The RSAD2 gene encodes the virus inhibitory protein, endoplasmic reticulum-associated, interferon-inducible (Viperin), also known as RSAD2 (radical SAM domain-containing 2). Viperin is an interferon-stimulated gene that functions as a multifunctional protein in viral activities. Viperin can be produced by either IFN-dependent or IFN-independent routes, and certain viruses may employ viperin to improve their infectivity.

Function

Viperin is an interferon-stimulated gene whose expression inhibits many DNA and RNA viruses including CHIKV, HCMV, HCV, DENV, WNV, SINV, influenza, and HIV. Initially identified as an IFN-γ induced antiviral protein in human cytomegalovirus (HCMV) infected macrophages, it was reported that viperin could be induced by HCMV glycoprotein B in fibroblasts, but inhibits HCMV viral infection and down-regulates viral structural proteins. The reason why virus protein would induce viperin against itself is still not clear; however, the viral induced redistribution of viperin may reflect the mechanism of virus evading its antiviral activities. Viperin may also be induced and interact with HCMV viral proteins and relocate to mitochondria in HCMV viral infected cells to enhance viral infectivity by disrupting cellular metabolism.

Viperin is a radical SAM enzyme which is capable of producing the chain terminator ddhCTP (3ʹ-deoxy-3′,4ʹdidehydro-CTP), which inhibits the viral RNA dependent RNA polymerase (RdRp). This activity appears to abolish metabolism of amino acids and mitochondrial respiration.

In the inhibition of influenza virus budding and release, viperin is suggested to disrupt the lipid rafts on the cell’s plasma membrane by binding to and decreasing the enzyme activities of farnesyl diphosphate synthase (FPPS), an essential enzyme in isoprenoid biosynthesis pathway. Viperin was suggested to inhibit the viral replication of HCV via its interaction with host protein hVAP-33 and NS5A and disrupting the formation of the replication complex.

Structure

Human viperin is a single polypeptide of 361 amino acids with a predicted molecular weight of 42 kDa. The N-terminal 42 amino acids of viperin forms amphipathic alpha-helix, which is relatively less conserved in different species and has a minor effect on the antiviral activity of viperin. The N-terminal domain of viperin is required for its localization to the ER and lipid droplets. Amino acids 77-209 of viperin constitute the radical S-adenosyl methionine (SAM) domain, containing four conserved motifs. Motif 1 has three conserved cysteine residues, CxxCxxC, which is the Fe-S binding motif and also essential for antiviral activity. The C-terminal 218-361 amino acids of viperin are highly conserved in different species and essential for viperin dimerization. The C-terminal tail appears to be critical for the antiviral activities against HCV since a C-terminal flag tagged of viperin lost its antiviral activity.

When viperin is bound to SAM and Cytidine triphosphate (CTP) or uridine triphosphate (UTP) is used as a substrate, different kinetic parameters are achieved. It is predicted that the CTP substrate binds much more tightly with viperin because of the low K_m value of the substrate. However, the overall structure of both UTP- and CTP-bound compounds are similar. The difference being that the uracil moiety is less effective then the cytosine moiety at binding and ordering turns A and B. Nucleotide-free viperin contains a (βα)₆ partial barrel and has a disordered N-terminal extension and a partially ordered C-terminal extension. When the C-terminal tail is ordered, a six-residue α-helix, an eight-residue P-loop (that binds the γ-phosphate of CTP), and a 3₁₀-helix are revealed.

Cellular localization

Viperin is normally localized to the endoplasmic reticulum (ER) via its N-terminal domain, and also localized to lipid droplet, which are derived from the ER. However, it is also found in mitochondria in the HCMV infected fibroblasts.

Nucleosides are glycosylamines that are similar to nucleotides but do not contain a phosphate group. A nucleoside is made up of just a nucleobase (also known as a nitrogenous base) and a five-carbon sugar (ribose or 2′-deoxyribose), whereas a nucleotide has a nucleobase, a five-carbon sugar, and one or more phosphate groups. The anomeric carbon of a nucleoside is linked to the N9 of a purine or the N1 of a pyrimidine by a glycosidic bond. DNA and RNA are made up of nucleotides, which are the basic building blocks.

Use in medicine and technology

In medicine several nucleoside analogues are used as antiviral or anticancer agents.The viral polymerase incorporates these compounds with non-canonical bases. These compounds are activated in the cells by being converted into nucleotides. They are administered as nucleosides since charged nucleotides cannot easily cross cell membranes.

In molecular biology, several analogues of the sugar backbone exist. Due to the low stability of RNA, which is prone to hydrolysis, several more stable alternative nucleoside/nucleotide analogues that correctly bind to RNA are used. This is achieved by using a different backbone sugar. These analogues include locked nucleic acids (LNA), morpholinos and peptide nucleic acids (PNA).

In sequencing, dideoxynucleotides are used. These nucleotides possess the non-canonical sugar dideoxyribose, which lacks 3′ hydroxyl group (which accepts the phosphate). It therefore cannot bond with the next base and terminates the chain, as DNA polymerases cannot distinguish between it and a regular deoxyribonucleotide.

Prebiotic synthesis of ribonucleosides

In order to understand how life arose, knowledge is required of the chemical pathways that permit formation of the key building blocks of life under plausible prebiotic conditions. According to the RNA world hypothesis free-floating ribonucleosides and ribonucleotides were present in the primitive soup. Molecules as complex as RNA must have arisen from small molecules whose reactivity was governed by physico-chemical processes. RNA is composed of purine and pyrimidine nucleotides, both of which are necessary for reliable information transfer, and thus Darwinian natural selection and evolution. Nam et al. demonstrated the direct condensation of nucleobases with ribose to give ribonucleosides in aqueous microdroplets, a key step leading to RNA formation. Also, a plausible prebiotic process for synthesizing pyrimidine and purine ribonucleosides and ribonucleotides using wet-dry cycles was presented by Becker et al. 

Nucleoside analogues are nucleosides which contain a nucleic acid analogue and a sugar. Nucleotide analogs are nucleotides which contain a nucleic acid analogue, a sugar, and a phosphate groups with one to three phosphates.

Nucleoside and nucleotide analogues can be used in therapeutic drugs, include a range of antiviral products used to prevent viral replication in infected cells. The most commonly used is acyclovir, although its inclusion in this category is uncertain, because it acts as a nucleoside but contains no actual sugar, as the sugar ring is replaced by an open-chain structure.

Nucleodide and nucleoside analogues can also be found naturally. Examples include ddhCTP (3ʹ-deoxy-3′,4ʹdidehydro-CTP) produced by the human antiviral protein viperin and sinefungin (a S-Adenosyl methionine analogue) procduced by some Streptomyces.

Function

These agents can be used against hepatitis B virus, hepatitis C virus, herpes simplex, and HIV. Once they are phosphorylated, they work as antimetabolites by being similar enough to nucleotides to be incorporated into growing DNA strands; but they act as chain terminators and stop viral DNA polymerase. They are not specific to viral DNA and also affect mitochondrial DNA. Because of this they have side effects such as bone marrow suppression.

A nucleoside and a phosphate make up nucleotides, which are organic compounds. They are monomeric units of the nucleic acid polymers deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), which are both fundamental macromolecules in all living things on Earth. Nucleotides are received from the diet and are also produced by the liver from common components.

Nucleotides are made up of three component molecules: a nucleobase, a five-carbon sugar (ribose or deoxyribose), and a one to three-phosphate phosphate group. Guanine, adenine, cytosine, and thymine are the four nucleobases of DNA; uracil replaces thymine in RNA.

Nucleotides also play a central role in metabolism at a fundamental, cellular level. They provide chemical energy—in the form of the nucleoside triphosphates, adenosine triphosphate (ATP), guanosine triphosphate (GTP), cytidine triphosphate (CTP) and uridine triphosphate (UTP)—throughout the cell for the many cellular functions that demand energy, including: amino acid, protein and cell membrane synthesis, moving the cell and cell parts (both internally and intercellularly), cell division, etc.^[2] In addition, nucleotides participate in cell signaling (cyclic guanosine monophosphate or cGMP and cyclic adenosine monophosphate or cAMP), and are incorporated into important cofactors of enzymatic reactions (e.g. coenzyme A, FAD, FMN, NAD, and NADP⁺).

Structure

Showing the arrangement of nucleotides within the structure of nucleic acids: At lower left, a monophosphate nucleotide; its nitrogenous base represents one side of a base-pair. At the upper right, four nucleotides form two base-pairs: thymine and adenine (connected by double hydrogen bonds) and guanine and cytosine (connected by triple hydrogen bonds). The individual nucleotide monomers are chain-joined at their sugar and phosphate molecules, forming two ‘backbones’ (a double helix) of nucleic acid, shown at upper left.

A nucleotide is composed of three distinctive chemical sub-units: a five-carbon sugar molecule, a nucleobase—the two of which together are called a nucleoside—and one phosphate group. With all three joined, a nucleotide is also termed a “nucleoside monophosphate”, “nucleoside diphosphate” or “nucleoside triphosphate”, depending on how many phosphates make up the phosphate group.

In nucleic acids, nucleotides contain either a purine or a pyrimidine base—i.e., the nucleobase molecule, also known as a nitrogenous base—and are termed ribonucleotides if the sugar is ribose, or deoxyribonucleotides if the sugar is deoxyribose. Individual phosphate molecules repetitively connect the sugar-ring molecules in two adjacent nucleotide monomers, thereby connecting the nucleotide monomers of a nucleic acid end-to-end into a long chain. These chain-joins of sugar and phosphate molecules create a ‘backbone’ strand for a single- or double helix. In any one strand, the chemical orientation (directionality) of the chain-joins runs from the 5′-end to the 3′-end (read: 5 prime-end to 3 prime-end)—referring to the five carbon sites on sugar molecules in adjacent nucleotides. In a double helix, the two strands are oriented in opposite directions, which permits base pairing and complementarity between the base-pairs, all which is essential for replicating or transcribing the encoded information found in DNA.

Nucleic acids then are polymeric macromolecules assembled from nucleotides, the monomer-units of nucleic acids. The purine bases adenine and guanine and pyrimidine base cytosine occur in both DNA and RNA, while the pyrimidine bases thymine (in DNA) and uracil (in RNA) occur in just one. Adenine forms a base pair with thymine with two hydrogen bonds, while guanine pairs with cytosine with three hydrogen bonds.

The Human Genome Initiative (HGP) was an international scientific research project that aimed to determine the base pairs that make up human DNA, as well as to identify and map all of the human genome’s genes, both physically and functionally. It is still the greatest collaborative biological effort in the world. After the US government picked up the idea in 1984, the project was formally launched in 1990, and it was declared complete on April 14, 2003. In May 2021, the level “full genome” was achieved.

The Human Genome Project originally aimed to map the nucleotides contained in a human haploid reference genome (more than three billion). The “genome” of any given individual is unique; mapping the “human genome” involved sequencing a small number of individuals and then assembling to get a complete sequence for each chromosome. Therefore, the finished human genome is a mosaic, not representing any one individual. The utility of the project comes from the fact that the vast majority of the human genome is the same in all humans.

Applications and proposed benefits

The sequencing of the human genome holds benefits for many fields, from molecular medicine to human evolution. The Human Genome Project, through its sequencing of the DNA, can help us understand diseases including: genotyping of specific viruses to direct appropriate treatment; identification of mutations linked to different forms of cancer; the design of medication and more accurate prediction of their effects; advancement in forensic applied sciences; biofuels and other energy applications; agriculture, animal husbandry, bioprocessing; risk assessment; bioarcheology, anthropology and evolution. Another proposed benefit is the commercial development of genomics research related to DNA based products, a multibillion-dollar industry.

The sequence of the DNA is stored in databases available to anyone on the Internet. The U.S. National Center for Biotechnology Information (and sister organizations in Europe and Japan) house the gene sequence in a database known as GenBank, along with sequences of known and hypothetical genes and proteins. Other organizations, such as the UCSC Genome Browser at the University of California, Santa Cruz, and Ensembl present additional data and annotation and powerful tools for visualizing and searching it. Computer programs have been developed to analyze the data because the data itself is difficult to interpret without such programs. Generally speaking, advances in genome sequencing technology have followed Moore’s Law, a concept from computer science which states that integrated circuits can increase in complexity at an exponential rate. This means that the speeds at which whole genomes can be sequenced can increase at a similar rate, as was seen during the development of the above-mentioned Human Genome Project.

Techniques and analysis

The process of identifying the boundaries between genes and other features in a raw DNA sequence is called genome annotation and is in the domain of bioinformatics. While expert biologists make the best annotators, their work proceeds slowly, and computer programs are increasingly used to meet the high-throughput demands of genome sequencing projects. Beginning in 2008, a new technology known as RNA-seq was introduced that allowed scientists to directly sequence the messenger RNA in cells. This replaced previous methods of annotation, which relied on the inherent properties of the DNA sequence, with direct measurement, which was much more accurate. Today, annotation of the human genome and other genomes relies primarily on deep sequencing of the transcripts in every human tissue using RNA-seq. These experiments have revealed that over 90% of genes contain at least one and usually several alternative splice variants, in which the exons are combined in different ways to produce 2 or more gene products from the same locus.

The genome published by the HGP does not represent the sequence of every individual’s genome. It is the combined mosaic of a small number of anonymous donors, of African, European and east Asian ancestry. The HGP genome is a scaffold for future work in identifying differences among individuals. Subsequent projects sequenced the genomes of multiple distinct ethnic groups, though as of today there is still only one “reference genome.

Once class 12th results are out and the school is over, it is time to make the strategies for higher education and think over what to do next. With numerous options available today, students often get confused in choosing a relevant career path for them. Many of the students might have already had plans for their future in place but for some the confusion still persists.

Here are some tips to keep in mind while choosing the most relevant career path.

>Know your interests

Before jumping on to look for the available options in the science, commerce or humanities stream, it is extremely important to consider your interests. If you don’t want to spend your time at job/work counting your days then look for the career which best suits and aligns with your interests and abilities. Deciding out of peer pressure or family pressure might not turn out to be beneficial in long run.

>Choose the right course

These days there are a number of ways to pursue the same course such as degree course, diploma course, correspondence mode, online mode and distance mode of education. By getting to know about the course structure, syllabus and methodology of teaching you can pick up the course which suits your needs.

>Look out for future scope and opportunities

It might happen that your interests direct you to your preferred career path but not a viable career. In order to overcome this major hurdle, you need to search for and know about the future scope and opportunities available for that particular field in your country and abroad.

>Maintain a balance between college preference and course of study

A college preference might be as important as the preferred course but a balance between the two is more important. A good college offering your preferred course is a steal deal. However, if things don’t go as per your will, consider the course above the college brand. Because it is only the course that is going to decide your future prospects and not the college’s brand value.

>Have a plan B

Just in case you doubt losing the opportunity to grab your preference of course or college always have a plan B. It would not only save your time from being wasted but also let you to explore other options. Who knows the unexplored opportunities come with hidden but favourable outcomes for you.

In times like today, health has become the primary concern for all. Good immunity proportionates healthy living which comes from eating the right food in the right amount. Superfoods are the go-to food items for strong immunity and good health.

Superfoods are high in nutrition having very few calorie count. They contain high value of vitamins, minerals and naturally occuring antioxidants which keep your body disease-free and make you healthier. When taken in the right quantity in your diet, superfoods can improve heart health and increase energy level in the body, detox the body, regulate metabolism, lower body cholestrol, reduce cardiovascular disease risks and also help in weight reduction.

>Green leafy vegetables

Green leafy vegetable are a great source of many nutrients that boost our immunity such as vitamin A, C, E and K, calcium, iron, fibre, zinc, potassium, magnesium etc. The fibres and nutrients present in green leafy vegetables are found useful in preventing heart diseases, type-2 diabetes and certain chronic diseases. Some well known green leafy vegetables include kale, spinach, beet greens, watercress etc.

>Citrus fruits

Citrus fruits are rich source of vitamin C and B6, ribloflavin, calcium, magnesium and a variety of phytochemicals. These nutrients are responsible for improved gastrointestinal function and vascular protection. Also, consuming citrus fruits reduces risk of diabetes, cancer and neurological diseases. Examples of citrus fruits are orange, sweet lime, tangerine, kinnow,pomelo etc.

>Berries and cherries

Berries are rich in vitamin C, minerals, manganese and antioxidants and are also low in calories. They also contain flavonoids which are responsible for protection of body cells. Similar to berries, cherries are a great source of antioxidants which help in protection against viruses. Potassium rich berries are also good for improved blood pressure.

>Turmeric

Known for its antibacterial properties, turmeric is a very commonly found and well known ingredient in Indian households. It is rich in proteins, carbohydrates and minerals like manganese, potassium and phosphorous. Scientifically proven health benefits of turmeric include prevention of heart diseases, cancer, Alzheimer’s and prevent symptoms of depression and arthritis.

>Honey

Honey, which is often considered a substitute of sugar, is a rich source of ascorbic acid, pantothenic acid, niacin and riboflavin and minerals like iron, copper, zin, calcium, phosphorous etc. It is also rich in antioxidants and helps regulate blood pressure and has benefits on heart health.

>Yogurt

Yogurt provides to the body good amount of vitamin B12, minerals like calcium, riboflavin, phosphorous etc and proteins. The fermentation process used to make yogurt makes it healthier than milk and easy to digest which cause the nutrients to get absorbed by the body more easily and quickly. This not just improves digestive health but also helps in weight management, strengthens immunity and prevents bone diseases like osteoporosis.

Forced migration can be described as mass movement of people of a particular area out of threat to their lives and livelihoods. People unwilling to leave their home towns and countries are forced to migrate to nearby, or sometimes far away, cities, towns and countries to have access to better facilities.

In context to Uttarakhand, forced migration or distressed migration has arisen as one of the major issues in recent times. In particular, male-specific outmigration has become a trend in the hills. The people have been migrating not just to seek better employment but also to have access to better healthcare and educational facilities. The educated ones are the first to leave as they get good opportunities in the cities and settle there forever. However, the elderly population is not yet ready to leave their home land because of the affection and attachment to the place.

More than 5 lakh people have migrated from Uttarakhand within the last 10 years. According to 2011 census, a total of 1,18,961 people from 6,338 village panchayats have migrated out of Uttarakhand permanently, while 3,83,726 people have migrated in search of work and prefer to visit their native places in the hills frequently. Out of 16,500 villages in Uttarakhand, 734 have become ghost villages. Also, there are 664 villages with negligible population and 3,900 other villages in the state that have a population of 50 or less.

The state of Uttarakhand was formed in the year 2000 after separation from Uttar Pradesh to ensure development in the hilly region. Though the purpose doesn’t seem to be served yet. Well structured roads and good health facilities continue as the basic requirements of the people. The lack of educational facilities is also among the majors reasons of migration.

Moreover, the decreased fertility of soil is a major concern for the locals affecting the agricultural productivity. Since it is an ecologically fragile state prone to natural disasters with half of the population’s workforce on farm, scope for other employment opportunities reduces.

Changing time brings along changes in basic needs which might not be fulfilled by the traditional methods and style of Uttarakhand. It proves to be a major cause of the shift. People now prefer to settle in the cities permanently in order to enjoy the relaxing life and lucrative opportunities offered there as compared to their home towns in the hills where the daily routine is tough and hectic and a decent livelihood has become a challenge.

Joe Biden’s statement was at odds with the long-held US policy known as “strategic ambiguity,” where Washington helps build Taiwan’s defenses but does not explicitly promise to come to the island’s help.

Baltimore, United States: 

President Joe Biden on Thursday said the United States would come to the defense of Taiwan if the island were attacked by China, which considers it part of its territory.

“Yes,” he responded when asked in a CNN town hall about defending Taiwan. “We have a commitment to that.”

Biden’s statement was at odds with the long-held US policy known as “strategic ambiguity,” where Washington helps build Taiwan’s defenses but does not explicitly promise to come to the island’s help.

He made a similar pledge in August during an interview with ABC, insisting that the United States would always defend key allies, including Taiwan, despite the withdrawal from Afghanistan in the face of the victorious Taliban.

Biden said the United States made a “sacred commitment” to defend NATO allies in Canada and Europe and it’s the “same with Japan, same with South Korea, same with Taiwan.”

The phenotype (from Greek o- (faino-)’showing’ and (tpos) ‘type’) is a set of observable features or qualities of an organism in genetics. The phrase refers to an organism’s morphology, or physical shape and structure, as well as its developmental processes, biochemical and physiological features, behaviour, and behavioural outcomes. The expression of an organism’s genetic code, or genotype, and the effect of environmental variables are the two primary components that determine its phenotype. Both factors may interact, altering phenotype even more. When two or more clearly different phenotypes exist in the same population of a species, the species is called polymorphic.

Phenotypic variation

Phenotypic variation (due to underlying heritable genetic variation) is a fundamental prerequisite for evolution by natural selection. It is the living organism as a whole that contributes (or not) to the next generation, so natural selection affects the genetic structure of a population indirectly via the contribution of phenotypes. Without phenotypic variation, there would be no evolution by natural selection.

The interaction between genotype and phenotype has often been conceptualized by the following relationship:genotype (G) + environment (E) → phenotype (P)

A more nuanced version of the relationship is:genotype (G) + environment (E) + genotype & environment interactions (GE) → phenotype (P)

Genotypes often have much flexibility in the modification and expression of phenotypes; in many organisms these phenotypes are very different under varying environmental conditions (see ecophenotypic variation). The plant Hieracium umbellatum is found growing in two different habitats in Sweden. One habitat is rocky, sea-side cliffs, where the plants are bushy with broad leaves and expanded inflorescences; the other is among sand dunes where the plants grow prostrate with narrow leaves and compact inflorescences. These habitats alternate along the coast of Sweden and the habitat that the seeds of Hieracium umbellatum land in, determine the phenotype that grows.

An example of random variation in Drosophila flies is the number of ommatidia, which may vary (randomly) between left and right eyes in a single individual as much as they do between different genotypes overall, or between clones raised in different environments.^{[citation needed]}

The concept of phenotype can be extended to variations below the level of the gene that affect an organism’s fitness. For example, silent mutations that do not change the corresponding amino acid sequence of a gene may change the frequency of guanine–cytosine base pairs (GC content). These base pairs have a higher thermal stability (melting point) than adenine–thymine, a property that might convey, among organisms living in high-temperature environments, a selective advantage on variants enriched in GC content.

The extended phenotype[edit]

Main article: The Extended Phenotype

Richard Dawkins described a phenotype that included all effects that a gene has on its surroundings, including other organisms, as an extended phenotype, arguing that “An animal’s behavior tends to maximize the survival of the genes ‘for’ that behavior, whether or not those genes happen to be in the body of the particular animal performing it.” For instance, an organism such as a beaver modifies its environment by building a beaver dam; this can be considered an expression of its genes, just as its incisor teeth are—which it uses to modify its environment. Similarly, when a bird feeds a brood parasite such as a cuckoo, it is unwittingly extending its phenotype; and when genes in an orchid affect orchid bee behavior to increase pollination, or when genes in a peacock affect the copulatory decisions of peahens, again, the phenotype is being extended. Genes are, in Dawkins’s view, selected by their phenotypic effects.

Other biologists broadly agree that the extended phenotype concept is relevant, but consider that its role is largely explanatory, rather than assisting in the design of experimental tests.

Epigenetics is the study of heritable phenotypic modifications that do not entail DNA sequence changes in biology. [1Epigenetics is defined by features that are “on top of” or “in addition to” the usual genetic foundation for heredity. The Greek prefix epi- (- “over, outside of, surrounding”) denotes traits that are “on top of” or “in addition to” the traditional genetic basis for inheritance. Modifications in gene activity and expression are the most common epigenetic changes, although the phrase can also refer to any heritable phenotypic change. External or environmental influences may have an effect on cellular and physiological phenotypic features, or they may be a normal aspect of development.

Molecular basis

Epigenetic changes modify the activation of certain genes, but not the genetic code sequence of DNA. The microstructure (not code) of DNA itself or the associated chromatin proteins may be modified, causing activation or silencing. This mechanism enables differentiated cells in a multicellular organism to express only the genes that are necessary for their own activity. Epigenetic changes are preserved when cells divide. Most epigenetic changes only occur within the course of one individual organism’s lifetime; however, these epigenetic changes can be transmitted to the organism’s offspring through a process called transgenerational epigenetic inheritance. Moreover, if gene inactivation occurs in a sperm or egg cell that results in fertilization, this epigenetic modification may also be transferred to the next generation.

Specific epigenetic processes include paramutation, bookmarking, imprinting, gene silencing, X chromosome inactivation, position effect, DNA methylation reprogramming, transvection, maternal effects, the progress of carcinogenesis, many effects of teratogens, regulation of histone modifications and heterochromatin, and technical limitations affecting parthenogenesis and cloning.

DNA damage

DNA damage can also cause epigenetic changes. DNA damage is very frequent, occurring on average about 60,000 times a day per cell of the human body (see DNA damage (naturally occurring)). These damages are largely repaired, but at the site of a DNA repair, epigenetic changes can remain. In particular, a double strand break in DNA can initiate unprogrammed epigenetic gene silencing both by causing DNA methylation as well as by promoting silencing types of histone modifications (chromatin remodeling – see next section). In addition, the enzyme Parp1 (poly(ADP)-ribose polymerase) and its product poly(ADP)-ribose (PAR) accumulate at sites of DNA damage as part of a repair process. This accumulation, in turn, directs recruitment and activation of the chromatin remodeling protein ALC1 that can cause nucleosome remodeling. Nucleosome remodeling has been found to cause, for instance, epigenetic silencing of DNA repair gene MLH1. DNA damaging chemicals, such as benzene, hydroquinone, styrene, carbon tetrachloride and trichloroethylene, cause considerable hypomethylation of DNA, some through the activation of oxidative stress pathways.

Foods are known to alter the epigenetics of rats on different diets.Some food components epigenetically increase the levels of DNA repair enzymes such as MGMT and MLH1and p53.Other food components can reduce DNA damage, such as soy isoflavones. In one study, markers for oxidative stress, such as modified nucleotides that can result from DNA damage, were decreased by a 3-week diet supplemented with soy. A decrease in oxidative DNA damage was also observed 2 h after consumption of anthocyanin-rich bilberry (Vaccinium myrtillius L.) pomace extract.

Techniques used to study epigenetics

Epigenetic research uses a wide range of molecular biological techniques to further understanding of epigenetic phenomena, including chromatin immunoprecipitation (together with its large-scale variants ChIP-on-chip and ChIP-Seq), fluorescent in situ hybridization, methylation-sensitive restriction enzymes, DNA adenine methyltransferase identification (DamID) and bisulfite sequencing. Furthermore, the use of bioinformatics methods has a role in computational epigenetics.

Aneuploidy is the presence of an aberrant number of chromosomes in a cell, such as 45 or 47 instead of the usual 46 in a human cell. A difference of one or more entire sets of chromosomes is not included. A euploid cell is one that has any number of full chromosomal sets.

Some genetic abnormalities are caused by an extra or missing chromosome. Atypical chromosomal counts can also be found in cancer cells. Aneuploid solid tumours account for roughly 68 percent of all human tumours. When the chromosomes do not separate properly between the two cells during cell division, aneuploidy occurs (nondisjunction). The majority of cases of autosomal aneuploidy result in miscarriage.

Mechanisms

Aneuploidy arises from errors in chromosome segregation, which can go wrong in several ways.

Nondisjunction usually occurs as the result of a weakened mitotic checkpoint, as these checkpoints tend to arrest or delay cell division until all components of the cell are ready to enter the next phase. For example, if a checkpoint is weakened, the cell may fail to ‘notice’ that a chromosome pair is not lined with the spindle apparatus. In such a case, most chromosomes would separate normally (with one chromatid ending up in each cell), while others could fail to separate at all. This would generate a daughter cell lacking a copy and a daughter cell with an extra copy.

Completely inactive mitotic checkpoints may cause nondisjunction at multiple chromosomes, possibly all. Such a scenario could result in each daughter cell possessing a disjoint set of genetic material.

Merotelic attachment occurs when one kinetochore is attached to both mitotic spindle poles. One daughter cell would have a normal complement of chromosomes; the second would lack one. A third daughter cell may end up with the ‘missing’ chromosome.

Multipolar spindles: more than two spindle poles form. Such a mitotic division would result in one daughter cell for each spindle pole; each cell may possess an unpredictable complement of chromosomes.

Monopolar spindle: only a single spindle pole forms. This produces a single daughter cell with its copy number doubled.

A tetraploid intermediate may be produced as the end-result of the monopolar spindle mechanism. In such a case, the cell has double the copy number of a normal cell, and produces double the number of spindle poles as well. This results in four daughter cells with an unpredictable complement of chromosomes, but in the normal copy number.

Somatic mosaicism in the nervous system

Mosaicism for aneuploid chromosome content may be part of the constitutional make-up of the mammalian brain. In the normal human brain, brain samples from six individuals ranging from 2–86 years of age had mosaicism for chromosome 21 aneuploidy (average of 4% of neurons analyzed).This low-level aneuploidy appears to arise from chromosomal segregation defects during cell division in neuronal precursor cells,and neurons containing such aneuploid chromosome content reportedly integrate into normal circuits.However, recent research using single-cell sequencing has challenged these findings, and has suggested that aneuploidy in the brain is actually very rare.

Partial aneuploidy

The terms “partial monosomy” and “partial trisomy” are used to describe an imbalance of genetic material caused by loss or gain of part of a chromosome. In particular, these terms would be used in the situation of an unbalanced translocation, where an individual carries a derivative chromosome formed through the breakage and fusion of two different chromosomes. In this situation, the individual would have three copies of part of one chromosome (two normal copies and the portion that exists on the derivative chromosome) and only one copy of part of the other chromosome involved in the derivative chromosome. Robertsonian translocations, for example, account for a very small minority of Down syndrome cases (<5%). The formation of one isochromosome results in partial trisomy of the genes present in the isochromosome and partial monosomy of the genes in the lost arm.

Genome instability (also known as genetic instability or genomic instability) is characterised by a high frequency of mutations in a biological lineage’s genome. Changes in nucleic acid sequences, chromosomal rearrangements, and aneuploidy are all examples of mutations. In bacteria, genome instability does occur. Genome instability is a key element in carcinogenesis in multicellular species, and it’s also a role in several neurological illnesses including amyotrophic lateral sclerosis and myotonic dystrophy in humans.

DNA Replication Defects

In the cell cycle, DNA is usually most vulnerable during replication. The replisome must be able to navigate obstacles such as tightly wound chromatin with bound proteins, single and double stranded breaks which can lead to the stalling of the replication fork. Each protein or enzyme in the replisome must perform its function well to result in a perfect copy of DNA. Mutations of proteins such as DNA polymerase, ligase, can lead to impairment of replication and lead to spontaneous chromosomal exchanges. Proteins such as Tel1, Mec1 (ATR, ATM in humans) can detect single and double-stranded breaks and recruit factors such as Rmr3 helicase to stabilize the replication fork in order to prevent its collapse. Mutations in Tel1, Mec1, and Rmr3 helicase result in a significant increase of chromosomal recombination. ATR responds specifically to stalled replication forks and single-stranded breaks resulting from UV damage while ATM responds directly to double-stranded breaks. These proteins also prevent progression into mitosis by inhibiting the firing of late replication origins until the DNA breaks are fixed by phosphorylating CHK1, CHK2 which results in a signaling cascade arresting the cell in S-phase. For single stranded breaks, replication occurs until the location of the break, then the other strand is nicked to form a double stranded break, which can then be repaired by Break Induced Replication or homologous recombination using the sister chromatid as an error-free template. In addition to S-phase checkpoints, G1 and G2 checkpoints exist to check for transient DNA damage which could be caused by mutagens such as UV damage. An example is the Saccharomyces pombe gene rad9 which arrests the cells in late S/G2 phase in the presence of DNA damage caused by radiation. The yeast cells with defective rad9 failed to arrest following radiation, continued cell division and died rapidly while the cells with wild-type rad9 successfully arrested in late S/G2 phase and remained viable. The cells that arrested were able to survive due to the increased time in S/G2 phase allowing for DNA repair enzymes to function fully.

Fragile Sites

There are hotspots in the genome where DNA sequences are prone to gaps and breaks after inhibition of DNA synthesis such as in the aforementioned checkpoint arrest. These sites are called fragile sites, and can occur commonly as naturally present in most mammalian genomes or occur rarely as a result of mutations, such as DNA-repeat expansion. Rare fragile sites can lead to genetic disease such as fragile X mental retardation syndrome, myotonic dystrophy, Friedrich’s ataxia, and Huntington’s disease, most of which are caused by expansion of repeats at the DNA, RNA, or protein level. Although, seemingly harmful, these common fragile sites are conserved all the way to yeast and bacteria. These ubiquitous sites are characterized by trinucleotide repeats, most commonly CGG, CAG, GAA, and GCN. These trinucleotide repeats can form into hairpins, leading to difficulty of replication. Under replication stress, such as defective machinery or further DNA damage, DNA breaks and gaps can form at these fragile sites. Using a sister chromatid as repair is not a fool-proof backup as the surrounding DNA information of the n and n+1 repeat is virtually the same, leading to copy number variation. For example, the 16th copy of CGG might be mapped to the 13th copy of CGG in the sister chromatid since the surrounding DNA is both CGGCGGCGG…, leading to 3 extra copies of CGG in the final DNA sequence.