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Microbiology 1

Chapter 1

Microbiology is the study of microorganisms, which are unicellular or cell-cluster microscopic organisms. This includes eukaryotes (with a nucleus) such as fungi and protists, and prokaryotes (without a nucleus) such as bacteria, protozoa and viruses.

The field of microbiology can be generally divided into several subdisciplines:

• Microbial physiology: The study of how the microbial cell functions biochemically. Includes the study of microbial growth, microbial metabolism and microbial cell structure.
• Microbial genetics: The study of how genes are organised and regulated in microbes in relation to their cellular functions. Closely related to the field of molecular biology.
• Medical microbiology: The study of the role of microbes in human illness. Includes the study of microbial pathogenesis and epidemiology and is related to the study of disease pathology and immunology.
• Veterinary microbiology: The study of the role in microbes in veterinary medicine.
• Environmental microbiology: The study of the function and diversity of microbes in their natural environments. Includes the study of microbial ecology, microbially-mediated nutrient cycling, geomicrobiology, microbial diversity and bioremediation.
• Evolutionary microbiology: The study of the evolution of microbes. Includes the study of bacterial systematics and taxonomy.
• Industrial microbiology: The exploitation of microbes for use in industrial processes. Examples include industrial fermentation and wastewater treatment. Closely linked to the biotechnology industry. This field also includes brewing, an important application of microbiology.

Stephen Giovannoni (1990): Identified in the Sargasso Sea, contains the most abundant organism on the planet---called SAR11( SAR fro Sargassso), this bacterium has been renamed Pelagibacter ubique.with the single species P. ubique, are possibly the most numerous bacteria in the world (perhaps 10²⁸ individual cells). They were originally named SAR11 and known only from their rRNA genes, which were first identified in environmental samples from the Sargasso Sea in 1990. The bacteria responsible were isolated in 2002 and given a specific name, although it has not yet been validly published according to the bacteriological code.Pelagibacter has a world-wide distribution and is found among the bacterioplankton. They are some of the smallest self-replicating cells known, with a diameter of only 0.12-0.20 µm.

Why this number of SAR11 were not observed until 2002?
The reason is that a lot of bateria could not be frown in the lad. SAR11 was discovered using techiniques that look for the prevalence of specific DNA fragments in water samples.

What is the significance of discovery of SAR11?
SAR11's success story suggests that the bacterium must have a signigican impact on the plant. Althought such role remain to be identified, Giovannoni belieces that they are responsible for up to 10 percent of all nutrient cyclcing on the planet, influncing the cycling of carbon, and even affecting global warming.

J. Craig Venter and his biotech team (Institute for Biology Energy): Plans on reading the DNA of every organism--microbial at least--in the Sargasso Sea. And they hope to isolate the microbial DNAs, fragment them into small, random pieces, and use a large array of seqencing machines to piece the DNA molecules back together to their respective microbes.

Microorganism(microbes): is an organism that is so small that it is microscopic (invisible to the naked eye). Microorganisms are often illustrated using single-celled, or unicellular organisms; however, some unicellular protists are visible to the naked eye, and some multicellular species are microscopic. The study of microorganisms is called microbiology.

What are the characteristics of microbes?
1, are present in vas numbers in bearly every enviornment and habitat on Earth. 2, By weight, they make up about 2/3 of Earth's living material. If a microbe can match its metabolism to a habitate or environment on Earth, microorganisms will be found there. 3, Microbes inhabit the soil and flourish in oceans and freshwater lokes where they recycle nutrients and help control our climate. They survie in many of the foods we eat; in the air we breath. The majority of these microbe are may actually be beneficial in keeping the dangerous microbes out.

Extremophile : is an organism, usually unicellular, which thrives in or requires "extreme" conditions. It is important to note that the definition of "extreme" in this context is anthropocentric; from the point of view of the organism, its environment is completely normal.

Pathogen: is a biological agent that causes disease or illness to its host.The term is most often used for agents that disrupt the normal physiology of a multicellular animal or plant. However, pathogens can infect unicellular organisms from all of the biological kingdoms. The term pathogen is derived from the Greek παθογένεια, "birth of pain."

Several substrates and pathways whereby pathogens can invade a host;
the principal pathways are: 1, air contact/respiration; 2, water contact/ingestion or dermal contact; 3, soil contact/dermal or ingestion; and 4, animal contact/bite or ingestion. All of these mechanisms have different episodic time frames, but soil contamination has the longest or most persistent potential for harboring a pathogen.

opportunistic infections: The human body has many natural defenses against some of the more common pathogens (such as Pneumocystis) in the form of the human immune system and by some "helpful" bacteria present in the human body's normal flora. However, if the immune system or "good" bacteria is damaged in any way (such as by chemotherapy, human immunodeficiency virus (HIV), or antibiotics being taken to kill other pathogens), pathogenic bacteria that were being held at bay can proliferate and cause harm to the host. Such cases are called opportunistic infections.

Some pathogens (such as Yersinia pestis, which may have caused the Black Plague, and the Variola virus) have been found to be responsible for massive amounts of casualties and have had numerous effects on afflicted groups. Plague is carried by fleas. Of particular note in modern times is HIV, which is known to have infected several million humans globally, as well as Severe Acute Respiratory Syndrome (SARS). Today, while many medical advances have been made to safeguard against infection by pathogens, through the use of vaccination, antibiotics and fungicide, pathogens continue to threaten human life.

Infectious disease or communicable disease is disease caused by a biological agent such as by a virus, bacterium or parasite. This is contrasted to physical causes, such as burns or chemical ones such as through intoxication.

What is the mechanism of Infectious diseases
the invasion of a host organism by a foreign replicator, generally microorganisms, often called microbes, that are invisible to the naked eye. Microbes that cause illness are also known as pathogens. The most common pathogens are various bacteria and viruses, though a number of other microorganisms, including some kinds of fungi and protozoa, also cause disease. Prions are borderline, and memes would not usually be considered in this scope. An infectious disease is termed contagious if it is easily transmitted from one person to another.

How does an organism infect human body?
An organism that a microbe infects is known as the host for that microbe. In the human host, a microorganism causes disease by either
1, disrupting a vital body process or stimulating the immune system to mount a defensive reaction. An immune response against a pathogen, which can include a high fever, inflammation, and other damaging symptoms, can be more devastating than the direct damage caused by the microbe.
2, Infectious disease requires an agent and a mode of transmission (or vector). A good example is malaria, which is caused by Plasmodial parasites, chiefly Plasmodium falciparum but does not affect humans unless the vector, the Anopheles mosquito, is around to introduce the parasite into the human bloodstream.
The vector does not have to be biological. Many infectious diseases are transmitted by droplets which enter the airway (e.g. common cold and tuberculosis).

Examples of infectious disease
The top three single agent disease killers are HIV/AIDS, TB, and malaria. Lower respiratory infections (which include various pneumonias) and diarrheal diseases are caused by many different viruses, bacteria or parasites.
Childhood diseases include pertussis, poliomyelitis, diphtheria, measles, and tetanus. Children also make up a large percentage of lower respiratory and diarrheal deaths.
Tropical diseases include trypanosomiasis, Chagas disease. schistosomiasis, leishmaniasis, lymphatic filariasis, and onchocerciasis.
From 1993 to 2002, the death ranking for AIDS went up from 7th to 2nd and Hepatitis B went down from 6th to 11th. While the number of deaths has decreased in almost every disease, it has increased four-fold in AIDS.

Historic pandemics

A pandemic (or global epidemic) is a disease that affects people over an extensive geographical area.

• The Influenza Pandemic of 1918 or Spanish Flu killed 25 to 40 million in 1 year (about 2% of world population of 1.7 billion).
  • Influenza now kills about 250,000 to 500,000 worldwide each year.
• The Black Death of 1347 to 1352 killed 25 million in Europe over 5 years (estimate of 25 to 50% of Europe, Asia, and Africa - world population was 500 million).

When does the study of microorganism begin?
The study of microorganism began in earnest with the work of Pasteur and Koch, although they were not the first to report microorganisms.

The beginning of microbiology: Robert Hooke, Anton Van Leeuwenhoek
Robert Hooke (English naturalist)------first account of "cells"
1665, Robert Hooke published a work called Micrographia.
1, a descrition of his microscope and its uses. Hooke's writings and his illustrations, awakened the learned of Europe to he world of the very small.
2, He also described a slice of cork and suggested that it was composed of tiny compartments, which he called "cells".

Anton Van Leeuwenhoek (Netherlands) ----- Obsessed observer, single lense microscope lenses 300 times.sound observation and experimentation
1, owner of a dry goods business in Dleft, Netherlands. head of the city coucil, inspector of weights and measures.
2, he ground pieces of glass into fine lenses, placing them between two silver or brass plates riveted together.
3, his lenses could magnify an object nearly 300 times.
4, He believed sound observation and experimentation is a requirment that remain a cornerstone of all sciences tody.
5, 1674 he examined a sample of greenish, he saw hundreds of tiny animals which he called animalcules
6, He cent letter to Royal Society. and this letter has special significance to microbiology because it contains the first description of what were probably bacteria.
7, He outlined structural details of protozoa and described threadlike fungi and microscopic algae.
8, became fellowship in the Royal Society in 1680. a very suspicious and secretive person.
9, opposed Jan Baptista's observation that rat originated from wheat. He suggested that they came from tiny eggs in the grain that he saw with his microscopes.

Why study of microbes progessed slowly after Anton Van Leeuwenhoek's death?
1, After his death, no one knew hot to grind lenses or construct a microscope. Such secrecy stalled the advancement of the knowledge of microorganism. It would take 100 years to grind lenses equal to or better than those of Leeuwenhoek.
2, Another reason is the natrual philosophers of 1700s saw microbes simple as cruiosities of nature and could not cause disease to lofty human being.

The transition period:
Louis Joblot (naturalist): published a review of protozoa in 1718.

Why most naturalists did not believe microscopic organims could cause infection?
They hypothesized that infectious disease, such as plague and malaria spread by an altered chemical quality of the atmosphere or a poisoning of the air, an entity called miasma.

What is miasma?
Miasma is considered to be a poisonous vapor or mist that is filled with particles from decomposed matter (miasmata) that could cause illnesses and is identifiable by its nasty, foul smell (which, of course, came from the decomposed material). A prominent supporter of the miasma theory was Abaris the Hyperborean, who famously cleaned Sparta under Mount Taygetus from miasmata coming downhill.The miasma idea figured prominently in medical thingking well into the 1800s.

Artistole (4th B.B.)Spontaneous generation and its basic doctrine.
He wrote the flies, worms and other small animals could arise from decaying matter. (without the need of parent organisms)

Jan Baptista van Helmont 1600s (Flemish): he observed that rats "originate" from wheat bran and old rag. Common people embraced the idea, for even they could see what appeared to be slime that produced toads and meat that generated wormlike maggots.

Francesco Redi (Florentine naturalist) Among the first to dispute the the spontaneous generation using experiment.
1, He noted Leeuwenhoek's descriptions, he reasoned that because flies had reproductive organs, they could land on pieces of exposed meat and lay their invisible eggs, which then hatch into visible maggots.
2, 1668 Redi performed one of the first experiemts in biology. He set up a series of test in which he coverd some jars of meat with line lace, thereby preventing the entry of flies. So protected, the meat should not produce maggots.

John Needham (British clergyman) :Reports of animals wre becoming widespread during the 1700s.in 1748, John Needham suggested they arise spontaneouly in the tubes of mutton gravy. He boiled several tubes of gravy and sealed the tubes with corks, as Redi had sealed his jars. Still, the tiny creature appeared. then he was elected membership of Royal Society of Landon.

Lazzaro Spallanzani (italian Cleric and naturalist) : First criticized Neeham's work.
Spallanzani boiled meat and vegetable broths for longer periods and then sealed the necks by melting the glass. As control experiments, he left some flasks open to the air, stopped some loosely with corks, and boiled some briefly, as Needham had done. After two days, he found the open flasks swarming with microorganisms, but the sealed flasks contained none. Spallanazani's experiemtn did not settle the issues, though.
Needham countered that the spallanzani had destroyed the "vital force" of the life with excessive heating. others also suggested that the air necessary for life had been excluded by sealing the flasks.

Louis Pasteur : finnally debunk the idea od spontaneous generation

When did people find out disease?
People had realized for centuries that disease could be contagiou and quarantines were used as early as the 1300s to combat the spread of diseases like Plague.

posted by C-T @ 7:49 PM