Category Archives: Biologi Molekuler

Top 7 in Molecular Biology

1. A glowing gene tag
A new, genetically-encoded fluorescent protein created in the lab of Roger Tsien, who shared a Nobel Prize for developing green fluorescent protein (GFP), is poised to revolutionize electron microscopy. Engineered from an Arabidopsis protein, “miniSOG” (for mini Singlet Oxygen Generator) is less than half the size of GFP, binds to a suite of well-characterized proteins, and can faithfully tag a variety of mammalian cells as well as cell in intact rodents and nematodes.

X. Shu, et al., “A genetically encoded tag for correlated light and electron microscopy of intact cells, tissues, and organisms,” PLoS Biology, 9:e1001041, 2011. Free F1000 Evaluation

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Phylogenetic Tree

ArchaeThe formal evolutionary hierarchy of groups of organisms proceeds from the largest to the smallest groups: domain – kingdom – phylum – order – class – family – genus – species. Living organisms are grouped according to the type of cells they consist of, either prokaryotic cells or eukaryotic cells. Prokaryotes have a simple internal architecture without a nucleus. Eukaryotes have a distinct internal structure with a nucleus containing the genetic material. A third group of living organismswas recognized in the late 1960s, the Archaea (also called archaebacteria). They differ from ordinary bacteria by their plasma membrane (isoprene ether lipids rather than fatty acid ester lipids) and lifestyle. They are assigned to two classes, Crenarchaeota and Euryarcheota.

Source : Thieme Color Atlas of Genetic 3ed (2007)

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Cell

I. Introduction

Cell (biology), basic unit of life. Cells are the smallest structures capable of basic life processes, such as taking in nutrients, expelling waste, and reproducing. All living things are composed of cells. Some microscopic organisms, such as bacteria and protozoa, are unicellular, meaning they consist of a single cell. Plants, animals, and fungi are multicellular; that is, they are composed of a great many cells working in concert. But whether it makes up an entire bacterium or is just one of trillions in a human being, the cell is a marvel of design and efficiency. Cells carry out thousands of biochemical reactions each minute and reproduce new cells that perpetuate life.

Animal Cell

Animal Cell

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PCR

Nucleic Acid Amplification Techniques

1. Introduction

Nucleic acid amplification techniques are based on 2 different approaches: 1.) amplification of a target nucleic acid sequence using, for example, polymerase chain reaction (PCR), ligase chain reaction (LCR), or isothermal ribonucleic acid (RNA) amplification, 2.) amplification of a hybridisation signal using, for example, for deoxyribonucleic acid (DNA), the branched DNA (bDNA) method. In this case signal amplification is achieved without subjecting the nucleic acid to repetitive cycles of amplification. In this general chapter, the PCR method is described as the reference technique.  Alternative methods may be used, if they comply with the quality requirements  described below.

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Sel

Penelitian menunjukkan bahwa satuan unit terkecil dari kehidupan adalah Sel. Kata “sel” itu sendiri dikemukakan oleh Robert Hooke yang berarti “kotak-kotak kosong”, setelah ia mengamati sayatan gabus dengan mikroskop.

Selanjutnya disimpulkan bahwa sel terdiri dari kesatuan zat yang dinamakan Protoplasma. Istilah protoplasma pertama kali dipakai oleh Johannes Purkinje; menurut Johannes Purkinje protoplasma dibagi menjadi dua bagian yaitu Sitoplasma dan Nukleoplasma

Robert Brown mengemukakan bahwa Nukleus (inti sel) adalah bagian yang memegang peranan penting dalam sel,Rudolf Virchow mengemukakan sel itu berasal dari sel (Omnis Cellula E Cellula).

ANATOMI DAN FISIOLOGI SEL

Secara anatomis sel dibagi menjadi 3 bagian, yaitu:
1.
Selaput Plasma (Membran Plasma atau Plasmalemma).
2. Sitoplasma dan Organel Sel.
3. Inti Sel (Nukleus).

1. Selaput Plasma (Plasmalemma)

Yaitu selaput atau membran sel yang terletak paling luar yang tersusun dari senyawa kimia Lipoprotein (gabungan dari senyawa lemak atau Lipid dan senyawa Protein).

Lipoprotein ini tersusun atas 3 lapisan yang jika ditinjau dari luar ke dalam urutannya adalah:
Protein – Lipid – Protein Þ Trilaminer Layer

Lemak bersifat Hidrofebik (tidak larut dalam air) sedangkan protein bersifat Hidrofilik (larut dalam air); oleh karena itu selaput plasma bersifat Selektif Permeabel atau Semi Permeabel (teori dari Overton).

Selektif permeabel berarti hanya dapat memasukkan /di lewati molekul tertentu saja.

Fungsi dari selaput plasma ini adalah menyelenggarakan Transportasi zat dari sel yang satu ke sel yang lain.

Khusus pada sel tumbahan, selain mempunyai selaput plasma masih ada satu struktur lagi yang letaknya di luar selaput plasma yang disebut Dinding Sel (Cell Wall).

Dinding sel tersusun dari dua lapis senyawa Selulosa, di antara kedua lapisan selulosa tadi terdapat rongga yang dinamakan Lamel Tengah (Middle Lamel) yang dapat terisi oleh zat-zat penguat seperti Lignin, Chitine, Pektin, Suberine dan lain-lain.

Selain itu pada dinding sel tumbuhan kadang-kadang terdapat celah yang disebut Noktah. Pada Noktah/Pit sering terdapat penjuluran Sitoplasma ng disebut Plasmodesma yang fungsinya hampir sama dengan fungsi saraf pada hewan.

2. Sitoplasma dan Organel Sel
Bagian yang cair dalam sel dinamakan Sitoplasma khusus untuk cairan yang berada dalam inti sel dinamakan Nukleoplasma), sedang bagian yang padat dan memiliki fungsi tertentu digunakan Organel Sel.

Penyusun utama dari sitoplasma adalah air (90%), berfungsi sebagai pelarut zat-zat kimia serta sebagai media terjadinya reaksi kirnia sel.
Organel sel adalah benda-benda solid yang terdapat di dalam sitoplasma dan bersifat hidup(menjalankan fungsi-fungsi kehidupan).
Organel Sel tersebut antara lain :
a. Retikulum Endoplasma (RE.)
Yaitu struktur berbentuk benang-benang yang bermuara di inti sel.
Dikenal dua jenis RE yaitu :
• RE. Granuler (Rough E.R)
• RE. Agranuler (Smooth E.R)
Fungsi R.E. adalah : sebagai alat transportasi zat-zat di dalam sel itu sendiri. Struktur R.E. hanya dapat dilihat dengan mikroskop elektron.
b. Ribosom (Ergastoplasma)
Struktur ini berbentuk bulat terdiri dari dua partikel besar dan kecil, ada yang melekat sepanjang R.E. dan ada pula yang soliter.
Ribosom merupakan organel sel terkecil yang tersuspensi di dalam sel.
Fungsi dari ribosom adalah : tempat sintesis protein.
Struktur ini hanya dapat dilihat dengan mikroskop elektron.
c. Miitokondria (The Power House)
Struktur berbentuk seperti cerutu ini mempunyai dua lapis membran.
Lapisan dalamnya berlekuk-lekuk dan dinamakan Krista
Fungsi mitokondria adalah sebagai pusat respirasi seluler yang menghasilkan banyak ATP (energi) ; karena itu mitokondria diberi julukan “The Power House”.
d. Lisosom
Fungsi dari organel ini adalah sebagai penghasil dan penyimpan enzim pencernaan seluler. Salah satu enzi nnya itu bernama
Lisozym.
e. Badan Golgi (Apparatus Golgi = Diktiosom)
Organel ini dihubungkan dengan fungsi ekskresi sel, dan struktur ini dapat dilihat dengan menggunakan mikroskop cahaya biasa.
Organel ini banyak dijumpai pada organ tubuh yang melaksanakan fungsi ekskresi, misalnya ginjal.
J. Sentrosom (Sentriol)
Struktur berbentuk bintang yang berfungsi dalam pembelahan sel (Mitosis maupun Meiosis). Sentrosom bertindak sebagai benda kutub dalam mitosis dan meiosis.
Struktur ini hanya dapat dilihat dengan menggunakan mikroskop elektron. 

g. Plastida
Dapat dilihat dengan mikroskop cahaya biasa. Dikenal 3 jenis plastida yaitu :
1.
Lekoplas
(plastida berwarna putih berfungsi sebagai penyimpan makanan),
terdiri dari:
• Amiloplas (untak menyimpan amilum) dan,
• Elaioplas (Lipidoplas) (untukmenyimpan lemak/minyak).
Proteoplas (untuk menyimpan protein).

2. Kloroplas
yaitu plastida berwarna hijau. Plastida ini berfungsi menghasilkan
klorofil dan sebagai tempat berlangsungnya fotosintesis.
3.
Kromoplas
yaitu plastida yang mengandung pigmen, misalnya :
Karotin (kuning)
Fikodanin (biru)
Fikosantin (kuning)
Fikoeritrin (merah)

h. Vakuola (RonggaSel)
Beberapa ahli tidak memasukkan vakuola sebagai organel sel. Benda ini dapat dilihat dengan mikroskop cahaya biasa. Selaput pembatas antara vakuola dengan sitoplasma disebut Tonoplas
Vakuola berisi :
• garam-garam organik
• glikosida
• tanin (zat penyamak)
• minyak eteris (misalnya Jasmine pada melati, Roseine pada mawar
Zingiberine pada jahe)
• alkaloid (misalnya Kafein, Kinin, Nikotin, Likopersin dan lain-lain)
• enzim
• butir-butir pati
Pada boberapa spesies dikenal adanya vakuola kontraktil dan vaknola non kontraktil.

i. Mikrotubulus

Berbentuk benang silindris, kaku, berfungsi untuk mempertahankan bentuk sel dan sebagai “rangka sel”.
Contoh organel ini antara lain benang-benang gelembung pembelahan Selain itu mikrotubulus berguna dalam pembentakan Sentriol, Flagela dan Silia.

j. Mikrofilamen
Seperti Mikrotubulus, tetapi lebih lembut.
Terbentuk dari komponen utamanya yaitu protein aktin dan miosin (seperti pada otot). Mikrofilamen berperan alam pergerakan sel.
k. Peroksisom (Badan Mikro)
Ukurannya sama seperti Lisosom. Organel ini senantiasa berasosiasi dengan organel lain, dan banyak mengandung enzim oksidase dan katalase (banyak disimpan dalam sel-sel hati).

3. Inti Sel (Nukleus)
Inti sel terdiri dari bagian-bagian yaitu :
• Selapue Inti (Karioteka)
• Nukleoplasma (Kariolimfa)
• Kromatin / Kromosom
• Nukleolus(anak inti).
Berdasarkan ada tidaknya selaput inti kita mengenal 2 penggolongan sel yaitu :
Sel Prokariotik (sel yang tidak memiliki selaput inti), misalnya dijumpai
pada bakteri, ganggang biru.
Sel Eukariotik (sel yang memiliki selaput inti).Fungsi dari inti sel adalah : mengatur semua aktivitas (kegiatan) sel, karena di dalam inti sel terdapat kromosom yang berisi ADN yang mengatur sintesis protein.

Bagi yang malas membaca  “doble clik below”

kuliah-sel

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Genetic Engineering

I   INTRODUCTION

Genetic Engineering, alteration of an organism’s genetic, or hereditary, material to eliminate undesirable characteristics or to produce desirable new ones. Genetic engineering is used to increase plant and animal food production; to help dispose of industrial wastes; and to diagnose disease, improve medical treatment, and produce vaccines and other useful drugs. Included in genetic engineering techniques are the selective breeding of plants and animals, hybridization (reproduction between different strains or species), and recombinant deoxyribonucleic acid (DNA).

II   SELECTIVE BREEDING

The first-known genetic engineering technique, still used today, was the selective breeding of plants and animals, usually for increased food production. In selective breeding, only those plants or animals with desirable characteristics are chosen for further breeding. Corn has been selectively bred for increased kernel size and number and for nutritional content for about 7,000 years. More recently, selective breeding of wheat and rice to produce higher yields has helped supply the world’s ever-increasing need for food.

Cattle and pigs were first domesticated about 8,500 to 9,000 years ago and through selective breeding have become main sources of animal food for humans. Dogs and horses have been selectively bred for thousands of years for work and recreational purposes, resulting in more than 150 dog breeds and 100 horse breeds.

III   HYBRIDIZATION

Hybridization (crossbreeding) may involve combining different strains of a species (that is, members of the same species with different characteristics) or members of different species in an effort to combine the most desirable characteristics of both. For at least 3,000 years, female horses have been bred with male donkeys to produce mules, and male horses have been bred with female donkeys to produce hinnies, for use as work animals.

IV   RECOMBINANT DNA

In recent decades, genetic engineering has been revolutionized by a technique known as gene splicing, which scientists use to directly alter genetic material to form recombinant DNA. Genes consist of segments of the molecule DNA. In gene splicing, one or more genes of an organism are introduced to a second organism. If the second organism incorporates the new DNA into its own genetic material, recombined DNA results. Specific genes direct an organism’s characteristics through the formation of proteins such as enzymes and hormones. Proteins perform vital functions—for example, enzymes initiate many of the chemical reactions that take place within an organism, and hormones regulate various processes, such as growth, metabolism, and reproduction. The introduction of new genes into an organism essentially alters the characteristics of the organism by changing its protein makeup.

In gene splicing, DNA cannot be transferred directly from its original organism, known as the donor, to the recipient organism, known as the host. Instead, the donor DNA must be cut and pasted, or recombined, into a compatible fragment of DNA from a vector—an organism that can carry the donor DNA into the host. The host organism is often a rapidly multiplying microorganism such as a harmless bacterium, which serves as a factory where the recombined DNA can be duplicated in large quantities. The subsequently produced protein can then be removed from the host and used as a genetically engineered product in humans, other animals, plants, bacteria, or viruses. The donor DNA can be introduced directly into an organism by techniques such as injection through the cell walls of plants or into the fertilized egg of an animal. Plants and animals that develop from a cell into which new DNA has been introduced are called transgenic organisms.

Another technique that produces recombinant DNA is known as cloning. In one cloning method, scientists remove the DNA-containing nucleus from a female’s egg and replace it with a nucleus from an animal of a similar species. The scientists then place the egg in the uterus of a third animal, known as the surrogate mother. The result, first demonstrated by the birth of a cloned sheep named Dolly in 1996, is the birth of an animal that is nearly genetically identical to the animal from which the nucleus was obtained. Such an animal is genetically unrelated to the surrogate mother. Cloning is still in its infancy, but it may pave the way for improved farm animals and medical products.

A   Applications

The use of recombinant DNA has transformed a number of industries, including plant and animal food production, pollution control, and medicine.

A1   Food Production

Recombinant DNA is used to combat one of the greatest problems in plant food production: the destruction of crops by plant viruses or insect pests. For example, by transferring the protein-coat gene of the zucchini yellow mosaic virus to squash plants that had previously sustained great damage from the virus, scientists were able to create transgenic squash plants with immunity to this virus. Scientists also have developed transgenic potato and strawberry plants that are frost-resistant; potatoes, corn, tobacco, and cotton that resist attacks by certain insect pests; and soybeans, cotton, corn, and oilseed rape (the source of canola oil) that have increased resistance to certain weed-killing chemicals called herbicides. Recombinant DNA has also been used to improve crop yield. Scientists have transferred a gene that controls plant height, known as a dwarfing gene, from a wheat plant to other cereal plants, such as barley, rye, and oats. The transferred gene causes the new plant to produce more grain and a shorter stalk with fewer leaves. The shorter plant also resists damage from wind and rain better than taller varieties.

Scientists also apply gene-splicing techniques to animal food production. Scientists have transferred the growth hormone gene of rainbow trout directly into carp eggs. The resultant transgenic carp produce both carp and rainbow trout growth hormones and grow to be one-third larger than normal carp. Other fish that have been genetically engineered include salmon, which have been modified for faster growth, and trout, which have been altered so that they are more resistant to infection by a blood virus.

Recombinant DNA also has been used to clone large quantities of the gene responsible for the cattle growth hormone bovine somatotropin (BST) in the bacterium Escherichia coli. The hormone is then extracted from the bacterium, purified, and injected into dairy cows, increasing their milk production by 10 to 15 percent.

A2   Pollution Control

Genetically altered bacteria can be used to decompose many forms of garbage and to break down petroleum products. Recombinant DNA also can be used to monitor the breakdown of pollutants. For example, naphthalene, an environmental pollutant present in artificially manufactured soils, can be broken down by the bacterium Pseudomonas fluorescens. To monitor this process, scientists transferred a light-producing enzyme called luciferase, found in the bacterium Vibrio fischeri, to the Pseudomonas fluorescens bacterium. The genetically altered Pseudomonas fluorescens bacterium produces light in proportion to the amount of its activity in breaking down the naphthalene, thus providing a way to monitor the efficiency of the process (see Bioremediation).

A3   Medicine

In 1982 the United States Food and Drug Administration (FDA) approved for the first time the medical use of a recombinant DNA protein, the hormone insulin, which had been cloned in large quantities by inserting the human insulin gene into the genetic makeup of Escherichia coli bacteria. Previously, this hormone, used by insulin-dependent people with diabetes mellitus, had been available only in limited quantities from hogs.

Since 1982 the FDA has approved other genetically engineered proteins for use in humans, including three cloned in hamster cell cultures: tissue plasminogen activator (tPA), an enzyme used to dissolve blood clots in people who have suffered heart attacks; erythropoetin, a hormone used to stimulate the production of red blood cells in people with severe anemia; and antihemophilic human factor VIII, used by people with hemophilia to prevent and control bleeding or to prepare them for surgery. Another important genetically engineered drug is interferon, a chemical that is produced by the body in tiny amounts. Engineered interferon is used to fight viral diseases and as an anticancer drug.

Scientists also have employed recombinant DNA to produce medically useful human proteins in animal milk. In this procedure, the human gene responsible for the desired protein is first linked to specific genes of the animal that are active only in its mammary (milk-producing) glands. The egg of the animal is then injected with the linked genes. The resulting transgenic animals will have these linked genes in every cell of their body but will produce the human protein only in their milk. The human protein is finally extracted from the animal’s milk for use as medicine. In this way, sheep’s milk is used to produce alpha-1-antitrypsin, an enzyme used in the treatment of emphysema; cow’s milk is used to produce lactoferrin, a protein that combats bacterial infections; and goat’s milk is used as yet another way to produce tPA, the blood-clot-dissolving enzyme also cloned in hamster cell cultures.

Recombinant DNA also is used in the production of vaccines against disease. A vaccine contains a portion of an infectious organism that does not cause severe disease but does cause the body’s immune system to form protective antibodies against the organism. When a person is vaccinated against a viral disease, the production of antibodies is actually a reaction to the surface proteins of the coat of the virus. With recombinant DNA technology, scientists have been able to transfer the genes for some viral-coat proteins to the cowpox virus, which was used against smallpox in the first efforts at vaccination in the late 18th century. Vaccination with genetically altered cowpox is now being used against hepatitis, influenza, and herpes simplex viruses. Genetically engineered cowpox is considered safer than using the disease-causing virus itself and is equally as effective.

In humans, recombinant DNA is the basis of gene therapy, in which genes within cells are removed, replaced, or altered to produce new proteins that change the function of the cells. The use of gene therapy has been approved in more than 400 clinical trials for diseases such as cystic fibrosis, emphysema, muscular dystrophy, adenosine deaminase deficiency, and some cancers. While gene therapy is a promising technique, many problems remain to be solved before gene therapy can reliably cure disease.

B   Patenting Genetically Engineered Products

It takes an average of seven to nine years and an investment of about $55 million to develop, test, and market a new genetically engineered product. Because of this great cost, companies have sought to patent the results of their discoveries. In 1980 the Patent and Trademark Office of the U.S. Department of Commerce issued its first patent on an organism that had been produced with recombinant DNA. The patent was for an oil-eating bacterium that could be used to clean up oil spills from ships and storage tanks. Since then, hundreds of patents have been granted for genetically altered bacteria, viruses, and plants. In 1988 the first patent was issued on a transgenic animal, a strain of laboratory mice whose cells were engineered to contain a cancer-predisposing gene. The mice are used to test low doses of suspected carcinogens, or cancer-causing substances, and to test the effectiveness of anticancer therapies.

C   Controversies

Public reaction to the use of recombinant DNA in genetic engineering has been mixed. The production of medicines through the use of genetically altered organisms has generally been welcomed. However, critics of recombinant DNA fear that the pathogenic, or disease-producing, organisms used in some recombinant DNA experiments might develop extremely infectious forms that could cause worldwide epidemics. In an effort to prevent such an occurrence, the National Institutes of Health (NIH) in the United States has established regulations restricting the types of recombinant DNA experiments that can be performed using such pathogens. In Canada, recombinant DNA products are regulated by various government departments, including Agriculture and Agri-Food Canada, Health Canada, Fisheries and Oceans Canada, and Environment Canada.

Animal rights groups have argued that the production of transgenic animals is harmful to other animals. Genetically engineered fish raise problems if they interbreed with other fish that have not been genetically altered. Some experts fear that this process may change the characteristics of wild fish in unpredictable and possibly undesirable ways. A related concern is that engineered fish may compete with wild fish for food and replace wild fish in some areas.

The use of genetically engineered bovine somatotropin (BST) to increase the milk yield of dairy cows is particularly controversial. Some critics question the safety of BST for both the cows that are injected with it and the humans who drink the resulting milk. In the United States, a large percentage of dairy cows are treated with BST, but in Canada, BST cannot legally be sold. Scientists at Health Canada rejected the legalization of BST in 1999 based on evidence that BST causes health problems for cows. In particular, the Canadian scientists found that BST increases a cow’s likelihood of developing mastitis, or infection of the udder, and it also makes cows more susceptible to infertility and lameness. Nevertheless, the scientists consider the milk obtained from cows injected with BST to be safe for human consumption.

Transgenic plants also present controversial issues. Allergens can be transferred from one food crop to another through genetic engineering. In an attempt to increase the nutritional value of soybeans, a genetic engineering firm experimentally transferred into soybean plants a Brazil-nut gene that produces a nutritious protein. However, when a study found that the genetically engineered soybeans caused an allergic reaction in people sensitive to Brazil nuts, the project was canceled.

Environmentalists fear that the transgenic plants may interbreed with weeds, producing weeds with unwanted characteristics, such as resistance to herbicides. An example of such interbreeding has been demonstrated in experiments involving transgenic oilseed rape. Environmentalists also argue that, due to natural selection, insects quickly develop resistance to plants that have been engineered to incorporate biological pesticides.

Opponents of genetic engineering warn that the use of genetically modified food crops could result in unforeseen problems. They point to a 1999 study that found that genetically modified corn produced pollen that killed monarch butterfly caterpillars in the laboratory. Although the study results were preliminary, as a precaution the Environmental Protection Agency (EPA) established new regulations in January 2000 to reduce potential risks posed by the corn crop. Among the new rules, the EPA has asked farmers to plant unmodified corn crops around the edges of genetically engineered corn fields in order to create a buffer that may prevent toxic pollen from blowing into butterfly habitats.

Many European and developing nations have voiced concern about the health and environmental risks associated with imported genetically modified food crops from the United States and other countries. In early 2000, 130 nations devised the Protocol of Biosafety. Formally approved in June 2003, the treaty requires exporting nations to notify importers when products contain genetically modified organisms, including seeds, food crops, cattle, and fruit trees.

Some critics object to the patenting of genetically altered organisms because it makes the organisms the property of particular companies. For example, Costa Rica has enacted laws to prohibit the patenting of genes of native Costa Rican species by drug companies in other countries. To date, no laws are in place in the United States and Canada regulating the use of cloning technology, and some people fear the prospect of human cloning. If this technology remains unregulated, critics fear that it will provide the ability to create an “improved” human being with characteristics predetermined according to a scientist’s particular bias.

 

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Virology

I   INTRODUCTION

Virus (life science), infectious agent found in virtually all life forms, including humans, animals, plants, fungi, and bacteria. Viruses consist of genetic material—either deoxyribonucleic acid (DNA) or ribonucleic acid (RNA)—surrounded by a protective coating of protein, called a capsid, with or without an outer lipid envelope. Viruses are between 20 and 100 times smaller than bacteria and hence are too small to be seen by light microscopy. Viruses vary in size from the largest poxviruses of about 450 nanometers (about 0.000014 in) in length to the smallest polioviruses of about 30 nanometers (about 0.000001 in). Viruses are not considered free-living, since they cannot reproduce outside of a living cell; they have evolved to transmit their genetic information from one cell to another for the purpose of replication.

Viruses often damage or kill the cells that they infect, causing disease in infected organisms. A few viruses stimulate cells to grow uncontrollably and produce cancers. Although many infectious diseases, such as the common cold, are caused by viruses, there are no cures for these illnesses. The difficulty in developing antiviral therapies stems from the large number of variant viruses that can cause the same disease, as well as the inability of drugs to disable a virus without disabling healthy cells. However, the development of antiviral agents is a major focus of current research, and the study of viruses has led to many discoveries important to human health.

II   STRUCTURE AND CLASSIFICATION

Individual viruses, or virus particles, also called virions, contain genetic material, or genomes, in one of several forms. Unlike cellular organisms, in which the genes always are made up of DNA, viral genes may consist of either DNA or RNA. Like cell DNA, almost all viral DNA is double-stranded, and it can have either a circular or a linear arrangement. Almost all viral RNA is single-stranded; it is usually linear, and it may be either segmented (with different genes on different RNA molecules) or nonsegmented (with all genes on a single piece of RNA).

The viral protective shell, or capsid, can be either helical (spiral-shaped) or icosahedral (having 20 triangular sides). Capsids are composed of repeating units of one or a few different proteins. These units are called protomers or capsomers. The proteins that make up the virus particle are called structural proteins. Viruses also carry genes for making proteins that are never incorporated into the virus particle and are found only in infected cells. These viral proteins are called nonstructural proteins; they include factors required for the replication of the viral genome and the production of the virus particle.

Capsids and the genetic material (DNA or RNA) they contain are together referred to as nucleocapsids. Some virus particles consist only of nucleocapsids, while others contain additional structures.

Some icosahedral and helical animal viruses are enclosed in a lipid envelope acquired when the virus buds through host-cell membranes. Inserted into this envelope are glycoproteins that the viral genome directs the cell to make; these molecules bind virus particles to susceptible host cells.

The most elaborate viruses are the bacteriophages, which use bacteria as their hosts. Some bacteriophages resemble an insect with an icosahedral head attached to a tubular sheath. From the base of the sheath extend several long tail fibers that help the virus attach to the bacterium and inject its DNA to be replicated and to direct capsid production and virus particle assembly inside the cell.

Viroids and prions are smaller than viruses, but they are similarly associated with disease. Viroids are plant pathogens that consist only of a circular, independently replicating RNA molecule. The single-stranded RNA circle collapses on itself to form a rodlike structure. The only known mammalian pathogen that resembles plant viroids is the deltavirus (hepatitis D), which requires hepatitis B virus proteins to package its RNA into virus particles. Co-infection with hepatitis B and D can produce more severe disease than can infection with hepatitis B alone. Prions are mutated forms of a normal protein found on the surface of certain animal cells. The mutated protein, known as a prion, has been implicated in some neurological diseases such as Creutzfeldt-Jakob disease and Bovine Spongiform Encephalopathy. There is some evidence that prions resemble viruses in their ability to cause infection. Prions, however, lack the nucleic acid found in viruses.

Viruses are classified according to their type of genetic material, their strategy of replication, and their structure. The International Committee on Nomenclature of Viruses (ICNV), established in 1966, devised a scheme to group viruses into families, subfamilies, genera, and species. The ICNV report published in 1995 assigned more than 4000 viruses into 71 virus families. Hundreds of other viruses remain unclassified because of the lack of sufficient information.

III   REPLICATION

The first contact between a virus particle and its host cell occurs when an outer viral structure docks with a specific molecule on the cell surface. For example, a glycoprotein called gp120 on the surface of the human immunodeficiency virus (HIV, the cause of acquired immunodeficiency syndrome, or AIDS) virion specifically binds to the CD4 molecule found on certain human T lymphocytes (a type of white blood cell). Most cells that do not have surface CD4 molecules generally cannot be infected by HIV.

After binding to an appropriate cell, a virus must cross the cell membrane. Some viruses accomplish this goal by fusing their lipid envelope to the cell membrane, thus releasing the nucleocapsid into the cytoplasm of the cell. Other viruses must first be endocytosed (enveloped by a small section of the cell’s plasma membrane that pokes into the cell and pinches off to form a bubblelike vesicle called an endosome) before they can cross the cell membrane. Conditions in the endosome allow many viruses to change the shape of one or more of their proteins. These changes permit the virus either to fuse with the endosomal membrane or to lyse the endosome (cause it to break apart), allowing the nucleocapsid to enter the cell cytoplasm.

Once inside the cell, the virus replicates itself through a series of events. Viral genes direct the production of proteins by the host cellular machinery. The first viral proteins synthesized by some viruses are the enzymes required to copy the viral genome. Using a combination of viral and cellular components, the viral genome can be replicated thousands of times. Late in the replication cycle for many viruses, proteins that make up the capsid are synthesized. These proteins package the viral genetic material to make newly formed nucleocapsids.

To complete the virus replication cycle, viruses must exit the cell. Some viruses bud out of the cell’s plasma membrane by a process resembling reverse endocytosis. Other viruses cause the cell to lyse, thereby releasing newly formed virus particles ready to infect other cells. Still other viruses pass directly from one cell into an adjacent cell without being exposed to the extracellular environment. The virus replication cycle can be as short as a couple of hours for certain small viruses or as long as several days for some large viruses.

Some viruses kill cells by inflicting severe damage resulting in cell lysis; other viruses cause the cell to kill itself in response to virus infection. This programmed cell suicide is thought to be a host defense mechanism to eliminate infected cells before the virus can complete its replication cycle and spread to other cells. Alternatively, cells may survive virus infection, and the virus can persist for the life of its host. Virtually all people harbor harmless viruses.

Retroviruses, such as HIV, have RNA that is transcribed into DNA by the viral enzyme reverse transcriptase upon entry into the cell. (The ability of retroviruses to copy RNA into DNA earned them their name because this process is the reverse of the usual transfer of genetic information, from DNA to RNA.) The DNA form of the retrovirus genome is then integrated into the cellular DNA and is referred to as the provirus. The viral genome is replicated every time the host cell replicates its DNA and is thus passed on to daughter cells.

Hepatitis B virus can also transcribe RNA to DNA, but this virus packages the DNA version of its genome into virus particles. Unlike retroviruses, hepatitis B virus does not integrate into the host cell DNA.

IV   DISEASE

Most viral infections cause no symptoms and do not result in disease. For example, only a small percentage of individuals who become infected with Epstein-Barr virus or western equine encephalomyelitis virus ever develop disease symptoms. In contrast, most people who are infected with measles, rabies, or influenza viruses develop the disease. A wide variety of viral and host factors determine the outcome of virus infections. A small genetic variation can produce a virus with increased capacity to cause disease. Such a virus is said to have increased virulence.

Viruses can enter the body by several routes. Herpes simplex virus and poxviruses enter through the skin by direct contact with virus-containing skin lesions on infected individuals. Ebola, hepatitis B, and HIV can be contracted from infected blood products. Hypodermic needles and animal and insect bites can transmit a variety of viruses through the skin. Viruses that infect through the respiratory tract are usually transmitted by airborne droplets of mucus or saliva from infected individuals who cough or sneeze. Viruses that enter through the respiratory tract include orthomyxovirus (influenza), rhinovirus and adenovirus (common cold), and varicella-zoster virus (chicken pox). Viruses such as rotavirus, coronavirus, poliovirus, hepatitis A, and some adenoviruses enter the host through the gastrointestinal tract. Sexually transmitted viruses, such as herpes simplex, HIV, and human papilloma viruses (HPV), gain entry through the genitourinary route. Other viruses, including some adenoviruses, echoviruses, Coxsackie viruses, and herpesviruses, can infect through the eye.

Virus infections can be either localized or systemic. The path of virus spread through the body in systemic infections differs among different viruses. Following replication at the initial site of entry, many viruses are spread to their target organs by the bloodstream or the nervous system.

The particular cell type can influence the outcome of virus infection. For example, herpes simplex virus undergoes lytic replication in skin cells around the lips but can establish a latent or dormant state in neuron cell bodies (located in ganglia) for extended periods of time. During latency, the viral genome is largely dormant in the cell nucleus until a stimulus such as a sunburn causes the reactivation of latent herpesvirus, leading to the lytic replication cycle. Once reactivated, the virus travels from the ganglia back down the nerve to cause a cold sore on the lip near the original site of infection. The herpesvirus genome does not integrate into the host cell genome.

Virus-induced illnesses can be either acute, in which the patient recovers promptly, or chronic, in which the virus remains with the host or the damage caused by the virus is irreparable. For most acute viruses, the time between infection and the onset of disease can vary from three days to three weeks. In contrast, onset of AIDS following infection with HIV takes an average of 7 to 11 years.

Several human viruses are likely to be agents of cancer, which can take decades to develop. The precise role of these viruses in human cancers is not well understood, and genetic and environmental factors are likely to contribute to these diseases. But because a number of viruses have been shown to cause tumors in animal models, it is probable that many viruses have a key role in human cancers.

Some viruses—alphaviruses and flaviviruses, for example—must be able to infect more than one species to complete their life cycles. Eastern equine encephalomyelitis virus, an alphavirus, replicates in mosquitoes and is transmitted to wild birds when the mosquitoes feed. Thus, wild birds and perhaps mammals and reptiles serve as the virus reservoir, and mosquitoes serve as vectors essential to the virus life cycle by ensuring transmission of the virus from one host to another. Horses and people are accidental hosts when they are bitten by an infected mosquito, and they do not play an important role in virus transmission.

V   DEFENSE

Although viruses cannot be treated with antibiotics, which are effective only against bacteria, the body’s immune system has many natural defenses against virus infections. Infected cells produce interferons and other cytokines (soluble components that are largely responsible for regulating the immune response), which can signal adjacent uninfected cells to mount their defenses, enabling uninfected cells to impair virus replication. Some cytokines can cause a fever in response to viral infection; elevated body temperature retards the growth of some types of viruses. B lymphocytes produce specific antibodies that can bind and inactivate viruses. Cytotoxic T cells recognize virus-infected cells and target them for destruction. However, many viruses have evolved ways to circumvent some of these host defense mechanisms.

The development of antiviral therapies has been thwarted by the difficulty of generating drugs that can distinguish viral processes from cellular processes. Therefore, most treatments for viral diseases simply alleviate symptoms, such as fever, dehydration, and achiness. Nevertheless, antiviral drugs for influenza virus, herpesviruses, and HIV are available, and many others are in the experimental and developmental stages.

Prevention has been a more effective method of controlling virus infections. Viruses that are transmitted by insects or rodent excretions can be controlled with pesticides. Successful vaccines are currently available for poliovirus, influenza, rabies, adenovirus, rubella, yellow fever, measles, mumps, and chicken pox. Vaccines are prepared from killed (inactivated) virus, live (attenuated or weakened) virus, or isolated viral proteins (subunits). Each of these types of vaccines elicits an immune response while causing little or no disease, and there are advantages and disadvantages to each. (For a more complete discussion of vaccines, see the Immunization article.)

The principle of vaccination was discovered by British physician Edward Jenner. In 1796 Jenner observed that milkmaids in England who contracted the mild cowpox virus infection from their cows were protected from smallpox, a frequently fatal disease. In 1798 Jenner formally demonstrated that prior infection with cowpox virus protected those that he inoculated with smallpox virus (an experiment that would not meet today’s protocol standards because of its use of human subjects). In 1966 the World Health Organization (WHO) initiated a program to eradicate smallpox from the world. Because it was impossible to vaccinate the entire world population, the eradication plan was to identify cases of smallpox and then vaccinate all of the individuals in that vicinity. The last reported case of smallpox was in Somalia in October 1977. An important factor in the success of eradicating smallpox was that humans are the only host and there are no animal reservoirs for smallpox virus. The strain of poxvirus used for immunization against smallpox was called vaccinia. Introduction of the Salk (inactivated) and Sabin (live, attenuated) vaccines for poliovirus, developed in the 1950s by the American physician and epidemiologist Jonas Salk and the American virologist Albert Bruce Sabin, respectively, was responsible for a significant worldwide decline in paralytic poliomyelitis. However, polio has not been eradicated, partly because the virus can mutate and escape the host immune response. Influenza viruses mutate so rapidly that new vaccines are developed for distribution each year.

Viruses undergo very high rates of mutation (genetic alteration) largely because they lack the repair systems that cells have to safeguard against mutations. A high mutation rate enables the virus to continually adapt to new intracellular environments and to escape from the host immune response. Co-infection of the same cell with different related viruses allows for genetic reassortment (exchange of genome segments) and intramolecular recombination. Genetic alterations can alter virulence or allow viruses to gain access to new cell types or new animal hosts. Many scientists believe that HIV is derived from a closely related monkey virus, SIV (simian immunodeficiency virus), that acquired the ability to infect humans. Many of today’s emerging viruses may have similar histories.

VI   DISCOVERY

By the last half of the 19th century, the microbial world was known to consist of protozoa, fungi, and bacteria, all visible with a light microscope. In the 1840s, the German scientist Jacob Henle suggested that there were infectious agents too small to be seen with a light microscope, but for the lack of direct proof, his hypothesis was not accepted. Although the French scientist Louis Pasteur was working to develop a vaccine for rabies in the 1880s, he did not understand the concept of a virus.

During the last half of the 19th century, several key discoveries were made that set the stage for the discovery of viruses. Pasteur is usually credited for dispelling the notion of spontaneous generation and proving that organisms reproduce new organisms. The German scientist Robert Koch, a student of Jacob Henle, and the British surgeon Joseph Lister developed techniques for growing cultures of single organisms that allowed the assignment of specific bacteria to specific diseases.

The first experimental transmission of a viral infection was accomplished in about 1880 by the German scientist Adolf Mayer, when he demonstrated that extracts from infected tobacco leaves could transfer tobacco mosaic disease to a new plant, causing spots on the leaves. Because Mayer was unable to isolate a bacterium or fungus from the tobacco leaf extracts, he considered the idea that tobacco mosaic disease might be caused by a soluble agent, but he concluded incorrectly that a new type of bacteria was likely to be the cause. The Russian scientist Dimitri Ivanofsky extended Mayer’s observation and reported in 1892 that the tobacco mosaic agent was small enough to pass through a porcelain filter known to block the passage of bacteria. He too failed to isolate bacteria or fungi from the filtered material. But Ivanofsky, like Mayer, was bound by the dogma of his times and concluded in 1903 that the filter might be defective or that the disease agent was a toxin rather than a reproducing organism.

Unaware of Ivanofsky’s results, the Dutch scientist Martinus Beijerinck, who collaborated with Mayer, repeated the filter experiment but extended this finding by demonstrating that the filtered material was not a toxin because it could grow and reproduce in the cells of the plant tissues. In his 1898 publication, Beijerinck referred to this new disease agent as a contagious living liquid—contagium vivum fluid—initiating a 20-year controversy over whether viruses were liquids or particles.

The conclusion that viruses are particles came from several important observations. In 1917 the French-Canadian scientist Félix H. d’Hérelle discovered that viruses of bacteria, which he named bacteriophage, could make holes in a culture of bacteria. Because each hole, or plaque, developed from a single bacteriophage, this experiment provided the first method for counting infectious viruses (the plaque assay). In 1935 the American biochemist Wendell Meredith Stanley crystallized tobacco mosaic virus to demonstrate that viruses had regular shapes, and in 1939 tobacco mosaic virus was first visualized using the electron microscope.

In 1898 the German bacteriologists Friedrich August Johannes Löffler and Paul F. Frosch (both trained by Robert Koch) described foot-and-mouth disease virus as the first filterable agent of animals, and in 1900, the American bacteriologist Walter Reed and colleagues recognized yellow fever virus as the first human filterable agent. For several decades viruses were referred to as filterable agents, and gradually the term virus (Latin for “slimy liquid” or “poison”) was employed strictly for this new class of infectious agents. Through the 1940s and 1950s many critical discoveries were made about viruses through the study of bacteriophages because of the ease with which the bacteria they infect could be grown in the laboratory. Between 1948 and 1955, scientists at the National Institutes of Health (NIH) and at Johns Hopkins Medical Institutions revolutionized the study of animal viruses by developing cell culture systems that permitted the growth and study of many animal viruses in laboratory dishes.

VII   EVOLUTION

Three theories have been put forth to explain the origin of viruses. One theory suggests that viruses are derived from more complex intracellular parasites that have eliminated all but the essential features required for replication and transmission. A more widely accepted theory is that viruses are derived from normal cellular components that gained the ability to replicate autonomously. A third possibility is that viruses originated from self-replicating RNA molecules. This hypothesis is supported by the observation that RNA can code for proteins as well as carry out enzymatic functions. Thus, viroids may resemble “prehistoric” viruses.

VIII   IMPORTANCE OF VIRUSES

Because viral processes so closely resemble normal cellular processes, abundant information about cell biology and genetics has come from studying viruses. Basic scientists and medical researchers at university and hospital laboratories are working to understand viral mechanisms of action and are searching for new and better ways to treat viral illnesses. Many pharmaceutical and biotechnology companies are actively pursuing effective antiviral therapies. Viruses can also serve as tools. Because they are efficient factories for the production of viral proteins, viruses have been harnessed to produce a wide variety of proteins for industrial and research purposes. A new area of endeavor is the use of viruses for gene therapy. Because viruses are programmed to carry genetic information into cells, they have been used to replace defective cellular genes. Viruses are also being altered by genetic engineering to kill selected cell populations, such as tumor cells. The use of genetically engineered viruses for medical intervention is a relatively new field, and none of these therapies is widely available. However, this is a fast-growing area of research, and many clinical trials are now in progress. The use of genetically engineered viruses extends beyond the medical field. Recombinant insect viruses have agricultural applications and are currently being tested in field trials for their effectiveness as pesticides.

Contributed By:
J. Marie Hardwick

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