A Deadly Snps —

Genetic association studies with coronary artery diseases are showing that single nucleotide polymorphisms ( SNPs ) found close together on chromosome 9 are associated with an increase prevalence of common diseases.

Individuals with two copies of them have an increased risk of coronary heart disease but less in its impact than diabetes or heavy smoking but is equivalent to smoking 10 cigarettes a day.

One wrong SNP increases the risk by 40%, two doubles the risk.

These are not necessarily the causative mutation but indictors in the long genomic region on chromosome 9 ( 9p21.3.)

There have been many false dawns in these studies, with more to come but this is all very interesting. Family history is still very important in defining risk. And makes one look harder at the claims for correlations between nutrition intake and disease. . The answer will be a balance between environmental factors and genomic patterns.

Finding a gene or SNP abnormality is not the same as describing the biology.

Risk SNPs

RS10811661 associated with diabetes found on chromosome 9

RS2241880 associated with Crohn’s disease on the long arm of chromosome 8

8Q24 associated with cancer of the breast, colorectal and prostate cancer on the long arm of chromosome 8

Baker 2008 Genetics by numbers Nature vol 451 pp516-7

Ageing

There are many theories of why we age, Curious we accept the ageing of a car or some tool more than ourselves. We accept growth but decline and its anticipation of death is less attractive. More personal perhaps.

Theories of ageing include the accumulation of toxins produced by gut bacteria (curable by eating yoghurt) and reduced secretions from the testicles (curable by transplants of testicular tissue from monkeys. ).

Jan Vijg has written a book Aging of the Genome: the dual role of DNA in life and death published by Oxford University Press Reviewed by Linda Partridge Nature 2007, vol 447, pp 262-3

The current accepted theory is that ageing is caused by the accumulation of random alterations to DNA in somatic tissues (all tissues other than the reproductive germline cells). What is not known is the damage responsible for functional impairment and death, and the processes that generate this damage and protect against it. Though the usual culprits ,( smoking reduces life expectation by 11 years, excess alcohol, weight , blood pressure and poor diet) must get a look in .

DNA is being constantly bombarded with chemical and physical challenges that induce random alterations, including structural damage and changes in nucleotide sequence and organization. But unlike proteins and lipids, the damaged DNA cannot be simply broken down completely and remade, because it holds unique information. Instead, cellular pathways detect alterations and dependent on the type of cell and the nature of the changes, this variously leads to DNA repair, arrest of the cell cycle (preventing cell division), cellular senescence or death, or toleration of the change. In some cell types, some forms of DNA alterations accumulate with age, with evidence for genomic hotspots and considerable variation between individuals. Cancer is a clear case where DNA alterations can give rise to age-related pathology; their role in other aspects of functional decline is less clear, with the exception of mutations in DNA within mitochondria, the organelles that power cells.

Vijg : Aging of the Genome: the dual role of DNA in life and death published by Oxford University Press Reviewed by Linda Partridge Nature 2007, vol 447, pp 262-3

Cancer Genetics

John D. Carpten et al A transforming mutation in the pleckstrin homology domain of AKTl in cancer

Nature 2007, vol 448, 439-444

It is important for Nutritionists to appreciate the profound discoveries which are being made in Molecular Biology . There are so many naïve statements associating all manner of dietary excesses or deficiencies and cancer aetiology, based on epidemiological studies. To my mind these statements demean Nutrition in an increasingly sophisticated Scientific environment.

The enzyme AKTl (v-akt murine thymoma viral oncogene homologue 1) kinase is important in the most frequently proliferation and survival pathway in cancer, yet mutations of AKTl have not been reported. In the paper Carpten and his colleagues report the identification of a somatic mutation in human breast, colorectal and ovarian cancers that results in a glutamic acid to lysine substitution at amino acid 17 (E17K) in the lipid-binding pocket of AKTl. Lys17 alters the electrostatic interactions of the pocket and forms new hydrogen bonds with a phosphoinositide ligand. This mutation activates AKTl by means of pathological localization to the plasma membrane, stimulates downstream signalling, transforms cells and induces leukaemia in mice. This mechanism indicates a direct role of AKTl in human cancer, and adds to the known genetic alterations that promote oncogenesis through the phosphatidylinositol-3-OH kinase/AKT pathway.

Cancer Genome

Many claims have been made that nutrition has a causative or preventive role in the aetiology of cancer. Some of these claims can be seriously considered, others dismissed as fabrications of fertile imaginations. Unfortunately this is a complex area and one to be looked at with care. However some silly claims turn out to be well founded and the reverse.

The prospect of the entire cancer genome being described offers a basis for rational thoughts and experiments for nutritionists

Abnormalities in some 350 genes have been shown to be associated with human cancer.

.A recent paper in Nature ( Greenman Nature 446, 153-158, 2007 ) has identified mutations in protein kinases, regulators of proteins through adding a phosphate and another in Science has identified the whole cancer genome in breast and colorectal cancer ( Sjoblom Science 314, 268-274, 2006 ) .

The variety of defects underlying human cancer include

Activating intragenic mutations

Gene amplification

Gene translocations

Epigenetic silencing

Gene deletions

Inactivating mutations

By the time that a cancer is diagnosed billions of cells carry the DNA abnormality which initiated the malignant transformation plus others accumulated along the way. Some of these secondary mutations are due to selective pressures ( drivers ) others incidental ( passengers). Passengers are the chance result of mutation exposures, genome instability, or through the rapid rate of proliferation.

It is the drivers that are the initiators and the subject of significant research. Mind you the passengers may turn out to be important in giving malignancy some of the significant characteristics.

Kinases have a probable role in cancer development eg BCR-ABL in chronic myeloid leukaemia. Cellular kinase mutations are common in cancer of the lung, stomach, ovary, colon and kidney and rare in breast and testes.

Each cancer genome carries many singular abnormalities and not all mutations identified contribute to the manifestations of the associated cancers.

Drivers and passengers.

From Haber and Settleman Nature 446, 145-146, 2007

Cell Structure

A very interesting problem is that of why do cells differ in their formation and in structures. Bone cells in bone being different to say liver cells in liver.

Yet they have identical genome structure. Even more complicated are multicellular structures.

The basis of this different form lies in the chromatin state. Chromatin is the combination of histones and other proteins in a package with the DNA. In an explanatory article Baylin and Schuebel ( The epigenomic era opens 2007 Nature 448, 548-9 )describe chromatin as the software for the readout of the DNA hard drive.

If there is a change in the hard drive ie in the primary sequence of the DNA then a genetic alteration or mutation occurs

If the change is due to a change in the chromatin then there is an epigenetic change which is an alteration in the heritable states of DNA function. This is the expression and interaction of genes especially during the development process. There is no change in gene structure. Epigenetic change is the mechanism whereby there is flexibility in gene expression and the same genome package produces different cellular structures in the same organism.,

The central unit of chromatin is the nucleosome, which is constructed from short regions of DNA wound around an octet of histone proteins. This unit can modulate the readout from DNA in at least three ways.

nucleosomes can be physically rearranged on DNA by complexes known as chromatin-remodelling proteins, the greater the distance between nucleosomes, and hence the ‘openness’ of chromatin, the higher the likelihood that such regions of DNA will be transcribed into RNA.
many nucleosomes can be compacted into higher-order aggregates to form closed chromatin, or heterochromatin, thereby preventing transcription. The balance between the open and closed parts of the genome facilitates proper gene-expression patterns in given cell types, and also prevents unwanted gene transcription.
there is a complex interplay between enzymes that can modify particular amino acids in the histone component of the nucleosomes, and those that reverse the modifications. The modifications, or histone ‘marks’ interact with proteins that bind to and interpret them. The marks were initially seen as a histone code’, the idea being that a restricted number of them would specify the ‘on’ or off state of RNA production from DNA .
the constituents of chromatin, and nucleosome structure, position and modification, are highly complex. It is a balance between these factors that marks an individual gene, or groups of genes, for various levels and states of expression”.

. Mikkelsen T S, et al in a paper entitled

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells 2007 Nature 448 553-9 report the application of single-molecule-based sequencing technology for profiling histone modifications in mammalian cells. They found that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation.

Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions.This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.

DNA Control

This paper in Nature 2008, vol 454 7th August p 711-2 is an easy read account of epigenomics, the physiology of molecular biology

Epigenomes, is all the epigenetic marks in a given cell type. Epigenetic processes are essential for packaging and interpreting the genome, are fundamental to normal development and are increasingly recognized as being involved in human disease. Epigenetic mechanisms include, among other things, histone modification, positioning of histone variants, nucleosome remodelling, DNA methylation, small and non-coding RNAs. These mechanisms interact with transcription factors and other DNA-binding proteins to regulate gene-expression patterns inherited from cell to cell. The patterns underlie embryonic development, differentiation and cell identity, transitions from a stem cell to a committed cell and responses to environmental signals such as hormones, nutrients, stress and damage.

Although epigenomic changes are heritable in somatic cells, drug treatments and presumably nutrients could potentially reverse them. This has significant implications for the prevention, diagnosis and treatment of major human diseases and for ageing.

Dna Methylation

Differential expression of the eukaryotic genome through cell differentiation or response to environmental changes requires specific modulation of its nuclear organization. These processes enable regulated genes to prevail against regulatory constraints of chromatin structure in which DNA is wrapped around core nucleosomes consisting of octamers of histones H2A. H2B, H3 and H4 Overcoming the structural restriction of chromatin upon gene expression is achieved in part through the modulation of particular marks that define active or inactive chromatin domains.

DNA methyl transferases establish and maintain the pattern of genomic DNA methylation on cytosines of CpG dinucleotides. This cpigenetic mark is linked to gene repression: hypomethylated DNA is associated with active genes, whereas hypermethylated genes are silent.

Although gene expression correlates with CpG demethy-lation, processes that either remove the 5-methyl group or that exchange methylated cytosines with cytosines are unclear.

Processes that regulate gene transcription are directly under the influence of the genome organization. The epigenome contains additional information that is not brought by DNA sequence, and generates spatial and functional constraints that complement genetic instructions.

Metivier et al in Nature 6th march 2008 show present evidence of an unanticipated dynamic role for DNA methylation in gene regulation in human cells. Periodic, strand-specific methylation/demethylation occurs during transcriptional cycling of the pS2/Tl gene promoter on activation by oestrogens.

DNA methyltransferases exhibit dual actions during these cycles, being involved in CpG methylation and active demethylation of 5mCpGs through deamination. Inhibition of this process precludes demethylation of the pS2 gene promoter and its subsequent transcriptional activation. Cyclical changes in the methylation status of promoter CpGs may thus represent a critical event in transcriptional achievement.

The interesting point here for nutritionists is that if oestrogen act in this manner then soy products which have an mild oestrogenic activity might also

Metivier et al 2008 Cyclical DNA methylation of a transcriptionally active promoter Nature vol 452, pp 45-50

DNA Repair

The role of some nutrients in metabolism is explained by their anti-oxidant influence on the molecular biological framework of the cell. This very useful series of reviews

In Nature 2007, vol 447, pp 923-958

give an insight into the systems which antioxidants might be protecting. A really good read.

Replication and protection of telomeres

R.E. Verdun SJ.Karlseder p 925-931

The ends of chromosomes need special protection against cellular processes that alter their genetic content It is essential to protect the chromosome ends to prevent triggering of the DNA-damage repair machinery and enzymatic attack. These processes include digestion by enzymes, inappropriate repair by the DNA-damage repair machinery and the failure of DNA polymerases to replicate DNA strands completely. Protection is provided by telomeres. Telomeres are tightly regulated complexes consisting of repetitive G-rich DNA and specialized proteins Telomeres not only conceal linear chromosome ends from detection and inappropriate repair but also provide a buffer to counteract replication-associated shortening They are highly regulated and specialized and their structure and length contribute to chromosomes integrity. The review discusses how telomeres interact and cooperate with the DNA replication and DNA-damage repair machineries.

Expandable DNA repeats and human disease

S. M Mirkin p 932-940

Nearly 30 hereditary disorders in humans result from an increase in the number of copies of simple repeats in genomic DNA. These DNA repeats seem to be predisposed to such expansion because they have unusual structural features, which disrupt the cellular replication, repair and recombination machineries which affects gene coding or expression and leads to disease. The underlying disruption is that repeat-containing regions can form hairpins and other unusual structures when the DNA duplex separates. Repeat-associated diseases develop not only in response to the structural characteristics of repetitive DNA but also to those of the corresponding RNA. Many of these debilitating diseases result from repeat expansions in the non-coding regions of their resident genes.

Base-excision repair of oxidative DNA damage

S. S. David. V L. O’Shea & S. Kundu p 941-950

The specific pairing of DNA bases is crucial for the maintenance of genetic integrity. Bases are susceptible to oxidation by environmental agents and endogenous products, which modify the chemical structure and therefore the base-pairing properties of DNA

Base-excision repair has an important role in preventing mutations associated with a common product of oxidative damage to DNA, 8-oxoguani’ne. Recent structural studies have shown that 8-oxoguanine DNA glycosylases use an intricate series of steps to locate and excise 8-oxoguanine lesions efficiently against a high background of undamaged bases. The importance of preventing mutations associated with 8-oxoguanine is shown by a direct association between defects in the DNA glycosylase MUTYH and colorectal cancer. The properties of other guanine oxidation products and the associated DNA glycosylases that remove them are now also being revealed.

Chromatin dynamics and the preservation of genetic information

J A. Downs, M C. Nussenzweig and A Nussenzweig p 951-958

The genome is frequently damaged by double-strand breaks in the DNA. Changes in the cellular response to double-strand breaks are an important cause of cancer and other age-related pathologies. It is important to understand the enzymatic mechanisms involved in recognizing, signalling and repairing double-strand breaks. Chromatin has an important role in initiating, propagating and terminating this cellular response to DNA damage.

Genetic material in cells is organized into chromatin, which consists of DNA in association with histone proteins . This packaging makes damaged sites in the DNA relatively inaccessible to the repair machinery. The density of chromatin is reduced in the region of double-strand breaks, enabling access of DNA-damage sensor proteins to the lesion and initiation of repair. Much is known about how chromatin is ‘remodelled’ during gene transcription, and it is becoming evident that some of the same machinery is involved in the response to DNA damage.

DNA and Damage

This is a fascinating review by Jackson and Bartekon the DNA-damage response in human biology and disease in Nature .

Tens of thousands of DNA in each of the 1013 cells in the human body is damaged each day. These lesions can block genome replication and transcription, and if they are not repaired or are repaired incorrectly, they lead to mutations or wider-scale genome aberrations that threaten cell or organism viability. Some DNA aberrations arise through physiological processes, such as DNA mismatches occasionally introduced during DNA rep¬lication and DNA strand breaks caused by abortive topoisomerase I and topoisomerase II activity. In addition, hydrolytic reactions and non-enzymatic methylations generate thousands of DNA-base lesions per cell per day. DNA damage is also produced by reactive¬oxygen compounds arising as by-products from oxidative respira¬tion or through redox-cycling events involving environmental toxic agents and Fenton reactions mediated by heavy metals. Reactive oxygen and nitrogen compounds are also produced by macrophages and neutrophils at sites of inflammation and infections. Such chemicals can attack DNA, leading to adducts that impair base pairing and/or block DNA replication and transcription, base loss, or DNA single-strand breaks. Furthermore, when two single-strand breaks s arise in close proximity, or when the DNA-replication apparatus encounters a single-strand breaks or certain other lesions, double-strand breaks single-strand breaks are formed. Although double-strand breaks do not occur as frequently as the other lesions listed above, they are difficult to repair and extremely toxic. The most pervasive environmental DNA-damaging agent is ultra¬violet light. Although the ozone layer absorbs the most dangerous part of the solar ultraviolet spectrum (ultraviolet C), residual ultra¬violet A and ultraviolet B in strong sunlight can induce -100,000 lesions per exposed cell per hour. Ionizing radiation also generates various forms of DNA damage, the most toxic of these being double-strand breaks. Some ionizing radiation results from radioactive decay of naturally occurring radioactive compounds. For example, uranium decay pro¬duces radioactive radon gas that accumulates in some homes and contributes to lung-cancer incidence. Exposure to natural or man¬made radioisotopes also occurs during cancer radiotherapy, whereas the radioactive compounds iodine-131 and technetium-99m are exploited to diagnose and treat benign and malignant thyroid diseases. Lessons about the health consequences of excessive radiation exposure are provided by the aftermaths of the Chernobyl nuclear-reactor disasterand nuclear detonations over Japan in the Second World War.

Today, probably the most prevalent environmental cancer-causing chemicals are those produced by tobacco products, which trigger various cancers, most notably those of the lung, oral cavity and adja¬cent tissues. Cancer-causing DNA-damaging chemicals can also contaminate foods, such as aflatoxins found in contaminated pea¬nuts and heterocyclic amines in over-cooked meats. DNA-damaging chemicals have also been used in warfare, and on a more positive note, are widely used to treat cancers and ailments such as psoriasis.

They describe how DNA lesions are dealt with at the molecular level. The presence of a lesion in the DNA, which has consequences for replication is recognised by various sensor proteins. These proteins initiate many cellular pro¬cesses, with biological significance which have roles in preventing human diseases. These include DNA repair pathways, DNA damage signalling and cell cycle checkpoints, a DNA damage response system.

Jackson and Bartek 2009 The DNA-damage response in human biology and disease Nature vol 461 pp 1071-78

DNA Shapes

The genetic information embodied in DNA must be decoded at the right time and in the right type of cell. To achieve this, proteins that control such processes have to bind to specific places in the genome. How a protein finds the correct spot to bind to among all the possi¬ble sites (3 billion base pairs in the human genome, for example) has been the preoccu¬pation of molecular and structural biologists for decades.

A protein could recognize its binding site in the genome by somehow ‘reading’ the DNA and this is the case from study¬ing structures of protein- DNA complexes. The DNA double helix has two grooves, a major and a minor one, that wind around the central axis of the molecule, and reading is achieved using hydrogen bonds that form between protein side chains and the edges of the DNA nucleo¬tides that are exposed in the major groove. But unlike the genetic code, a simple code for protein recognition of DNA has not emerged despite years of effort.

DNA is a mol¬ecule with a three-dimensional shape that is not perfectly uniform. Rohs et al. in Nature (2009 p 1248-53 vol 461 1248-1253) show that one structural feature of DNA, the shape of its minor groove, can be exploited by proteins for specific recognition.

A particular sequence of nucleotides presents a unique array of hydrogen-bond donors and acceptors in the major groove, providing a clear mechanism for reading that sequence,

The width of the minor groove varies depending on which nucleotides are present in a segment of DNA. The width of the minor groove has a physi¬cal consequence that goes beyond the merely structural, stemming from the charged groups (phosphates) that are arrayed along the outer edge of the DNA backbone, one per nucleotide . Where the minor groove is narrow, the electric-field lines due to the negatively charged phosphates are focused into the groove, leading to an enhanced negative electrostatic potential in that segment of the double helix.

Rohs and colleagues have looked at the databases of three-dimensional structures of protein-DNA complexes and found many examples of proteins that use amino acids containing positively charged side chains, principally arginines, to read the electrostatic potential of the minor groove. Where the groove width and electrostatic potential are optimal, an arginine side chain of a DNA-binding protein is often seen to sit in the minor SI groove

The shape of the minor groove of DN A can direct the binding of proteins to specific sites.

Negatively charged phosphate groups are arrayed along the outer edge of the D A major and minor grooves that spiral around the axis of the double helix. The width of the minor groove varies depending on the sequence of nucleotides. This variation leads to differences in the distance between phosphates across the groove, which in turn lead to variation in the negative electrostatic potential along the minor groove.

Tullius 2009 DNA binding shapes up Nature vol 461 pp 1225-6

Dog Muscle Mass

Whippets are very fast runners, can reach 60 km an hour and have traditionally been used for racing. A rather unfortunate complication has arisen in that some whippets are experiencing doubling muscling, a cramp in the shoulders and thighs.

This is due to a mutation on the MSTN gene which encodes myostatin, a protein important in muscle composition. This mutation involves the deletion of only two DNA bases.

If the dog has mutations in both copies of the MSTN gene then they have the double muscling problem. The parents will have only one mutation.

There is a relationship between speed, muscle mass and a single mutation of the MSTN.

Selective breeding of whippets but not other heavy muscled dog breeds leads to this double muscle condition.

Reported by Shadam in Nature 2007, vol 447, p 274

Epigenetics

I know this review is almost a year old but is very important.

The science of Epigenetics was in part developed by Waddington and his influence flows through these articles.

This is an important area for nutrition and is a rich source of ideas and research projects.

Epigenetics is the study of heritable changes in gene expression that are not due to changes in DNA sequence. Epigenetic changes allow for the differentiation of various cell types in an organism and cellular processes. X-chromosome inactivation in the female mammal is an example. This control may be upset by the aging process, neoplastic transformation, chronic inflammation and exposure to noxious influences and even by nutrition though this an unexplored area.

Epigenetic change may be de to chemical changes in the DNA or histones and also there is a role for RNA in this mechanism.

There are two well known epigenetic systems the Polycomb and Trithorax and DNA methylation.

The Polycomb and Trithorax are a group of proteins which maintain repressed or active transcription states of developmentally important genes. This system has a memory which can be transmitted to the next generations.

DNA methylation is associated with stable gene silencing eg the inactivation of the second X chromosome in the female mammal.

There are additional complex changes in protein complexes which regulate transcription. Changes in chromatin packing and histone modification the protein that packs around the DNA modify transcription.

A further modifying influence on gene activity is its position in the three dimensional structure of the chromosome, that is the manner in which the chromosome is shaped and the position of the chromosome in the nuclear structure and whether the gene is available for biochemical activity or hidden. This may vary from cell to cell and the activity of that cell and determine the cell’s function.

During development, cells are in a genetic state, from which they can differentiate into many cell types, and progressively become differentiated. . Their gene-expression programmes become more defined, restricted and fixed. . Pluripotent stem cells express genes that encode a set of core transcription factors, while genes that are required later in development are repressed by histone marks, with short-term, and flexible, epigenetic silencing. The methylation of DNA gives long-term epigenetic silencing of particular sequences — transposons, imprinted genes and pluripotency-associated genes in somatic cells. Long-term silencing can be reprogrammed by demethylation of DN A, and this process might involve DNA repair.

When there is change in these processes then disease may occur. The interesting situation is in repair and response to injury and inflammation and possibly malnutrition.

Nature Insight editor Campbell,2007 Epigenetics Nature vol 447, pp395-440

Evolution

Many of the classical studies in genetics have used the fruit fly Drosophila. Why the Drosophila?. It has been suggested that the original scientist who used Drosophila was intending to study another insect but as he ate his lunch there was a fruit fly on his banana.

The sequence of the genomes of 12 fly species has now been completed. During evolution, protein coding genes are conserved but show variation. . The vast majority of multigene families are found in all the 12 genomes Drosophila studies. Though there are novel genes peculiar to a particular species.

A major review in Nature looks at the genes involved in genetic selection. And why the different Drosophila species emerge and indeed why they are different. They have examined the traditional protein coding genetics, motifs that regulate gene expression and additional possible mechanisms for the pre-translational processing of mRNAs or alternative modes of translation.

Rapid evolution has occurred in the genes involved in olfaction, immunity and insecticide resistance.

The Drosophila has a simple metabolic system for example the control of glucose and lipid metabolism. Studies in Drosophila metabolic processes have equivalence in mammalian tissue and hence are a good model to study the gene protein metabolic systems. Similarly the control of total size, organ size, cell competition and apoptosis, control of cell division , cell shape and arrangement can be studied in the fruitfly. The feedback systems coordinating various processes are similarly well studied in the fly.

Gunter et al Editor 2007 Genome labour bear fruit. Nature vol 450 pp 183-241

Gene Control

In cells genes are turned off or on according to the requirements and type of cell. Clearly an intestinal cell will behave differently to a nerve cell yet arising from the same germinal cell line. Yet the genes are the same.

The silencing of genes can be controlled by the Polycomb group of proteins. These alter the structure of chromatin the DNA – histone complex. Such silencing may be thorough the addition of specific small molecular weight molecules to the histone. This can be reversible.

The manner in which genes are arrayed within the cell determines transcription. The suppressing tags include acetyl, methyl and phosphate groups added to specific amino acids in histones. Methylation is the most stable addition and be retained through many life cycles. There are histone demethylase enzymes which remove the methyl additions to the histone.

A newly described demethylase enzyme acts with a retinoic acid receptor to prevent expression of retinoic acid responsive genes. Retinoic acid can signal to the Polycomb group proteins to remove histone tags in nerve cell releasing more specialised stem cells. Retinoic acid also has a role in bone marrow and macrophage gene unlocking .

Jones (2007) Reversing the irreversible Nature vol 450 pp 357-9

Epigenome

What makes two individuals different.? Less the genome sequence , which has a minor place but the epigenome , a set of chemical modifications, not encoded in DNA , which dictate how and when genes are expressed. There are many ways of epigenetic modification, which includes methylation of the DNA , histones that wind around DNA to create a packed cluster of chromosomes and the activation of small non coding RNA. DNA methylation reduces gene expression.

Katsnelson 2010 Genomics goes beyond DNA sequence Nature vol 465 p 145

Gene Flexibility

Nutrition has had to come to terms with the domination of science by molecular biology. Can Nutrition find a place in the science of the post translational events by providing substrates for the modulation of these genetic metabolic programme?.

Hints are given by studies describing small molecular transfer reactions.

Acetylation as a regulatory post translational modifier. The general transcription factor TFIIB which is prerequisite for the initiation of polymerase II activity is acetylated. Acetyl CoA is involved in this reaction ( Choi et al Nature 2003, vol 424, pp 965-9 )

Methylation is involved in cancer linked epigenetic alteration , either through hypomethylation or hypermethylation . The breast cancer drug tamoxifen is a drug with distinct genomic activity and gene transcriptional regulation. ( Wu et al Nature 2005, vol 438, , pp 981- 987

Nicotinamide riboside increases the concentrations of nicotinamide adenine dinucleotide which activates the age related protein Sir2, well anyhow in yeast. Nature 2007, vol 447, p 118

Folic acid is a determinant of DNA methylation which is important in DNA activity. Ageing is associated with DNA hypomethylation. ( Choi et al 2005, British Journal of Nutrition vol 93,pp31-35)

The inhibition of histone deacetylases can improve memory capabilities in a genetically engineered mouse model of neurodegenera-tion in the central nervous system . Histone deacetylases remove acetyl groups from lysine amino acids in proteins, including the cell nucleus histones. Histones interact with DNA to form chromatin which control the accessibility of DNA for gene transcription. Acetylated histones form active chromatin complexes with DNA, which makes the DNA accessible to RNA polymerases, thereby regulating gene transcription
Inhibitors of Histone deacetylases block the ability of these enzymes to deacetylate histones, promoting histone acetylation in the nucleus and thus altering gene expression. Because altered transcription is known to be necessary for the formation of long-term memories, Histone deacetylases inhibitors have the potential to boost memory formation. This has been demonstrated in normal rats and mice

Sweatt Nature 2007, vol 447, pp151-152

Fischer et al Nature 2007, vol 447 pp 178-182.

There is much potential here for exciting studies.

Gene Variation

There is a great game being played in the molecular biology world genome analysis . It is possible to trace the migration of peoples across he world and long standing theories for the migrations are being tested. It is quite a thought that mankind evolved in Africa and then was able o slowly move to Australia and down the Americas to geographical isolation thereafter.

In addition here are the great Trade route, eg the Silk Road wherein traders brought goods to and from China to the coast of the Mediterranean Sea.

Arabia has served as a strategic crossroads for human dissemination , providing natural connection between the distant populations: of China and India in the east to the western civilizations along the Mediterranean.

In the paper the authors explore this region’s critical role in the migratory episodes leaving Africa to Eurasia and back, using high resolution Y chromosome analysis of males from the United Arab Emirates. Qatar and Yemen .

With the exception of Yemen, southern Arabi, South Iran and South Pakistan show high diversity in their Y-haptogroup substructure possibly as a result of gene flow along the coastal crescent shaped corridor of the Gulf of Oman facilitating human dispersals. Increased rates of marriages between close relatives may have an impact in Yemen and Qatar, which experience significant heterozygote deficiencies at various hypervariable autosomal STR loci.

What interest is this to an nutritionist. Wel, any theory which purports to attribute environmental change eg diet to a particular health problem must bear in mind the diversity of the human population or lack of diversity in a particular population.

Cadenas et al 2008 Y-chromosome diversity characterizes the Gulf of Oman , European Journal of Human Genetics. Vol 16, 374-386

Genes, Obesity

Ling Yang1, et al (2008) Potential association of INSIG2 rs7566605 polymorphism with body weight in a Chinese subpopulation European Journal of Human Genetics 16, 759–761

Herbert et al reported association with obesity of a common DNA variant rs7566605 at 10 kb upstream of the INSIG2 gene. Ling Yang analyzed rs7566605 polymorphism in 3125 Chinese in a cross-sectional study. They found no significant association of rs7566605 polymorphism with body mass index (BMI) and waist circumference among all participants (P=0.52). However, if geographic location is considered, the C/C genotype of rs7566605 was marginally associated with increased levels of BMI and risk of obesity among individuals living in Shanghai (P=0.06), indicating that the C/C genotype may contribute to obesity in certain subpopulation among Chinese under certain environmental settings.

INSIG2, cross-sectional study, obesity, body weight; Chinese population

Genetic Reviews

Life at the top of any intellectual discipline is not necessarily a kindly experience. The very bright can be bold brash characters.

Two men who have radically changed our knowledge of genetics are James Watson and Craig Venter.

Watson and Crick were the first to adequately describe DNA and in doing so transform our understanding of biology.

Craig Venters organised a privately funded project to decode the human genome.

Each have written an account of their lives and experiences.

Craig Venters , A life decoded: My genome: My life

Allen Lane

James Watson Avoiding boring people. And other lessons from a life in science.

Oxford University Press

Well reviewed and worth looking at.

Genetics And TB

The balance between nature and nurture and the development of disease is complex. Nutrition clearly has a major role in the health of an individual.

However infections are another major factor.

An article in Nature

Kaufmann 2008, Deadly combination Nature vol 453 p 295-6

describes that not only does the genetic make up of the individual dictate vulnerability to tuberculous infection but also the genetic structure of the tubercle strain.

Normally when a tubercle bacteria reaches the lungs as a droplet, the immune mechanism of the lungs removes the infection. If however the tubercle can bypass this response then an infection results. Detection of the pathogen is through recognition receptor TLR-2 on the surface of the macrophages followed by a signalling cascade mediated by the TLR-2 adaptor protein. T cell white cells are involved.

If the tubercle can bypass this process then infection ensues.

Polymorphism is a feature of tuberculosis and hence the threat from infection persists

I have always felt that the ravages of tuberculosis in 19th century Europe have altered the genetic structure of the surviving families. The survivors for whatever reason were different from the population entering the 19th century.

Many factors would affect survival. Overcrowding, awful working conditions, nutrition and sunlight to name but a few.

Genome Diabetes

In 1913, RA Fisher, an evolutionary biologist and pioneer of modern statistics, published a paper on the genetic causes of disease that brought together two rival factions.

Geneticists who proposed a theory that diseases worked like Mendel’s pea plants, with just one or two genes responsible for each condition.
Biometricians, however, advocated a continuous distribution of phenotypes.
Fisher suggested that many mendelian traits could result in the continuous distribution of a disease.

But Fisher’s theories had been difficult to substantiate. Even the much-heralded Human Genome Project in the 1980s didn’t help as much as expected.

The two methods traditionally used to hunt down disease genes are linkage analysis, which uses large family trees to work out which genes are shared by affected individuals, and the candidate-gene approach, which uses physiological clues to narrow down potential culprits. But when it comes to complex conditions such as heart disease or diabetes, in which multiple environmental and genetic factors combine, neither method is very powerful- Scientists have identified just a handful of disease genes, along with lots of weak, unconfirmed hits.

Modern gene-chip technology combined with recently published maps of human genetic variants that groups together related variants single nucleotide polymorphisms enables the entire genomes of thousands of people to be scanned. The GWA approach ( genome wide association )

Yet new results, including a stud)- en type 2 diabetes published this week (R. Sladek et al. .(Nature doi :10.1038/nature05616;2007 ) suggest that the GW’A approach will bear fruit, and lots of it This study on large numbers of type 2 diabetics and normals show . four genomic regions that confer a significant risk to developing the disease. Along with the previously identified TCF7L2 gene, these regions together account for 70% of the genetic risk for the disease.

Of the four new genes, the best hit is SLC30A8, a zinc transporter, which is important because zinc assists with insulin secretion

Other diseases in the pipeline include coronary heart disease and rheumatoid arthritis.

Gene Russo Nature vol 445, 15 February 2007 pp 688-9

Genome & Disease

Genome susceptibility to diseases.

The Welcome Trust Case Control Consortium has made a large case control comparison of the gene structure of 14000 cases of seven common diseases with 2000 controls.

One wonders if the control group size is sufficiently large.

Nevertheless

They have identified 24 independent control association signals

1 for coronary artery disease

9 for Crohns disease

3 for rheumatoid arthritis

7 for type 1 diabetes

3 in type 2 diabetes

They are also have association studies for tuberculosis , breast cancer, multiple sclerosis ankylosing spondylitis and autoimmune thyroid disease.

All of these conditions have other aetiological theories grouped around them, including diet.

The old Chinese curse, to live in a time of change

The Welcome Trust Case Control Consortium 2007, Genome-wide association study of 14,000 cases of seven common diseases and 3000 shared controls. Nature vol 447, 661-678.

Genotype

One of the rewards of the avalanche of genome information are the findings that there are associations between diseases, behaviour patterns and genotype, the genotype- phenotype association. The genotype-genotype association .

However one should take such findings with a pinch of salt until

The report has been repeated and hence more likely to be true, ie replication d
that vigorous statistical analyses have been performed
The study information is sufficient to make a judgement on the work
The data presented is sufficient to make independent statistical analysis.
The methodologies used are proper.
The control population is truly a control population and sufficiently large to make a significant comparison.
An expert working party has reported in Nature with criteria for accepting studies of genotype-phenotype associations assessed by genome-wide or candidate-gene approaches.

Statistical analyses demonstrating the level of statistical significance of a finding should be published or at least available so that others can attempt to reproduce the reported results
Explicit information should be provided about the study’s power to detect a range of effects
¦The study should be epidemiologically sound, with careful accounting for potential biases in selection of subjects, characterization of phenotypes, comparability of environmental exposures’ (when possible) and underlying population structure in cases and controls

■ Phenotypes should be assessed according to standard definitions provided in the report

Associations should be consistent (within the range of expected statistical fluctuation) and reported for the same phenotypes across study subgroups or across similar phenotypes in the entire study group
Significance should not depend on altering the quality control methods beyond standard approaches that could change inclusion or exclusion of large numbers of samples or loci
¦ Measures to assess the quality of genotype data should include results of known study sample duplicates or publicly available samples

The results for concordance between duplicate samples (if applicable) as well as completion and call rates per SNP and per subject should be disclosed, along with rates
of missing data
A subset of notable SNPs should be evaluated with a second technology that verifies the
same result with excellent concordance, because no technology is error-free
¦ Associations with nearby SNPs in strong linkage disequilibrium with the putatively associated SNP should be reported (and should be similar)

The results of replication studies of previous findings should be reported even if the results are not significant.

Testing for differences in underlying population structure in case and control
groups should be performed and reported
Appropriate correction for multiple comparisons across all statistical tests
examined should be reported.
Comparison to genome-wide thresholds should be described. Similarly, for bayesian approaches, the choice of prior probabilities should be described
Not easy stuff, but do not accept any of these widely publicised associations without thinking, is this sensible.

NGI-NHGRI working Group on Replication in Association studies (2007 Replicating genotype –phenotype associations Nature vol 447, 655-660

Growth Control

The control of organ (or organism) size is a fundamental aspect of life ? What makes an elephant grow a million times larger than a mouse? How do our two hands develop independently of each other yet reach very similar size? How does a liver precisely regenerate its original mass when two-thirds of it is removed? The coordination of cell proliferation and cell death is essential for proper organ size during development and for maintaining tissue homeostasis throughout postnatal life

The recent discovery of a novel signaling network in Drosophila, known as the Hippo (Hpo) pathway, might provide an important entry point to these fascinating questions. The Hpo pathway consists of several negative growth regulators acting in a kinase cascade that ultimately phosphorylates and inactivates Yorkie (Yki), a transcriptional coactivator that positively regulates cell growth, survival, and proliferation. Components of the Hpo pathway are highly conserved throughout evolution, suggesting that this pathway may function as a global regulator of tissue homeostasis in all metazoan animals.

(Pan D ( 2007) Genes Devel. Hippo signalling in organ size control.vol 21, : 886-97)

In Drosophila, cell proliferation and cell death are orchestrated by the Hippo kinase cascade, a growth-suppressive pathway that ultimately antagonizes the transcriptional coactivator Yorkie (Yki). A single phosphorylation site in Yki mediates the growth-suppressive output of the Hippo pathway. Hippo-mediated phosphoryiation inactivates Yki by excluding it from the nucleus, whereas loss of Hippo signaling leads to nuclear accumulation and therefore increased Yki activity. A mammalian Hippo signaling pathway also culminates in the phosphorylation of YAP, the mammalian homolog of Yki. The mammalian Hippo pathway is a potent regulator of organ size, and that its dysregulation leads to tumorigenesis. ( Dong J ( 2007,) Elucidation of a universal size-control mechanism in Drosophila and mammals. Cell, 130, 1120-33 )

Which is part of the explanation for why a mouse and an elephant are somewhat different in size.

As an aside it is fascinating how such complex and far reaching are controlled by phosphorylation, acetylation and methylation.

Histones and Cancer

Post-translational modification of histones provides an important regulatory platform for processes such as gene transcription and DNA damage repair. It has become increasingly apparent that the misregulation of histone modification, which is caused by the deregulation of factors that mediate the modification installation, removal and/or interpretation, actively contributes to human cancer. In this Review, the authors summarize recent advances in understanding the interpretation of certain histone methylations by plant homeodomain finger-containing proteins, and how misreading, miswriting and mis-erasing of histone methylation marks can be associated with oncogenesis and progression. These observations provide a greater mechanistic understanding of epigenetic alterations in human cancers and might also help direct new therapeutic interventions in the future.

Chi et al (2010 ) Covalent histone modifications — miswritten, misinterpreted and mis-erased in human cancers Nature Reviews Cancer 10, 457-469

Lung Cancer

Variation in the human genome and the consequences for health are giving exciting result, largely through genome-wide association studies (GWAS). Such studies need to be large and repeatable.. Since early 2007, variations at nearly 100 regions of the genome have been associated with an increased risk for diseases with a complex genetic background, such as diabetes, inflammatory bowel disease, cancer (most notably breast, colorectal and prostate) and heart disease.

Lung cancer is associated with smoking and hence has a considerable environmental factor in its aetiology. Not everyone who smokes heavily gets lung cancer Three recent studies identify variation in the same region of the long arm of chromosome 15 (15q24/15q25.1) as having a key role in the aetiology of lung cancer. Among the genes in this region are those that encode subunits of nicotinic acetylcholine receptors, which have an affinity for nicotine. The genetic variation are as single nucleotide polymorphisms (SNPs, with DNA sequence variations that arise from the substitution of one nucleotide base for another, and contribute approximately 90% of common variation in the human genome.

The three studies are all large and appropriately replicated, but they differ on whether the connection is direct or mediated via smoking behaviour — that is, characteristics such as the duration and ‘dose’ of lifetime smoking, and/or the propensity for nicotine addiction. Previous studies ‘had identified the genes encoding subunits of nicotinic acetylcholine receptors as strongly associated with smoking behaviour. The association between smoking and lung cancer is very strong , and any gene variant that is modestly linked with smoking behaviour will seem to be associated with lung cancer unless the matching of cancer cases and controls by smoking behaviour is close to perfect.

The reports vary in their interpretation of the results. One says that the association between the SNP variations is with the number of cigarettes smoked per day and a nicotine dependence scale. They argue that the link with cancer is though nicotine dependence.

The other two groups interpret their results as an association with lung cancer and not smoking.

These result s indicate the complexity of the subject. It is also indicates that it is easy to jump to conclusions about the aetiology of disease and environmental influences.

Nutrition studies are not sufficiently careful in this area.

Chanock and Hunter 2008 When the smokes clears Nature vol 452, pp 537-538

Metabolic Clock

The activities of our bodies follow cycles of repeated oscillations, examples are the sleep-wake cycle, the feeding rhythm and variations in body temperature and hormonal levels. The anatomical centre of the mammalian circadian clock lies within the suprachiasmatic nucleus region of the brain in the anterior hypothalamus.

Many of these cyclic oscillations are circadian (of around 24-hour periodicity), and are controlled by an interplay of numerous molecular factors which ensure the accuracy of the ‘body clock’. The body clock is , organized in complex feedback loops that involve gene transcription and the events that follow it.

The peripheral tissues of many creatures contain independent pacemakers involved in a ‘synchronization web’ that coordinates timing in all the tissues. The transcription of at least 10% of all cellular genes oscillates in a circadian manner indicates how the circadian transcriptional mechanisms influence a wide array of cellular functions.

PGC-1α is a transcriptional coactivator with an essential role in the maintenance of glucose, lipid and energy homeostasis.. It is highly responsive to a variety of environmental cues, temperature, nutritional status and physical activity. Liu and colleagues have shown that the transcriptional regulator PGC-1α is a key factor in the molecular pathways in the circadian control of energy metabolism,.

Several genes contribute to the regulation of the circadian rhythm, including Clock, Bmall, Per. Cry and Rev-erba. The findings of Liu et al showed in Nature that PGC-l α, has a central role in connecting the expression and function of these circadian clock genes in the regulation of energy metabolism, including gluconeogenesis (the synthesis of glucose from non-.sugar substrates), oxidative phosphorylation, oxidation of fatty acids and the biosynthesis of haem.

This function of PGC-l α seems to be mediated by nuclear receptors, such as ROR α, and other, unidentified, transcription factors.

Liu et al 2007 Transcriptional coactivator PGC-1α integrates the mammalian clock and energy

metabolism Nature vol 447pp 477- 81

Grimaldi and Sassone-Corsi (2007) metabolic clockwork Nature vol 447pp 386-7

Methylation

Methylation and all that

Mammals use methylation for the heritable silencing of retrotransposons and imprinted genes and for the inactivation of the X chromosome in females.

The establishment of patterns of DNA methylation during gametogenesis depends upon DNMT3L, an enzymatically inactive regulatory factor that is related in sequence to the DNA methyltransferase DNMT3A and DNMT3B. DNMT3L interacts with the end of a histone H3 which in turn is inhibited by methylation of the histone H3.

Histone methylation is central for regulating chromatin structure, gene transcription and the epigenetic state of the cell.

This is not obscure yawn material but has significance in

1.this is how the heritable factors held in DNA are controlled, and the role of the proteins histones.

2. Methylation may well be dependent upon dietary elements , folic acid, vitamin B12 comes to mind. Clearly this is a guess but this is fascinating

Ooi et al DNMT3L ( 2007 ) connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature vol 448, 714-717

Lan et al ( 2007 ) Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-medaited gene expression. Nature vol 448, 718-722

Micro RNA

MicroRNAs ( m1RNAs) are RNA sequences some 23 nucleotides long. They are crucial to gene expression. As part pf a RNA-protein complexes they form complementary bas pairs with their target complementary RNA sequences. These influence mRNA degradation and repress the translation of the mRNA into protein. Individual micro RNA sequences can suppress the production of hundreds of proteins, the effect is subtle and modest but very important in the fine tuning of protein synthesis. An important route whereby miRNA interact with the target mRNAs is through “seed sites”. These are specific short sequences in both miRNA and the corresponding sequence in the mRNA.

Selbach et al have shown many of these control systems in a recent paper in Nature. Does this matter to a nutritionist. First it is important biology and somewhere in her food must have a role

Selbach et al Nature 2008 Widespread changes in protein synthesis induced by microRNAs vol 455 pp 58-63

Baek et al Nature 2008 The impact of microRNAs on protein output vol 455 pp 64-71

Mourelatos Z Nature 2008 The seeds of silence vol 455 pp 44-45

More Stem Cell

This is not easy stuff but if read slowly drinking a cup of tea can be is at least comprehended. Again a complex system controlled by a methylation process.

The stem cell complex is capable of differentiating into most if not all tissues. The differentiation is determined by histone modification . Histones are the protein wrapping around the DNA.

Bone and fat are somewhat different and their formation involves osteoblasts and adipocytes respectively. The production of osteoblasts and adipocytes from common mesenchymal stem cells is under transcriptional control. Peroxisome proliferator receptor-γ is an marrow . inducer of fat tissue formation

Takada and colleagues have shown that a pathway using CaMKII-TAKl-TAB2-NLK transcriptionally represses PPAR-γ transactivation and induces Runx2 expression, promoting osteoblastogenesis in preference to adipogenesis in bone marrow mesenchymal progenitors. Wnt-5a activates NLK (Nemo-like kinase), which in turn phosphorylates a histone methyltransferase, SETDB1 (SET domain bifurcated 1), leading to the formation of a co-repressor complex that inactivates PPAR-γ function through histone H3-K9 methylation. The signalling pathway suppresses PPAR-γ function through chromatin inactivation triggered by recruitment of a repressing histone methyl transferase, thus leading to an osteobtastic cell lineage from mesenchymal stem cells.

Takarda et al 2007 A histone lysine methyltransferase activated by a non-canonical Wnt signalling suppresses PPAR-γ trans activation. .Nature Cell Biology 9, 1273-1285

Multigenes

As the molecular biologists discover more genes which predispose on to diseases the more evident it becomes that some common conditions are associated with more than one gene. What cannot be over emphasised is that these are susceptibilities which not always directly causal. No matter how many predisposing genes one has for obesity , food must be available in luxious amounts to generate fatty tissue.

There are at least seven genetic variants associated with symptomatic coronary heart disease. Three important ones are found on chromosomes 2, 6 and 9 and apparently these account for 38% of coronary heart disease in that population. The paper describing this is from Germany it is possibly different in other populations.

( Rosenzweig A in New Engl J Med 2007, vol 357, August 2nd ; Scanning the Genome for Coronary risk

And Samani N et al New Engl J Med vol 357 August 2nd Genomewide association analysis of coronary artery disease

Another condition or group of conditions with a genetic basis is inflammatory bowel disease. The genes which have been associated with Crohns disease are involved in barrier function and innate and adaptive immunity. There have been 7 and maybe more genes described with a role in this susceptibility or vulnerability.

The current aetiological concepts in the aetiology include the balance between commensal microbes and the immune response of the person. The nature of the host defences is all important. The mucosal barrier is all important.

So we have nice indicators that susceptibility and disease engendering circumstances interplay.

Xavier RJ and Podolsky DK 2007, Unravelling the pathogenesis of inflammatory bowel disease Nature 2007, vol 448, 427-434

Molecular Biology Update

Chromosomal structural abnormalities are now being studied as a result of the completion of the Human Genome Project. much of the structural variation in the genome has gone unrecognised until recently. Deletions and duplications of DNA strands of between a few hundred base pairs and several million base pairs (copy number variants) are widespread. Human genomic variation, as single nucleotide substitutions has been catalogued since the completion of the draft human genome sequence in 2000. The HapMap project, which by 2007 had documented more than 3 •1 million single nucleotide polymorphisms (SNPs) and their inter-relation, has underpinned subsequent successful genome-wide association studies. Since 2007, genome-wide association studies based on single nucleotide polymorphisms show replicated associations to several common diseases. Some copy number variants explain rare, previously uncharacterised disorders, and they are now expected to explain some of the genetic contribution to common diseases. This review by Wain et al reviews current work to map copy number variants and discusses the of further understanding human health and disease.

Large deletions, duplications, and other structural rearrangements have a role in the aetiology of specific diseases (genomic disorders)

In addition intermediate scale structural variation, caused by a variable number of copies of a particular DNA segment are referred to as copy number variants. The influence of these on disease aetiology is now being studied.

The potential role of copy number variation in complex diseases, includes susceptibility to autism, shizophrenia, Crohn’s disease, psoriasis,” systemic lupus erythematosus. amyotrophic lateral sclerosis, and HIV-l . Such variation has also been associated with vertical transmission of HIV-l, and the progression and response to treatment of HIV-l/ AIDS.

Some of these associations could be false positives, others have had either technical validation or replication of findings in different study populations, or both. These validated associations are probably a direct or an indirect result of changes to the copy number of the relevant genomic sequence.

The location, size, and boundaries (breakpoints) of these variants documented in public databases have been very imprecise, although the new generation of maps of copy number variants are providing much improvement. Scalable methods to characterise copy number variation in association studies have been inexact. In this Review, Wain et al introduce copy number variation, examine advances in our understanding, and discuss the inferences that can be reasonably drawn from association studies of copy number variation.

Wain et al 2009genomic number variation, human health and disease. Lancet vol 374 pp 340-350

Nutrition

Genetics, nutrition, environment and health

Can a well established known environmental or dietary threat or precipitant of ill health affect a person who does not have the innate genetic predisposition?

Obesity & Genes

Adipose-tissue contains the largest store of energy in the body and has important roles in regulating energy partitioning. Adipose tissue is also seen as an active biological tissue rather than a mass of fat.

Developments in genomics, in particular microarray-based expression profiling have: provided scientists with a number of new candidate genes whose expression in adipose tissue is regulated by obesity- Integrating expression profiles with genome-wide linkage and/or association analyses is a promising strategy to identify new genes underlying susceptibility to obesity.

An article by Dahlman and Arner gives a comprehensive review of adipose-tissue expressed genes possibly involved in predisposition to human obesity

The following genes are of potential note.

peroxisome proliferator-activated receptor gamma

INSIG2 acting in adipogenesis;

the adrenoreceptors beta 2 and 3,

hormone-sensitive lipase acting on lipolysis:

uncoupling protein a acting in mitochondria energy expenditure ;

and among secreted molecules the cytokine tumor necrosis factor alpha and the hormone leptin.

Whilst this is in part inspired speculation, the concept of predisposition is an interesting thought. But obesity is the result of an imbalance between food intake and energy expenditure resulting in the storage of energy as fat. No food, no obesity. Or is that the case?

Dahlman and Arner 2007, Obesity and polymorphisms in genes regulating human adipose tissue. International Journal of Obesity vol 31, 1629-1641

P53 Function

P53 is regarded as the guardian of the genome, which regulates the cellular response to stress. It is a tumour suppressor gene , but does p53 have a physiological role? It has a function in maternal reproduction. Sufficient LIF ( leukaemia inhibitory factor) a cytokine is required for implantation of the fertilised ovum and the embarkation on a successful pregnancy. This is regulated by p53.

What the role in the male is remains to be seen? Also from LIF’s name there are other functions attributable to LIF which must be the start of an interesting story.

Hu et al 2007, p53 regulates maternal reproduction through LIF. Nature vol 450 pp721-724

Phenotypes

The genetic make up of populations and even apparently similar races is not uniform. The exciting developments in mapping populations reveal all manner of varieties.

Fuzhong Xue et al report a molecular biological which analyses the presence of a significant boundary between the populations of north and south in China.. This had previously been indicated by archeological, anatomical, linguistic, and genetic data which suggested the presence of a significant boundary between the populations of north and south in China. However, the exact location and the strength of this boundary have remained controversial. In this study, the authors systematically explored the spatial genetic structure and the boundary of north–south division of human populations using mtDNA data in 91 populations and Y-chromosome data in 143 populations. Their results highlight a distinct difference between spatial genetic structures of maternal and paternal lineages. A substantial genetic differentiation between northern and southern populations is the characteristic of maternal structure, with a significant uninterrupted genetic boundary extending approximately along the Huai River and Qin Mountains north to Yangtze River. On the paternal side, however, no obvious genetic differentiation between northern and southern populations is revealed.

This indicates the static nature of female populations in the past. And supports the contention that mobility of males has led to population diversity.

Fuzhong Xue et al (2008) A spatial analysis of genetic structure of human populations in China reveals distinct difference between maternal and paternal lineages. European Journal of Human Genetics) 16, 705–717;

Keywords:

spatial genetic structure, maternal and paternal lineages, mitochondrial DNA, Y-chromosome, GIS, China

Population Genes

There are papers being published with quite sweeping statements about genetic make up and disease liability. This is an interesting and thought provoking paper.

An investigation into fine-scale European population structure was carried out using high-density genetic variation on nearly 6000 individuals originating from across Europe. The individuals were collected as control samples and were genotyped with more than 300 000 SNPs in genome-wide association studies using the Illumina Infinium platform. A major East–West gradient from Russian (Moscow) samples to Spanish samples was identified as the first principal component (PC) of the genetic diversity. The second PC identified a North–South gradient from Norway and Sweden to Romania and Spain. Variation of frequencies at markers in three separate genomic regions, surrounding LCT, HLA and HERC2, were strongly associated with this gradient. The next 18 PCs also accounted for a significant proportion of genetic diversity observed in the sample. We present a method to predict the ethnic origin of samples by comparing the sample genotypes with those from a reference set of samples of known origin. These predictions can be performed using just summary information on the known samples, and individual genotype data are not required. We discuss issues raised by these data and analyses for association studies including the matching of case-only cohorts to appropriate pre-collected control samples for genome-wide association studies.

Simon C Heath et al ( 2008 ) Investigation of the fine structure of European populations with applications to disease association studies. European Journal of Human Genetics (2008) 16, 1413–1429;

RNA And Genes

RNA interference, or RNAi. When a gene is to be expressed, it sends instructions to the cell’s protein synthesis machinery. The intermediary is messenger RNA (mRNA), which has a structure complementary to that of the gene. In their paper, published in Nature in 1998, Fire and Mello, and colleagues, demonstrated that these mRNAs can be targeted for destruction by specific double-stranded forms of RNA (A. Fire et al , Nature 391,806-811; 1998).

It was already known that ‘antisense’ RNA — an artificial molecule whose sequence complements the mRNA could silence specific genes when taken up by a cell. But the effect was modest and inconsistent. And, to complicate the picture the same effect was obtained with ‘sense’ RNA.

In a series of experiments on a muscle gene in the nematode worm Caenorhabditis elegans Fire and Mello showed that a powerful and consistent effect required the sense and antisense RNAs to be stuck together, as double-stranded RNA. When injected with the double-stranded RNA, the worms twitched awkwardly, just like mutant worms lacking the muscle gene. The researchers also showed that mRNA was destroyed by the treatment, rather than being masked as others had believed. And they showed that the double stranded RNA can cause more copies of itself to be made, can spread between cells and can even be inherited by progeny. It is now known that organisms use this mechanism to control the expression of their genes. RNAi is an important way to control genes which insert themselves throughout the genome, jumping genes and disrupt gene function .

This mechanism of RNAi is a universal mechanism throughout all the species studied.

Nature collection December 2006

RNA Interference

The discovery of DNA and RNA was to describe the anatomy of the mechanism whereby heritable information was transferred from generation to generation.

Now the physiology and biochemistry of the mechanism is being described.

Ericka Check in Nature 2007, Hitting the on switch , 448, pp 855-868 discusses RNA interference. This is the process whereby small pieces of RNA regulates the expression of genes. RNA has been seen as the carrier pigeon of the system, that DNA is all. RNA however is important in controlling the transfer of information held by DNA.

Small strands of RNA stick together in pairs and can turn off specific genes. Short interfering RNAs ( siRNAs ) ( also known as short hair pin RNAs ( shRNAs). These act by using a protein (RISC) to cut up the longer messenger RNAs. The small RNAs are able to target messenger RNA through their sequence matches and destroy the messenger RNA. There are also more than 500 miRNA which are directly encoded by DNA.

Methylation has been seen as a prime silencer of gene activity.

It is also possible that the interference pathway may activate genes. if this is the case then a whole new approach to molecular Biology is waiting to be discovered.

ribosomes

A ribosome in action

The manufacture of proteins by ribosomes involves complex interactions of diverse nucleic-acid and protein ligands. Single-molecule studies allow us, for the first time, to follow the synthesis of full-length proteins in real time.

Protein synthesis involves a complex interplay of various cellular components. Ribosomes are the cell’s protein-production factories, and interact with messenger RNA (the template), amino-acylated transfer RNAs (which act as adaptors between mRNA and amino-acid residues) and diverse co-factors (for the ini¬tiation of synthesis, elongation of the nascent chain and release of the mature polypeptide). Uemura et al. report the use of an extremely sensitive single-molecule detection technique to observe this process at unprec¬edented resolution: the stepwise synthesis of a single protein.

Ribosomes are evolutionarily conserved molecular nanomachines with a diameter of about 25 nanometres and a molecular weight of around 2.5 megadaltons. In functional terms, they are amino-acid polymerase enzymes with an RNA ‘heart’. They accelerate the rate of pro¬tein synthesis by at least one millionfold, owing exclusively to entropic effects that involve the positioning of aminoacyl- tRNAs, the shielding of the reaction from bulk solvent and the organ-ization of their own active site. Ribosomes also check the quality of their polypeptide products – as inaccurate amino-acid sequences could result in an altered three-dimensional protein structure and even cellular toxicity.

Structural analyses of functional ribosome complexes have formed the basis of a consistent biochemical model for the mechanism of protein synthesis, suggesting that this process depends on large-scale conformational changes in the ribosome. But the nature, timescale and magnitude of these dynamic changes have until now remained undefined.

Brakmann 2010 A ribosome in action Nature vol 464 987-8

Uemura et al 2010 Real time t RNA transit on single translating ribosomes at codon resolution Nature vol 464, 1012-1017

Sirtuins Update

This Review in Nature 30th July 2009 is a very important review for Nutritionists to appreciate. It suggests that a family of enzymes the sirtuins have a role in governing the control of both metabolism and genetics. This review looks at sirtuin biology, and the role these proteins have in various age-related diseases

The sirtuins are a highly conserved family of NAD+ -dependent enzymes that regulate lifespan in lower organisms. Recently, the mammalian sirtuins have been connected to a activities that include cellular stress resistance, genomic stability, tumorigenesis and energy metabolism..

In 1914, F. Peyton Rous described the beneficial effects of rats placed on a calorie-restricted diet. Over time, however, other scientists demonstrated the benefits of caloric restriction in species ranging from humans to yeast. Studies in yeast showed that the molecular basis of caloric restriction involves a family of NAD+ -dependent enzymes, the sirtuins.

The first described member of the sirtuin family, yeast Sir2 (silent information regulator 2), was originally isolated in a screen for silen¬cing factors. Then , four proteins (named Sir1-Sir4) were shown to be important regulators of silencing at the mating type locus as well as telomeric DNA.

The Sir family are also key regulators of lifespan .

Sir2 also acts as a histone deacetylase, requiring NAD+ as a co-factor.

In yeast and flies, Sir2levels increased following caloric-restriction treatment.

In sirtuins deficient yeast and mice, this extension of lifespan by caloric restriction is abolished.

To date, seven mammalian homologues have been identified. SIRT6 and SIRT7 being nuclear proteins, SIRT3, SIRT4 and SIRTS mitochondrial proteins, and SIRTl and SIRT2 being found both in the nucleus and the cytoplasm, in a cell¬ and tissue-dependent context.

Sirtuins have a role in maintaining genomic integrity . Yeast and mammalian Sir2 has been shown to inhibit recombination of ribosomal DNA, delocalises to sites of DNA breaks and are involved in deacetylating histone proteins and the absence of this activity results in silencing defects, increased genomic instability and sensitivity to DNA damage.

Mammalian SIRT1 also influences genomic stability. SIRTl can deacetylate various factors linked to the repair of DNA damage, SIRTl appears to regulate epigenetic silencing and chromatin modification, and recent evidence suggests this is achieved, at least in part, through direct regulation of modifying enzymes, such as the histone methyltransferase SUV39Hl.

Mammalian sirtuins also appear to have an important role in regu¬lating cellular stress resistance and modulating the threshold for cell death. In part, this increased stress resistance comes from the inter¬action ‘with the Forkhead box class 0 (FOXO) family of transcription factors. These mammalian transcription factors regulate both energy status and stress resistance, two properties intimately connected to lifespan extension.

In mammals, blood glucose concentration is maintained within a narrow range under a variety of physiological conditions. During starvation, serum glucose control is achieved in part by hepatic gluconeogenesis. Sirtuins have a role in in this physiological adaptation. The peroxisome proliferator-activated receptor gamma¬coactivator-1a (PGC-la.) is a known target of SIRTl-dependent dea¬cetylation, and this coactivator also plays a fundamental part in regulating gluconeogenesis and fatty acid oxidation pathways within the liver. The ability of PGC-la. to modulate these latter two path¬ways appears to require SIRTl

The sirtuin family has a much broader role in metabolism than the regulation of glucose homeostasis. SIRTl through its regulation of PPAR-y and PGC-la activity has a significant regulatory role in fat mobilization and fatty acid oxidation The regulation of PGC-la. activity also suggests a role for sirtuins in the generation of new mitochondria, SIRTS, another mitochondrial sirtuin, is an important regu¬lator of the urea cycle.

Why is the sirtuin family a key regulator of so many seemingly varied processes. The common actor is NAD+, linking sirtuin activity to the underlying metabolic state of the cell. Ingested sugar, fat and protein eventually reduce to a single, simple and versatile intermediate, acetyl¬CoA, which also modifies histones and hence regulates gene expression. Acetylation and NAD + -dependent deacetylation are perhaps the most immediate and versatile connection between intracellular energetics and intracellular fate.

Finkel, Deng & Mostoslavsky 2009 Recent progress in the biology and physiology of sirtuins Nature vol 460 pp 587-591

Small Rnas

A new development in our understanding of metabolism as controlled by our genome is the finding of a large family of small non coding RNAs.

In a clear summary in Nature Grobhans and Filopwicz explain their biology

There arc three main types of well characterised RNA:

Messenger RNA, transfer RNA and ribosomal RNA.

Messenger mRNAs are translated into proteins, whereas transfer tRNAs and ribosomal rRNAs have housekeeping roles during mRNA translation

Small RNAs (20-30-nucleotides) are not translated into proteins, but regulate biological processes, often by interfering with mRNA translation.

Small RNAs include small interfering RNAs (siRNAsJ, microRNAs (miRNAs) and Piwi-associated RNAs (piRNAs).

A summary of RNAs

Messenger RNAs (mRNAs) act as templates for protein synthesis.

Ribosomal RNAs ( rRNAs ) are found in ribosomes, and mediate the decoding of mRNAs to the amino-acid sequences of proteins.

Transfer RNAs (tRNAs ) carry individual amino acids to the site of protein synthesis that recognize specific codons in -mRNA.

Non-coding regulatory RNA

Small interfering RNAs ( siRNAs)

Small RNAs (20-25 nucleotides in length)are formed by cleavage of long double-stranded RNA molecules. These are important in modulating of transposons activity and combating viral infection, and regulate protein-coding genes

.MicroRNAs (miRNAs) Small RNAs (20-25 nucleotides in length) are encoded by specific genes from long, single-stranded RNA sequences and fold into hairpin structure. The are important in repressing mRNA translation or mRNA degradation

Piwi-associated RNAs (piRNAs ) are small RNAs (25-3nudeotides in length) and are essential for the development of germ cells.

Longer non-coding RNAs of of 70 to thousands of nudeotides lengths which are involved in various cellular processes, including mRNA splicing and ribosome biogenesis.

Small RNAs are generally produced by fragmentation of longer precursors eg from double-stranded RNAs form ed by base-pairing of complementary RNAs by the enzyme Dicer into shorter double-stranded siRNAs some 20 base pairs long.

Each strand assembles into an effector complex known as an RNA-induced silencing complex (RISC, finds a mRNAs with a sequence perfectly complementary to the siRNA. RISC then cleaves the mRNA in the middle of the mRNA-siRNA duplex, and the resulting mRNA halves are degraded by other cellular enzymes

MicroRNAs are processed from specific genome-encoded precursors, in two steps, catalysed by the enzymes Drosha (in the nucleus) and Dicer (in the cytoplasm).

Pi w i – assoc ia ted R N As are generated from long, single-stranded precursors in a process independent of Drosha and Dicer. There are tens of thousands of these and are important in the development of the germ cell.
Grobhans and Filipowicz 2008 The expanding world of small RNAs vol 451, 414-416

Starvation

It is always satisfying when the hints developed by epidemiology ae shown in experiments to be true.

Some epidemiological observations ( e.g. smoking and cancer of the lung and jumping form the 22nd floor of a building is fatal) stand in their own right.

Others point the direction

One such indicator is that starvation reduces the chances of tumour development.

Lee and his colleagues in a difficult paper show a relationship between tumour development and energy starvation.

Tumour formation is a process in which the normal control mechanisms are lost. A serine/threonine kinase ( mTOR) is central to a diverse range of cellular processes important in growth and proliferation. mTOR is increased in a number of malignant processes. There are two forms of mTOR with different regulatory functions. The tumour suppressors TSC1 and TSC2 regulate mTOR.. Loss of TSC1 or TSC2 leads to a tumour called hamartoma syndrome which is a none malignant growth.

By phosphorylating TSC2, the low energy response mediator AMPK inactivates mTOR dependent growth and proliferation. This phosphorylation of TSC2 has a protective role against energy starvation mediated apoptosis ( cell death ). Other substrates phosphorylated by AMPK lead to anabolic processes being inhibited and catabolic processes being activated.

AMPK also protects the cell cycle from stress by phosphorylation of the gene p53. Protein synthesis is also prevented.

Both energy starvation and DNA damage lead to p53 activation. mTOR activity increases p53 synthesis and activation in response to both glucose starvation and DNA damage. There is phosphorylation of p53 . p53 is a potent activator of apoptosis.

By means of the AMPK-TSC-mTOR pathway , p53 forms a negative feedback loop which keeps its own synthesis in check. Cells that cannot inhibit mTOR have increased p53 activity when activated.

Lee et al (2007) Constitutive mTOR activation in TSC mutants sensitises cells to energy starvation and genomic damage via p53. The EMBO Journal vol 26, 4812-4823.

Stem Cells

Several fines of evidence have suggested extensive proliferaton activity and pluripotency of germline stem cells, including spermatogonial stem cells .

In an early embryo a cell has the potential to generate many different cell types. During development cells generally lose this potential or ’potency’, and become restricted to making one or a few cell types. Cells can become undetermined and undifferentiated in special circumstances. These Undifferentiated cells which are capable of self-renewal and differentiation into more specialised cells are called stem cells . . Stem cells have the potential to develop into many different cell types in the body They might act as a repair system for the body, they can theoretically divide without limit to replenish other cells as long as the person or animal is still alive. When a stem cell divides, each new cell has the potential to either remain a stem cell or become another type of cell with a more specialized function, such as a muscle cell, a red blood cell, or » brain cell.

Karin Nayernia ( 2007 : Stem cell derived from testis show promise for treating a wide variety of medical condition’ Cell Research 17, 895-897 )

Has written a review showing the possibility of using the continued presence of stem cells in the testis for the repair of medical problems. The maturation of such stem cells may well have needs for nutritional support in as yet unsuspected ways.

Telomeres

Nutrition now and in the future is about understanding biological proceses and how the constituents of food may affect these processes. An obvious statement.

A very interesting article in the Lancet ( Spyridopoulos and Dimmeler 2007 , 369, 81-2

Can telomere length predict cardiovascular risk ? )

Telomeres—TTAGGG DNA are the repeats at the ends of chromosomes—and are widely regarded to be the internal biological clock of a living organism as they shorten with every cell division.1 Telomeres in human blood cells contain about 10000-20000 nucleotides at birth. This length decreases by about 50 bp a year, thereby being reduced to a few thousand bp in elderly individuals. Critically short telomeres are assumed to have functional implications, such as the induction of cellular senescence, which is characterised by the expression of specific markers of ageing and the inability of the cell to divide further.1 Although age is an important independent predictor for the development of cardiovascular disease, shortening of age-corrected telomere length in leucocytes exposes individuals to an additional substantial risk of mortality from cardiovascular and infectious complications.’1

In the Lancet, Scott Brouilette and colleagues ( Lancer 2007, 369, 107-114 ) report the correlation between telomere length and risk of developing coronary heart disease/ Telomere length was measured in white blood cell DNA from a subgroup of more than 1500 patients in the West of Scotland Primary Prevention Study (WOSCOPSJ, in which the use of pravastatin was tested in men with raised concentrations of LDL cholesterol to prevent cardiovascular events. This substudy shows that individuals with shorter telomere length have about a two-fold increased risk of developing coronary artery disease in the 5 years from the start of treatment. Interestingly, pravastatin completely attenuated this telomere-attributed risk. The randomised case-control design of the study is better than to all previous studies on the association of telomere length and cardiovascular risk.

Several aspects of Brouilette and colleagues’ study merit special attention. The first is the potential mechanism behind the correlation between mean telomere length and coronary heart disease. One might speculate that shorter telomeres could indicate functional changes within cell populations—eg, senescent lymphocytes that produce higher amounts of inflammatory cytokines. Furthermore, telomere shortening in stem or progenitor cells could limit the repair capacity of the vessel wall. Telomere shortening associated with a dysfunction of circulating endothelial progenitor cells, which contribute to endothelial repair and seem to be atheroprotective, could aggravate atherosclerotic disease progression.

Interestingly also smoking and obesity accelerate this shortening process.

What a rich field for nutritional studies.

The Brain

As vertebrate embryo grows, the development of its brain and spinal cord is controlled by complex and precisely regulated patterns of gene activity. Writing in Nature Lacalli ( Nature 2003, vol 424 , pp263-4) reviews a paper discussing the genes responsible for patterning the body along its antero-posterior axis (that is, from front to back), notably Hox genes and the like. These genes are highly conserved in evolution, with similar expression patterns in animals and such anatomically different creatures as insects and vertebrates. Insects and vertebrates are advanced members, respectively, of the two major divisions of animals, protostomes and deuteros tomes

These genes are expressed in the vertebrate brain and spinal cord and appear on the surface nerve net of a closely related group of invertebrates.

Understanding of the brain is fundamental to nutrition but is so complex as to be daunting If the brain has a common evolutionary basis with worms where in all of this comes the characteristics of the human brain. Intelligence, thought, creativity , emotions, wanting, perception of self, language, understanding free will , communication to name but a few.

Baum in his book “What is thought” published by Bradford Books 2004 , MIT Press Cambridge Massachusetts proposes a computational explanation of thought. That life must be explainable at a fundamental level by physics and chemistry, Baum argues that the complexity of mind is the outcome of evolution, which has built thought processes that act unlike the standard algorithms of computer science, and that to understand the mind we need to understand these thought processes and the evolutionary process that produced them in computational terms.

Baum proposes that underlying mind is a complex but compact program that corresponds to the underlying structure of the world. He argues further that the mind is essentially programmed by DNA. We learn more rapidly than computer scientists have so far been able to explain because the DNA code has programmed the mind to deal only with meaningful possibilities. Thus the mind understands by exploiting semantics, or meaning, for the purposes of computation; constraints are built in so that although there are myriad possibilities, only a few make sense. Evolution discovered corresponding subroutines or shortcuts to speed up its processes and to construct creatures whose survival depends on making the right choice quickly. Baum argues that the structure and nature of thought, meaning, sensation, and consciousness therefore arise naturally from the evolution of programs that exploit the compact structure of the world.

He draws heavily on that basic principle oft disregarded in Nutrition namely Occam’s razor, the dictum of the 14th Century philosopher, “Entities should not be multiplied unnecessarily”, and he is looking for straight forward simple laws to govern this complexity. His other basic rule is Bayesian statistics which is a rational way of calculating and revising probabilities and beliefs during change .The concept of meaningful possibilities which he relates to the flexibility of change during evolution. It makes sense that brain structure is modelled on a template of DNA. The complex inter connections by which the brain functions are a different matter. Theories based on systems that we have created e.g. the computer are forms of anthropomorphism. Heady or even brainy stuff

It does not help us however with .

Where does consciousness start?.

What is thought or creativity?

Why do some have convergent and others divergent minds?

If we ensure that the developing mind receives a sufficiency of long chain fatty acids and other nutrients what element of intelligence do we improve or is it an overall improvement. Is creativity or memory changed? Does the spectrum of long chain fatty acids matter.? .

Tumour Genes

Lung cancer is the major and most preventable cause of cancer world wide. 80% of these tumours are non-small cell lung cancers. An article and a summarising article in Nature

Meyerson M Broken genes in solid tumours |Nature 2007, 448, 545-6

Soda M Identification of the transforming EML4-ALK fusion gene in non small cell lung cancer. Nature 2007, 448,561-566

Shows that a position change of a gene associated with this form of cancer on chromosome 2 activates the gene ALK which encodes ALK tyrosine kinase. Tyrosine kinase regulate the activity of other proteins by adding phosphate to their tyrosine groups. The inhibition of such a gene expression has great potential in cancer therapy. And for a nutritionist these findings indicate that these transfer reactions may be amenable to some dietary change . Who know?.