Diseases of Mushrooms

Diseases of Mushrooms

I.                   Fungal diseases:

a.      Dry Bubble disease: Caused by a fungus called Verticillum. Hence it’s also called Verticillum disease

Symptoms: whitish mycelia develop which then turn to yellowish colored. Later become grey. The infected mushroom becomes dry and show cracks

Control:

Physical: sterilization of culture

Biological : a fungus called Trichoderma is used against verticillum.

Chemical: A chemical agent called Zineb is used against this disease.

b.      Wet Bubble disease:

Also called white mold.

Pathogen: Mycogone perniciosa

Symptoms:

Stipes become thickened and gills become detached from the fruiting body. All infected parts exude water drops on the surface. So its called wet bubble.

Control:

Chemical: Benomyl spray is used to control wet bubble.

Biological:  a bacteria called Acremonium strictum is used as against this disease

Physical: Pasteurisation and sterilization.

c.       Cob web disease:

Also called Dactylium disease

Pathogen:Cladobotrynum dendroides or dactylium dendroides

Symptoms:

Cob web appears first as small patches of grey white mycelium. In dense cases of attack a dense whiote mold develops which looks like  cob web.

Control:

Physical: sterilization and Pasteurisation

Biological: leaf extracts of Ricinus (in Malayalam AAVANAKK, plz don’t write this in answer sheet!!! Aavanakk ennonnum answer sheetil ezhutharuthu.) is used

Chemical:Terraclor is used against cob web disease.

d.      Green mold disease:

Pathogen: Trichoderma ; hence disease is also called Trichoderma spot.

Symptoms: Green mycelia appear on infected parts.

Control:

Chemical: Zineb is used.

II.                 Bacterial diseases:

a.      Bacterial blotch disease:

Pathogen: Pseudomonas fluorescens

Brown spots appear on Infected area.

Control: Streptomycin is used against this disease

b.      Yellow blotch:

Pathogen: Pseudomonas agarici

Symptom: Yellow-orange patches appear at infected area.

Control:Oxytetracycline is used to control the disease.

First Genetic Map by Sturtevant

First Genetic Map by Sturtevant

Mendel's Original Published Paper on Inheritance

Mendel's Original Published Paper on Inheritance

Koch's postulates

Koch's postulates ( /ˈkoʊk/) are four criteria designed to establish a causal relationship between a causative microbe and a disease. The postulates were formulated by Robert Koch and Friedrich Loeffler in 1884 and refined and published by Koch in 1890.

Koch's postulates are:

1.   The microorganism must be found in abundance in all organisms suffering from the disease, but should not be found in healthy organisms.

2.   The microorganism must be isolated from a diseased organism and grown in pure culture.

3.   The cultured microorganism should cause disease when introduced into a healthy organism.

4.   The microorganism must be reisolated from the inoculated, diseased experimental host and identified as being identical to the original specific causative agent.

The Bergey Classification of Bacteria

The Bergey’s Manual of Systematic Bacteriology is the main resource for determining the identity of bacteria species, utilizing every characterizing aspect. First published in 1923 by David Hendricks Bergey, it is used to classify bacteria based on their structural and functional attributes by arranging them into specific familial orders.

It was published in four volumes

Volume 1 included information on all types of Gram-negative bacteria that were considered to have "medical and industrial importance."

Volume 2 included information on all types of Gram-positive bacteria.

Volume 3 deals with all of the remaining, slightly different Gram-negative bacteria, along with the archaea.

Volume 4 has information on filamentous actinomycetes and other, similar bacteria

• Bergey Division I = The Cyanobacteria (formerly the blue-green alga) - These bacteria can use light as their energy source under aerobic conditions. The use carbon dioxide and produce oxygen.
• Bergey Division II = The Bacteria (includes the photobacteria and all other classical bacteria) - See the 19 parts below.
• Archeobacteria = in the 8th Edition (1974) the archeobacteria were mixed within the 19 parts of the book. I have not yet decided how to handle these bacteria.

The Bergey Classification of Bacteria into 19 parts.

• Phototrophic Bacteria: Rhodospirillum - Rhodopseudomonas - Chromatium
• Gliding Bacteria: Myxococcus - Beggiatoa - Simonsiella - Leucothrix
• Sheathed Bacteria: Sphaerotilus - Leptothrix
• Budding / Appendaged Bacteria: Caulobacter - Gallionella
• Spirochetes: Spirochaeta - Treponema - Borrelia
• Spiral and Curved Bacteria: Spirillum - Auqaspirillum - Oceanospirillum - Bdellovibrio
• Gram-negative Aerobic Rods and Cocci: Pseudomonas - Xanthanomonas - Zoogloea - Gluconobacter - Azotobacter - Rhizobium - Agrobacterium - Halobacterium - Acetobacter
• Gram-Negative Facultative Anaerobic Rods: Escherichia - Citrobacter - Salmonella - Shigella - Klebsiella - Enterobacter - Serratia - Proteus - Yersinia - Erwinia - Vibrio - Aeromonas - Zymomonas - Chromobacterium - Flavobacterium -
• Gram-negative anaerobes: Bacteriodes - Fusobacterium - Desulfovibrio - Succinimonas
• Gram-Negative cocci: Nisseria - Branhamella - Acinetobacter - Paracoccus
• Gram-negative anaerobic cocci: Veillonella - Acidaminococcus
• Gram-Negative Chemolithotrophic: Nitrobacter - Thiobacillus - Siderocapsa
• Methane producing:
• Gram-Positive Cocci: Micrococcus - Staphylococcus - Streptococcus - Leuconostoc - Pediococcus - Aerococcus - Peptococcus - Ruminococcus - Sarcina
• Endospore-forming Rods and cocci: Bacillus - Clostridium - Sporosarcina
• Gram-positive, non-sporing rods: Lactobacillus - Listeria - Erysipelothrix - Caryophanon
• Actinomycetes and Related: Corynebacterium - Arthobacter - Brevibacterium - Cellumonas - Kurthia - Propionibacterium - Eubacterium - Actinomyces - Archina - Bifidiobacterium - Rothia - Mycobacterium - Frankia - Streptosporangia - Nocardia - Streptomyces - Streptoverticillium - Micromonospora
• Rickettsias: Rickettsia - Erhlichia - Wollbachia - Bartonella - Chlamydia
• Mycoplasmas: Mycoplasma - Acoleplasma - Thermplasma – Spiroplasma

History of Cell Biology

1595 – Jansen credited with 1st compound microscope
1655 – Hooke described ‘cells’ in cork.
1674 – Leeuwenhoek discovered protozoa. He saw bacteria some 9 years later.
1833 – Brown descibed the cell nucleus in cells of the orchid.
1838 – Schleiden and Schwann proposed cell theory.
1840 – Albrecht von Roelliker realized that sperm cells and egg cells are also cells.
1856 – N. Pringsheim observed how a sperm cell penetrated an egg cell.
1858 – Rudolf Virchow (physician, pathologist and anthropologist) expounds his famous conclusion: omnis cellula e cellula, that is cells develop only from existing cells [cells come from preexisting cells]
1857 – Kolliker described mitochondria.
1879 – Flemming described chromosome behavior during mitosis.
1883 – Germ cells are haploid, chromosome theory of heredity.
1898 – Golgi described the golgi apparatus.
1938 – Behrens used differential centrifugation to separate nuclei from cytoplasm.
1939 – Siemens produced the first commercial transmission electron microscope.
1952 – Gey and coworkers established a continuous human cell line.
1955 – Eagle systematically defined the nutritional needs of animal cells in culture.
1957 – Meselson, Stahl and Vinograd developed density gradient centrifugation in cesium chloride solutions for separating nucleic acids.
1965 – Ham introduced a defined serum-free medium. Cambridge Instruments produced the first commercial scanning electron microscope.
1976 – Sato and colleagues publish papers showing that different cell lines require different mixtures of hormones and growth factors in serum-free media.
1981 – Transgenic mice and fruit flies are produced. Mouse embryonic stem cell line established.
1995 – Tsien identifies mutant of GFP with enhanced spectral properties
1998 – Mice are cloned from somatic cells.
1999 – Hamilton and Baulcombe discover siRNA as part of post-transcriptional gene silencing (PTGS) in plants

First Cells Seen in Cork

While the invention of the telescope made the Cosmos accessible to human observation, the microsope opened up smaller worlds, showing what living forms were composed of. The cell was first discovered and named by Robert Hooke in 1665. He remarked that it looked strangely similar to cellula or small rooms which monks inhabited, thus deriving the name. However what Hooke actually saw was the dead cell walls of plant cells (cork) as it appeared under the microscope. Hooke’s description of these cells was published in Micrographia. The cell walls observed by Hooke gave no indication of the nucleus and other organelles found in most living cells. The first man to witness a live cell under a microscope was Anton van Leeuwenhoek, who in 1674 described the algae Spirogyra. Van Leeuwenhoek probably also saw bacteria.

Formulation of the Cell Theory

In 1838, Theodor Schwann and Matthias Schleiden were enjoying after-dinner coffee and talking about their studies on cells. It has been suggested that when Schwann heard Schleiden describe plant cells with nuclei, he was struck by the similarity of these plant cells to cells he had observed in animal tissues. The two scientists went immediately to Schwann’s lab to look at his slides. Schwann published his book on animal and plant cells (Schwann 1839) the next year, a treatise devoid of acknowledgments of anyone else’s contribution, including that of Schleiden (1838). He summarized his observations into three conclusions about cells:

1.    The cell is the unit of structure, physiology, and organization in living things.

2.    The cell retains a dual existence as a distinct entity and a building block in the construction of organisms.

3.    Cells form by free-cell formation, similar to the formation of crystals (spontaneous generation).

We know today that the first two tenets are correct, but the third is clearly wrong. The correct interpretation of cell formation by division was finally promoted by others and formally enunciated in Rudolph Virchow’s powerful dictum, Omnis cellula e cellula,: “All cells only arise from pre-existing cells”.

Modern Cell Theory

1.    All known living things are made up of cells.

2.    The cell is structural & functional unit of all living things.

3.    All cells come from pre-existing cells by division. (Spontaneous Generation does not occur).

4.    Cells contains hereditary information which is passed from cell to cell during cell division.

5.    All cells are basically the same in chemical composition.

6.    All energy flow (metabolism & biochemistry) of life occurs within cells.

As with the rapid growth of molecular biology in the mid-20th century, cell biology research exploded in the 1950′s. It became possible to maintain, grow, and manipulate cells outside of living organisms. The first continuous cell line to be so cultured was in 1951 by George Otto Gey and coworkers, derived from cervical cancer cells taken from Henrietta Lacks, who died from her cancer in 1951. The cell line, which was eventually referred to as HeLa cells, have been the watershed in studying cell biology in the way that the structure of DNA was the significant breakthrough of molecular biology.

In an avalanche of progress in the study of cells, the coming decade included the characterization of the minimal media requirements for cells and development of sterile cell culture techniques. It was also aided by the prior advances in electron microscopy, and later advances such as development of transfection methods, discovery of green fluorescent protein in jellyfish, and discovery of small interfering RNA (siRNA), among others.

Chi-Square test

Chi-square is a statistical test commonly used to compare observed data with data we would expect to obtain according to a specific hypothesis. For example, if, according to Mendel's laws, you expected 10 of 20 offspring from a cross to be male and the actual observed number was 8 males, then you might want to know about the "goodness to fit" between the observed and expected. Were the deviations (differences between observed and expected) the result of chance, or were they due to other factors. How much deviation can occur before you, the investigator, must conclude that something other than chance is at work, causing the observed to differ from the expected. The chi-square test is always testing what scientists call the null hypothesis, which states that there is no significant difference between the expected and observed result. 

The formula for calculating chi-square ( χ²) is:

χ²= Σ (o-e)²/e

That is, chi-square is the sum of the squared difference between observed (o) and the expected (e) data (or the deviation, d), divided by the expected data in all possible categories. 

For example, suppose that a cross between two pea plants yields a population of 880 plants, 639 with green seeds and 241 with yellow seeds. You are asked to propose the genotypes of the parents. Your hypothesis is that the allele for green is dominant to the allele for yellow and that the parent plants were both heterozygous for this trait. If your hypothesis is true, then the predicted ratio of offspring from this cross would be 3:1 (based on Mendel's laws) as predicted from the results of the Punnett square 

Eg:i f the ratio is 3:1 and the total number of observed individuals is 880, then the expected numerical values should be 660 green and 220 yellow. 

 Note that we get a value of 2.668

1. Determine degrees of freedom (df). Degrees of freedom can be calculated as the number of categories in the problem minus 1. In our example, there are two categories (green and yellow); therefore, there is I degree of freedom.

2. Determine a relative standard to serve as the basis for accepting or rejecting the hypothesis. The relative standard commonly used in biological research is p >0.05. The p value is the probability that the deviation of the observed from that expected is due to chance alone (no other forces acting). In this case, using p >0.05, you would expect any deviation to be due to chance alone 5% of the time or less.

3. Refer to a chi-square distribution table (Table B.2). Using the appropriate degrees of 'freedom, locate the value closest to your calculated chi-square in the table. Determine the closestp (probability) value associated with your chi-square and degrees of freedom. In this case (χ²=2.668), the p value is about 0.10, which means that there is a 10% probability that any deviation from expected results is due to chance only. Based on our standard p > 0.05, this is within the range of acceptable deviation. In terms of your hypothesis for this example, the observed chi-squareis not significantly different from expected. The observed numbers are consistent with those expected under Mendel's law.

Interference and coincidence

In genetics, the coefficient of coincidence (c.o.c.) is a measure of interference in the formation of chromosomal crossovers during meiosis. It is generally the case that, if there is a crossover at one spot on a chromosome, this decreases the likelihood of a crossover in a nearby spot. This is called interference.

The coefficient of coincidence is typically calculated from recombination rates between three genes. If there are three genes in the order A B C, then we can determine how closely linked they are by frequency of recombination. Knowing the recombination rate between A and B and the recombination rate between B and C, we would naively expect the double recombination rate to be the product of these two rates.

The coefficient of coincidence is calculated by dividing the actual frequency of double recombinants by this expected frequency

c.o.c. = actual double recombinant frequency / expected double recombinant frequency

Interference is then defined as follows

interference = 1 - c.o.c.

This figure tells us how strongly a crossover in one of the DNA regions (AB or BC) interferes with the formation of a crossover in the other region.

Mendelian genetics Notes

Mendel's First Law of Genetics (Law of Segregation)

Genetic analysis predates Gregor Mendel, but Mendel's laws form the theoretical basis of our understanding of the genetics of inheritance.

Mendel made two innovations to the science of genetics:

1.   developed pure lines

2.   counted his results and kept statistical notes

Pure Line - a population that breeds true for a particular trait [this was an important innovation because any non-pure (segregating) generation would and did confuse the results of genetic experiments]

Results from Mendel's Experiments

Parental Cross	F1Phenotype	F2 Phenotypic Ratio	F2Ratio
Round x Wrinkled Seed	Round	5474 Round:1850 Wrinkled	2.96:1
Yellow x Green Seeds	Yellow	6022 Yellow:2001 Green	3.01:1
Red x White Flowers	Red	705 Red:224 White	3.15:1
Tall x Dwarf Plants	Tall	l787 Tall:227 Dwarf	2.84:1

Terms and Results Found in the Table

Phenotype - literally means "the form that is shown"; it is the outward, physical appearance of a particular trait

Mendel's pea plants exhibited the following phenotypes:

• - round or wrinkled seed phenotype
• - yellow or green seed phenotype
• - red or white flower phenotype
• - tall or dwarf plant phenotype

Seed Color: Green and yellow seeds.

Seed Shape: Wrinkled and Round seeds.

What is seen in the F₁ generation? We always see only one of the two parental phenotypes in this generation. But the F₁ possesses the information needed to produce both parental phenotypes in the following generation. The F₂ generation always produced a 3:1 ratio where the dominant trait is present three times as often as the recessive trait. Mendel coined two terms to describe the relationship of the two phenotypes based on the F₁ and F₂ phenotypes.

Dominant - the allele that expresses itself at the expense of an alternate allele; the phenotype that is expressed in the F₁ generation from the cross of two pure lines
Recessive - an allele whose expression is suppressed in the presence of a dominant allele; the phenotype that disappears in the F₁ generation from the cross of two pure lines and reappears in the F₂ generation

Mendel's Conclusions

1.   The hereditary determinants are of a particulate nature. These determinants are called genes.

2.   Each parent has a gene pair in each cell for each trait studied. The F₁ from a cross of two pure lines contains one allele for the dominant phenotype and one for the recessive phenotype. These two alleles comprise the gene pair.

3.   One member of the gene pair segregates into a gamete, thus each gamete only carries one member of the gene pair.

4.   Gametes unite at random and irrespective of the other gene pairs involved.

Mendelian Genetics Definitions

• Allele - one alternative form of a given allelic pair; tall and dwarf are the alleles for the height of a pea plant; more than two alleles can exist for any specific gene, but only two of them will be found within any individual
• Allelic pair - the combination of two alleles which comprise the gene pair
• Homozygote - an individual which contains only one allele at the allelic pair; for example DD is homozygous dominant and dd is homozygous recessive; pure lines are homozygous for the gene of interest
• Heterozygote - an individual which contains one of each member of the gene pair; for example the Dd heterozygote
• Genotype - the specific allelic combination for a certain gene or set of genes

Using symbols we can depict the cross of tall and short pea plants in the following manner:

The F₂ generation was created by selfing the F₁ plants. This can be depicted graphically in a Punnett square. From these results Mendel coined several other terms and formulated his first law. First the Punnett Square is shown.

	D	d
D	DD (Tall)	Dd (Tall)
d	Dd (Tall)	dd (Short)

The Punnett Square allows us to determine specific genetic ratios.
Genotypic ratio of F₂: 1 DD : 2 Dd : 1 dd (or 3 D_ : 1 dd)
Phenotypic ratio of F₂: 3 tall : 1 dwarf

Mendel's First Law - the law of segregation; during gamete formation each member of the allelic pair separates from the other member to form the genetic constitution of the gamete

Confirmation of Mendel's First Law Hypothesis
With these observations, Mendel could form a hypothesis about segregation. To test this hypothesis, Mendel selfed the F₂ plants. If his law was correct he could predict what the results would be. And indeed, the results occurred has he expected.

From these results we can now confirm the genotype of the F₂ individuals.

Phenotypes	Genotypes	Genetic Description
F2 Tall Plants	1/3 DD 2/3 Dd	Pure line homozygote dominant Heterozygotes
F2 Dwarf Plants	all dd	Pure line homozygote recessive

Thus the F₂ is genotypically 1/4 Dd : 1/2 Dd : 1/4 dd

This data was also available from the Punnett Square using the gametes from the F₁ individual. So although the phenotypic ratio is 3:1 the genotypic ratio is 1:2:1

Mendel performed one other cross to confirm the hypothesis of segregation --- the backcross. Remember, the first cross is between two pure line parents to produce an F₁ heterozygote.

At this point instead of selfing the F₁, Mendel crossed it to a pure line, homozygote dwarf plant.

Backcross: Dd x dd

		Male Gametes
		d
Female Gametes	D	Dd (Tall)
	d	dd (Short)

Backcross One or (BC₁) Phenotypes: 1 Tall : 1 Dwarf

BC₁ Genotypes: 1 Dd : 1 dd

Backcross - the cross of an F₁ hybrid to one of the homozygous parents; for pea plant height the cross would be Dd x DD or Dd x dd; most often, though a backcross is a cross to a fully recessive parent
Testcross - the cross of any individual to a homozygous recessive parent; used to determine if the individual is homozygous dominant or heterozygous
So far, all the discussion has concentrated on monohybrid crosses.
Monohybrid cross - a cross between parents that differ at a single gene pair (usually AA x aa)
Monohybrid - the offspring of two parents that are homozygous for alternate alleles of a gene pair
Remember --- a monohybrid cross is not the cross of two monohybrids.
Monohybrids are good for describing the relationship between alleles. When an allele is homozygous it will show its phenotype. It is the phenotype of the heterozygote which permits us to determine the relationship of the alleles.
Dominance - the ability of one allele to express its phenotype at the expense of an alternate allele; the major form of interaction between alleles; generally the dominant allele will make a gene product that the recessive can not; therefore the dominant allele will express itself whenever it is present

Mendel's Law of Independent Assortment

To this point we have followed the expression of only one gene. Mendel also performed crosses in which he followed the segregation of two genes. These experiments formed the basis of his discovery of his second law, the law of independent assortment. First, a few terms are presented.

Dihybrid cross - a cross between two parents that differ by two pairs of alleles (AABB x aabb)

Dihybrid- an individual heterozygous for two pairs of alleles (AaBb)

Again a dihybrid cross is not a cross between two dihybrids. Now, let's look at a dihybrid cross that Mendel performed.

Parental Cross: Yellow, Round Seed x Green, Wrinkled Seed

F₁ Generation: All yellow, round

F₂ Generation: 9 Yellow, Round, 3 Yellow, Wrinkled, 3 Green, Round, 1 Green, Wrinkled

At this point, let's diagram the cross using specific gene symbols.

Choose Symbol	Seed Color: Yellow = G; Green = g
	Seed Shape: Round = W; Wrinkled = w

The dominance relationship between alleles for each trait was already known to Mendel when he made this cross. The purpose of the dihybrid cross was to determine if any relationship existed between different allelic pairs.

Let's now look at the cross using our gene symbols.

Now set up the Punnett Square for the F₂ cross.

		Female Gametes
		GW	Gw	gW	gw
Male Gametes	GW	GGWW  (Yellow, round)	GGWw  (Yellow, round)	GgWW  (Yellow, round)	GgWw  (Yellow, round)
	Gw	GGWw  (Yellow, round)	GGww  (Yellow, wrinkled)	GgWw  (Yellow, round)	Ggww  (Yellow, wrinkled)
	gW	GgWW  (Yellow, round)	GgWw  (Yellow, round)	ggWW  (Green, round)	ggWw  (Green,
	gw	GgWw  (Yellow, round)	Ggww  (Yellow, wrinkled)	ggWw  (Green, round)	ggww  (Green, wrinkled)

The phenotypes and general genotypes from this cross can be represented in the following manner:

Phenotype	General Genotype
9 Yellow, Round Seed	G_W_
3 Yellow, Wrinkled Seed	G_ww
3 Green, Round Seed	ggW_
1 Green, Wrinkled Seed	ggww

The results of this experiment led Mendel to formulate his second law.
Mendel's Second Law - the law of independent assortment; during gamete formation the segregation of the alleles of one allelic pair is independent of the segregation of the alleles of another allelic pair
As with the monohybrid crosses, Mendel confirmed the results of his second law by performing a backcross - F₁dihybrid x recessive parent.
Let's use the example of the yellow, round seeded F₁.

                            Punnett Square for the Backcross

	Female Gametes
		GW	Gw	gW	gw
Male Gametes	gw	GgWw (Yellow, round)	Ggww (Yellow, wrinkled)	ggWw (Green, round)	ggww (Green, wrinkled

		Female Gametes
		GW	Gw	gW	gw
Male Gametes	gw	GgWw (Yellow, round)	Ggww (Yellow, wrinkled)	ggWw (Green, round)	ggww (Green, wrinkled

The phenotypic ratio of the test cross is:

• 1 Yellow, Round Seed
• 1 Yellow, Wrinkled Seed
• 1 Green, Round Seed
• 1 Green, Wrinkled Seed

Backcross with a recessive is called test cross