Friday, April 29, 2011

IB Biology on Genetics and Stem Cells

Cloning is producing genetically identical copies of genes, organisms or stem cells.
Cloning of genes ( gene cloning ), an organisms ( reproductive cloning ) or therapeutic cloning ( to harvest the embryonic stems cells for research)
A clone is a group of genetically identical cells derived from a single parent cell.
First Clone Mammal (Dolly the sheep )
picture taken from
http://worldofwords.blogia.com/2010/diciembre.php

List of cloned animals from frog, cat , dog, goat and click HERE to view the latest.
Scientists from Korea (SNU) that cloned (Dog) Snuppy and (Wolf) Snuwolf. 
Click HERE by BBC


Embryonic Stem Cells can be obtained from SCNT or IVF
A claim by South Korean scientists to have created the first cloned wolves is being investigated by officials at the team's university.The group is led by Lee Byeong-chun, a former collaborator of disgraced scientist Hwang Woo-suk. In 2005, a Seoul National University panel concluded stem cell research by Dr Hwang had been fabricated.......................................................................................................BBC
Keywords for Somatic Cell Nuclear Transfer (SCNT)
Enucleated egg from female donor, Differentiated Somatic Cell, Electric pulse, Fused cell forming embryo, Somatic to Stem cell, Genetically identical, Surrogate mother, Dolly sheep 
SCNT needs enucleated egg which may be obtained from female donor by IVF


Video on SCNT

Cloning is controversial as it involves harvesting Embryonic Stem Cells and Destruction of a life.


From Dolly to Human Cloning using SCNT
Human Cloning was suggested by Prof Antinori  with Dr Zavos in 1998
Human Cloning, Right or Wrong
How Human Cloning work with SCNT 
Egg taken from IVF
Ethical Debate Human Cloning, For or Against


picture taken from
http://www.success4dummies.com/?tag=human-cloning









Human Cloning proposed by Prof Antinori and Dr Zavos in 1998

cropped with SnipSnip
Information on Human Cloning, click HERE to view

Stem Cells into Heart Cells by SCNT, click HERE to view
Embryonic Stem Cells is controversial involving Human Embryo using SCNT and IVF but now Scientist developed new method called IPSC. Read on to find out.
............................................................................................................
Induced Pluripotent Stem Cells  (without any Human Embryos)
In an interview with The Times, Professor Sir Ian Wilmut said that the “ethical” production of induced pluripotent stem (IPS) cells, developed from human skin cells and not from human embryos, represented an opportunity to tackle some of the hundreds of inherited diseases that could prove as important as the way that medical science had conquered many infectious diseases over the past 200 years..................................................................................................By The Times
Video on Turning Adult/Somatic Cell (iPSC) to Stem Cells


Video, Power of Induced Pluripotent Stem Cells (iPSC)

Timeline on induced pluripotent stem cells
Click HERE to get in
Thanks to EdYong and all video contributors

Tuesday, April 26, 2011

IB Biology on Genetics and Stem Cells

IB Biology on Stem Cell and Induced Pluripotent Stem Cells
FUTURE of  STEM CELL RESEARCH and INDUCED PLURIPOTENT STEM CELL
Picture taken from
http://www.adult-stemcell-research.com/
Brief Introduction on Stem Cells.
  • Self Renewal and Unspecialised cells which are able to specialised into any 220 cell types
  • Able to give rise to any 220 cells type
  • Two types Embryonic Stem Cell and Adult Stem Cell
  • Totipotent give rise to all cells
  • Pluripotent give rise to all cell types
  • Multipotent give rise to limited cell types
  • Unipotent only one cell type
Stem Cell Research
Click  HERE  for more info
Latest Update on Obama Administration on Stem Cell Research
On March 9, 2009, President Barack H. Obama issued Executive Order 13505: Removing Barriers to Responsible Scientific Research Involving Human Stem Cells. The Executive Order states that the Secretary of Health and Human Services, through the Director of NIH, may support and conduct responsible, scientifically worthy human stem cell research, including human embryonic stem cell (hESC) research, to the extent permitted by law.
Video on Latest update on Stem Cell Research

Keynotes from Obama
False choice between Sound Science and Moral values. We need to ease human suffering and must have the capacity to care. Humanity and Conscience to conduct research in a responsible manner. Some strongly opppose but the potential it offers is great. Stem Cell Research has open up!
Potential for great benefits with opening of many Stem Cell lines

Keynotes from CNN on Moral and Ethical Issues
IVF embryonic stem cells are discarded if not used. Use them for Stem Cell Research for treatment of Spinal cord and many  diseases. Throw them away or Use to Save Lifes
Embryos come from IVF and used for therapeutic research

 Keynotes
Surplus or excess embryos in IVF  will be discarded. Why not donate for Research. Embryonic Stem Cells will benefit Stem Cell Research if donated instead of throwing them away. 
What is Stem Cell ? Click HERE to get more info about


Why Embryonic Stem Cells (ESC) are pluripotent and far better than Adult Stem Cells (ASC) which are multipotent. Click HERE to get more info about


Induced Pluripotent Stem Cell , Turning Skin cells into Stem Cells 


.........................................Click HERE to continue on Pluripotent Stem Cell..............

IB Biology on Genetics and Stem Cells

IB Biology on Induced Pluripotent Stem Cell
Induced Pluripotent Stem Cells made by inducing Somatic Adult Cells into Embryonic Stem Cells (by inserting 4 genes using retrovirus) 
Picture taken from
http://www.rndsystems.com/cb_detail_objectname_cb09i2_induced_pluripotent_stem_cells.aspx
Induced pluripotent stem cells were first generated by Shinya Yamanaka's team at Kyoto University, Japan in 2006. Yamanaka used genes that had been identified as particularly important in embryonic stem cells (ESCs), and used retroviruses to transduce mouse fibroblasts with a selection of those genes. Eventually, 4 key pluripotency genes essential for the production of pluripotent stem cells were isolated; Oct-3/4, SOX2, c-Myc, and Klf4
Source taken from 
http://en.wikipedia.org/wiki/Induced_pluripotent_stem_cell

Embryonic Stem Cells Vs Induced Pluripotent Stem Cells (IPS)
Benefits of IPS Cells
  • No embryos needed
  • Making stem cells from normal adult/somatic cells
Danger of IPS Cells
  • Causes cancer as genes introduced using retrovirus( viral transfection) may cause tumor
  • Low yield of stem cells, time consuming and highly unpredictable
Named as Method of Year 2009 ( Induced Pluripotent Stem Cells )


Induced Pluripotent Stem Cells Explained

Timeline, Stem Cell/Induced pluripotent Stem Cells by SciDaily
ScienceDaily (Feb. 12, 2007) — For cells that hold so much promise, stem cells' potential has so far gone largely untapped. But new research from Rockefeller University and Howard Hughes Medical Institute scientists now shows that adult stem cells taken from skin can be used to clone mice using a procedure called nuclear transfer.
ScienceDaily (Oct. 9, 2010) — Researchers at Karolinska Institutet have shown how stem cells, together with other cells, repair damaged tissue in the mouse spinal cord.
ScienceDaily (Feb. 28, 2011) —  According to new research published online in The FASEB Journal, scientists have successfully fused human stem cells derived from subcutaneous adipose (fat) tissue with muscle cells from rat hearts. 
ScienceDaily (Mar. 7, 2011) — "Pluripotent" stem cells -- which have the potential to mature into almost any cell in the body -- are being widely studied for their role in treating a vast array of human diseases and for generating cells and tissues for transplantation.
ScienceDaily (Apr. 7, 2011) — People who use in vitro fertilization to conceive children often have leftover embryos and must decide whether to store them, dispose of them or possibly donate them for research.
ScienceDaily (Apr. 10, 2011) — Researchers at the University of Pennsylvania School of Medicine have devised a totally new and far more efficient way of generating induced pluripotent stem cells (iPSCs), immature cells that are able to develop into several different types of cells or tissues in the body
News from Stem Cell Research by Medical News
In two papers published on April 25 in the Proceedings of the National Academy of Sciences, Sheng Ding, PhD, reveals novel and safer methods not only for transforming embryonic stem cells into large numbers of brain cells with multiple uses, but also for transforming adult skin cells into so-called neural stem cells
A group of scientists at Marshall University is conducting research that may someday lead to new treatments for repair of the central nervous system. Dr. Elmer M. Price, who heads the research team and is chairman of Marshall's Department of Biological Sciences, said his group has identified and analyzed unique adult animal stem cells that can turn into neurons
................Click HERE to continue on Cloning using iPSC..............................

Sunday, April 24, 2011

IB Biology on Microbes and Bacteria Option F

IB Biology on Microbes, Nitrogen Cycle, Gram Staining and Haber Process.

Picture taken from
http://bettersoils.soilwater.com.au/module2/images/27.gif
Bacteria Involved in Nitrogen Cycle 
picture from
http://www.splammo.net/bact102/102exp091011.html
Keywords are 
Nitrogen Fixation, Nitrification, Denitrification, Ammonification, Nitrites, Nitrates, 


Microbes Involved
  • Nitrogen Fixing bacteria, Azotobacter and Rhizobium ( mutualistically ) in root nodules in legume plts Convert Nitrogen to Ammonia
  • Nitrifying Bacteria, Nitrosomonas and Nitrobacter (aeration) needed. Nitrosomonas convert Ammonia to Nitrites, Nitrobacter convert Nitrites to Nitrates
  • Denitrifying Bacteria, Pseudomonas ( anaerobic ) convert Nitrates to Nitrogen
Microbes make Ammonia (Naturally) Vs  Haber Process Ammonia Production (Industry)
Do you know..........
Ammonia Plant in Korea ( Ulsan ), Fritz Haber Father of Chemical Warfare, Nobel Prize Chemistry, Haber Process is Link to World War I and Ammonia used to make BOMB


Fritz Haber awarded Nobel Prize for his contribution in Chemistry in the production of ammonia which is crucial in making fertilisers.
Click HERE if you want to know more about Haber






Ammonia Production in Korea

Excess nitrate and phosphate ions leached from soil due to over use of fertilisers causes 
( Fertiliser have NPK content ). What does it means to have 20:20:20 NPK content?
1. Eutrophication leads to algal bloom, overuse/depletion of oxygen cause hypoxia/deoxygenation, kills fish due to low oxygen level.
2. BOD up. Bacteria decomposes dead algae, increase in BOD (Biochemical Oxygen Demand) High BOD will decrease the dissolve oxygen concentration in water.

Gram Positive and Gram Negative Bacteria
Keywords are
Lipid layer, Differences, Lysozymes protection, Porins, Stain with Violet, Peptidoglycans, Ethanol, Safranin, Thick and thin, Which bacteria is more dangerous?
Gram staining is done by using crytal violet, iodine, ethanol, safranin and cell wall will be stained purple or pink depending on the cell structure. 


Keywords are
Peptidoglycan, Gram Positive, Gram Negative, LPS, Eubacteria, 
Gram Postive (thick wall) will be purple/violet
Gram Negative (thin wall/LPS) will be pink
Gram Staining in YouTube


Gram Staining Explained in Detail


Friday, April 22, 2011

IB Biology on Microbes and Bacteria Option F

IB Biology on Microbes, Sources of energy and Carbon
Types of bacteria
Click HERE to get in
Photo taken from
http://microbewiki.kenyon.edu/index.php/MicrobeWiki
Photo from
http://en.wikipedia.org/wiki/Photoheterotroph
Keywords are 
Energy source, Carbon source, Photoautotroph, Chemoautotroph,, Photoheterotroph, Chemoheterotroph
........................................................................................................................................................
Photoautotrophs
Energy from light, Carbon source from inorganic substances (CO2), Producers,
Sulfur/purple green bacteria (H2S as reducing agent) and blue green algae ,cyanobacteria (H2O as reducing agent)
Click  MicrobeWIKI for more  infomation
Cyanobacteria
Anabaena is a filamentous cyanobacteria, or blue-green algae, found as plankton. Known for its nitrogen fixing abilities, and they form symbiotic relationships with certain plants
Cyanobacteria is an Oxygenic Photosynthetic Bacteria
Picture taken from
http://www.tutorvista.com/content/biology/biology-iii/kingdoms-living-world/cyanobacteria.php
Cynanobacteria  is believe to be the main origin of Chloroplast found in plant.


Chloroplast (Eukaryotes) comes from Cyanobacteria ( Bacteria)  based on Endosymbiotic Theory


Video on Cyanobacteria shaping our world in producing oxygen . 
Adaptation, Evolution , Endosymbiotic Theory, Cyanobacteria from Sea, Land now found in Plant

Click HERE to get in to animation on Endosymbiotic Theory
........................................................................................................................................................
Chemoautotroph
Energy(ATP) from chemical reaction( hydogen sulfide, iron, ammonia and nitrite), Carbon source from inorganic subtances ( CO2 )
Nitrosomonas ( oxidises ammonia to nitrite to get energy), 
Nitrobacter (oxidises nitrite to nitrate to get energy)
picture taken from
http://copepodo.wordpress.com/2011/02/25/reforma-en-el-acuario-4-ciclo-del-nitrogeno/
........................................................................................................................................................
Photoheterotroph
Energy(ATP) from Light, Not capable of reducing CO, Carbon source from organisms,
Purple non sulfur bacteria (purple bacteria) are proteobacteria that are phototrophic, that is capable of producing energy through photosynthesis. Pigmented with bacteriochlorophyll a or b, together with various carotenoids. These give them colours ranging between purple, red, brown, and orange. Do not produce oxygen because the reducing agent ,electron donor  involved in photosynthesis is not water. In some, calledpurple sulfur bacteria Purple non-sulfur bacteria uses hydrogen.
........................................................................................................................................................
Chemoheterotroph
Saprotrophic or decomposers
Energy(ATP) from chemical reaction, Carbon source  from organisms, 2 method of energy production ( respiration and fermentation), Fermenters are anaerobic, Many organic compound like alcohol, hydrocarbon, cellulose can be metabolised by chemoheterotrophs.
.......................................................................................................................................................
Click HERE to get into Origin of Life
Archaea Bacteria
  • Halophiles live in salt condition
  • Thermophiles in hot spring and thermal vent
  • Methanogens live in anaerobic where organic matter is available.
Video on Thermophiles bacteria oxides inorganic substances like H2S to get energy in deep sea


Video on Methanogens in Biogas Production

How Biogas Works from Nathan Ranney on Vimeo.
Usefulness of Bacteria in Bioremediation
Keywords are
Breakdown of pollutants to harmless substances, removing pollutants, oxidise it, degrade, breakdown contaminants.
  • oil spill/hydrocarbon broken down by microbes
  • selenium ions/toxic is oxidised by bacteria to insoluble selenium metal/less toxic
  • pesticides or chlorinated solvent pollution removed by bacteria
Click HERE to get in
Video on removal of oil spill by bacteria


Methane gas was consumed by bacteria during the BP Oil Spill in 20 April 2010( worst oil spill)
Click HERE to see how microbes ( methanogens) consume the methane gas released

Wednesday, April 20, 2011

IB Biology and IB Chemistry on Enzymes and Kinetics for IA

IA Biology/Chemistry on Enzymes and Kinetics done using Vernier Pressure Sensor and Logger Pro

Research question.............
How will changing hydrogen peroxide concentration affect the rate of its decomposition due to a change in pressure (oxygen)  released measured with a pressure sensor.
(Complete)


Video tutorial on Decomposition of Hydrogen Peroxide with Catalase using Pressure Sensor


Using Logger Pro to measure the Initial Rate


 Tips when using data logging with Pressure Sensor
  • Make sure it is time based for 300s
  • Press collect button to obtain the base line pressure
  • Add magnesium ribbon or catalase enzyme
  • Close the cap and pressure will build up
  • ALWAYS COLLECT THE INITIAL AVERAGE RATE for first 50s
  • Use linear regression to find the gradient for the first 50s
  • This will represent the INITIAL AVERAGE RATE for 50s
  • MUST ALWAYS TAKE INITIAL AVERAGE RATE........Why?
  • If possible take instantaneous rate at time zero which is the INITIAL RATE
  • Perform all trials and compute the initial average rate using linear regression 


All the best on your IA journey.Have fun and learn along the way, find joy in what you do and do it well. If a task is once begun, never leave it till it is done. Be the labor great or small, do it well or  not at all...........

IB Biology and IB Chemistry on Enzymes and Kinetic experiment for IA

 IA Biology/Chemistry on Enzymes and Kinetics done using Vernier Sensor and Logger Pro

Research Question.......

How will changing hydrochloric acid conc affect the rate of reaction due to a change in pressure  (hydrogen gas) in a reaction between magnesium ribbon and acid measured using a Pressure Sensor.
(Complete)


Video Tutorial on Magnesium with Acid using Pressure Sensor
Video Tutorial on Hydrogen Peroxide with catalase enzyme using Pressure Sensor

Tips for successful data collection
  • use test tube of same size ( constant variable )
  • measure initial rate initial average rate
  • let the expt run to collect the base pressure
Finding the slope or gradient using linear regression in Logger Pro.
Initial Rate must be taken for the first 50-100s


Video Tutorial on measuring Initial Rate using linear regression in Logger Pro


 Tips when using data logging with Pressure Sensor
  • Make sure it is time based for 300s
  • Press collect button to obtain the base line pressure
  • Add magnesium ribbon or catalase enzyme
  • Close the cap and pressure will build up
  • ALWAYS COLLECT THE INITIAL AVEARGE RATE for first 50s
  • Use linear regression to find the gradient for the first 50s
  • This will represent the INITIAL AVERAGE RATE for 50s
  • MUST ALWAYS TAKE INITIAL AVERAGE RATE........Why?
  • If possible take instantenous rate at time zero, INITIAL RATE.
  • Perform all trials and compute the initial average rate using linear regression 


All the best on your IA journey.Have fun and learn along the way, find joy in what you do and do it well. If a task is once begun, never leave it till it is done. Be the labor great or small, do it well or  not at all...........

IB Biology and IB Chemistry on Enzyme and Kinetics Experiment for IA

IA, using Oxygen, Conductivity and Temp Sensor
Research Question with Pressure Sensor
How will changing concentration of hydrogen peroxide affect the rate of reaction in a reaction using enzyme catalase .
( PARTIAL )


How will changing  hydrogen peroxide conc affect the pressure change due to the released of oxygen gas catalased by enzyme catalase measured using a pressure sensor 
(Complete ) 
Research Question with Conductivity Sensor.......
How will changing sodium chloride conc in a Visking Tubing  affect the rate of diffusion
(Partial )


How will changing sodium chloride conc in a Visking Tubing affect the rate of conductivity change due to the diffusion of sodium ions out from Tubing measured with a conductivity sensor 
(Complete )

Research Question with Temperature Sensor
How will changing  types of alcohol from methanol to pentanol affect the rate of its evaporation.
(Partial)


How will changing molar mass of alcohol from methanol to pentanol affect its rate of evaporation due to drop in temperature measured using a temperature sensor. 
(Complete )


IB Biology and IB Chemistry on Enzymes and Kinetic experiment for IA

Using Vernier Pressure sensor for Data Logging
Research Question
How will changing hydrogen peroxide concentration affect the rate of enzyme catalase activity. (Partial)


How will changing hydrogen peroxide concentration affect the pressure change due to released of oxygen in a hydrogen peroxide catalased solution measured using pressure sensor.
(Complete )


Video tutorial on using Pressure Sensor to measure the rate of gas production.


 Tips when using data logging with Pressure Sensor
  • Make sure it is time based for 300s
  • Press collect button to obtain the base line pressure
  • Add magnesium ribbon or catalase enzyme
  • Close the cap and pressure will build up
  • ALWAYS COLLECT THE AVERAGE INITIAL RATE for 50s
  • Use linear regression to find the gradient for the first 50s
  • This will represent the AVERAGE INITIAL RATE for 50s
  • MUST ALWAYS TAKE INITIAL RATE ( INSTANTANEOUS RATE AT TIME 0 )
  • Perform all trials and compute the initial rate or average rate  using linear regression 
Video tutorial  using Pressure Sensor for Gas Production Explained In Detailed

All the best on your IA journey.Have fun and learn along the way, find joy in what you do and do it well. If a task is once begun, never leave it till it is done. Be the labor great or small, do it well or not at all. .......................

Tuesday, April 19, 2011

IB Biology and IB Chemistry on enzyme and kinetic experiments for IA

Visible Spectrophotometer for IA experiments in Chemistry and Biology
Below is a sample of my Video tutorial on using Visible spectrophtometer for quantification.
  • Need to calibrate 
  • prepare standard calibration curve
  • prepare a serial dilution
Video on Visible Spectrophotometer and Standard Calibration Curve with Beer Lambert's Law


Sample IA done using Visible Spectrophotometer 
Research question..........
How will changing salt concentration affect amylase activity in its hydrolysis of stach into simple sugar measured using visible spectrophotometer by monitoring its blueblack colouration over time.


Research Question......


How will changing temperature affect the activity of invertase enzyme measured using visible spectrophotometer by monitoring the change in absorbance over time.

IB Biology and IB Chemistry on enzyme kinetics using pressure and pH sensor

Rate of reaction or enzyme activity can be measured using Vernier Lab Pro Pressure Sensor or pH sensor
Vernier sensors for IA experiments


IA which involves the released of any gases, hydrogen, oxygen, carbon dioxide or any change in pressure, Pressure Sensor is used while any change in pH a pH sensor can be used.


Hydrogen Peroxide with catalase can be measured using an oxygen /pressure sensor
Digestion of fat/milk with lipase can be measured using pH sensor.


Some good sample IA for your reference............
Research Question.........
How will changing concentration of hydrochloric acid affect the pressure change due to released of hydrogen gas in a reaction between magnesium ribbon and hydrochloric acid measured using pressure sensor?


Research Question.........
How will changing albumin concentration affect the rate of diffusion of water into a Visking Tubing  containing albumin solution measured using a pressure sensor.
Research Question......
How will changing temperature of pancreatic lipase with bile affect the rate of digestion of milk into glycerol and fatty acids measured using a pH sensor?

Monday, April 18, 2011

IB Chemistry and IB Biology on Kinetics and Rate of reaction for IA

Kinetics is appropriate for Complete Design for IB Chem IA.
Research Question for kinetics must have the 4 criteria to score a complete
  • IV and DV 
  • Well defined
  • Measureable
  • Focus
How will changing concentration of HCI affect the rate of reaction in a reaction between HCI and magnesium ribbon? (  partial because it is not well defined and focus )

How will changing concentration of HCI affect the pressure change due to release of hydrogen gas measured using a pressure sensor in a reaction between hydrocloric acid and magnesium ribbon ?
 (Complete )

How will changing concentration of thiosulphate affect the rate of sulfur formation in a reaction between sodium thiosulphate and hydrochloric acid ( is only Partial )

How will changing concentration of thiosulphate affect the rate of disappearance of cross X due to formation of sulphur in a reaction between sodium thiosulphate and hydrochloric acid 
(Complete )


Using ICT  Vernier Lab Pro for Quantification.


How will changing concentration of thiosulphate affect the change in light intensity due to formation of sulphur measured using a light sensor in a reaction between sodium thiosulphate and hydrochloric acid (Complete)

How will changing concentration of potassium iodide affect the change in absorbance/ transmittance due to formation of blue black colouration measured using a visible spec in an iodine clock reaction ( potassium iodide with H2O2 ) is a ( Complete )


Iodine Clock reaction is a very good experiment for Chem IA
Reagent used are H2O2, KI, S2O3, starch, and stop watch or visible spectrophotometer

Below are 2 good samples of IA on iodine clock reaction measured using stop watch
A better way to quantify is to use ICT visible spectrophotometer not a stopwatch. 
See slideshare for sample.



Related Posts Plugin for WordPress, Blogger...