Welcome to JAAN's science class!!

Big hi to all of you! I'm an undergraduate following a Bsc in bioscience. Trust me I know the feeling of surfing around the net for ages and getting nothing in return! Or getting something worthless for the time we spent surfing. So I started this blog adding the science stuff I have noted which I think might help someone in their home work. Ok then enjoy!
Showing posts with label bioscience. Show all posts
Showing posts with label bioscience. Show all posts

01 January 2014

Mushroom poisoning

Ingestion of potentially poisonous mushrooms leads to the harmful health effect of mushroom poisoning which is also known as Mycetism. Previous experience and observation make it possible to discriminate between poisonous and non-poisonous mushrooms. Depending on the type of mushroom, the adverse effects range from mild gastrointestinal (GI) symptoms to major cytotoxic effects resulting in organ failure and death. Toxicity may also vary depending on the amount and age of the mushroom, the season, the geographic location and the way in which the mushroom was prepared prior to ingestion. Consumption of poisonous mushrooms can cause various types of reactions, such as allergic gastroenteritis, psychological relaxation and fatal liver intoxication. Mushroom poisoning occurs among four main groups of individuals: young children who ingest mushrooms inadvertently, wild-mushroom foragers, individuals attempting suicide or homicide and individuals looking for a hallucinatory high. Mushroom poisoning cannot be made nontoxic by cooking, freezing or any other way other than avoiding the consumption of the poisonous species.

i.                    Protoplasmic poisoning
Poisoning by the poisonous mushrooms can severely affect the protoplasm of cell resulting disturbances in the essential life functions of a cell. Chemical toxins such as Amatoxins, Hydrazines and Orelanine in mushrooms cause the protoplasmic poisoning.
  • Amatoxins

Amatoxins (cyclic octapeptides) represent 1 of the 3 major groups of cyclopeptides (in addition to phallotoxins and virotoxins); they are heat-stable, insoluble in water, and not destroyed by drying. The most significant of these are the alpha and beta subtypes of amanitin. Currently 10 types of amatoxins are recognized.
α-Amanitin                        Amanullin                               
Amanullinic acid               Proamanullin
Amaninamide                   Amanin
β-Amanitin                        γ-Amanitin                  ε-Amanitin     
Mushrooms that contain amatoxins;
-       Death cap: Amanita phalloides
Native to Europe. The smell has been described as initially faint and honey-sweet, but strengthening with time. Introduced to Africa, North America and Australia by importation of hardwoods and conifers especially Oak which the mushroom is associated with.
-        Destroying angel: Amanita bisporigera, A. ocreata, A. virosa
Amanita bisporigera and A. ocreata can be found in North America while A. virosa is native to Europe. Can be mistaken to button and horse mushrooms.
-        Fool’s mushroom: Amanita verna
Found in Europe.
-        Autumn skullcap: Galerina autumnalis
Found throughout the world but especially in America. Commonly grows on wood, and when on the ground when it has preference to mossy habbitats.

  • Hydrazines

False morel mushrooms contains a carcinogenic hydrazine, gyromitrin. It is unstable and is easily hydrolyzed to the toxic compound monomethylhydrazine. Consuming a large amount of gyromitrin can in worst case cause liver damage leading to death. Most of this toxin is removed when the mushroom is double boiled and rinsed, rendering it relatively safe for consumption. Main species of false morel is Gyromitra esculenta which is widely distributed in Europe in North America.

  • Orellalnine

A mycotoxin which is a pyridine N-oxide. An intense, burning thirst (polydipsia) and excessive urination (polyuria) are the first symptoms. This may be followed by nausea, headache, muscular pains, chills, spasms, and loss of consciousness. In severe cases, severe renal tubular necrosis and kidney failure may result in death (15%) several weeks after the poisoning. Caused by the Sorrel Webcap mushroom (Cortinarius orellanus) and some of its relatives.

ii.                  Neurotoxins
Poisonings by mushrooms that cause neurological problems are divided into three groups, based on the type of symptoms produced, and named for the substances responsible for these symptoms.
  • Muscarine Poisoning

This is due to the substance Muscarine which is particularly found in Inocybe and Clitocybe mushroom species. It is a highly toxic alkaloid related to the cholines and nonselective agonist of the muscarinic acetylcholine receptor. Within 15 to 30 minutes after ingestion of the mushroom increased salivation, perspiration, and lacrimation occur. Abdominal pain, severe nausea, diarrhea, blurred vision and breathing difficulties occur with large doses.
  • Ibotenic acid/Muscimol Poisoning

Ibotenic acid is a powerful neurotoxic isoxazole substance and Muscimol is a psychoactive alkaloid. Both substances cause the same effects, but muscimol is approximately 5 times more effective than ibotenic acid. Naturally occurring in Fly Agaric (Amanita muscaria) and Panthercap (Amanita pantherina) mushrooms Drowsiness and dizziness are the main symptoms of this type of poisoning.
  • Psilocybin Poisoning

Psilocybin is a tryptamine compound with a chemical structure containing an indole ring linked to an ethylamine substituent. It is structurally similar to the neurotransmitter serotonin. This is a naturally occurring toxin in mushrooms known as Psilocybin mushrooms. When consumed this cause a syndrome similar to alcohol intoxication.

iii.                Gastro-Intestinal irritants
The gastrointestinal irritants are the least defined and most widespread of the mushroom toxins.  Symptoms are mild, short-lived stomach discomfort to vomiting and diarrhea. The specific responsible toxins are generally unknown, but can be due to mushrooms of unusual sugars, amino acids, peptides, resins, and other compounds. Ex: Green Gill (Chlorophyllum molybdites), Tigertop (Tricholoma pardinum), Jack O'Lantern (Omphalotus illudens), Naked Brimcap (Paxillus involutus), Sickener (Russula emetica)

iv.                Disulfiram-like poisoning
The disulfiram-like compound coprine, an amino acid produced by mushrooms of the genus Coprinus, notably C. atramenarius, the Alcohol Inky causes this type of poisoning. Coprine is converted to cyclopropanone hydrate in the human body. This compound interferes with the breakdown of alcohol. The symptoms are generally mild, consisting of flushing of the head and neck, tingling of the extremities, heart palpitations, headache and nausea.  It is regarded as edible, with caution as  it has no adverse side effects if alcohol is not consumed for about three days.

v.                  Miscellaneous poisoning

Young fruiting bodies of the sulfur shelf fungus Laetiporus sulphureus are regarded as edible but ingestion of it has caused digestive problems and allergies in some people. It is recommended not to it in raw form. 

Aflatoxins
Aflatoxin belongs to a group of fungal toxins known as mycotoxins, and is widespread in agricultural products and food.

Toxin producing agent:  Produced primarily by the fungi Aspergillus;
·         Aspegillus flavus
·         parasiticus
·         nomius and A. niger

Associated food: Corn, figs, nuts, cereals, milk and milk products, peanuts, cottonseed, spices.


Characteristics and chemical mechanism of the toxin:
·        
Classified into a number of subtypes. The most important ones are B1, B2, G1 and G2, distinguished by their fluorescent colour under ultraviolet light. In addition, aflatoxin M1 and M2 are hydroxylated metabolites of aflatoxin B1 and B2.
·         Odourless, tasteless and colourless.
·         Chemically stable in foods and resistant to degradation under normal cooking procedures.
·         Accumulation is dependent upon weather conditions. Before harvest, the risk for the development of aflatoxin is greatest during major droughts as the number of Aspergillus spores in the air increases. These spores infect crops through areas of damage caused by insects, and inclement weather. Once infected, plant stress occurs; the production of aflatoxin is favoured. During post-harvest stage, production of aflatoxin can be worsened under storage conditions such as hot and humid storage atmosphere.

Natural occurrence:
·         Aspergillus sp infect agricultural supplies either before harvest or at post-harvest stages under favourable conditions of temperature and humidity.
·         The aflatoxigenic moulds are mainly found in soils and decaying vegetation.
·         Occur in warmer parts of the world such as tropical/sub-tropical regions where temperature and moisture are high.
·         Milk, eggs, and meat products can be contaminated because of the animal consumption of aflatoxin-contaminated feed.

Impact:
·         Associated with both acute and chronic toxicity in animals and humans.
·         Include acute liver damage, liver cirrhosis, and liver cancers. Symptoms may include fever, vomiting and jaundice.
·         Chronic toxicity associated with consumption of low dose aflatoxin mainly in peanuts and grains.
·         Epidemiologically implicated as a carcinogen in humans and an environmental contaminant which is widespread in nature.
·         Recent medical research indicates that a regular diet including apiaceous vegetables such as carrots, parsnips and parsley, may reduce the carcinogenic effects of aflatoxin.
·         Aflatoxin B1 can permeate through the skin. Dermal exposure to these aflatoxin in particular environmental conditions can lead to serious health risks.
·         As aflatoxin B1 can cause immune suppression, exposure is associated with an increased viral load in HIV positive individuals.

20 September 2012

Biology of two common phyto-pathogenic Oomycetes


Phytophthora infestans
Obligate parasite.
Infect potatoes and tomatoes with late blight disease.

imageslateblight
downloadpotato   

Life cycle
Mycelium:  Non septate, coenocytic

Asexual reproduction
In the host tissue inter-cellular somatic hyphae colonizes and club shaped haustorias penetrate the tissues, feeding the parasite.
Sporangiophores are produced from the hyphae and emerge through stomata.
Sporangiophores produce lemon-shaped sporangia laterally and at the terminal end/apex of the sporangiphore. A Sporangium possesses a papilla on its tip.
Outcome of the sporangium depends on the temperature and humidity.
Low humidity or high temperature: Sporangium germinates by a germ tube that later results the somatic hapha.  
High humidity (when raining) or low temperature (120C or below: Cytoplasm of the sporangium divides and gives rise to biflagellate Zoospores. Either by dissolution of papilla or through its opening tip, zoospores are released to outside. Zoospores directly penetrate host tissue and undergo encystment in cells. They develop into germ tubes that later result the hyphae.
Sexual reproduction
Plasmogamy occurs as oogonium punches the antheridium, going through that antheridium, oogonium grows above it. The antheridium therefore appears as a funnel at the base around the oogonium. Karyogamy and meiosis occurs respectively. Oospore is spherical and adapted to adverse environmental conditions. It results out a sporangiophore that again develops into a sporangium.

photo
via www.apsnet.org


Plasmopara viticola
Obligate parasite.
Infect grape vines with Downy mildews.

imagesgrapes

Life Cycle
Mycelium is non septate and coenocytic.
Life cycle is much similar to Phytophthora infestans as both are oomycites.

Asexual reproduction
Somatic hyphae develops in inter cellular space host tissue penetrating with haustoria.
Hyphae give rise to sporangiophores that emerge through stomata, branching and producing sporangia at each apex of the branches.
Sporangia may either germinate directly into mycelium or produce kidney shaped, biflagellate zoospores, depending on humidity and temperature just like the Phytophthora infestans. Zoospores encyst in cells, germinate and result the somatic hyphae.
Sexual reproduction
Sexual phase is taken place at unfavorable conditions. Plasmogamy occurs by gametangial copulation as oogonium and anthredium come close together. Karyogamy results zygote that later gives the spherical oospore. Oospore divides by meiosis and undergoes germination producing a sporangium.



13 July 2012

Insect Abdomen: Appendages found on the abdomen


Insect abdomen is the third functional region of insect body. It is located behind the thorax and contains 6-10 segments. There are various types of appendages arise from the abdomen.

Cerci
Located close to anus.

-Blattodea: simple and jointed cerci
ediacaran.mech.northwestern.edu
Via ediacaran.mech.northwestern.edu


-Orthoptera: simple and not jointed cerci
-Dermaptera: Sclerotized, forceps like cerci
gallurapestcontrol.com
Dermaptera forcep like cerci via gallurapestcontrol.com

-Thysanura: Long filamentous cerci
untitled
Long filamentous cerci of Thysanura

-Ephemeroptera larvae: Wing like cerci that helps to move forward in water.
untitled
Wing like cerci -Ephemeroptera larva

Styles
Can be seen in Cockroach and Lepisma. It is regarded as the vestige of the walking limb.
microscopy-uk.org.uk
via microscopy-uk.org.uk

Median caudal filament
This is a thread like projection arising from he center of the last abdominal segment between the cerci.
untitled

Abdominal Prolegs
Can be seen in Lepidopera.
entomology.umn.edu
via entomology.umn.edu
images (1)

Abdominal Gills
These are respiratory organs and found in nymphs of some aquatic insects.
untitled

Cornicles
These are located dorsally on the abdomen as paired secretory structures.
images (2)      images (3)

Female External Genitalia
Ovipositors are used for oviposition and it is formed by the modification of 8-9 abdominal segments. Thysanura, Orthoptera, Thysanoptera and some Hymenoptera insects contain true ovipositors.
images (5)
Ovipositor places egg inside caterpillar 
naturecloseups.com
Egg is released (naturecloseups.com)

-The ovipositor is modified as a poison injecting sting ( Wasps, bees..etc)
amazingnature.us
via amazingnature.us
-Hind end of the abdomen is extended to work as an ovipositor

Male genitalia
Modification of 9th abdominal segment makes the copulatory organ of males which is consist of aedeagus and pair of lateral claspers to grasp and hold the abdomen of the female during mating. 

25 June 2012

Polymerase Chain Reaction ( PCR )


This is a method to produce very large numbers of copies of specific DNA sequences without cloning. Therefore PCR can amplify specific sequences or add sequences such as  endonuclease  recognition  sequences as primers to cloned DNA.

PCR consists of 5 main components.
-Target DNA
-Single stranded Oligonucleotides (primers)
-d NTPs (dATP, dCTP, dTTP, dGTP)
-Taq DNA polymerase
-Termocycler

There are three main steps in PCR.

Step1:  Denaturation. The mixture of excess primer and DNA fragment is heated to about 95° C causing the double strands of target DNA to be denatured into single strands.

Step 2: Annealing of Primers. The temperature is dropped down between about 350- 65°C
As the temperature decreases the single strands of DNA reassociate into double strands. Large excess of primer allows two primers anneal or bind to their complementary sequences on the target DNA leaving the rest of the fragment single-stranded.

Step 3: Primer Extension. The temperature is raised to 700- 75°C Taq  polymerase is added. Taq polymerase extends the primer into a complementary copy of the entire single-stranded fragment, in the 5’-3’ direction.  As both the DNA strands are replicated, two copies of the original fragment are gained.

This process is repeated many times. At each time, the number of DNA copies doubles. This is continued until enough copies are gained for the analysis. 


photo





23 June 2012

Different kinds of bacteriophages (phages)


M13
Filamentous.
About 870nm in length and 6nm in width.
Consists of single stranded DND (ssDNA).
Three kinds of capsomeres build the capside.
Infects E. coli by adsorbing to the cell and entering through F pilli. Therefore only infect F+ and HFr cells. Also male specific.
Does not kill the host. Particles are released by budding, therefore when the particles are released, the host cell is alive.
An efficient vector in gene cloning as it can hold longer pieces of foreign DNA.

T phage
Structure is composed of icosahedral head, double stranded DNA and a tail.
Infects E.coli
 Main types of T phages are T2, T4 and T12.
In the infection linear DNA of the phage is released to the host cell and becomes circular by replicating that later produces a long DNA chain known as ‘Concatamen’. This coils into the phage’s head by headfull mechanism while packaging.
Infection kills the host cell as the new particles are released outside by bursting the host cell.

Lambda (λ)
Composed of head and tail.
Head is consisting of double stranded linear DNA.
At both 5’ ends of the DNA strand, 12 complementary base pair, single stranded segments are present. These two ends are known as “cos ends”.
Because of the cos ends, phage chromosome circularizes before replication. Concatamen is produced during the replication and during the packaging, Terminase enzyme cuts off the cos ends.
Host cell is E.coli.

MS2
Contains the smallest known genome.
Super coiled single stranded DNA.
Infect only through sex pilli. Therefore male specific.
Infect E.coli.

Phi×174(ΦX174)
Contains a single stranded circular DNA.
After adsorption, synthesizes the complementary strand and becomes double stranded.
Use as a positive control in DNA sequencing.

G4
Structurally similar to ΦX174 phage.
Can infect susceptible E.coli cells. 



06 May 2012

Serotonin the neurotransmitter


Serotonin i.e. 5-hydroxytryptamine (5-HT) is a monoamine neurotransmitter that is said to be helping to relay signals from one area of the brain to another. However its primary functions are found in gastrointestinal tract as 90% of total serotonin is located in the enterochromaffin cells in the gut. 

Serotonin is made via a unique biochemical conversion process that begins with Tryptophan. Tryptophan is a building block to proteins. In the synthesis of serotonin, Tryptophan hydroxylase the enzyme combines with tryptophan to form 5-hydroxytryptophan metabolite that later converts to Serotonin.

 On top a L-tryptophan molecule with an arrow down to a 5-HTP molecule.  Tryptophan hydroxylase catalyses this reaction with help of O2 and tetrahydrobiopterin which becomes water and dihydrobiopterin. From the 5-HTP molecule goes an arrow down to a serotonin molecule. Aromatic L-amino acid decarboxylase or 5-Hydroxytryptophan decarboxylase catalyses this reaction with help of pyridoxal phosphate. From the serotonin molecule goes an arrow to a 5-HIAA molecule at the bottom ot the image. Monoamine oxidase catalyses this reaction, in the process O2 and water is consumed, and ammonia and hydrogen peroxide is produced.
Via wikipedia.org

As mentioned earlier serotonin helps to distribute messages across the brain. Brain cells related to mood, appetite, sleep, memory, learning, temperature regulation, sexual desire and some social behaviour are influenced either directly or indirectly by serotonin due to the widespread distribution in the brain. 
It can also affect the functioning of the cardiovascular system, muscles, and various elements in the endocrine system.

When it comes to mental health, it is widely believed that a serotonin deficiency plays a role in depression but there is no way to measure its levels in the living brain. Therefore, there have not been any studies proving that brain levels of this or any neurotransmitter are in short supply when depression or any mental illness develops. People who suffer from depression shows lower serotonin levels in blood levels but still it is not revealed that whether the blood levels reflect the brain's level of serotonin.

Antidepressant medications such as SSRIs (selective serotonin reuptake inhibitors) and SNRIs (serotonin and norepinephrine reuptake inhibitors) that work on serotonin levels are believed to lower the symptoms of depression, but their exact function is not fully understood.

Recent studies show that when the Mycobacterium vaccae, which occurs naturally in soil and is often breathed in when spending much time nature, is injected into mice, it stimulates neuron growth and causes serotonin levels in blood to increase. So that the bacteria could have antidepressant benefits but it is not yet revealed whether it has an effect on human.


02 May 2012

Simple facts about Betalain


Betalains are alkaloid pigments which are found in some families of plants belonging to the order Caryophyllales, but in no other plants.
They are named after the Beet family of plants (Beta).


photo


Betalains are not found in plants containing anthocyanin pigments. Structurally they are unrelated. Unlike anthocyanins, they are not pH indicators as their colour is stable over a wide range of pH.  They are oxidised over time going brown in colour. This can be prevented by 0.1% ascorbic acid.

They have also been found in some fungi too e.g. Fly Agaric (mushroom)
Betalains can be divided into two types as betacyanins and betaxanthins; based upon their molecular structure.
Betacyanins
Usually appear red to red violet in colour (absorbance in 535-550nm)

Betaxanthins
Usually appear yellow in colour (absorbance in 475-480nm)

Betalains are found in the vacuole and they are water-soluble.
Also they cause colour in both flowers, fruits and sometimes vegetative organs
Beetroot contains 2 Betacyanins. Thay are Betanin and a derivative.

Not much is known about the role of betalains. Commercially they are sometimes used as food colourants. As a food dye it’s cheap and no all allergic side effects are figured out yet.

Basic structure of betalain



21 March 2012

Physiology of Synapse:- Excitatory synapses and Inhibitory synapses


Synapse is simply a junction between two neurons. There are two types of synapses in central nervous system.
·         Excitatory synapses
·         Inhibitory synapses


Excitatory synapses
Pre synaptic knob secretes as excitatory substance. (Ex: Acetyl choline, Noradrinalin, Gutamic acid)

Transmission:

Nerve impulse à pre synaptic knob releases acetyl choline (Ach)àAch diffuse across synaptic cleftàAch combine with receptor sites of post synaptic membraneàpermeability of post synaptic membrane changesà permeability to Na+ increases and Na+ enter the post synaptic knobà Excitatory post synaptic potential (EPSP) is obtainedàthreshold potential is reachedà action potential is formedà distribution of action potential

A combined EPSP depolarize the membrane to a threshold value to generate an action potential is known as summation. Summation can occur in two ways as temporal summation which is obtained by repeat discharge of single pre synaptic knob and spatial summation which is obtained by numerous pre synaptic knobs.

Inhibitory synapses
Pre synaptic knob secretes an inhibitory substance. (Ex: alpha butric acid and glycine)
This inhibitory synapses function in two ways as post synaptic inhibition and pre synaptic inhibition.

Post synaptic inhibition
Nerve impulseà pre synaptic knob release an inhibitory substance (GABA)àGABA diffuse across synaptic cleftà GABA binds with receptor sites on post synaptic membraneà permeability of post synaptic membrane changesà permeability to K+ and Cl- ions increaseà K+ leaves and Cl- ions enteràInhibitory post synaptic potential (IPSP) is obtainedà membrane hyperpolarizedà no action potential initiated

Pre synaptic inhibition
Nerve impulseà pre synaptic knob release inhibitory substancesàhyperpolarize the pre synaptic  excitatory membraneà prevent excitatory substances releasingà no excitation occurs on post synaptic membrane     

Sequence of events take place during action potential in brief


>In resting state, membrane is permeable to K+ and relatively impermeable to Na+.

>When a stimulus depolarize the membrane into the threshold value the voltage gated Na+ channels open, vastly increasing the membrane’s permeability to Na+.

>Na+ enters the cell across the membrane under the influence of both concentration gradient and the electric gradient.

>Na+ makes the membrane more depolarized and that makes more voltage gated sodium channels to open.

>As the membrane potential approaches equilibrium potential of Na+ the driving force of Na+ is reduced. Therefore less number of Na+ reach into the cell.

>After a short time the voltage gated Na+ channels are inactivated and stop the taken in of the Na+.  Here the membrane potential rise to +45mV.

>As this occurs, the voltage gated K+ channels open and greatly increases the permeability to K+ ions. Therefore K+ leaves the cell under the influence of concentration gradient and electric gradient.

>As K+ leaves, the positive charge inside the cell is reduced. After awhile the equilibrium potential of K+ is obtained and the membrane is hyperpolarized. Now the membrane potential is -75mV. Hyperpolarization is due to the delay of closing the K+ channels compared to Na+ channels.

>The voltage gated K+ channels close and by then the Na+ channels recovered by inactivation.


12 March 2012

Biosynthesis and function of aromatic amino acids in plants


Most aromatic amino acids in plants are formed by three main types of aromatic acids;
  •    Phenylalanine
  •     Tyrosine
  •     Tryptophan

These three important aromatic amino acids are exclusively synthesized by Shikimic acid pathway that is unique to plants and microbes. This pathway got its name by an important intermediate forms,called Shikimic acid.

Shikimic acid pathway starts from the condensation of Erythrose-4-phosphate with Phosphoenolpyruvate (PEP). PEP is provided by the glycolysis while Erythrose-4-P comes from either oxidative pentose phosphate pathway or Calvin cycle. Therefore Shikimic acid pathway is combined with other important metabolic pathways of the cell. 
The condensation produces 3-deoxy-D-arabinoheptulosonic acid-7-phosphate (DAHP). DAHP undergoes another series of reactions including condensation with another molecule of PEP to give out Chorismic acid. Shikimic acid forms as an intermediate in this reaction and regarded as the key intermediate.
Chorismate is a central intermediate giving rise to two products; Prephenate and Anthranillic acid. Shikimic acid pathway is shown simply as below.

photo


The synthesis of aromatic amino acids is important as these amino acids are the precursors for the synthesis of defense and repair compounds.

Phenylalanine
·         Flavonoids: in plant pigments (eg: Anthocyanine), act against pathogens. Antioxidants.
·         Coumarins: Has appetite-suppressing properties.
·         Liginin: In lignicolous fungi

Tyrosine
·         Tocopherol: Antioxidant in cornifers.
·         Plastoquinone: Important in photosynthesis.
·         Cyanogenic glucosides: Phytoanticipants. Important in plant defense against herbivores due to bitter taste and release of toxic hydrogen cyanide upon tissue disruption.

Tryptophan
·         Alkaloides: provides protection as it prevents insects and herbivores eating the plant.
·         Plant growth regulators