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7 Major Steps of Scientific Method in Biology with explanation

7 Major Steps of  Scientific Method in Biology
Definition of Scientific Method
Scientific method is an organized and systematized effort to gain knowledge that uses observation and experimentation to describe and explain nature or natural phenomenon. It includes collection of data through observation and experimentation and formulation and testing of hypothesis.
Steps involved in a scientific method or research
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7 Major Steps of  Scientific Method in Biology with explanation

Step I: Define the problem through observation and by asking questions.
Make an observation. Based on the observation, ask questions. Why, how, what?.  Preliminary answers to these questions will help you to define the problem.  The observation should be correct and repeatable. Observation can be direct using senses or indirect with the help of instruments.

Step II: Research the problem or Review of literature
Research the problem:  This step is often called as review of literature. It is the process of collecting all available information on the selected topic from available authentic sources. It includes research journals, books, periodicals etc. Review of literature will give the researcher a clear picture about the selected topic, helps in making good hypothesis and also helps in avoiding repetition of the work.

Step III: Formulate a Hypothesis
Based on review of literature, the researcher will formulate a hypothesis. Hypothesis is an educated guess, a possible answer or a predictive statement that can be tested by scientific methods or scientifically testable or measurable. This statement is based on our previous experience on the topic or based on existing knowledge (review of literature).
Null Hypothesis
·         The null hypothesis is a hypothesis which the researcher tries to disprove, or nullify.
·         It is denoted by H0  
·         Accepting the null hypothesis suggest that researchers hypothesis needs revision

Alternative Hypothesis
·         The alternative hypothesis is a hypothesis which the researcher tries to prove.
·         It is denoted by H1 
·         Accepting the alternate hypothesis proves that the researchers reasoning is true.

Step IV: Test Hypothesis by conducting experiments.
Here we have to design the experiment and execute the project. We often call the methodology adopted for conducting the experiment as procedure. It should be properly designed to get unbiased results. We need to determine the variables in the experiment
A variable is any factor, trait, or condition that can have different values, change in variable influences the outcome of experimental research
The variable is the factor you might measure in an experiment
1. Independent variable: The variable that researcher changes or the researcher think it will affect the dependent variable
        2. Dependent variable: The variable that is affected by change  in independent variable
      3. Controlled variable: The variable that is kept constant or same throughout the experiment.
If possible, the experiment should have a control group.
Step V: Collect and record data. Data collection may be direct (using our senses) or indirect (using scientific instruments). 

Step VI: Analyze and interpret data and draw conclusions.
Analyze data using mathematical tools or statistical software like SPSS for finding out the significance of the result. At the end of the experiment, null hypothesis may be accepted or rejected. Accepting the null hypothesis suggest that researchers hypothesis needs revision

Step VII: Report results or Publish the result. This includes preparation of report, scientific paper or presentation of results or publish it in scientific journals so that your finding is open to public. A theory is a hypothesis supported by large body of observation and experimental evidences. All scientific theories are subjected to revisions or modifications.
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7 Steps of Scientific Method with Explanation Poster

 7 Steps of scientific method in biology poster. 
 7 Steps of scientific method in biology poster

Scientific method is an organized and systematized effort to gain knowledge that uses observation and experimentation to describe and explain nature or natural phenomenon. It includes collection of data through observation and experimentation and formulation and testing of hypothesis.
7 steps of scientific method in Biology with explanation

Watch this simple 5 min video
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5 Cell wall Synthesis Inhibitors and their Mode of Action


5 Cell wall Synthesis Inhibitor Drugs and its Mode of action
Cell wall is a rigid layer of polysaccharides present outside the plasma membrane of the cells of plants, fungi, and bacteria. In the algae and higher plants it consists mainly of cellulose.
  • In fungus, cell wall is primarily made up of chitin
  • In Bacteria, cell wall is primarily made up of peptidoglycan except in archaebacteria
  • Cell wall offers protection to the cell and maintains its structure and shape
  • Many drugs target cell wall as cell wall is essential for the survival of infectious pathogens
5 Cell wall Synthesis Inhibitors and their Mode of Action

Cell wall synthesis inhibitors
1. Penicillin
  • β lactam antibiotics (beta-lactam ring in their structure)
  • effective against gram positive bacteria
  • Inhibits bacterial cell wall formation by blocking cross linking of the cell wall structure.
  • Inhibits transpeptidase enzyme
  • Bacteria formed in the presence of beta-lactams lack cell-wall.
Mode of action: Beta-Lactam Antibiotics bind to specific receptors on bacterial cell membrane called Penicillin Binding Proteins (PBPs) thus inhibiting transpeptidase enzyme that catalyzes cross- linking of peptidoglycan chains of the bacterial cell wall. The target bacterium undergo lysis or cell breakage without cell wall.
2. Cephalosporin
  • β lactam antibiotics but broad spectrum antibiotic
  • Broad spectrum antibiotic generally effective against both Gram positive and Gram negative bacteria.
  • having 7- aminocephalosporanic acid nucleus

Mode of action: Similar to penicillin
3. Vancomycin
  • Vancomycin is a unique glycopeptide structurally unrelated to any currently available antibiotic.
  • Narrow spectrum antibiotic which inhibits the second phase of cell wall synthesis
  • Effective against Gram positive bacteria

Mode of action
Vancomycin Mode of Action
Vancomycin recognizes and binds to the two D-ala residues on the end of the peptide chains. Thus prevent cross linking of cell wall strands by preventing the binding of cross linking enzyme
There is also evidence that vancomycin alters the permeability of the cell membrane and selectively inhibits ribonucleic acid synthesis.
4. Bacitracin
  • polypeptide antibiotic derived from B. subtilis
  • primarily effective against gram positive bacteria
  • Inhibits peptidoglycan strand synthesis

Bacitracin Mode of Action
Mode of action
Peptidoglycan monomers - consisting of the sugars NAM and NAG with a pentapeptide coming off the NAM - are synthesized in the cytosol of the bacterium. These monomers are then transported across the cytoplasmic membrane and inserted into the growing peptidoglycan chain by membrane transporters called bactoprenols.
Bacitracin binds to bactoprenol after it inserts the peptidoglycan monomer transported into the growing cell wall. It subsequently prevents the dephosphorylation of the bactoprenol. Bactoprenol molecules that have not lost the second phosphate group cannot assemble new monomers and transport them across the cytoplasmic membrane. As a result, no new monomers are inserted into the growing cell wall.
Without the active dephosphorylated bactoprenol, peptidoglycan synthesis cannot be completed and the cell lyses occurs*
5. Fosfomycin
  • Phosphonic acid derivative produced by Streptomyces sps
  • Broad spectrum antibiotic effective against both Gram positive and Gram negative bacteria.
  • Acts as phosphoenolpyruvate (PEP) analogue inhibiting the enzyme MurA involved in the first committed step of peptidoglycan cell wall biosynthesis
Mode of action:
Fosfomycin is a phosphoenolpyruvate (PEP) analog that irreversibly inhibits of MurA (UDP-N-acetylglucosamine-3-enolpyruvyl transferase), the cytosolic enzyme responsible for the first step in the peptidoglycan biosynthesis pathway that produces UDP-N-acetylmuramic acid. 
MurA is responsible for catalyzing the transfer of  enolpyruvate moiety of phosphoenolpyruvate (PEP) to the 3′-hydroxyl group of UDP-N-acetylglucosamine in the pathway that produces UDP-N-acetylmuramic acid 
References
Castañeda-García, A., Blázquez, J., & Rodríguez-Rojas, A. (2013). Molecular mechanisms and clinical impact of acquired and intrinsic fosfomycin resistance. Antibiotics2(2), 217-236.
Zhanel, G. G., Walkty, A. J., & Karlowsky, J. A. (2016). Fosfomycin: a first-line oral therapy for acute uncomplicated cystitis. Canadian Journal of Infectious Diseases and Medical Microbiology2016.
http://faculty.ccbcmd.edu/courses/bio141/lecguide/unit2/control/bacresillus.html
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Causes and Effects of Ozone depletion - Ozone Hole

  • Ozone is present mainly in the stratosphere extending 16 kms -50 kms.
  • Also known as ozone umbrella, or protective layer.
  • The presence of ozone layer in the stratosphere is of vital importance for all living organisms, because the harmful solar radiation, such as ultraviolet rays(UV-B), which are lethal to life on the earth are absorbed by it.
  • The ozone umbrella does not allow these harmful UV rays to enter the earth’s atmosphere.
Ozone depletion
Ozone hole
  • The thickness of ozone layer is measured in Dobson unit (DU),where 
                                 1 DU =0.01mm
  • The average thickness of the stratosphere ozone layer is estimated to be 32 Du
  • A fall in thickness or concentration of spring time ozone layer is termed as ozone hole.
  • It was discovered by Farman et al 1985, who coined  the term ozone hole.
Causes of Ozone depletion
  • The main cause of ozone layer depletion is the build-up of CFCs (chlorofluorocarbons) in the atmosphere.
  • When the CFCs reach the upper atmosphere, high UV radiation reacts with CFCs and releases chlorine atoms. These free chlorine atoms react with ozone thereby leading to the depletion of the ozone layer.
CFCl3-> CFCl2+Cl
CFCI2 ->CFCI+CI
CI+O3->CIO+O2
CIO+O3->CI+2O2
  •  An individual chlorine atom can on average destroy nearly a thousand ozone molecules before it is converted into a form harmless to ozone this is why CFCs are extremely damaging to the ozone layer.
  •  The build-up of CFCs is caused by many applications like the production of refrigerants, anesthetics, aerosol sprays.


Ozone Depleting Substances (ODS)
  • The green house gases like CFC, Methane and nitrous oxide in the stratosphere destruct ozone layer.
  • Substances that cause the depletion of the ozone layer are called Ozone Depleting Substances (ODS).
The different ODS are
  • CFCs (14% of total depletion)
  • Nitrogen oxides(3.5% depletion)
  • Halons (Used in fire extinguishers)
  • Methyl Chloroform
  • Carbon Tetrachloride
  • Hydrofluorocarbons (HCFCs)
Effects of Ozone Depletion
  • Due to depletion of ozone layer the dangerous UV B radiation passes through this layer and reaches the earth.
  • Cornea absorbs UV b radiations and becomes inflamed. The disorder is called ‘snow blindness’ cataract
  • The incidence of UV B radiation damage skin cells cause ageing of skin and skin cancer.
  • Decreased photosynthetic activity will increase CO2 concentration of the atmosphere resulting in global warming.
September 16: International  Ozone Day
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Green House Gases, Global Warming and its Effects

Green house effect
Industrial and domestic coal burning release high amount of carbon dioxide,carbon monoxide, chloroflurocarbons, methane, nitrous oxide etc from various sources.They are acting as greenhouse gases.
Green House Gases
The various green house gases are 
  • Carbon Dioxide, CO2(warming effect 60%),
  • Methane, CH4 (effect 20%)
  • Chloroflurocarbons or CFCs(14%),
  • Nitrous Oxide, N2O  (6%)
  • Others of minor significance are water vapours and ozone.
  • The excessive increase in the amount of green house gases in the atmosphere raises the temperature by retaining more infrared radiations.
  • This excessive green house effect is referred to as global warming.
  • CO2 is the most important green house gas that plays   a major role in increasing global warming.
  • 60% of the global warming is caused by carbon dioxide. Chloroflourocarbon (CFC), nitrous oxide and methane constitute the remaining 40%of the global warming.
Effects of global warming
  • Drought is one of the most serious problems arising from major climate change resulting from global warming. 
  • Decrease in precipitation.
  • Increased evaporation reduces water available for agricultural , and other uses. It may affect the food production.
  • Sea level rise: the melting of glaciers
  • Rising of sea level produces negative impacts on human existence, freshwater resources, agricultural and dry lands, animals and bird existence etc.
  • Effect on range of species distribution.
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Acid rain: Definition, Causes and Effects - Acid Rain Formula

The term acid rain was first used by Robert Angus Smith (1872).
It is described as ‘man’s chemical warfare on nature”.

•Also known as Acid precipitation
Acid rain Definition, Causes and Effects   Acid Rain Formula
What is Acid Rain:
Acid rain refers to the presence of excessive acid content in the atmosphere and also in the precipitation water(rain, snow, mist, fog etc).
It is the rain fall and other forms of precipitation with a pH of less than 5 of normal rain is 5.6-6.5.
Two forms: Wet and Dry
Wet deposition: Rain, snow and fog
Dry deposition: it is settle down of wind blown acidic gases and particles over trees, various articles and soil. about 50 of acidity is passed to earth as dry deposition.
Causes of Acid Rain: 
      1. Sulphuric acid and nitric acid are the major agents of acid rain.
a) Formation of Sulphuric acid:
2SO2+O2->2SO3
SO3+H2O->H2SO4   (Sulphuric acid)
b) Formation of nitric acid
2NO+3[O]->N2O5
N2O5+H2O->2HNO3 (Nitric acid
2. Hydrochloric acid, nitrous acid and carbonic acid also contribute to acid rains.
a) Formation of carbonic acid
             CO2+H2O-> H2CO3 (Carbonic acid)
             b)Formation of nitrous acid
NO+O3->NO2+O2
NO+NO2->N2O3
                           N2O3+H2O-2HNO2 (Nitrous acid)
Oxides of nitrogen come from combustion of fuels in automobiles as well as in power plants.
Oxides of sulphur are released from smokestacks of coal fired power plants, smelters and other industries (oil furnaces).

Effects of Acid Rain (Acid precipitation):
Acid rain is very harmful to agriculture, plants, and animals. It washes away all nutrients which are required for the growth and survival of plants. Acid rain affects agriculture by the way how it alters the composition of the soil.
Effect on nitrogen cycle: Nitrogen cycle is highly sensitive to the acidification of soil.  Acidity suppresses denitrification, high  pH increases the volatilization of ammonia, Alkalinity affects the survival of nitrogen fixing bacteria.
Effect on fresh water ecosystems: due to acid rain many lakes in Germany and other European countries have a pH of less than 5, an acidity level considered lethal for many species of fish. Acidic water can carry dissolved aluminum to lakes and streams which clogs the gills of fish and deprives them of oxygen.
Effects on soil: It causes leaching of essential minerals of soil
Effects  on terrestrial ecosystems: It causes extensive damage to forest trees and all vegetation.
Effects on buildings, stone structures (stone leprosy) etc: Acid rain corrodes metals, marble, painted surfaces, slate, stone etc. This phenomenon is called Stone leprosy. In Greece and Italy, valuable stone statues have been partially dissolved and Taj Mahal in India is affected by the acid rain.
Before and After Effects of Acid Rain on The Taj Mahal
. Acid rain has the following reaction with the marble (calcium carbonate):
                                 CaCO3 +  H2SO4 -> CaSO + H2O + CO 
Acid rain damages plants  direct effect on foliage and growing point; necrosis, dieback, chlorosis, defoliation. It causes reduced rates of photosynthesis and growth, increased sensitivity to drought and disease.
Effects on human health: Acidification of soil may leads to the aluminum toxicity of drinking water, which may cause kidney failure, bone softening, Alzheimer’s disease  etc.
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Causes and Effect of Climate Change

Climate: the weather conditions prevailing in an area in general or over a long period.
A number of factors affect and alter the climate.
It may be natural and anthropogenic(man made)
Causes and Effect of Climate Change
Image credit
Causes of climate change:
The quantum of solar energy reaching the earth.
Increasing concentration of green house gases in the atmosphere.
Snow, ice and glaciers which reflect solar radiation back to the atmosphere.


•Ocean currents which play a significant role in heating the earth.
• Volcanic eruptions which can directly influence the  temperature and climate of the earth


Effects of climate change:
        1.Increasing heat stress
2.Abnormal changes in the pattern of rainfall which may result in drought.
3.Depletion of freshwater
4.Melting of polar ice caps and mountain glaciers
5.Rise in  sea level, submergence of coastal lands and islands.
6.Loss of natural habitats and biodiversity.
7. The climate changes which result in tsunamies, El Ninos, cyclones and storms have become increasingly higher.


Pollution:
•  Undesirable change in physical, chemical and  biological characteristics of air, water and soil which may cause any harm to man and other living organisms of the environment is known as pollution.
• Various types of pollution occur on earth which includes water, air, soil, noise and radioactive pollution. These pollutants lead to global environmental changes like green house effect, global warming, acid rain, ozone layer depletion etc.
(El-Nino: It is warm water current in the pacific that periodically flows southwards along the coasts of Eduador. It causes a chin of climatic changes and often induces great storms. )
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Antigen Presenting Cells (APC)-Definition,Mechanism of action and Examples

Definition of APC: Any cell that can process and present antigenic peptides in association with class II MHC molecules and deliver a co-stimulatory signal necessary for T cell activation.
These cells possess class II MHC molecules on the surface.
APCs include macrophages (monocytes as blood macrophages and histiocytes as tissue macrophages), B cells and dendritic cells.
Mechanism of APC (Antigen Presenting Cells)
Mechanism of APC (Antigen Presenting Cells) -  Immunology
B cell as Antigen presenting cell
Step 1: B cell activation=Antigen binding to Naïve B cell receptor followed by Antigen degradation inside B cell

Step 2: B cell acts as antigen presenting cells (APCs). Degrades antigenic peptides are displayed on MHC Class II recetor.
-T cell receptor (TCR) of Th cell binds to MHC class II bound antigenic peptide
-TCR activates B cells by secreting chemokines such as interleukins.

Step 3: Clonal selection and Differentiation: That activated B cell  divide continuously forming clone of B cells with that specificity.
Late these B cells differentiate into Plasma cells and memory B cells.

Step 4: Plasma cells produce antibodies and are released into the blood stream that binds to the antigen and neutralize it. Thus preventing further infection
-Memory B cells produced are responsible for immunologic memory. (when the same antigen attacks the body for the second time, memory B cells recognizes it quickly and trigger an enhanced immune response, thus preventing further infection).
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