Information

11.12: Genetic Information - Biology


The genetic information of an organism is stored in DNA molecules. For example, the E. coli bacterium carries its genetic instructions in a DNA molecule that contains more than five million nucleotides. The human genome (all the DNA of an organism) consists of around three billion nucleotides divided up between 23 paired DNA molecules, or chromosomes.

The information stored in the order of bases is organized into genes: each gene contains information for making a functional product. The genetic information is first copied to another nucleic acid polymer, RNA (ribonucleic acid), preserving the order of the nucleotide bases. Genes that contain instructions for making proteins are converted to messenger RNA (mRNA). Some specialized genes contain instructions for making functional RNA molecules that don’t make proteins. These RNA molecules function by affecting cellular processes directly; for example some of these RNA molecules regulate the expression of mRNA. Other genes produce RNA molecules that are required for protein synthesis, transfer RNA (tRNA), and ribosomal RNA (rRNA).

In order for DNA to function effectively at storing information, two key processes are required. First, information stored in the DNA molecule must be copied, with minimal errors, every time a cell divides. This ensures that both daughter cells inherit the complete set of genetic information from the parent cell. Second, the information stored in the DNA molecule must be translated, or expressed. In order for the stored information to be useful, cells must be able to access the instructions for making specific proteins, so the correct proteins are made in the right place at the right time.

Both copying and reading the information stored in DNA relies on base pairing between two nucleic acid polymer strands. Recall that DNA structure is a double helix (see Figure 1).

The sugar deoxyribose with the phosphate group forms the scaffold or backbone of the molecule (highlighted in yellow in Figure 1). Bases point inward. Complementary bases form hydrogen bonds with each other within the double helix. See how the bigger bases (purines) pair with the smaller ones (pyrimidines). This keeps the width of the double helix constant. More specifically, A pairs with T and C pairs with G. As we discuss the function of DNA in subsequent sections, keep in mind that there is a chemical reason for specific pairing of bases.

To illustrate the connection between information in DNA and an observable characteristic of an organism, let’s consider a gene that provides the instructions for building the hormone insulin. Insulin is responsible for regulating blood sugar levels. The insulin gene contains instructions for assembling the protein insulin from individual amino acids. Changing the sequence of nucleotides in the DNA molecule can change the amino acids in the final protein, leading to protein malfunction. If insulin does not function correctly, it might be unable to bind to another protein (insulin receptor). On the organismal level of organization, this molecular event (change of DNA sequence) can lead to a disease state—in this case, diabetes.

Practice Questions

The order of nucleotides in a gene (in DNA) is the key to how information is stored. For example, consider these two words: stable and tables. Both words are built from the same letters (subunits), but the different order of these subunits results in very different meanings. In DNA, the information is stored in units of 3 letters. Use the following key to decode the encrypted message. This should help you to see how information can be stored in the linear order of nucleotides in DNA.

ABC = aDEF = dGHI = eJKL = f
MNO = hPQR = iSTU = mVWX = n
YZA = oBCD = rEFG = sHIJ = t
KLM = wNOP = jQRS = pTUV = y

Encrypted Message: HIJMNOPQREFG – PQREFG – MNOYZAKLM – DEFVWXABC – EFGHIJYZABCDGHIEFG – PQRVWXJKLYZABCDSTUABCHIJPQRYZAVWX

[practice-area rows=”2″][/practice-area]
[reveal-answer q=”236947″]Show Answer[/reveal-answer]
[hidden-answer a=”236947″]This is how DNA stores information.

[/hidden-answer]

Where in the DNA is information stored?

  1. The shape of the DNA
  2. The sugar-phosphate backbone
  3. The sequence of bases
  4. The presence of two strands.

[reveal-answer q=”767717″]Show Answer[/reveal-answer]
[hidden-answer a=”767717″]Answer c. The sequence of the bases codes for the instructions for protein synthesis. The shape is DNA is not related to information storage. The sugar-phosphate backbone only acts as a scaffold. The presence of two strands is important for replication, but their information content is equivalent, as they are complementary to each other.

[/hidden-answer]

Which statement is correct?

  1. The sequence of DNA bases is arranged into chromosomes, most of which contain the instructions to build an amino acid.
  2. The sequence of DNA strands is arranged into chromosomes, most of which contain the instructions to build a protein.
  3. The sequence of DNA bases is arranged into genes, most of which contain the instructions to build a protein.
  4. The sequence of DNA phosphates is arranged into genes, most of which contain the instructions to build a cell.

[reveal-answer q=”363484″]Show Answer[/reveal-answer]
[hidden-answer a=”363484″]Answer c. The sequence of DNA bases is arranged into genes, most of which contain the instructions to build a protein. DNA stores information in the sequence of its bases. The information is grouped into genes. Protein is what is mainly coded.[/hidden-answer]


Biology Question Bank – 57 MCQs on “Biological Classification” – Answered!

57 Questions with Answers and Explanations on Biological Classification for Biology Students.

1. Static concept of species was put forward by

Answer and Explanation:

1. (c): Linnaeus, 1758 developed “Binomial system of nomenclature”, de Candolle gave the term taxonomy. Theophrastus, father of botany, gave names and descriptions of 480 plants in his book. ‘Histuria plantarum’ and Darwin proposed the theory of natural selection or origin of species.

2. The term “New Systematics” was introduced by

Answer and Explanation:

2. (c): The term “New Systematics” was given by Julian Huxley (1940). This classification takes into account the cytological, morphological, genetical, anatomical, palynological and physiological characters.

3. Classification given by Bentham and Hooker is

Answer and Explanation:

3. (b): Classification given by Bentham and Hooker is Natural System. Monocots were placed after dicots closely related families were seperated gymnosperms were placed between dicots and monocots.

4. The causal organism for African sleeping sickness i is

Answer and Explanation:

4. (d): Trypanosoma gambiense was first observed by Forde in 1901. It causes African sleeping sickness. The disease, also called trypanosomiasis, is found in western and central parts of Africa. The parasite is transmitted by blood sucking tse-tse fly, Glossina palpalis. Mouth and contractile vacuole are absent. Food is absorbed through the body surface.

The parasite multiplies by fission. In human beings the parasite lives in the blood plasma. It causes trypanosoma fever. It is accompanied by glandular swelling. Later the parasite enters cerebrospinal fluid and damages the brain. It makes the patient lethargic and unconscious. Because of it, the disease is called sleeping sickness. If untreated, the disease leads to death.

5. The vector for sleeping sickness is

Answer and Explanation:

5. (b): Trypanosoma gambiense was first observed by Forde in 1901. It causes African sleeping sickness. The disease, also called trypanosomiasis, is found in western and central parts of Africa. The parasite is transmitted by blood sucking tse-tse fly, Glossina palpalis. Mouth and contractile vacuole are absent. Food is absorbed through the body surface.

The parasite multiplies by fission. In human beings the parasite lives in the blood plasma. It causes trypanosoma fever. It is accompanied by glandular swelling. Later the parasite enters cerebrospinal fluid and damages the brain. It makes the patient lethargic and unconscious. Because of it, the disease is called sleeping sickness. If untreated, the disease leads to death.

6. Trypanosoma belongs to class

Answer and Explanation:

6. (b): On the basis of locomotory organelles the protozoan protists are divided into four groups : Mastigophora, Sarcodina, Sporozoa and Ciliata. Trypanosoma belongs to class zooflagellata which comes under the group mastigophora. The characteristics are:

(i) These zooflagellates are generally uninucleate, occasionally multinucleate.

(ii) The body is covered by a firm pellicle.

(iii) Nutrition is holozoic, parasitic and saprobic.

(iv) Reserved food is glycogen.

7. Malaria fever coincides with liberation of

Answer and Explanation:

7. (b): Symptoms of malaria first appear several days after the infection of the malaria parasite in man. This interval of time or the incubation period is utilized by the parasites to increase their progeny. To establish malarial symptoms, it is necessary that a large number of organisms must continue erythrocytic cycle at a time.

A healthy person acquires infection when a female Anopheles mosquito, containing infective stages of parasite (sporozoites) in its salivary glands, bites him for sucking his blood. Once within the numan blood, the sporozoites get into liverto invade the hepatic cells. Here they multiply asexually by schizogony.

Liver schizogony has two phases, pre-erythrocytic and exo-erythrocytic: Pre-crythrocytic phase: After penetrating a hepatic cell each sporozoite becomes a cryptozoite. It grows for a number of days and becomes a spherical and non- pigmented schizont.

It divides by schizogony (multiple fission) and forms a large number of uninucleate cells, the cryptomerozoites. During pre-erythrocytic schi7ogony, blood remains sterile and its inoculation does not produce infection.

Exo-erythrocvic phase: Cryptomerozoites enter fresh liver cells to become metacryptozoites. They undergo schizogony similar to the previous one producing enormous number of metacrypto-merozoites. Metacryptonierozoites, after escaping into blood stream, invade the erythrocytes or red blood corpuscles. This starts the erythrocytic schizogony. With erythrocytic schizogony, the symptom of malaria starts appearing.

8. A bite of Tse-tse fly may pass to humans

Answer and Explanation:

8. (b): The main vertebrate host is human. The principle invertebrate’s hosts are tsetse fly of the genus Glossina. T. gambiense is transmitted to human by biting of an infected tsetse fly after the cyclic development of the parasite.

9. Artificial system of classification was first used by

Answer and Explanation:

9. (a): Artificial system of classification was first used by Linnaeus. The cryptogams were included in flowering plants. Linnaeus system is known as sexual system of classification. He classified on the basis of number, size and union of sex organs.

10. System of classification used by Linnaeus was

Answer and Explanation:

10. (b): Linnaeus put forward an “Artificial system” of plant classification which was based on sexual characters like cryptogamia, monoecia, monandria, diandria, polyandria etc. It is commonly also called as sexual system of plant classification.

11. The infective stage of malaria parasite, Plasmodium that enters human body is

Answer and Explanation:

11. (b): The infective stage of Plasmodium is a minute organism called sporozoite. When the mosquito bites man, sporozoites present in the salivary gland of female Anopheles mosquito are injected into the blood of the man. These sporozoites are spindle-shaped or sickle- shaped uninucleate organisms capable of wrigging (worm­like) movements. Each sporozoite consists of elastic pellicle, cytoplasm and nucleus.

12. Genetic information in Paramecium is contained in

(c) both micronucleus and macronucleus

Answer and Explanation:

12. (a): Paramaecium contains a single large macronucleus and one small micronucleus. The macronucleus controls metabolism such as feeding and maintaenance, whereas the macronucleus takes and important role in reproduction and stores genetic information, hence it is also termed as reproductive nucleus whereas macronucleus is termed as vegetative nucleus.

13. Which is true about Trypanosoma?

Answer and Explanation:

13. (a): Trypanosoma is polymorphic i.e. it has more than one form. It has at least four forms that are recognized on the basis of the positions of kinetoplast and blepharoplast and the course taken by the tlagellum. Two or more such forms occur either in one or both the hosts in the life cycles of various species of Trypanosoma. These i forms are

(i) Leishmanial (amastigote): Round or oval form with a nucleus, blepharoplast and kinetoplast. Flagellum reduced and fibril-like embedded in cytoplasm.

(ii) Leptomonad (promastigote): Body elongate, nucleus large and anteriorly located blepharoplast and kinetoplast. Flagellum short and unattached.

(iii) Crithidial (epimastigote): Body elongate. Blepharoplast and kinetoplast placed immediately anterior to nucleus. Undulating membrane inconspicuous.

(iv) Trypanosomid (trypomastigote): Body elongate and slender. Blepharoplast and kinetoplast situated at or near posterior end. Undulating membrane conspicuous.

Tiypanosoma is digenetic i.e. it completes its life cycle in two hosts. It is an obligate parasite and is pathogenic.

14. Amoebiasis is prevented by

(b) eating plenty of fruits

Answer and Explanation:

14. (c): Amoebiasis can be prevented by drinking boiled water as it mainly occurs by ingestion of cysts of E. histolytica in food or drinks. The contamination of food or drinks occurs by (i) unhygienic habits of food handlers who by habit scratch the anus and then put the fingers in the food which they serve, (ii) habit of defecating in open fields causing contamination of vegetables and then washing the bottom in ponds causing the contamination of water, (iii) transmission of cysts from stools to food and drinks by flies and cockroaches. So, one should take following preventive measures:

(I) Proper sanitation of roads, streets, lanes and open drains.

(II) Purification of drinking water (by boiling).

(III) Proper disposal of sewage.

(IV) Covering of the food articles by the traders.

(V) Chemical trcatent of huma faeces to be used as fertilizer.

15. Plasmodium, the malaria parasite, belongs to class

Answer and Explanation:

15. (c): These protozoans are adapted to parasitic mode of life. All of them are endoparasites. Locomotory organelles (cilia, flagella. pseudopodia, etc.) are absent. Organelles connected with ingestion are absent. Nutrition is parasitic (absorptive). Sexual reproduction takes place through syngamy.

It is followed by spore formation, hence sporozoans. Life cycle consists of two distinct asexual and sexual phases. They may be passed in one (monogenetic) or two different hosts (digenetic).

16. Linnaeus evolved a system of nomenclature called

Answer and Explanation:

16. (c): Binomial nomenclature is the formal system of naming species. The essence of it is that each species name is in (modern scientific) Latin and has two parts, so that it is also sometimes popularly known as the ‘Latin name of the species’, although this terminology is frowned upon by biologists, who prefer the phrase scientific name.

17. Basic unit or smallest taxon of taxonomy/ classification is

Answer and Explanation:

17. (a): Basic unit or smallest taxon of taxonomy/ classification is species. Species is a group of individuals that remain relatively constant in their characteristics can be distinguished from other species and do not normally interbreed.

(a) a group of related families

(b) a group of related species

(c) a type of living organisms

(d) a taxonomic group of any ranking.

Answer and Explanation:

18. (d): The word taxon signify a taxonomic group of any rank which represents the real biological organisms included in a category. The term taxon was coined by Adolf Meyer (1926) for animals and H.J Lam (1948) used this term in plant Science.

19. Who discovered Plasmodium in R.B.C. of human beings?

Answer and Explanation:

19. (c): Laveran discovered that malaria is caused by protozoan parasite (Plasmodium) in 1880. He discovered Plasmodium and got Nobel Prize in 1907.

Sir Ronald Ross in 1897, a doctor in Indian Army, established that malaria parasite is transmitted by the bite of a female Anopheles mosquito and in 1902 he got Nobel Prize for this discovery.

20. Malignant tertian malaria parasite, belongs to class

Answer and Explanation:

20. (a): Plasmodium falciparum is the greatest killer of human beings over most parts of Africa and elsewhere in tropics. It causes malignant (or pernicious or cerebral or tropical) tertian malaria.

This malaria is most harmful. Plasmodium vivax causes benign tertian malaria. Plasmodium malariae causes quartan malaria. Plasmodium ovale is the rarest of the four species which infect man and it causes mild tertian malaria.

21. African sleeping sickness is due to

(a) Plasmodium vivax transmitted by Tsetse fly

(b) Trypanosoma lewsii transmitted by Bed Bug

(c) Trypanosoma gambiense transmitted by Glossina palpalis

(d) Entamoeba gingivalis spread by Housefly.

Answer and Explanation:

21. (c): Trypanosoma gambiense is the parasitic zoo flagellate which causes one of the deadliest ailments in human beings called sleeping sickness or trypanosomiasis. The disease is common in humid and subhumid zones of the African continent. The disease is transmitted by shade loving tsetse fly (Glossinapalpalis) which acts as the vehicle that carries the culprit protozoan parasite.

22. In Amoeba and Paramecium osmoregulation occurs through

Answer and Explanation:

22. (c): In Amoeba and Paramecium osmoregulation occurs through contractile vacoule. Osmoregulation is a phenomenon in which contractile vacuole plays an important role in maintaining the water balance of the cell. Paramaecium contains two contractile vacuoles which have fixed position.

One contractile vacuole is present near the anterior end while another is present towards posterior end of the body. Each contractile vacuole is surrounded by 5-12 radial canals. Excess of water is transferred from the cytoplasm to the radial canals. The latter pour water into the contractile vacuole. The contractile vacuole expels water outside the body.

Thus the contractile vacuoles and radial canals are for osmoregulation. In Amoeba the endoplasm, at its posterior end, contains a single, clear rounded and pulsating contractile vacuole, filled with a watery fluid and enclosed by a unit membrane. Surrounding this membrane is a region containing many tiny feeder vacuoles and mitochondria. It helps in the osmoregulatory and excretory activities of the animal.

23. A group of plu.nts or animals with siuilar traits of any rank is

Answer and Explanation:

23. (d): A taxon (plural taxa) or taxonomic unit, is a name designating an organism or group of organisms. A taxon is assigned a rank and can be placed at a particular level in a systematic hierarchy reflecting evolutionary relationships.

24. An important criterion for modern day classification is

(a) resemblances in morphology

(b) anatomical and physiological traits

(d) presence or absence of notochord.

Answer and Explanation:

24. (b): Taxonomy and classification are a part of the broader field of systematics which is the study of diversity of organisms. Classification of a part of systematics as it lists the unique characters of each taxon.

25. The part of life cycle of malaria parasite Plasmodium vivax, that is passed in female Anopheles is

(b) pre-crythrocytic schizogony

(c) exoerythrocytic schizogony

(d) post-erythrocytic schizogony.

Answer and Explanation:

25. (a): Plasmodium has two hosts.

(i) Female Anopheles mosquito: Here the sexual phase of the malaria parasite occurs and it is considered the definitive host of material parasite, (ii) Human beings: Here the asexual phase of malaria parasite occurs. It is considered as the intermediate host. Options (b), (c) and (d) are the stages of the asexual phase of Plasmodium.

26. The term phylum was given by

Answer and Explanation:

26. (a): The term phylum was given by Cuvier.

27. Sequence of taxonomic categories is

(a) class-phylum-tribe-order family- genus species

(b) di vision-class-family-tribe-order-genus- species

(c) division-class-order-family-tribe-genus- species

(d) phylum-order-class-tribe-family-genus- species

Answer and Explanation:

27. (c): To construct the hierarchy of classification, one or more species are grouped into a genus, one or more of genera into a family, families are clubbed into order, order into class, classes into phylum and various phyla into kingdom.

28. If all ponds and puddles arc destroyed, the organism likely to be destroyed is

Answer and Explanation:

28. (d): Plasmodium is digenetic i.e. it completes its life cycle in two hosts, asexual cycle in man and sexual cycle in Anophelesmosquito. The breeding place of this mosquito is ponds, marshes, swampy areas etc. So, if all the ponds and puddles are destroyed, Anopheles will not be able to survive leading to destruction of its parasite, Plasmodium.

29. Schizont stage of Plasmodium occurs in human cells

(c) erythrocytes and liver cells

(d) erythrocytes, liver cells and spleen cells.

Answer and Explanation:

29. (c): Schizont stage of Plasmodium occurs in human erythrocytes and liver cells. Within the human blood the sporozoites, circulates about half an hour and enters into the liver cell. The kupffer cells of the liver clear the sporozoites from the blood stream and kill many of the organisms. A fraction of sporozoites escape destruction, however, and penetrate the hepatocytes where they take up the residence. Here they multiply by schizogony.

30. Linnaeus is credited with

(c) discovery of microscope

(d) discovery of blood circulation.

Answer and Explanation:

30. (a): Binomial nomenclature of scientific naming was first given by C. Linnaeus (1735) in his book System a Naturae and later in “Species Plantarum” (1753). He used two Latin words for any organism, the first being generic name and the second is specific name. The generic name begins with capital letter and the species name with small letter.

(a) only free nucleic acid aggregates

(b) membrane bound nucleo proteins lying embedded in the cytoplasm

(c) gene containing nucleoproteins condensed together in loose mass

(d) nucleoprotein in direct contact with the rest of the cell substance.

Answer and Explanation:

31. (b): Protists include all unicellular and colonial eukaryotes except those of green and red algae. They are broadly divided into three groups – photosynthetic, slime moulds and protozoans. The protistan cells are typically eukaryotic having membrane bound organelles like mitochondria, chloroplasts, Golgi bodies, endoplasmic reticulum, nucleus etc. Nucleus is well defined. Protists can be uninucleate, binucleate or multinucleate. The genetic material is linear DNA, enclosed by nuclear envelope, complexed with proteins and organised into distinct chromosomes.

32. Phylogenetic classification is one which is basea

(d) common evolutionary descent.

Answer and Explanation:

32. (d): Phylogenetic systems of classification bring out evolutionary relationships of organisms. Phylogenetic
systems of classification came into existence after acceptance of doctrine of evolution and natural selection propounded by Charles Darwin in his book “On the origin of Species” by means of Natural Selection. Darwin had put forward the view that the present day plants/animals originated from some ancestral ones after undergoing some periodical changes.

So the phylogenetic classification is based on the evolutionary descent of a group of organisms and the relationships are depicted through a phylogram and a cladogram.

33. Tobacco mosaic virus (TMV) genes are

Answer and Explanation:

33. (a): Tobacco Mosaic Virus is a ribovirus and contains single stranded RNA. It was proved by the experiments ofFrankel Conart that RNA is the genetic material in this virus. It does not contain any DNA and is composed of 6 % RNA surrounded by a hollow cylinder of portion subunits.

Double stranded RNA is found in Reovirus and Tumor virus.

Retroviruses have two copies of single stranded RNA.

34. The tailed bacteriophages are

(a) motile on surface of bacteria

(c) motile on surface of plant leaves

(d) actively motile in water.

Answer and Explanation:

34. (a): The tailed bacteriophages contain a hollow helical tail which serves both as cell attachment organ and as a tube that facilitates the entry of nucleic acid into the host cell. The tail consists of tail plate and the caudal fibres.

35. BGA (blue green algae) is included in which of the following groups?

Answer and Explanation:

35. (b): According to Whittaker’s system, blue green algae are placed in kingdom monera which is the kingdom of prokaryotes. This is because they lack nucleus, DNA is naked and is folded variously to form nucleoid in the centre of the protoplast. In addition they lack membrane bound organelles including endoplasmic reticulum and ribosomes are of 70s type. So they are included under prokaryotes.

36. ‘Taxon’ is the unit of a group of

Answer and Explanation:

36. (b): Taxon refers to all the categories in the taxonomic hierarchy. It may be a kingdom, class, order, family, genus or species. It is any level of grouping of organisms. Each of these categories has been divided further into intermediate categories like subkingdom, subdivision, superclass, subgenus, subspecies etc. This term was coined by ICBN in 1956.

37. What is the genetic material in influenza virus?

Answer and Explanation:

37. (b): Influenza viruses are spherical in shape measuring about 800-1200A in diameter. It has a protein capsid that encloses a single stranded RNA. The single stranded RNA is generally linear and constitutes about 10% of the virus particle. RNA is genetic material in other viruses like poliomyelitis, foot and mouth disease virus and tobacco mosaic virus etc.

(a) ribosomes to synthesize protein

(b) organelle for its vitamin mechanism

39. In the five kingdom system of classification, which single kingdom out of the following can include blue-green algae, nitrogen fixing bacteria and methanogenic archaebacteria?

Answer and Explanation:

39. (c): R.H. Whittaker had proposed a five kingdom system of biological classification in 1969. It is based on complexity of cell structure, body organization and mode of nutrition. The kingdom monera includes all prokaryotes. They are basically unicellular with peptidoglycan in cell wall. Naked circular DNA coiled to form nucleoid without association with histones, ribosomes 70s, thylakoids present in photoautotrophs but other membrane bound organelles are absent.

These are heterotrophic, phototrophic or chemotrophic in their mode of nutrition. The blue-green algae, nitrogen fixing bacteria and methanogenic archaebacteria are all unicellular prokaryotes so they are included in the kingdom monera.

40. The book ‘Genera Plant arum’ was written by

Answer and Explanation:

40. (b): Bentham and Hooker in their monumental work Genera Plantarum (1862-1883) have provided elaborate keys for the easy identification of202 natural orders and genera. Engler and Prantl wrote Die naturlichen pflanzen familien. Huchinson wrote a book titled “The Families of Flowering Plants.”

41. A system of classification, in which a large number of traits are considered, is

Answer and Explanation:

41. (a): There are three systems of classification – artificial, natural and phylogenetic. In the natural system of classification the organisms are arranged on the basis of all known taxonomic characters instead of one or first few. These include morphological, anatomical, cytological, and physiological and biochemical characters of the organisms.

The artificial system is based on one or a few characters that are easily observable. The phylogenetic system tries to organize organisms on the basis of their genetic and phylogenetic relationships besides taxonomic characters.

42. Which of the following is less general in characters as compared to genus?

Answer and Explanation:

42. (a): A taxonomic hierarchy is the sequence of arrangement of taxonomic categories in a descending order during the classification of an organism. There are seven obligate categories – kingdom, division, class, order, family, genus and species. Species is the lowest category while kingdom is the highest category.

The number of common characters is maximum in case of organisms placed in the lowest category. Number of common characters decreases with the rise in category. Species are the smallest group of individuals which can be recognized by ordinary methods as groups and which arc consistently and persistently different from other groups because their characters are less general.

43. Cauliflower mosaic virus contains

Answer and Explanation:

43. (c): Cauliflower mosaic virus contain ds DNA. It is circular and shows semidiscontinuous type of replication.

44. In five kingdom system, the main basis of classification of

Answer and Explanation:

44. (b): Whittaker’s system is based on the following three criteria –

• complexity of cell structure.

• complexity of the body organization.

On the basis of these criteria, Whittaker divided organisms into five kingdoms. These five kingdoms are monera, protista, algae, fungi and animalia. In the five kingdom classification all, prokaryotes have been placed in kingdom monera, all unicellular eukaryotes in kingdom protista, fungi (except slime moulds and water moulds) in their separate kingdom while kingdom plantae and kingdom animalia have been retained for multicellular, autotrophic and multicellular holozoic organisms respectively.

45. Biosystematics aims at

(a) the classification of organisms based on broad morphological characters

(b) delimiting various taxa of organisms and establishing their relationships

(c) the classification of organisms based on their evolutionary history and establishing their phylogeny on the totality of various parameters from all fields of studies

(d) identification and arrangement of organisms on the basis of their cytological characteristics

Answer and Explanation:

45. (c): Biosystematics is the study of identification, nomenclature classification and relationships amongst living beings. In other words, it is the study of diversity of organisms, their comparative and evolutionary relationships based on comparative anatomy, ecology, physiology, biochemistry and other fields.

46. In which kingdom would you classify the archaea and nitrogen-fixing organisms, if the five-kingdom system of classification is used?

Answer and Explanation:

46. (d): The kingdom monera includes all prokaryotes. They are basically unicellular but can be mycelial, colonial and filamentous. They contain peptidogycan in cell wall. Naked circular DNA coiled to form nucleoid without association with histones, ribosomes 70s, thylakoids present in photoautotrophs but other membrane bound 1 organelles are absent. Nutrition is of various types – parasitic, chemoautotrophic, photoautotrophic and saprobic.

Some monerans have the ability to fix nitrogen. Due to presence of these characters in arehaea and nitrogen- fixing organisms they are placed under monera.

All others fungi, plantae, protists and animalia are eukaryotic.

47. Phenetic classification is based on

(a) the ancestral lineage of existing organisms

(b) observable characteristics of existing organisms

(c) dendrograms based on DNA characteristics

Answer and Explanation:

47. (b): Phenetic classification is a type of numerical taxonomy. In this type of classification the organisms are arranged according to overall similarity of existing organisms based on available characters.

It is also called adansonian taxonomy because the same was first attempted by Adanson (1763), of course on the basis of external traits only. Numerical taxonomy evolved around 1950.

It has received impetus with the availability of calculating machines and computers. In numerical taxonomy as many characters as possible are employed for evaluating degree of similarity and difference. All characteristics used in analysis are given equal weightage and importance.

A proper selection of characters, their organisation and analysis in the light of current knowledge is key to success of this method. A lot of subjectivity can creep in depending upon the judgement of the biosystematist. No weightage is given to the quantity of the character present.

48. Species are considered as

(a) real basic units of classification

(b) the lowest units of classification

(c) artificial concept of human mind which cannot be defined in absolute terms

(d) real units of classification devised by taxonomists

Answer and Explanation:

48. (a): Species is a natural population or group of natural populations of individuals which are genetically distinct and reproductively isolated with similar essential morphological traits. Species is also a genetically closed system because its members do not interbreed with members of other species. Species is lowest or basic taxonomic category, e.g., mango

Here indica, tuberosum, Leo are species of genera Mangifera, Solatium and Pantera respectively. All other taxonomic categories are defined and described in relation to species. For example, a genus is a group of species and a subspecies or a variety is a part of species. New species originate from already existing species. Species is considered basic unit of taxonomy since in the greater majority of cases we do not have intraspecific names.

49. Viruses are no more “alive” than isolated chromosomes because

(a) they require both RNA and DNA

(b) they both need food molecules

(c) they both require oxygen for respiration

(d) both require the environment of a cell to replicate

Answer and Explanation:

49. (d): Viruses contain a protein coat that encloses a single type of nucleic acid, either RNA or DNA. They multiply only inside the living host cells and for this they take over the machinery of the host cell. They lack cell division and enzymes for protein synthesis. They do not have cell 01 ganclles like mitochondria, Golgi complex, lysosomes ribosomes etc. so they cannot live or reproduce separately.

50. Tobacco mosaic virus is a tubular filament of size

Answer and Explanation:

50. (c): TMV is rod shaped measuring 300 20 nm. It is made of RNA and proteins.

51. Which one of the following statements about viruses is correct?

(a) viruses possess their own metabolic system

(b) all viruses contain both RNA and DNA

(c) viruses are obligate parasites

(d) nucleic acid of viruses is known as capsid

Answer and Explanation:

51. (c): Viruses contain a protein coat known as capsid which encloses a single type of nucleic acid, either RNA or DNA. They do not have enzymes for protein synthesis. They multiply only inside the living host cell and for multiplication they take over the machinery of the host cell. Thus viruses are obligatory intercellular parasites.

52. Phenetic classification of organisms is based on

(a) observable characteristics of existing organisms

(b) the ancestral lineage of existing organisms

(c) dendogram based on DNA characteristics

Answer and Explanation:

52. (a) Refer to Explanation 47

53. Viruses that infect bacteria multiply and catise their lysis, are called

Answer and Explanation:

53. (c): Viruses like bacteriophage T4 undergo lytic cycle that involves lysis of bacteria. The replication cycle of bacteriophage T4 consists of following phases –

(i) Adsorption of the phage to bacterial or host cell. Then the viral genetic material penetrates into the host cell.

(ii) Eclipse period involves the synthesis of new phage DNA and proteins.

(iii) Maturation involves the assembly of phage DNA into the protein coat.

(iv) Lysis of host cell occurs and releases infective progeny phases.

54. Which of the following statements is not true for retroviruses?

(a) DNA is not present at any stage in the life cycle of retroviruses

(b) Retroviruses carry gene for RNA-dependent DNA polymerase

(c) The genetic material in mature retroviruses is RNA

(d) Retroviruses are causative agents for certain kinds of cancer in man.

Answer and Explanation:

54. (a): Retroviruses contain RNA as genetic material and this RNA is converted to DNA using enzyme reverse transcriptase.

55. One of the most important functions of botanical gardens is that

(a) they provide a beautiful area for recreation

(b) one can observe tropical plants there

(c) they allow ex-situ conservation of germ plasm

(d) they provide the natural habitat for wild life.

Answer and Explanation:

55. (c): Ex situ conservation means “offsite conservation”. It is the process of protecting endangered species of plants and animals by removing it from an unsafe or threatened habitat and placing it or part of it under the care of humans. Botanical gardens serve as ex situ conservation of germplasm of different plants, to maintain rare and endemic plant species and also to provide recreation and knowledge about plants to a comnian man.

(a) International Code of Botanical Nomenclature

(b) International Congress of Biological Names

(c) Indian Code of Botanical Nomenclature

(d) Indian Congress of Biological Names.

Answer and Explanation:

56. (a): The International Code of Botanical Nomenclature (ICBN) is a set of rules and recommendations dealing with the formal botanical names given to plant. The foundations of ICBN are given in book written by C. Linnaeus named Philosophia Botanica. It is independent of zoological nomenclature, i’lie rank of species is basic and relative orders of the ranks of taxa are as: species, genus, tribe, family, order, series, class, division and kingdom.

The different ranks or categories have following specific endings of their names as division – phyla, class, and family-aceae.

57. Which one of the following is a slime mould?

Answer and Explanation:

57. (a): Slime moulds are peculiar protista that normally take the form of amoebae, but under certain conditions develop fruiting bodies that release spores, superficially similar to the sporangia of fungi.

The order physarales include Physarum species. The fruiting bodies (sporangia) are characterized by the presence of abundant amount of calcium salt. The order comprises 142 species which are placed under 12 genera. Physarum polycephalam is the best known. The somatic phase is multinucleate, diploid holocarpic Plasmodium which is the product of syngamy.


11.12: Genetic Information - Biology

The role of public health is to ensure that the basic conditions required for people to be healthy are present. Until recently, public health focused mostly on environmental causes and risk factors for disease, such as infections, cigarette smoking, diet, etc. Since the sequencing of the human genome has been completed, high hopes rest on the potential to prevent the impact of genetic risk factors or susceptibilities to disease. Advances in genetic knowledge and technology could be used to try to prevent disease and improve population health.

The perceived role of genetics in public health is changing, as is the definition of what is a genetic disease. The role of genetics in public health is broadened if we consider all the diseases for which genetics might play a role, either by the presence of a genetic susceptibility for the development of this disease or for response to treatment, or by the presence of protective genetic factors, such as in resistance to infection.

One day, it might be possible to determine for each individual which genetic susceptibilities and protective factors each individual possesses, and act accordingly to prevent the occurrence of disease. In the meantime, the role of genetics in public health is mostly limited to monogenic diseases.

II - Populations targeted by public health genetics interventions

Public health considers the overall health of the population as a group, and not the health of each individual. Since resources for public health interventions are limited, priorities need to be established to determine which interventions will be most beneficial to the population as a whole. These priorities will be based on the characteristics of the disease, such as its prevalence, its severity, and treatment availability, as well as the amount of resources needed for the intervention.

Monogenic diseases are rare. Is it justifiable to implement population-based interventions to identify a few rare cases of a particular genetic disease? There is no single right answer to this question. It depends on the burden these rare cases represent for society, on our ability to act to attenuate this burden, and on the value we place on obtaining an early diagnosis, compared to the complexity of detecting these cases and the amount of resources needed to detect them. For example, newborn screening for phenylketonuria is considered beneficial because it makes it possible for the children identified through screening, who would otherwise have developed severe mental retardation, to develop normally by following a special diet. In the majority of developed countries, all newborns are screened for phenylketonuria to detect a handful of cases, because the impact of treatment on these children’s potential ability to contribute to society is so great. On the other hand, similar newborn screening for Huntington disease is not being considered, because it is a late-onset disease for which there is no treatment and no clear benefit to an early diagnosis. Screening would not change the impact of the disease on the affected individuals or its burden on society.

To improve the yield of a screening program for a genetic disease, one option is to target a population at higher risk of disease, often the families of affected cases. This approach limits the amount of resources needed for screening and increases the yield of screening. It unfortunately is limited by the fact that many new cases of genetic disease occur in individuals with no family history who would not be identified by family-based screening. In some cases, ethnic groups can be the target population of screening programs, when prevalence of the disease in questions is particularly high in that ethnic group. For example, Ashkenaze Jewish populations are screened for Tay-Sachs disease. In programs targeted at specific communities, it is important to ensure that the community is in favor of screening and that it does not become a source of stigmatization for the community.

III - Ethical, legal, and social implications of public health genetic interventions

III - 1. Use of genetic information: confidentiality and discrimination

The issue of confidentiality of genetic information is frequently raised. Genetic information is different from other types of personal information found in a medical chart. First, genetic information does not change over time: the presence of a mutation or a polymorphism in an individual is immutable. Second, genetic information about one individual has implications not only for the individual in question, but also for his/her family members, since the genetic abnormalities are heritable in most cases. In some cases, genetic information is used to confirm a clinical diagnosis, but it is increasingly used to confer a level of risk or susceptibility for the development a specific condition. In that context, it is not surprising that some are worried that information about a specific genetic susceptibility might be used by insurers or employers as a source of discrimination.

III - 2. DNA banks

Genetic research often requires the collection of DNA samples. Many DNA banks were formed from DNA samples collected for specific research projects or from blood samples collected for newborn screening. Once they have served their intended use, what should now be done with these samples? Who do they belong to? Can the researcher use them for other purposes without the consent of those who gave these samples? Can he only do it if he anonymizes the samples first? Or does the researcher need to contact each individual to renew his/her consent? To respect the autonomy of individuals who participated in previous research projects, it would be necessary to contact them again to obtain renewed consent before using their samples for other research projects. On the other hand, these samples are easily accessible and could be used to further scientific knowledge for the benefit of society without major negative impact on the individual who provided the sample, especially if the samples are anonymized. In some cases, the nature of the prospective research will also influence the decision to use or not use samples from a DNA bank. Researchers and ethicists all over the world are faced with these issues. Institutional review boards are assessing each research project based on its specific context, because no consensus has been reached for now on procedures for the use of DNA banks in research.

III - 3. Prenatal diagnosis, assisted reproduction and embryo selection

Assisted reproduction has made it necessary to redefine fundamental concepts, such as paternity and maternity. We now use the terms biological mother, gestational mother (or surrogate mother), and social mother. We also differentiate between biological father and social father. Before DNA tests, paternity was always assumed, but it is now possible to determine with strong certainty whether an individual is or isn’t a given child’s biological father. In the past, maternity was simply attributed to the woman who had given birth to the child. But these days, it is possible for a woman to have an embryo conceived with her own eggs carried to term by another woman. The first woman is then the biological mother, and the second the gestational mother. The social mother will be the one acting as a parent to the child in question.

Assisted reproduction is not reserved for infertile couples anymore, but is also used by couple who want to ensure that their child will be born without a specific hereditary disease, or even to make sure that their child will be a matched donor for an older sibling in need of a bone marrow transplant. Genetic tests performed on embryos make it possible to select only embryos that fit certain criteria. For now, this technology is mostly used to avoid the birth of children with severe hereditary childhood diseases, but it is feared that it opens the door to embryo selection based on other criteria, such as physical appearance or intellectual ability.

When a pregnant woman is offered the possibility of undergoing prenatal diagnosis for genetic diseases through amniocentesis or chorionic villous sampling, it implies that selective abortion is an option they will consider if the fetus is indeed affected with a genetic disease. For some, this option is unacceptable for ethical, moral, and/or religious reasons. It raises the question of the legal status of the embryo, the definition of human life and of a human being.

IV - Examples of the role of public health in genetics

There are already many examples of the role of public health in genetics. Better known examples deal with reproductive technologies (prenatal screening, carrier screening) and newborn screening. More recent examples in the adult setting concern genetic susceptibility screening and pharmacogenetics.

IV - 1. Folic acid and neural tube defects

Neural tube defects (NTD) account for an important part of birth defect-related infantile mortality and morbidity. Their incidence tends to be decreasing over time (secular trend). During the 1980s, studies have shown a decrease in the recurrence of NTD in subsequent pregnancies with the use of folic acid for women having already had a child with a NTD. Since then, studies done in women with no family history of NTD have also shown lower incidence rates of children born with NTD in women who took folic acid supplements. Even though the way in which folic acid acts to prevent NTD has not been elucidated, these observed findings have led to the hypothesis that folic acid supplementation would be beneficial to all women planning a pregnancy, to prevent the birth of a child with a NTD.

Because the neural tube closes during the fourth week of gestation, it is recommended to start folic acid supplementation before conception. The minimal dose needed to obtain an effect has not been established, but the usually recommended daily dose is 400 micrograms in women with no specific risk factor, and should be started at least 3 months before conception. However, supplementation often does not occur, either because women are not aware of the benefits of folic acid supplementation or because pregnancy was not planned.

To address this problem, some countries have decided to add folic acid to the food supply, most often in flour. This type of public health intervention has occurred in the past to prevent other diseases: iodized salt to prevent goiter, and vitamin D in milk to prevent rickets.

Folic acid fortification of flour has not been done without controversy. Some fear that folic acid fortification will mask vitamin B12 deficiency and delay its diagnosis. Others worry about long-term effects of a folic acid-fortified diet or about potential interactions between folic acid and prescribed drugs. No study has shown that this fortification strategy would be sufficient to reduce the incidence of NTD in the population. In spite of all that, many professional organizations have declared themselves in favor of fortification. Folic acid fortification has been established at the end of the 1990s in many developed countries, most often in flour. Studies done since fortification seem to show a significant reduction in the incidence of NTD in the population, even when accounting for the secular trend.

IV - 2. Newborn screening

for phenylketonuria (PKU) is the first example of population-based genetic screening. It was put in place in the U.S.A. in the early 1960s, thanks to the development by Dr Robert Guthrie of a technique allowing the measurement of blood phenylalanine levels using blood samples collected on filter paper. Samples collected in this way are easy to store and ship, and can be preserved for extended periods of time. The technique itself is cheap and easy to perform. These characteristics have made it possible to develop large-scale screening programs. Newborn screening for PKU is now performed by the state in most developed countries.

In the wake of newborn screening tests, a screening “system” was developed. Today, a newborn screening system includes sample collection and shipment to screening facilities, performance of the screening test in the laboratory, diffusion of test results to parents and referring physicians, and, for newborns with abnormal results, rapid access to specialized evaluation and appropriate care. In parallel, severe quality control criteria have been established and voluntary laboratory quality control programs are managed by government agencies, such as the Center for Disease Control in the U.S.A.

Since the 1960s, other diseases have been added to newborn screening panels. The list varies by region, but it almost always includes congenital hypothyroidism, and often includes galactosemia, tyrosinemia, sickle cell anemia, and/or congenital adrenal hyperplasia. For all these diseases, a dietary-based or drug-based treatment is available to prevent the effects of the disease or attempt to control their progression, and it seems preferable to start these treatments as early as possible.

In the last few years, a new technology, tandem mass spectrometry (MS/MS), makes it possible to detect over 30 metabolic diseases during the newborn period, such as aminoacidemias, organic acidurias, and urea cycle defects, to name a few. The use of this technology for newborn screening is controversial for several reasons. Among the diseases that can be detected with MS/MS, some have a poorly defined natural history. In those cases, it is difficult to predict what will happen to the affected newborn and the impact that early diagnosis and treatment could have. It is not clear whether dietary treatment will be as effective in all cases. However, newborn screening using MS/MS would make it possible to learn more about these diseases, which might otherwise go undetected (even if symptomatic). In the U.S.A., advocacy groups formed by parents of children with diseases detectable with MS/MS are lobbying for the addition of this technology to state-run newborn screening programs. Those opposed to using MS/MS for newborn screening argue that there is no evidence that early diagnosis and treatment of these diseases will improve their natural course, which goes against the criteria largely used to decide whether or not to add new diseases to newborn screening programs. They stress that the availability of the technology and its capacity to detect disease does not mean that the information it provides is valuable for newborns.

Newborn screening for cystic fibrosis is also currently debated. Newborn screening programs for cystic fibrosis already exist in many regions of the world: in Wisconsin and Colorado (USA), in Brittany (France), and some regions of the United Kingdom and Australia. Some studies have shown that children identified through newborn screening achieve better nutritional status and/or better respiratory function than those diagnosed through symptoms, but these differences are mild and tend to disappear over time. The main newborn screening criteria, as defined by the World Health Organization, state that an effective treatment must be available and that the early application of that treatment must improve the health outcome of the child. Even though long term impact of early diagnosis of cystic fibrosis on the evolution of disease has not been irrevocably established, some argue that early diagnosis is of benefit to parents because it avoids unnecessary anxiety related to delayed diagnosis in a symptomatic child, and enables them to make informed reproductive decisions for future pregnancies. The benefit is not for the child itself, but for parents, and it is not related to the early onset of effective treatment. According to this argument, it would be justifiable to screen for genetic conditions with no known effective treatment but whose early diagnosis would be of value to the parents. In the case of cystic fibrosis, early diagnosis can possibly be of value to the child, but this would not be the case for other diseases for which newborn screening has been advocated, such as Duchenne muscular dystrophy and Fragile X syndrome.

IV - 3. Carrier screening in the context of reproductive decisions

The first carrier-screening program for recessive diseases was developed in the Ashkenazi Jewish communities in New York and Washington, D.C., in the U.S.A. With the support of the community and religious officials, a carrier-screening program for Tay-Sachs disease was established in the early 1970s, shortly after the discovery of the enzyme whose deficiency is the cause of the disease. Tay-Sachs disease then had a relatively high prevalence in the Ashkenazi Jewish community. This disease causes progressive neurodegeneration starting in the first year of life and inevitably leading to the child’s death, usually by four years of age. Both the community members and the health professionals involved agreed that this disease is so severe that it would be preferable to take measures to avoid the birth of affected children. The screening strategy has been adapted to the needs and realities of the different communities: in orthodox communities where selective abortion was not acceptable, premarital screening is performed and results are taken into account in the rabbi’s decision to bless the marriage or not, which has been deemed acceptable by the community. Carrier screening programs for Tay-Sachs disease now exist in Ashkenazi Jewish communities around the world. Thanks to these programs, the incidence of the disease has decreased by over 90% in these communities. In the wake of this success, other diseases with relatively high prevalence in Ashkenazi Jewish communities have been added to carrier screening panels, such as Canavan disease and Gaucher disease, to name a few.

In response to the success of Tay-Sachs carrier screening in Ashkenazi Jewish communities, similar programs have been developed in other communities where an autosomal recessive disease was highly prevalent in children, such as carrier screening for beta-thalassemia in Cyprus and Sardinia. These programs have also led to drastic reductions in disease prevalence in these communities. Carrier screening programs for sickle cell anemia in African Americans in the U.S.A. in the 1970s have not had the same success, partly because the distinction between being a healthy carrier and having the disease was not made clear. This had led to discrimination against carriers.

Recently, the American College of Obstetrics and Gynecology has recommended that all pregnant women be offered carrier screening for cystic fibrosis. This recommendation has been questioned by some, because screening is routinely offered when pregnancy is already ongoing and because cystic fibrosis is not considered as severe as Tay-Sachs disease.

IV - 4. Prenatal screening for aneuploidy and neural tube defects

For a detailed discussion of what is available in prenatal diagnosis, see “Prenatal Diagnosis” section.

In terms of population health, it is of note that prenatal screening for chromosomal abnormalities and neural tube defects is offered to pregnant women in many countries. These screening programs may be targeted at women with specific risk factors (i.e. according to maternal age), or to all pregnant women. In most cases, newborns with chromosomal abnormalities or neural tube defect are born of mothers with no specific risk factors. A screening test done during pregnancy can identify those women at higher risk of carrying a fetus with one of these conditions. This blood test, which measures a combination of serum and/or ultrasound markers, is not a diagnostic test: like all screening tests, it tends to be highly sensitive, but not necessarily very specific. The role of a screening test is to detect all cases of the targeted condition, at the expense of a certain amount of false positive results. For prenatal screening, the test result is usually given as the probability that the fetus is affected, and the result is considered “positive” when this probability is higher than a specific threshold, usually between 1/400 and 1/200. Since this threshold is relatively low, there is inevitably a high proportion of false positive results, i.e. pregnancies with test results above the threshold and considered at high risk of having an affected fetus, but whose fetus is actually not affected. In a screening context, we tolerate a certain amount of false positive results that will have to undergo definitive diagnostic testing through amniocentesis and incur the associated risk of miscarriage. It is the price to pay to reduce as much as possible the rate of false negative results, i.e. a result placing the risk below the threshold when the fetus is actually affected. These screening programs have been developed to give women the possibility of terminating the pregnancy if the fetus is found to be affected. In general, this option is considered acceptable because most people consider these conditions to be severe enough and prevalent enough to justify a population-based screening program. Those who consider termination to be unacceptable can select out of the screening process.

IV - 5. Screening for genetic susceptibilities in adults

Since the sequencing of the human genome, advances in genetic knowledge has led us to consider the potential use of genetic information to assess individual susceptibilty to disease. Although this is not widely possible yet, there are some examples of the use of genetic tests for that purpose. These examples raise questions about the real clinical utility of that type of information at the individual level.

Hereditary hemochromatosis is an autosomal recessive disease. Individuals who suffer from this disease can develop cirrhosis of the liver, diabetes, and cardiomyopathy. Symptoms are caused by a defect in iron metabolism, which leads to iron deposition in tissues. Two main mutations in the hemochromatosis gene have been identified, C282Y and H63D. Most cases are C282Y homozygotes. Regular phlebotomies reduce iron deposition and can help prevent or reduce symptoms. For that reason, hemochromatosis is considered an ideal target for population-based screening. The use of a genetic test as a screening test for hereditary hemochromatosis is justified if we assume that penetrance of the disease is high, i.e. that most C282Y homozygotes will develop symptoms of hemochromatosis in their lifetime if untreated, and that they would benefit from early diagnosis and preventive treatment. Unfortunately, penetrance seems lower than previously thought: it seems that only a minority of C282Y homozygotes actually develop symptoms of hemochromatosis in their lifetime. The value of population-based genetic screening for hemochromatosis is being questioned. It is currently recommended to use transferrin saturation level as a screening test for hemochromatosis. This is a biochemical index of iron overload, and is closer to the phenotype of hemochromatosis than the genetic test.

Factor V Leiden (FVL) is a variant of factor V, a coagulation factor. This variant is associated with an increased risk of thrombosis. Even though the presence of FVL in an individual with a history of thrombosis can help explain the cause of the thrombosis, it does not usually change immediate treatment or long-term management of that individual, who will be treated as any other individual with a personal history of thrombosis. On the other hand, not all individuals who have FVL will develop thrombosis. It is difficult to justify population-based screening for FVL, and especially to submit them to long-term prophylactic anticoagulation treatment, which is associated with significant risks of bleeding. Other factors also influence the risk of thrombosis in these individuals, such as smoking and hormonal therapy, and make it difficult to predict risk of thrombosis on an individual basis.

As our knowledge of gene-environment interactions increases, it might be possible to improve our assessment of individual disease susceptibility by using predictive models based on combinations of genetic and environmental risk factors. For now, the impact of genetic susceptibility is difficult to assess, especially on an individual basis.

IV - 6. Pharmacogenetics and ecogenetics

Pharmacogenetics is a field of genetics focusing on the role of genetics in individual variability of drug response and side effect occurrence. If we can predict the pharmacologic response of a given individual to a specific drug based on the presence or absence of a given genetic polymorphism, we could adjust dosage accordingly. Most genetic polymorphism studied until now have been in genes involved in the metabolism or elimination of drugs. It is thought that these polymorphisms might accelerate or slow drug metabolism or drug elimination.

Ecogenetics is similar to pharmacogenetics, but focuses on the role of genetics in explaining the individual variability of response to environmental factors (carcinogens, pesticides, food products, industria pollutants, etc.), instead of response to drugs. This information could be used in the workplace to identify individual workers at risk of developing complications related to occupational exposure to specifc agents. There is the danger that this might be used to discriminate against those with genetic susceptibility to develop complications, who might be refused employment. On the other hand, workers at low-risk of complications might be exposed to higher levels of the agent in question if it gives them a false sense of security and protective measures are lessened, which would paradoxically put them at higher risk of actually developing complications.

IV - 7. Personalized Health Care and Genetic Information

Some hope that a better understanding of genetic variability will help adapt treatments on the basis of an individual’s genetic characteristics and the risks and benefits of the many treatment options available for that individual. This will depend on how fast knowledge will grow in pharmacogenetics and ecogenetics. In some cases, the treatment will be the same, but the dose, duration or timing of treatment will be different according to the individual’s genotype. In other cases, treatment itself will be tailored for specific individual genotypes, targeting specific genetic differences. Over time, a better understanding of genetic susceptibilities might help target preventive measures to individuals who can potentially benefit from them the most. But, in the context of increasing health care costs, the use of resources to personalize health care based on genetic characteristics will have to be balanced against its benefits.

Conclusion

The impact of genetics in public health is still limited, but is expected to grow in the near future, as genetic knowledge rapidly increases. Current examples of the use of genetics in public health can serve as lessons for the future.


aaRSs (aminoacyl-tRNA synthetases), 115

abstract euclidean vector space, 59

   BH distance of separation, 65

algorithmic information theory, 168, 170

Alice in Wonderland (Carroll), 164

American Standard Code for Information Interchange. See ASCII

   in abstract euclidean vector space, 59󈞰

   cyclic imino acids versus, 83

   functionally equivalent, 57, 60, 77󈞼, 88

   Hamming distances within, 76, 82

   primitive coding templates for, 131

   protein synthesis for, 110

   protein-folding pathways for, 57

   thyroid gland deficiency and, 57

aminoacyl-tRNA synthetases. See aaRSs

Ansatz, 59. See also prescriptions

Arrowsmith (Lewis), 121

ASCII (American Standard Code for Information Interchange), 14, 17, 19, 117

Astrobiology (journal), 142

Atlas of Protein Sequence and Structure 5, 57

Bacillus subtilis, 110

Bada, Jeffrey, 116, 119, 123, 128, 146, 148

banded iron formation. See BIF

Baudisch, Oskar, 124, 127, 148

BIF (banded iron formation)

   in electronic communications, 97

blending inheritance theory, 3

   error detection properties of, 39󈞔

Bovine pancreatic trypsin inhibitor, 82

Bryan, William Jennings, 178

Bungenberg de Jong, H.G., 146, 157, 188

   in United States Postal Code, 16

   compound composition for, 138

The Central Dogma, 20, 21, 23, 52, 134, 160

   absolute temperature in, 25

   energy dissipation and, 24

   Sequence Hypothesis vs., 23

Chaitin, Gregory, 2, 168, 169

Channel Capacity Theorem, 4, 42󈞚, 47, 49, 158, 162, 181, 184

   communication systems within, 42

   conditional entropy and, 42

Chironomus thummi, 36

clostridial type ferrodoxins

Clostridium butyricum, 98

Clostridium thermoaceticum, 106

   United States Postal Code, 14

   Universal Product Bar Code, 14

   white noise applications, 37

   biosynthetic pathways for, 107

   for mitochondria, 94, 103, 112

   information theory and, 169

conditional entropy, 42, 43󈞚

   Intelligent Designer as part of, 176

Crick, Francis H.C., 3, 8, 9, 10, 13, 17, 20, 21, 24, 96, 97, 104, 112

   sequence hypothesis of, 57

Critique of Judgment (Kant), 150

Darwin, Charles, 4, 119�, 141, 150, 177

   on blended characteristics, 179

Darwin’s Black Box (Behe), 178

dialectical materialism, 12, 151�

   Law of the Transformation of Quantity into Quality, 151

   Shklovskii, Iosef Samuilovich, and, 155�

Dialectics of Nature (Engels), 156

The Dialectics of Nature (Engels), 151

Die Koazervation und ihre Bedeutung für die Biologie (Bungenberg de Jong), 157

Directed Panspermia theory, 142

discrete memoryless source, 43

DNA-mRNA-proteome communication system, 33󈞎

Dodgson, Charles Lutwidge. See Carroll, Lewis

Drosophilia melanogaster, 86

Drosphilia yakuba, 105

Duve, Christian de, 119, 187

The Dynamics of Living Matter (Loeb), 121

   radioactive decay series and, 138

electron transfer pathways

   in The Central Dogma, 24

Engels, Friedrich, 118, 151, 156, 157

entropy of probability theory, 14, 185

Entscheidungsproblem (decision problem), 170

“error catastrophe,” 162�, 184

   Gompertz function within, 162

“Experiments on plant hybrids” (Mendel), 156

Five Billion Vodka Bottles to the Moon (Shklovskii), 155

Five Proofs (Aquinas), 176

Gamow, George, 8, 10, 11, 14, 58, 93, 180, 184

   genetic specificity for, 11

   quantum mechanical tunnelling applications of, 12

   sequence hypothesis of, 58

Gatlinburg Symposium on Information Theory in Biology, 11󈝸

   error correction effects in, 41󈞖, 94

   Hamming distances in, 105, 109

   instantaneous factors for, 107�

   mapping relationships within, 96

   Markov states in, 101, 103, 109

   transmission as part of, 35

   vocabulary expansion of, 103�

genetic communication systems

   gene duplication rates in, 38, 181

   majority logic redundancy within, 38

   sense code letters within, 39

   stochastic Markov process within, 37

   longevity interactions, 163

   tunnelling processes in, 180

Gilbert, William S., 115, 116

“Great chain of being” (Aristotle), 181

GULAG Archipelago (Solzhenitsyn), 157

Gulliver’s Travels (Swift), 147

Haeckel, Ernst H.P.A., 114, 115, 126, 132, 156, 157, 186

   on Urschleim, 117, 146�, 160, 182

Haldane, John B.S., 115, 126, 146, 148, 175

   synonymous source code letters and, 40

Helmholtz, Hermann Ludwig Ferdinand von, 142

Hertzsprung–Russell diagram, 135

homologous protein families, 47󈞜

horizontal gene transfer, 174, 181

Human Genome Project, 23, 186

Incompleteness Theorem, 174

information theory, 3, 6, 31, 158, 184

   instantaneous genetic codes for, 108

   transmission as part of, 34

Intelligent Designer, 178, 181

Intelligent Life in the Universe (Sagan/Shklovskii), 118, 155

“irreducible complexity,” 178

isoǃ-cytochrome c, 29󈞊, 53, 62, 65, 68, 83, 87

   amino acid predictions for, 68

   Cys amino acid sites in, 82

   in electron transfer pathways, 59, 81

   oligonucleotide mutagenesis in, 82

   polypeptide sequences in, 64

   Shannon–McMillan–Breiman theorem and, 84, 118

   site-directed mutagenesis in, 82

Journal of the Chemical Society, 122

   clostridial type ferrodoxins in, 98

   Hamming distances within, 98

Just So Stories (Kipling), 1, 146

Krankenhaus, Rudolf Virchow, 124

Law of the Transformation of Quantity into Quality, 155

   in dialectical materialism, 151

Lawrence, Ernest Orlando, 125

LIFE: Its Nature, Origin and Development (Lysenko), 156

“Light and Life” (Bohr), 5

   corona discharge during, 131

Löb, Walther, 122, 123, 124, 126, 128�, 148

   biometric synthesis apparatus, 127

Logic and the understanding of nature (Hilbert), 172

majority logic redundance

   in genetic communication system, 38

   in DNA-mRNA-proteome communication system, 33

   in genetic codes, 101, 103, 109, 181

   carbonate minerals on, 140

“master sequence” proposal, 30, 159

The Mathematical Appendix, 53

Maxwell–Boltzmann–Gibbs entropy, 26, 32, 185

mechanist–reductionism, 5, 150�

   on segregated inheritance, 3

Methanosarcina barkeri, 17

Miller, Stanley, 124, 125, 127, 130, 132, 186

   on amino acid formation, 128

Miller–Urey experiments, 118, 126, 130

   endosymbiotic theory of, 111

   surface metamorphism for, 137

Morgano–Weismannite genetics, 154�

   mitochondrial codons and, 106�

mutual entropy, 43, 45, 48󈞝, 92

   binary alphabet similarity within, 47

   as information content measure, 53󈞤

Mycoplasma capricolum, 112

Mycoplasma caprolium, 104, 111

Mycoplasma genitatilium, 85, 174

Mycoplasma pneumoniae, 85

NASA (National Aeronautic and Space Administration), 142

National Aeronautic and Space Administration. See NASA

Nature (magazine), 21, 85, 139, 148

Naturphilosophie, 149, 151

   Shannon entropy theorem and, 32, 185

negentropy. See negative entropy

Neurospora crassa, 104

non-sense code letters, 16, 37, 39

Oparin, Alexandr Ivanovich, 115, 126, 146, 152, 153, 155, 156

   Western True Believers and, 154

Origin of Life (Haldane), 128

“origin of life” events, 103

   The Central Dogma and, 147

   evolutionary process during, 103

Origin of Species by Means of Natural Selection or the Preservation of Favored Races in the Struggle for Life (Darwin), 120, 177, 179, 182

overlapping genes, 85󈟂, 87

Pasteur, Louis, 114, 115, 117

   scientific discoveries of, 2

Perron-Frobenius Theorem, 53, 56

prebiotic soup theory, 97, 114, 182

probability amplitudes, 173

   prebiotic elements of, 123

protein-protein recognition, 24

The Protein Information Resource, 65, 68, 76

protoplasmal primordial atomic globules, 115, 122, 147, 157, 184, 187

The Purloined Letter (Poe), 2

Pythagorean Theorem, 64, 65

quantum mechanical tunnelling, 12

   dialectical materialism and, 12

   number generation and, 166

   transcendental numbers and, 167

The Republic (Plato), 1

reverse transcription, 21, 22, 183

reversible computation, 22

   in Urschleim (primeval slime), 145

The Road Not Taken (Frost), 27

Saccharomyces cerevisiare, 38

Science (magazine), 85, 148, 187

Search for extraterrestrial intelligence. See SETI

   The Central Dogma versus, 23

SETI (search for extraterrestrial intelligence), 187

Shannon entropy theorem, 21, 22, 24, 28, 30, 32, 43, 52, 159, 160

   complexity as part of, 168

   information flow within, 34

Shannon–McMillan–Breiman Theorem, 8, 29, 30, 59, 85, 118, 158, 185

   isoǃ-cytochrome sequences in, 84, 118

Shklovskii, Iosef Samuilovich, 117, 155, 156

   dialectical materialism and, 155�

Simpson, George Gaylord, 143, 186

Solzhenitsyn, Aleksandr, 157

spontaneous generation, 114

   in genetic communication system, 33

Stop Codon Takeover Model, 105, 107

“superiority parameters,” 159

supernumerary amino acids, 110

Thermal Emission Spectrometer, 140

“Through the Looking Glass” (Carroll), 6𔃅

Turing machines, 170, 171, 179

   Godel’s Incompleteness Theorem and, 171

unconstrained channels, 43

United States Postal Code, 14, 15, 16, 17, 19

Universal Product Bar Code, 14, 15, 17, 19

Universe, Life, and Mind (Shklovskii), 118, 155

   for genetic code origins, 173

Urschleim (primeval slime), 114, 116, 117, 118, 130�, 132, 144

   Haeckel, Ernst H.P.A., and, 117, 146�, 160, 182

Vavilov, Nikolai Ivanovich, 153, 156

Versuche über Pflanzen-Hybriden (Experiments on plant hybrids) (Mendel), 179

   sequence hypothesis of, 57

“Watson–Crick Theory” (of inheritance), 22

Western True Believers, 154

   coding theory applications for, 37

   stochastic process and, 37

The Worker’s Paradise, 12

Zeitschrift für Elektro-Chemie (Journal for Electro-Chemistry), 122


Genetic Clues in the Goop of a COVID Swab

U.S. Marines with Ground Combat Element, Marine Rotational Force - Darwin undergo a COVID-19 swab test on the Royal Australia Air Force Base Darwin, NT, Australia, July 19, 2020. Marines will receive at least two negative COVID-19 tests before completing their 14-day quarantine. (U.S. Marine Corps photo by Cpl. Sarah Marshall)

The components of certain things are meant to remain mysterious. The ingredients of sausage. A burger&rsquos slimy secret sauce. The recipe for Coke or Kentucky Fried Chicken.

Researchers from Stanford University are tackling the make-up of another entity, something rather new to our world: the stuff retrieved from swabs shoved up nostrils to sample genetic material from SARS-CoV-2, the virus behind COVID-19. A swab actually samples much more than the virus&rsquos RNA, required for diagnosis.

John Gorzynski and colleagues describe the &ldquomulti-omic data repositories&rdquo from deployed swabs in a preprint (not yet peer-reviewed) and at the recent virtual annual meeting of The American Society of Human Genetics.

&ldquoA single nasopharyngeal swab can reveal substantial host and viral genomic information in a high-throughput manner that will facilitate public health pandemic tracking and research into the mechanisms underlying virus-host interactions,&rdquo they write.

That&rsquos a mouthful. I&rsquoll just call them super swabs.

Amplifying Viral Sequences

Extracting clues from the stuff on the swabs is a little like collecting evidence at a crime scene. Several things happen.

The polymerase chain reaction (PCR) rapidly ramps up the number of viral genomes to detectable levels, copying the RNA like documents flying out of an old-fashioned Xerox machine. At least 32 PCR cycles must run to yield enough genome copies to register as a positive test, a metric called cycle threshold (CT) value. A low CT can lead to a false negative test result.

The Stanford technology also scrutinizes swabs for genetic material from 40 other respiratory viruses. The list of usual suspects includes rhinoviruses, respiratory syncytial viruses, influenza viruses and other coronaviruses, which are RNA-based, as well as common cold DNA-based adenovirus, and a few others.

Considering Our Genomes and More

Next from the super swabs comes a quickie genome sequencing of the &ldquohost&rdquo &ndash the person attached to the nose being probed. Cells lining the nose and throat, sloughed off and floating amidst the mucus, provide the genomes. A shortcut technology requires only a brief and limited amplification of the DNA.

Human genome information will become important once we figure out which genes control susceptibility to and severity of COVID-19. A few candidates are popping up in multiple investigations: a section of chromosome 3 found in Neanderthals and some of us a variant of a gene near the one that determines ABO blood type and genes that encode antibody parts and interferon receptors.

Swab analysis pays special attention to eleven genes that encode proteins called the human leukocyte antigens. The HLA proteins dot cell surfaces and are traditionally used in tissue typing for transplants. For COVID, HLA typing can be used to predict and monitor the immune response &ndash possibly life-or-death information.

Beyond health associations, our DNA on swabs also indicates how people are related, which could be important in contact tracing. Our gene and genome sequences reflect ancestry. These data, when synced with electronic health records, might point to population groups at elevated risk of severe COVID, likely confirming what we already know from epidemiology and just looking at what&rsquos happening at hospitals.

The swabs also yield human RNA, aka the transcriptome. This is the set of mRNAs present in a specific cell, which indicates the genes that are actively instructing the cell to synthesize their encoded proteins. Host transcriptomes hold clues to the specific choreography of COVID in an individual. In the virus, RNA is the genetic material, but in us, it is the purveyor of the information in the DNA.

The original use of a nasopharyngeal swab &ndash to detect SARS-CoV-2 RNA &ndash continues. But researchers are also using the RNA sequences to chart the evolution of the pandemic, paying special attention to mutations. The best studied mutation is D614G, which increases transmissibility.

The D614G mutation has entered the US on several occasions, from Europe. It partly explains why the number of cases has been slowly rising and now is skyrocketing, even as the percentage of deaths decreases. The now notorious mutation alters a single DNA base in a place that changes a critical amino acid in the spike protein, which is what the virus uses to latch onto our cells. The rather unglamorous name D614G is code for the location of the glitch in the viral spike gene.

D614G isn&rsquot the only mutation. The genome of SARS-CoV-2 is changing, as all genomes do. Mutation is a normal consequence of errors in replication of genetic material. But most mutations do no harm. The effect depends upon what part of a protein a mutation perturbs.

Researchers compare different versions of a genome &ndash those with different mutations &ndash to deduce which begat which, connecting viral strains (and the animals that carry them) by their shared mutations, essentially building family trees. This computational approach, called phylodynamic tracking, comes from decades of evolutionary biology research. Now with the more pressing goal of handling pandemic dynamics at local levels, viral tree-building is enabling public health systems to prepare.

Fertilizer for building the viral family trees comes from the data of newly-sequenced SARS-CoV-2 strains posted frequently to a website called the GISAID Initiative. The speed at which the database is building is astonishing.

The first genome sequence of the &ldquonovel coronavirus&rdquo was published on January 10. When I posted &ldquoCOVID Genomes Paint Portrait of an Evolving Pathogen&rdquo on July 30, GISAID listed 75,000 viral genomes. Now it&rsquos nearing 200,000!

Comparing viral genomes over time has been critical in tracking and predicting outbreaks. Frantic physicians in Washington State, back at the beginning of the pandemic, were initially alerted to community spread from asymptomatic individuals from viral genome sequences.

The information held in seemingly low-tech nasal swabs can serve as a crystal ball during this most challenging of times. And that&rsquos crucial because future infectious disease outbreaks, epidemics, and pandemics are inevitable, the Stanford team warns.