Post on 15-Apr-2017
TDC TRAINING IISC, KUDAPURA CAMPUS,
CHALLAKERE, KARNATAKA, INDIA
CoordinatorProf. M.S. Hegde
Biology CoordinatorsProf. S.Shishupala, HOD, Dept of Microbiology,
Davangere University, Davangere &
Dr. Aravinda, Crystallographer, IISC, Bangalore
TraineeDr. Mousumi DasAsst Professor,
Dept of Biotechnology, SIT, Tumkur
WHY TDC, IISC Challakerere ?
• Indian Institute of Science - Challakere Campus at Kudapura
• Indian Institute of Science Bangalore celebrated its centenary in the year
2009. To expand its activities, need for a second campus was felt at that
time.
• Indian Institute of Science has acquired a second campus at Kudapura,
Challakere, Chitradurga district of Karnataka.
• The creation of the second campus has been greatly facilitated by the
Government of Karnataka.
• The campus is located at Kudapura 15 Km from Challakere on the
Challakere - Nayakanahatti Road. Kudapura campus is 220 Km away from
the Bangalore campus.
Talent Development Centre (TDC)The Institute conceived the idea of starting a Talent Development Centre mainly to impart training to science teachers at all levels, to conduct discussion meetings, seminars, winter and summer schools, provide academic and research facilities for the young high school, college, and University students. High School Science Teachers Training Program is considered a priority because it is in the high schools the students are introduced to science. Science education is crucial for the development of our Nation. It is the experience of the Institute that if the teachers are trained, vast number of students gets benefitted for a long period of time.
Vision of High School teachers TrainingThe primary vision of this program is teaching and training teachers to teach students with passion. Motivating them to have higher level of intellectual activity is more important than just giving lectures to the participating teachers and covering the course syllabus. The hallmark of the IISc academic program is in its rigor, honesty of purpose, simplicity, humility, sincerity, time consciousness, hard work and delivery. It is the research and the research attitude that drives the Institute. If an event is announced in IISc it takes place at the scheduled time. Can we inculcate IISc's culture of learning in these teachers ?
Non Teaching Staffs , TDC, IISC, Kudapura Campus,Challakere
IISC , TDC , KudapuraOutside and InsideClassrooms and Well Facilitated Lab with all necessaru basic amenities
Biology and Chemistry Lab
Entrance
IISC , TDC , Kudapura campus ;Outside view
Biology and Chemistry Lab
Biology Lab Biology Lab with a trainee
TDC Entrance
Theory lectures scheduled from 23rd Nov to 13th Dec.,2016
Practicals scheduled from 23rd Nov to 13th Dec.,2016 represented in a Lab Manual
List of Practicals Carried out from 23rd Nov to 13th Dec,2016
Topics covered in theory lectures by resource persons
Topics covered in theory lectures by resource persons
Topics covered in theory lectures by resource persons
List of experiments covered in practicals
List of experiments covered in practicals
Dr. S. Shishupala, HOD, Dept of Microbiology, Davangede Univ. Davangede; Biology Coordinator at TDC
Prof. Dipak Saini , Dept of Biological Sciences, IISC, Bangalore
Prof. D.N Rao, Dept of BiochemistryIISC, Bangalore
Prof. P.Kondaiah, Dept of Reproductive Biology and Gene Expression Unit
IISC, Bangalore
Prof. P.Kondaiah, Cancer BiologistIISC, Bangalore
Prof. M.R.N. Murthy, IISC, Bangalore
Some of the Resource Persons… In camera
Prof. Upendra Nongthomba, DBGL Lab, IISC, Bangalore
Prof. R .Manjunath, Associate Professor, Dept of Biochemistry, IISC Bangalore
Associate ProfessorJNCASR ,Jakkur, Bangalore 560 064, India
Dr. Hemalatha Balaram
Persons behind the hardships of training being conducted in TDC,IISC,Kudapura, Challakere
Brief Glimpses of TDC , IISC, Kudapura, Challakere from 23rd Nov to 13th Dec,2016
ESTABLISHMENT OF LAB FOR BIOTECHNOLOGY WITH BASIC AND HIGHEND INFRASTUCTURE WITH A
NOMINAL COSTING
Instruments Approximate Costing(Rupees)
Glasswares Miscellaneous ( Rupees) Funds and Collaborative agencies suggested
Total costing
Microscopes and Autoclave and pressure cooker
50,000 Conical flasks -50 ml to 1000 ml (Borosil)
Micro Pippettes (0.0 to 5 ml) Tarsons - 5,000
CSR –corporate Social Research funds from near industries
4.0 -6.0 lakhs
Hot Air Oven 8,000 Beakers (10-1000 ml; Borosil),
Pippette stand, Cuvette stand, Testtube stand ,Eppendorfs tubes (1 ml to 5 ml) and stands, micropippete tips and (0-5 ml),rubber bands, dialysis bag,forceps, needles, spatula, centrifuge tubes, , etc
India Bioscience KSITBTVGST
Plastic beakers (500 to 1000 ml) - Tarsons
Shaker Incubator/ Vortex mixers
10,000 Glass pippettes (1 ml to 10 ml)-Borosil
Disposable autoclavable bags,
LAF/pH meter (digital) 48,000 Funnels (small, medium and big size) – glass and plastic made
micropippete tip boxes
Cooling Centrifuge/ Table top centrifuge and microcentrifuge
65,000 BOD bottles (100 ml – 1000 ml)
gel staining and destaining box,
Dessicators for chemical storage
8,000 Storage bottles Blubber for acid pippeting
PCR or Thermocycler and Powerpack combined PAGE unit
30,000-40,000
Volumetric flask Columns for chromatography
Spectrophotometer/ Colorimeter
47,000 Separating funnel Blotting papers, Whattmann Filetre paper, pH strips (core and decibel range 1.0 to 14.0)
DNA gel running machine or Gelrocker and illuminator
Glass slides, cavity slides, coverslips etc
Total- 1.0to 4.5 lakhs
Total-1.5 lakhs Total-– 30,000 to 50,000
Some lab amenities starting from very basic to highend
Fluorescence Microscope StereoBinocular
Microscope
Sterilization efficiency checking materials for autoclave
Filter sterilization and bacteriophage filter elements
Eppendorf tube stand to keep in waterbath
SDS PAGE UNIT
Shaker Incubator
Gas Chromatographer
Shaker Waterbath
Arrangements and designing of feasible accomodation of chemicals and glasswares with a brief systematic planning
Infrastucture facilities with maximum utilization in minimum space
Glimpses of theory lectures on some basic theoretical issues – common perspective of Lifesciences including all branches
Mass is the amount of matter in an object.Difference Between Mass and WeightStudents of physics often confuse mass and weight of an object and many also feel that there is no difference between the two, while the fact is that there is a lot of difference between the two.Mass is the amount of matter present in a body and is an intrinsic property of the body. Mass of an object remains the same always at any place.Weight on the other hand is the force which a given mass feels due to the gravity at its place. Weight is measured in units of Force like Newton (which is the SI unit of Force).If your mass is 60 kgs then your weight is approximately 60 x 10 = 600 Newtons. This is becauseForce = mass x acceleration (From Newton's second Law)Thus, weight = mass x acceleration due to gravityIf you go to moon your mass remains same, i.e 60 kgs, but your weight becomes less by 1/6 amount, since moon's gravity is 1/6 that of earth.Mass of a body is measured by balancing it equally with another known amount of mass. You keep known amount of masses like blocks of 1 kg, 2 kg etc on one side till both the sides balance and then add up the numbers on the known side of mass and thus calculate the unknown mass. This works because, when the masses are equal on both the sides of the balance the effect of gravity cancels out for both (i.e weight cancels out) and hence we can calculate the mass on one side of the balance if we know the mass on the other side of the balance.Weight is measured using a scale which effectively measures the pull on the mass exerted by the gravity of the earth.
Ion type Composition M/z ratio Frequency
A Σ +H –CO S-27 quite common
B Σ +H S+1 common
C Σ +H +NH +H +H S+18 rare
X Σ +OH +CO S+45 rare
Y Σ +OH +H +H S+19 very common
Z Σ +OH –NH very rare
doubly-charged parent parent ion +H+ (parent M/z + 1) / 2 very common
trebly-charged parent parent ion +H+ +H+ (parent M/z + 2) / 3 rare
internal ion Σ +OH +H +H S+19 rare
immonium ion Σ +H -CO S-27 rare
Table 1. Masses of ions found in tandem spectra.'Σ' here denotes the total mass of the constituent amino acids, as given in table 2.The Frequency column applies to low-energy collisions in a modern QTOFspectrometer, higher-energy collisions in older spectrometers gave rise to agreater variety of ions.
S+2
letter name mass,DaG glycine 57.02A alanine 71.04S serine 87.03P proline 97.05V valine 99.07T threonine 101.05C cysteine 103.01I isoleucine 113.08L leucine 113.08N asparagine 114.04D aspartic acid 115.03Q glutamine 128.06K lysine 128.09E glutamic acid 129.04M methionine 131.04H histidine 137.06F phenylalanine 147.07R arginine 156.10Y tyrosine 163.06W tryptophan 186.08
carboxymethyl cysteine 161.05carbamidated cysteine 160.03oxidised methionine 147.04
Table 2. Masses of amino acids to two decimal places.
Parent ion mass 1275.67
Parent++
Step 1. Identify doubly charged parent ion(1275.67 + 1)/2 = 638.33
We do this to just eliminate this peak and not associate it with a fragment ion. This has no other purpose
Parent++
Yn-1
Y
•Step 2. Identify high mass peaks at right end of spectrum•These could be Y ions•1112.70 – could be Yn-1 arising from cleavage of amino terminal amino acid from parent ion Yn•Parent ion is +19 (18+1(singly charged))•1275.67-1112.70 = 162.97•162.97 could correspond to a single amino acid or the sum of masses of a small number of amino acids.•162.97 = mass of tyrosine
Parent++
Yn-1
YG
Yn-2
Yn-3
Yn-4
Yn-5
I/L
V
T
•Identify Yn-2 and Yn-3•1112.70-1055.67 = 57.03 G•1055.67 – 1014.52 = 41.15 not consistent with any amino acid, peak small, we skip it.•1055.67 – 947.67 = 113.05 I/L•Similarly the next two are valine and threonine•942.62-843.48 = 99.14 Valine•843.48 – 742.46 = 101.02 threonine
Ion Sequence predicted mass
A1 Y 136.08
A2 YG 193.10
A3 YGI 306.18
A4 YGIV 405.25
A5 YGIVT 506.30
B2 YG 221.09
B3 YGI 334.18
B4 YGIV 433.25
B5 YGIVT 534.29Table 3.
B1 cannot form
Parent++
Yn-1
YG
Yn-2
Yn-3
Yn-4
Yn-5
I/L
V
TA1
A5
A3A2
A4
B2
B3
B4
B5
Parent++
Yn-1
YG
Yn-2
Yn-3
Yn-4
Yn-5
I/L
V
TA1
A5
A3A2
A4
B2
B3
B4
B5
Parent++
Yn-1
YG
Yn-2
Yn-3
Yn-4
Yn-5
I/L
V
TA1
A5
A3A2
A4
B2
B3
B4
B5
Y0 Y0Y0
•Peaks at 843, 942, 1055 all have peaks 18 Da to the left of them•Due to loss of water•These are designated as Y0
•Ser or Thr following(?) YGIVT
Parent++
Yn-1
YG
Yn-2
Yn-3
Yn-4
Yn-5
I/L
V
TA1
A5
A3A2
A4
B2
B3
B4
B5
Y0 Y0Y0
++Parent0
++Parent*
•Small peaks at 629.33 and 629.87•Other doubly charged ions Parent0/parent’•Drop of water (-18) (S or T)•Drop of ammonia (-17) (Q, N, K, R)•Tryptic peptides contain K/R
Chemistry for Biology
Problems and solutions derivations on pH, pka, % dissociation, molarity, molality, preparation of buffers ; evaluation of kw etc.
HOW DOCK WORKS
Step 1: Start with crystal coordinates of target receptor
In this example, HIV-1 protease is the target receptor, with its active site aspartyl
groups identified in red.
Step 2: Generate molecular surface for receptorThis is performed using Mike Connolly's ms program. Note that only the surface for the active site needs to be generated
For the rest of this overview, we'll use a a blow up of the active site
Step 3: Generate spheres to fill the active site
The shape of cavities in the receptor is used to define spheres; the centers of the spheres become potential localtions for ligand atoms.
In the following picture, the sphere centers are identified by cyan triangles, and the sphere surfaces are shown:
Side view of spheres
Step 5: Scoring
Each oriented molecule is then scored for fit. There are currently 3 scoring schemes:
·Shape scoring -- which uses a loose approximation to the Lennard-Jones potential
·Electrostatic scoring -- which uses the program DELPHI to calculate electrostatic potential ·Force-field scoring, which uses the AMBER potential
In this example, this is the top-scoring orientation for the molecule thioketal in the HIV1-protease active site, using force-field scoring. (please note, this is a different orientation than previously published, as those runs were done using the shape scoring scheme, and a different version of the protease crystal structure
Final notes Here is a comparison of the top scoring orientation of the molecule thioketal with the orientation found in the crystal structure.
The journey of Lab…………from 23rd Nov. to13th Dec,2016At Biology Training in TDC, IISC,Kudapura, Challakere
Pollen germination test represented by bud formation as observed Under 40X in Light Microscope
Pollen germinationEmploying
Catharanthus roseus
Pollens Initiation of bud formation
Maturation and elongation
of bud from pollen
SEED HEALTH TESTING
INFECTED SEED INFESTED WITH FUNGAL HYPHAE
Negative stainining
Catalase test
Stages of mitosis from Onion root tip
Bacterial Motility testing 3% KOH test for preliminary identification of Gram +Ve and
Gram –Ve Bacterial colony
Slide with mashed root tip after staining with acetocarmine
Principles of biology experiments meet the end at real life exposures …….
Pregnancy detection kit -
Sugar and protein estimation by urine detection kit
the presence or absence of hCG hormone in urine sample by immonodiffusionVISIPREG strip sandwich immune assay which uses anti-hCG inboth native and conjugated forms
Sugar normally is not found in urine. But when blood sugar level rise well above a target range which can occur in type 1 and type 2 diabetes, the kidneys sometimes releases sugar into the urine even when blood sugar levels are within a range
ODD assay in iimunotechnology
Different anitgen and antibody samples used for ODD assay in iimunotechnology
Ring of precipitation depends on conc. of antigen and antibody
Agarose gel
Distance of the wells leads to time dependent Precipitation ring development Antige
nAntibody Antibody
Determination of ESR count ESR is represented as fall of RBCs in mm per hour
Determination of heamoglobin conc. In blood in terms of percentage
Blood grouping Total count of WBC And RBC in different chambersOf Newbauer slide in Haemocytometer
Neutrophil
Basophil
Neutrophil
Lymphocyte
Monocyte Differential count of WBC by Giemsa staining
Thymus in dissected mouse
White transparent lobes above heart
Thymus, spleen and bonemarrow afterdissection
T cells and undiffrentiated lymphocyrte cells In bonemarrow extrafct after differential staining
WBC’s in thymus extract after differential staining
Ammonification in soil employing different soil samples
Control
Test
After 15 days Callus culture
Conductance of Callus culture
Amplified DNA after PCR
Purity checking of DNA after PCR in agarose gel electrophoresis
Development of peak employing MS software to check purity of amplified DNA PCR in progress
Polymerase chain reaction
Non amplified DNA as control
Bacterial growth curve Slide culture for study of autotrophs
Methyl Red test
Cell immobilization and inveratse assay from immobilized yeast cells on calcium alginate
SDS PAGE PROCESS AND DETERMINATION OF Mr FROM GRAPHICAL CALCULATIONS
Study of Barr Body from human cheek cells
Sterilized spatula
Staining of cheek cells (saliva samples)
Saliva sample from male – barr body absentAs one X chromosome absent
Sterilized spatula
Saliva sample from female – barr body presentAs two X chromosomes present
Barr body
Nucleus with no barr body
Nucleus
Barr body
Nucleus
Study of Drosophila, polytene chromosome and mitotic chromosome
Drosophila culturing
Chloroform application
Collected Drosophila after chloroform applied
Identification of male and female Drosophila
Microtomy of Drosophila 3rd Instar larvae for salivary gland dissection
Male and female Drosophila under Sterio Binocular Microscope at 4X
S…
Salivary gland
Neural Lobes ( frontal)
Poytene chromosome followed by saivary gland mashing and staining
Poytene chromosome
Mitotic chromosome followed by neural lobe mashing and staining
All cells are in metaphase stage
Qualitative estimation of Proteins
Quantitative estimation of Proteins
Lowry Method
Colorimeter
Quantitative estimation of carbohydrate
DNS Method
Study of protease activity from bromelein obtained form pine apple juice emplpying
gelatinase test
Control Test – Liquification of gelatin followed by incubation at 250C
Estimation of Microbial load on handscrubbing method
Antibiotic susceptibility test
Study of fungi
Colony of Rhodotorula an yeast Branched fungal hyphae
Estimation of chlorophyll
Agarose gel electrophoresis, restriction digestion, ligation of DNA
Pla B P R L
Pla- Plant DNA B- Bacterial DNAP- Plasmid DNA R- Restriction Digestion markersL- Ligated DNA
First test before initiation of the training (Answer key) date: 23.11.2016
Assignments based on each day lectures delivered by resource persons (key answers with questions)
Assignments based on each day lectures delivered by resource persons (key answers with questions)
Post training evaluation ( questions with key answers of test II)12.12.2016
ACKNOWLEDGEMENT
The training would not be successful even initiated by me
…
If I don’t thank the following persona…………..
TDC Training centre, IISC, Challakere for selecting me
1. Dr. B.S. Gowrishankar, HOD, Dept of Biotechnology,
SIT , Tumkur
2. Dr. Shivakumaraiah, Principal , SIT,. Tumkur and
Management of SIT, Tumkur
3. Faculty Staffs of Dept of Biotechnology, SIT, Tumkur
4. Non teaching staffs
5. My Family for support all the time invisibly
6. All my well wishers