifying the molecule on which the germs relies for its survivalThen we develop another molecule i.e. drug which will bind to the targetSo the germ will not be able to interact with the target.Proteins are the most common targetsDrug Discovery:

21. 21For example HIV produces HIV protease which is a protein and which in turn eat other proteinsThis HIV protease has an active site where it binds to other moleculesSo HIV drug will go and bind with that active siteEasily said than done!Drug Discovery:

22. BiostatisticsIt encompasses the design of biological experiments, the collection and analysis of data from those experiments and the interpretation of the results.

23. Biostatistics covers applications and contributions not only from health, medicines and, nutrition but also from fields such as genetics, biology, epidemiology, and many others. O It is mainly consists of various steps like generation of hypothesis, collection of data, and application of statistical analysis

24. Branches of Biostatistics Descriptive Biostatistics  Methods of producing quantitative summaries of information in biological sciences.  Tabulation and Graphical presentationBranches of BiostatisticsInferential Biostatistics Methods of making generalizations about a larger group based on information about a sample of that group in biological sciences. Primarily performed in two ways: 1. Estimation 2. Testing of hypothesis

25. Sir Francis Galton is considered as the Father of Biostatistics He was the first to apply statistical methods to the study of human differences and inheritance of intelligence, and introduced the use of Questionnaires and Surveys for collecting data on human communities, which he needed for genealogical and biographical works and for his anthropometric studies.

26. ApplicationsAs a Science In Physiology And Anatomy O To define what is normal or healthy in a population. To find the limits of normality in variables such as weight and pulse rate etc. in a population.To find the difference between means and proportions of normal at two places or in different periods. To find the correlation between two variables X and Y such as height and weight.  whether weight increases or decreases proportionately with height and if so by how much, has to be found.

27. Application in pharmacologyTo find the action of drug – a drug is given to animals or humans to see whether the changes produced are due to the drug or by chance.To compare the action of two different drugs or two successive dosages of the same drug. To find the relative potency of a new drug with respect to a standard drug.

28. Application in medicineTo compare the efficacy of a particular drug, operation or line of treatment – for this, the percentage cured, relieved or died in the experiment and control groups, is compared and difference due to chance or otherwise is found by applying statistical techniques.To find an association between two attributes such as cancer and smoking or filariasis and social class –an appropriate test is applied for this purpose.To identify signs and symptoms of a disease or syndrome. Cough in typhoid is found by chance and fever is found in almost every case. The proportional incidence of one symptom or another indicates whether it is a characteristic feature of the disease or not.To test usefulness of sera and vaccines in the field – percentage of attacks or deaths among the vaccinated subjects is compared with that among the unvaccinated ones to find whether the difference observed is statistically significant.

29. CLINICAL MEDICINE Documentation of medical history of diseases. Planning and conduct of clinical studies. Evaluating the merits of different procedures. In providing methods for definition of ‘normal’ and ‘abnormal’.PREVENTIVE MEDICINE To provide the magnitude of any health problem in the community. To find out the basic factors underlying the ill- health. To evaluate the health programs which was introduced in the community(success/failure). To introduce and promote health legislation.

30. Role of biostatisticsRole of Biostatistics in Health Planning and EvaluationStatistics arising out of biological sciences, particularly from the fields of Medicine and Public health. O The methods used in dealing with statistics in the fields of medicine, biology and public health for planning, conducting and analyzing data which arise in investigations of these branches.In carrying out a valid and reliable health situation analysis, including in proper summarization and interpretation of data. O In proper evaluation of the achievements and failures of a health programs.

31. Bioaugmentationpractice of adding cultured microorganisms into the subsurface for the purpose of biodegrading specific soil and groundwater contaminants.

32. Bioaugmentation of chlorinated contaminants:cultured microorganisms used for bioaugmentation are “specialists” in degrading specific target contaminants. For example, some microbes may be able to degrade the chlorinated compounds cis-1,2 dichloroethylene (cDCE) and vinyl chloride (VC) more quickly than the naturally-occurring microbial community at a particular site. As a result, the remediation community has shifted toward a more prescriptive approach with the use of bioaugmentation to accelerate the reductive dechlorination process, achieve remediation targets, and realize cost savings.Specific strains of anaerobic microorganisms have been isolated, cultured and are commercially available for the biodegradation of the chlorinated contaminants cDCE and VC. Bio-Dechlor INOCULUM® Plus is a widely used bioaugmentation culture designed specifically for this purpose. It is typically co-applied with electron donor solutions such as 3-D Microemulsion® and HRC® to facilitate full and rapid reductive dechlorination.

33. Bioaugmentation of petroleum hydrocarbons :Relative to bioaugmentation for the degradation of petroleum hydrocarbons or any aerobically degradable contaminants in soil and groundwater, it is rare if ever that aerobic degrader augmentation is required to facilitate enhanced aerobic biodegradation.Research has shown that aerobic microrganisms are ubiquitous and are typically limited by the availability of oxygen to sustain and grow their populations. REGENESIS recommends the use of Oxygen Release Compound (ORC®) or ORC Advanced® stimulate the existing aerobic microbial community through enhanced aerobic biodegradation.

34. THANKS