Recognition of Pathogenic and Infectious Elements

What is a bacterium?
Bacteria are a group of microscopic single-celled organisms that are surrounded by a relatively thick outer covering. These organisms have a simple structure and belong to the Prokaryote group. They are the first living things to come to earth. The first signs of life on Earth, about three and a half billion years ago, are related to the emergence of prokaryotic bacterial cells. Bacteria are the most diverse and important microorganisms. Few of them are pathogenic in humans, animals and plants. In general, life on Earth is disrupted without their activity. Eukaryotes must have evolved from bacterial-like organisms. Because bacteria are simple in structure and many of them can be easily cultured and controlled in the laboratory, microbiologists have done extensive research on their vital processes. The simplest asexual reproduction (binary fission) is found only in bacteria. In binary fission, the bacterium divides in half every twenty minutes, provided there are suitable conditions (food, air, proper temperature, and absence of chemical compounds). If conditions are not favorable, the bacterium forms a thick layer around its chromosome, known as the endospore. The endospore protects the bacterium from adverse conditions, and the bacterium may resume its activity hundreds of years later. The method of removing the endospore is sterilization. Bacteria can be found in all climates and in almost all places, including hot springs, polar ice caps, or lakes with high salinity.

Fungi
Fungi are a group of eukaryotic organisms that include microorganisms such as yeasts, molds, and basidiomycotes. These organisms are classified in the kingdom of fungi, which are a separate group of animals and plants. The fungal lineage is a series of eukaryotes that contain chitin in their cell walls and do not have photosynthetic power. Another name for the mushroom in Persian was Samarogh. Ordinary people also call it “terrace canopy” and “snake umbrella”.  Fungi are all heterotroph and need organic compounds for energy and carbon dioxide to grow and multiply. Fungi are aerobic or anaerobic are optional. Most fungi are saprophytic, living in soil and water, and in these areas, decompose plant and animal remains. Fungi, like bacteria, are involved in the breakdown of substances and the circulation of elements in nature. The science of studying fungi is called mycology and the science of studying parasitic fungi for humans is called medical mycology. These parasites cause many diseases. Fungi play a key role in the ecosystem. Fungi have many different effects on nature. A species of fungus ferments grapes to turn it into wine. Another species kills grapes on the vine. Other species cause the bathroom tiles to turn dark, and other fungal species cause or cure disease, or cause wood to rot or the roots of the plant to grow back. Unlike plants, fungi cannot produce their own food; Therefore, in order to survive, they have to be consumers (heterotrophs).

What is a virus and what are its types?
A virus is a small pathogen that only grows in the living cells of an organism. The word virus has its roots in Latin and means poison or any toxic substance. Viruses can infect all forms of life, from animals and plants to microorganisms, including bacteria and Archaea. There are millions of types of viruses among living things and in different habitats and places, and so far more than 6,000 different types of viruses have been accurately identified and introduced. The virus is not a living organism, but a piece of nucleic acid enclosed in a protein coating (capsid). Viruses are much smaller than bacteria and can only be seen with an electron microscope. The virus multiplies using the host cellular facilities and disrupts the main activity of the host cells. Viruses infect many animals, plants, and bacteria, but only some of them infect humans. Also, viruses multiply only in a neutral environment in living cells and are forced intracellular parasites. Because viruses lack all biological characteristics except the genetic phase, biologists did not consider them alive until the end of the last century. Viruses do not grow, are not homeostatic, and do not have metabolic reactions due to the lack of major enzymes. Only two enzymes are found in them, the ATP enzyme and the reverse transcriptase enzyme (for RNA carriers). Today, however, given the possibility of culturing and replicating viruses in the laboratory, the notion that parasites are obligatory is questionable. Scientists are skeptical about the evolutionary origin of viruses. One group of viruses appears to have evolved from plasmids and the other group of bacteria evolved from bacteria. Viruses play a very important role in the evolution of species and the horizontal transmission of genes, resulting in recombination and genetic diversity. In recent decades, virological developments have begun to reveal information that suggests that viruses may be living organisms. One of these discoveries was mimiviruses; Giant viruses with large genomic libraries that were even larger than some bacteria. Some viruses, such as the Ebola virus, have a small number of the seventh gene. Some of these giants have protein genes that are necessary to make a new virus. Based on this, the fact that this case remains unknown is a reason for placing those viruses in the classification of non-living organisms. Because of some of the characteristics of living organisms and the lack of others, scientists have recently defined viruses as "creatures on the edge of life," or in other words, "self-reproducing." Viruses exist in the form of independent particles of a virus or virions that exist: (i) genetic material, ie molecules, while they are not yet inside an infected cell (host), or are not infecting a cell. Long DNA or RNA that encodes the structure of the proteins that the virus works with. (ii) a protein coat, called a capsid, that surrounds and protects the genetic material; And in some cases (iii) an outer sheath of lipids. The shapes and forms of these virus particles vary from simple helical and icosahedron forms to more complex structures: viruses may be spherical, spiral, or polyhedral. A special feature of animal viruses is that they have a coating of cell membranes (protein, lipid, and glycoprotein). They get this cover from their previous host, and this is because animal viruses enter the host through endocytosis. Bacteria that attack bacteria are called bacteriophages, which are more complex than other plant and animal viruses. This is because it consists of two polyhedral coatings (as capsid) and a spiral coating (as a tail).

Structure of Viruses
A simple outline of the structure of a virus:
The general structure of viruses consists of nucleic acids (genomes) and a coating of a protein called a capsid. In some viruses, a layer of lipoprotein and lipopolysaccharide is placed around it to protect the protein coat. The genome of viruses is a type of nucleic acid according to which viruses are divided into two categories. Ribonucleic acid (RNA) viruses and Deoxyribonucleic acid (DNA) viruses. Infection of viruses is solely the result of the intracellular activity of nucleic acid or their genome, so outside the cell the virus and its genome are free of any activity and are a large molecule. The genomes of many viruses are stranded or coiled inside a protein called a capsid. This protein coating is not integrated but is made up of smaller particles or units called capsomers. Capsomers form a capsid when it joins, and its specific form depends on the type of virus and its structure. In some viruses, the genome is synthesized in a spiral, and the capsomers cover it regularly, so that the nucleocapsid of the virus becomes springy or helical. In addition, the genome and capsid (nucleocapsid) of more than half of the viruses contain envelope of lipoprotein and lipopolysaccharide. In this case, viruses are divided into two categories: enveloped group and nonenveloped group. envelope Viruses are very diverse. The size, shape, volume and structure of viruses vary widely. Viruses are some spherical, some conical, or similar to other geometric shapes, such as the cube or polyhedron. Virus diameters can range from 20 nanometers (smallest) to 450 nanometers (largest). Some filoviruses are 1,400 nanometers long, but only 80 nanometers in diameter. Large viruses, such as the smallpox virus, are large in size, have an unusual, relatively complex structure, and, like bacteria, do not pass through the Chamberland filter at all, while most viruses are able to pass through these filters. Viruses have no cellular structure and are isolated from host cells without any chemical, enzymatic, or cellular metabolism, and are never able to replicate due to a lack of cloning requirements. They should be considered as a composite macromolecule or an infectious unit outside the living cell. Because they are compound macromolecules, that is, they have a nucleic acid chain and a protein shield, and possibly an envelope of lipoprotein and lipopolysaccharide, they are ready as soon as they come in contact with the host cell and after the genome is absorbed, penetrated and released. Take control and arrange the general stages of their reproduction with the help of cellular transcription and translation systems. All living organisms, including eukaryotes and prokaryotes, can be forced hosts of viruses. Not every cell is receptive to any virus, it is exclusively receptive to a familiar virus.

Giant Viruses
Mimivirus is one of the largest known viruses. The virus has a capsid diameter of 400 nm and has surface protein strands of 100 nm. The structure of the virus is seen in a hexagonal electron microscope. In 2011, the largest known virus was discovered in the ocean floor off the coast of Chile. This virus is called Megavirus chilensis and can be seen using a conventional light microscope. In 2013, a genus of viruses called Pandoravirus was discovered in Chile and Australia. The genome size of this virus is twice the size of the Mimivirus and Megavirus genomes. The genome of all giant viruses is double-stranded DNA. These viruses are divided into seven different families.

Virus Replication
The virus replication cycle begins with the infection of the host cell and ends with the release of mature viral particles. Due to the lack of cell structure and any metabolism and chemical interaction, viruses are not able to replicate themselves and for this purpose they have to enter a sensitive cell and need energy and a protein cell-making device for living cells. Transmission of the virus into the cell is possible only by the cell, and this is done only by the sensitive cell carrying the receptors familiar to the virus. Cells that have these receptors ready to absorb the virus can probably transmit different types of viruses, otherwise the cell will be resistant to the virus and any contact with the virus will be ineffective. By entering the cell and being covered by cell enzymes, the nucleic acid activity of the virus begins. Virus nucleic acids have enough genes to inhibit host cell metabolism, thereby meeting the needs of vital chemical interactions for proliferation by the host cell. Once the host cell is infected, the virus can multiply in two cycles.

Lysogenic Cycle
Sometimes, after entering the cell during the early stages and releasing the genome or nucleic acid, instead of producing the virus genome and protein, the virus places itself inside the host chromosome, in which case it is called a Provirus. Each time a cell divides, the Provirus also splits. In this type of cycle, the viral genome multiplies without destroying the host cell; Sometimes this step produces the complete virus without destroying the host cell and directs the newly-formed virus out of the cell.

Lytic Cycle
At this stage, the host cell, after replicating the virus, is completely destroyed and many viruses are released from the host cell.

Stages of Virus Replication
Absorption and Attachment
The virus contacts the receptors in the cell membrane, causing the virus to be absorbed and attached to the cell, triggering the onset of infection. This binding of the virus to receptors and the presence of these receptors in specific tissues causes the virus to be specific to specific tissues and cause specific diseases in the same tissue cells. Ambient temperature, proper pH, electrostatic force and the presence of mineral salts are very important in virus uptake and binding to cell surface receptors. Binding of the virus to the receptor is a weak and non-covalent bond. The types of receptors are not the same for different viruses. For example, polio virus absorbs PVR and influenza virus absorbs sialic acid from respiratory cells. Also the HIV receptor is CD4 molecule and the Epstein – Barr virus receptor is CD21 molecule and the Rhinovirus receptor is ICAM-1 molecule. Each of the receptors has a normal function in the service of the body and is abused by the virus, so that CD4 in lymphocyte T cells plays a role as a stimulus to identify and respond to foreign antigens attached to the MHC.

Penetration or Entry to the Cell:
After attaching the virus to the cell surface with changes in the cell receptor, the virus looks for a way to enter the cell. In general, virus entry occurs either through membrane fusion (fusion of the viral coating with the cell membrane) or through endocytosis. Enveloped viruses often enter the cell through fusion with the help of viral proteins that play a role in fusion. Nonenveloped viruses also enter the cell through endocytosis, with each type of endocytosis including clathrin-mediated endocytosis, kaolin-mediated endocytosis, clathrin-independent endocytosis, and kaolin and macropinocytosis. Due to the presence of strong chitin and cellulose cell walls in fungi and plants, viruses enter these cells with difficulty, and viruses can only enter if the cell wall is damaged. In plant cells, viruses can travel directly from one cell to another through Plasmodesma cell pores.

Deenveloping
Once the virus enters the cell, inside the cytoplasm and under the influence of intracellular enzymes or the enzymes of the virus itself, the viral protein envelope is broken down and the nucleic acid is released. From the beginning to this stage can be tracked with the help of an electron microscope and observe the changes in the virus.

Disappearance
The released nucleic acid of the virus is broken down into smaller pieces, and after a short time the slightest trace of the virus genome will not be visible. From now on, the nucleic acid of the virus dominates the infected cell and controls the cell's protein-producing apparatus for proliferation. In these stages, the virus can be considered a living unit, or in other words, the nucleic acid of the virus is a living unit.

Replication or Biosynthesis
With the synthesis and construction of enzymes required for replication, the activity of the virus nucleic acid begins within the cellular cytoplasm, enzymes begin their activity to prevent the production of protein and cellular nucleic acid. In some cases, the production of protein and cellular nucleic acid is not stopped at all and is limited only in a controlled manner. The replication and translation steps for virus biosynthesis begin with the production and fabrication of virus proteins and nucleic acids at specific centers. Depending on the type of virus, the production centers are formed in a corner of the cell, sometimes inside the cytoplasm and sometimes inside the cell nucleus, to prepare and produce the virus and its next stage.

Completion
After the production and synthesis of the virus protein and nucleic acid in specific centers, the virus nucleic acid is placed inside the protective protein and the work of completing the virus proceeds in its own way. Completion of viruses is not generally the same and is done privately. The complementarity of enveloped or nonenveloped viruses and those with complex structures or helical nucleocapsids are quite different, and each has evolved differently. In short, spherical viruses, or icosahedral capsids, are complemented by the joining of capsomers and the placement of nucleic acid within it. Viruses with helical nucleocapsids are already coated on the nucleic acid with a capsule of capsules and take on their helical form when the virus is ready to leave the cell. Viruses that have a complex structure are not as complete as other viruses, as studies show that the nucleic acid and the preservative protein and their outer surface filaments and the lipid used in their structure are generally synthesized elsewhere and the virus forms and completes at the same site. Envelope of the enveloped viruses, those that multiply inside the cell nucleus after leaving the nucleus, and those that complete in the cytoplasm of the cell, are wrapped around and complete when the envelope leaves the cytoplasmic membrane.

Virus out of the cell
There are two methods for removing viruses from the cell. In some cases, the virus is released when the host cell disintegrates, depending on its type and cell type. In such cases, a large amount of virus is suddenly released after the cell is destroyed. This type of release is found in many bacteria and some animal cells. In some other cases, such as enveloped viruses, such as the HIV virus, the virus is released out of the cell without the cell being destroyed. In these cases, the virus separates from the cell like a bud. In the case of enveloped viruses, the envelopes are wrapped around them and out of the cell at the same time.

Viral Diseases in Humans
Examples of common human viral illnesses include colds, flu, chickenpox, and herpes, and examples of dangerous viral illnesses include rabies, Ebola, AIDS, SARS, and hepatitis. However, the role of viruses in some human diseases such as Multiple Sclerosis has not been proven and is still under investigation. Some viruses, such as the herpes virus, may remain hidden in the body and only become active under certain conditions. The presence of such viruses in the body can be beneficial due to the increased activity of the immune system. Some viruses, such as hepatitis B virus and hepatitis C virus, can have a permanent presence and infection in a person's body, and such people will be a permanent carrier of these diseases. There are generally two ways of transmitting the virus: vertical transmission means the transmission of the virus from mother to fetus, for example, the transmission of the AIDS virus and hepatitis or syphilis; In horizontal transmission, the disease is transmitted individually or through vectors such as mosquitoes in populations. Transmission may be through saliva, respiratory droplets, sex, or contaminated water and food.