What is a gene?

Genes are small sections of DNA within the genome that code for proteins. They contain the instructions for our individual characteristics – like eye and hair colour.

Pleiotropy !!!!!!

Pleiotropy refers to genes that can affect more than one character. A gene may make just one polypeptide, but that polypeptide can affect a number of different properties of an organism. The hemoglobin gene, sickled cells cause a breakdown of red blood cells and a higher likelihood of red blood cell clumping, which can block blood vessels and cause impaired mental function and kidney failure, and increase the risk of pneumonia. These are different phenotypic characteristics caused by a defect in a single, pleiotropic gene.

New Technique reveals unseen information in DNA code

Imagine reading an entire book, but then realizing that your glasses did not allow you to distinguish "g" from "q." What details did you miss?  


Geneticists faced a similar problem with the recent discovery of a "sixth nucleotide" in the DNA alphabet. Two modifications of cytosine, one of the four bases that make up DNA, look almost the same but mean different things. But scientists lacked a way of reading DNA, letter by letter, and detecting precisely where these modifications are found in particular tissues or cell types. The team used the technique to map 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) in DNA from human and mouse embryonic stem cells, revealing new information about their patterns of distribution. These studies have revealed that these DNA modifications play major roles in fundamental life processes such as cell differentiation, cancer and brain function. They regulate gene expression and have a broad impact on stem cell development, various human diseases such as cancer, and potentially on neurodegenerative disease, they may even shape the development of the human brain. Geneticists describes a method called TAB-Seq that directly measures 5-hmC, and presents the first map of the entire genome of 5-hmC at single-base resolution. It's a major breakthrough in that TAB-Seq allows precise mapping of all 5-hydroxymethylcytosine sites in a mammalian genome using well-established, next-generation DNA sequencing methods.  The study showed very clearly that deriving useful knowledge about this poorly understood epigenetic regulator requires determination of the exact locations of 5hmC with base-level accuracy. 

Epistasis?

The ability of one gene to influence the expression of another gene, or even a group of genes. The existence of epistasis should not be surprising if one considers biochemical pathways. Several different genes are involved in such pathways, and if an early step in the pathway is blocked, then the precursor for a later gene is not made, and thereby the action of the later gene is disrupted. Expressions of alleles at that later point in the pathway can be blocked by epistasis.

Genes Affect Sex Differences in Behavior

Men and women can seem like they’re from different planets sometimes. Hormones help drive those differences. A new study shows how genes pass on the message. Hormones are the body's signaling molecules. They affect many aspects of development and biology. Researchers have long known that the sex hormones, such as estrogen and testosterone, drive certain differences in behavior between men and women. How these hormones exert their effects on a molecular level, however, isn't well understood. A team of scientists used DNA microarrays to analyze gene expression across the mouse brain. They particularly focused on the hypothalamus, a region known to be involved with hormone sensing. The team reported finding 16 genes that were expressed differently between the brains of male and female mice. A closer look revealed that these sex differences in gene expression weren’t limited to the hypothalamus. They were also found in the amygdala, a region implicated in processing emotions. These results also suggest that other complex behaviors might be similarly constructed by gene networks. Of course, genes aren't the only things that drive how people behave. But this research shows that genes may play an important role in complex human behavior.

Dark Areas of DNA

A massive effort to sequence and compare 29 mammalian genomes has shed new light on the “dark matter” of the genome, the over 98% of DNA that doesn’t code for proteins. The DNA that lies outside of gene sequences was once called “junk DNA.” But researchers now know that these non-coding regions have important biological functions. Many disease-causing mutations have been found in these areas, and scientists have pieced together some clues to their functions. For example, some regions regulate the expression of genes, controlling when genes are turned on and off. Nevertheless, this vast genetic dark matter remains largely uncharted.To gain new insights, an international team of researchers set out to compare the sequences of several mammalian species. Regions that remain the same or have only gradually evolved, they reasoned, must have some function.

In the early online edition of Nature on October 12, 2011, the researchers reported the sequencing of 20 new mammalian genomes, including rabbit, dolphin and elephant. They compared these new sequences with 9 others that were previously described, including humans. The scientists found that at least 5% of the genome appears to be constrained by evolution. They were able to identify 3.6 million specific elements under constraint, which together make up over 4% of the human genome. These elements include hundreds of new families of RNA, thousands of previously undetected segments of protein-coding DNA, and 2.7 million elements thought to play a role in controlling gene expression.

Significantly, the researchers found that many of the elements they identified overlap with variants that were linked to diseases and conditions in previous genomics studies.

Gene Linked to Optimism and Self-Esteem

Why can some people make it through difficult times with little trouble while others crumble under the same circumstances? A new study suggests that the answer lies—at least in part—in your genes.Scientists have long known that people with certain psychological traits, or resources, can fare better in challenging situations. Three of the most widely studied psychological resources—optimism, self-esteem and mastery (the feeling that you can master your environment and achieve what you want)—are good predictors of a person’s physical and psychological health. These 3 resources have been shown to help people weather stressful events and beat back depression. Because these psychological resources tend to run in families, scientists had suspected a genetic component.

Earlier studies found evidence that particular variants, or alleles, of theOXTR gene might be linked to stress-related traits and other psychological characteristics. OXTR codes for the receptor for oxytocin, a hormone that contributes to positive emotion and social bonding.

The researchers found that people who had 1 or 2 copies of the OXTR gene with an “A” (adenine) allele at a particular location tended to have more negative measurements than those with 2 copies of the “G” (guanine) allele. People with an A allele were less optimistic, had lower self-esteem and felt less personal mastery than people with 2 G alleles. In addition, the A allele was linked to higher levels of depressive symptoms. Follow-up analyses suggested that the effects of OXTR variants on depression are largely mediated by the gene’s influence on psychological resources. The scientists say their findings are the first to link OXTR directly to specific psychological resources. But the gene itself is far from the only factor influencing these traits.

Genes and the Brain

Two related studies revealed gene activity in the brains of people of different genders and ethnicities, from fetal development to old age. The accomplishment provides a broad foundation for understanding both normal brain development and what goes awry in mental disorders.  Messenger RNAs, or transcripts, are transient copies of genes that carry instructions to the protein-making machinery within cells. Transcripts are made, or “expressed,” in patterns that are influenced by the approximately 1.5 million DNA variations unique to each of us. Researchers led a broad survey to find which genes are active in different areas in the brain at different stages of life and they found that different sets of genes are expressed during prenatal development, infancy and childhood. Three-fourths of genes change expression levels immediately after birth, with most decreasing. Gene expression gradually declines from there, eventually leveling off in middle age. It then surges again as the brain ages in the last decades of life. Individual genetic variations are profoundly linked to expression patterns. However, despite differences in the genetic code across individuals and ethnicities, the transcriptomes—the complete set of expressed transcripts—of human brains are generally similar.

Over 90% of the genes expressed in the brain are differentially regulated across brain regions and/or over developmental periods. Brain location and timing, the researchers found, affect gene expression far more than gender, ethnicity or individual variation.

Gene Therapy Helps Patients with Hemophilia

A single dose of an experimental gene therapy boosted production of a missing blood-clotting factor in people with hemophilia, a new study shows. The therapy might give patients a long-term solution for preventing dangerous bleeding episodes. Hemophilia is a rare, inherited disorder in which blood is unable to clot normally. As a result, people with hemophilia tend to bleed more than others after injury. They may also bleed without warning inside their bodies. This bleeding can damage organs and tissues and may be life threatening.

To find an alternative clotting factors replacement therapy, researchers investigated a potential gene therapy approach, focused on hemophilia B. This uncommon form of the disease affects about 1 in 5 patients with hemophilia. Hemophilia B is caused by defects in the gene that codes for human clotting factor IX. Scientists packaged a normal factor IX gene into a modified adeno-associated virus that targets liver cells. The liver is the only site that can produce a form of factor IX needed for the clotting process. The virus—acting as a delivery vehicle, or vector—was designed to transport the normal gene into liver cells and launch production of factor IX.

After gene therapy, each patient generated factor IX at between 2% and 11% of normal levels. In the short-term follow-up period (6 to 16 months), 4 of the 6 men no longer needed factor IX infusions for routine bleeding. Results from this study represent a promising step toward making gene therapy a viable treatment option for hemophilia B. 

DNA has its own genetic language !!!!

The amount of information in human DNA is roughly equivalent to 12 sets of The Encyclopedia Britannica, an amazing 384 volumes worth of detailed information that would fill 48 feet of library shelves! But the size of a DNA molecule is only two millionths of a millimeter thick. In order for there to be anything resembling a language it must meet the following criteria; an alphabet or coding system, correct spelling, grammar (a proper arrangement of the words), meaning (semantics) and an intended purpose. It has been discovered that DNA meets all of these requirements and in fact, it has all of the same properties as any computer code or language does.

DNA can be altered through diet and exercise...

A new study(study published in the journal Proceedings of the National Academy of Sciences) that was recently published sheds more evidence to what many have been saying for a long time, that DNA does not control the body or predestine you to being overweight, ill, sick, weak or anything else, but that the majority of our health and destiny lies within our own power. The men underwent three months of major lifestyle changes, including eating a diet rich in fruits, vegetables, whole grains, legumes and soy products, moderate exercise such as walking for half an hour a day, and an hour of daily stress management methods such as meditation. After the three months, the men had changes in activity in about 500 genes -- including 48 that were turned on and 453 genes that were turned off. The activity of disease-preventing genes increased while a number of disease-promoting genes, including those involved in prostate cancer and breast cancer, shut down,

Reverse Genetics ?

Reverse genetics is an approach to discovering the function of a gene by analyzing the phenotypic effects of specific gene sequences obtained by DNA sequencing.  This investigative process proceeds in the opposite direction of so-called forward genetic screens of classical genetics. Simply put, while forward genetics seeks to find the genetic basis of a phenotype or trait, reverse genetics seeks to find what phenotypes arise as a result of particular genes. Automated DNA sequencing generates large volumes of genomic sequence data relatively rapidly. Many genetic sequences are discovered in advance of other, less easily obtained, biological information. Reverse genetics attempts to connect a given genetic sequence with specific effects on the organism.

The History of the Intron

In the 25 years since they were first discovered, introns have puzzled molecular biologists because of their uncertain function and mysterious origin. Introns are non-coding DNA sequences that reside inside a gene, splitting it into discrete units called exons. The resulting disruption of coding sequence continuity would wreak havoc in protein assembly if eukaryotic cells did not dispose of introns in messenger RNAs—the intermediates in the decoding of gene sequences to produce protein chains—in a now well-described process known as splicing. At first glance, introns may seem like pesky parasites for which eukaryotes have cleverly evolved bypass mechanisms. But introns may also benefit their hosts. Evolutionary advantages of introns include the possibility to create new genes by cutting and pasting exons from existing genes or to diversify the protein output of a single gene by splicing the exons together in different ways. Thus, balancing intron gains and losses clearly has important evolutionary implications for a host. Organisms with low intron density display a bias for insertions at the beginning (5′ end) rather than the end (3′ end) of genes. A popular hypothesis is that in these organisms, genes lose their introns through a process that rewrites genomic DNA using as template the messenger RNAs purged of intron sequences. This process might preferentially remove 3′ introns because it relies on an enzyme called reverse transcriptase that can be primed to read RNAs starting at their 3′ end. 

In a new study, Cydney Nielsen and her colleagues present evidence that challenges this model. They address intron dynamics with a genome-wide survey of intron distribution among four Ascomycete fungi with recently completed genome sequences. The four fungi (Neurospora crassa,Magnoporthe grisea, Fusarium gramineum, and Aspergillus nidulans) form an evolutionary tree with branching points estimated at 200, 230, and 330 million years ago. The authors' approach is to tally intron gains and losses during the evolution of these four species and then plot their positions along the genes' length. They identify 3,450 gene regions that are clearly conserved in all four species and harbor an intron in at least one of them. To distinguish intron gains from losses, they rely on a simple parsimony principle, which they refine with additional probability analyses. In brief, an intron present in only one species counts as a gain; an intron absent from one species but present in its closest relative and in a cousin counts as a loss.

Nielsen and colleagues record between 150 and 350 intron losses in each lineage. Surprisingly, losses do not occur preferentially at the genes' 3′ end. The authors conclude that while a 3′ reverse transcriptase-based mechanism might be a factor, it cannot be the sole reason for the introns' 5′ bias. The other surprising result is that intron gains occur at almost the same rate as losses in all lineages. Intron gains therefore play an important role in the evolution of even intron-poor genomes. 

Exon Theory of Genes

A theory that holds that introns are extremely ancient characteristics of genes and that early genes were created through the intron-mediated shuffling of exons. The theory has existed since the late seventies. An uncompromising version of the theory, in which all introns were considered to be ancient, dominated the early work. However, in the late eighties and early nineties evidence arose that at least some introns are more recently acquired. Due to the previously overly polarized nature of the debate, many results that demonstrated the existence of recent introns have been interpreted by some as evidence that all introns are late, leading some to believe that the theory is no longer a viable theory. However, recent work emphasizes a mixed model, in which some introns are ancient and some new. This model has proven to provide impressive explanatory power for a broad array of observations. Thus, this moderated form of the Exon Theory of Genes still offers a coherent picture of the origin and evolutionary history of the intron-exon structure of eukaryotic genes.

What are the advantages of Step one Plus RT-PCR?

The step one plus RT-PCR ( 96 well platform, 4 color system, veriflex sample blocks) use fluorescent-based PCR reagents to provide 1) Quantitative detection of target nucleic acid sequences using real time analysis, 2) Qualitative detection of targets using post-PCR (end point) analsyis, 3) Qualitative analysis of the PCR product (achieved by melt curve analysis that occur post-PCR) and 4) Time saving ( one full run of PCR plate completed within 40minutes ). The step one plus RT-RCR instrument contains 6 independently thermally regulated "veriflex" blocks to help to optimize the thermal cycling conditions. We can set a different temperature for one or more of the veriflex blocks, (or) we can set the same temperature for each of the veriflex blocks. The following experiments can be perform using the step one plus RT-PCR:

• Quantitation - Standard curve
• Quantitation - Relative standard curve
• Quantitation - Comparative CT 
• Melt curve
• Genotyping
• Presence / Absence experiments
• Minimizing DNA contaminants

Following 4 filters can be used by the step one plus RT-PCR : 1) FAM dye - SYBR Green dye, 2) JOE dye - VIC dye, 3) TAMRA dye- NED dye, and 4) ROX dye.

Exon shuffling

Another mechanism that explains how the genome can encode for such a wide array of proteins is alterative splicing. Normally RNA splicing removes the introns and then reattaches the exons in sequence. However, in alternative splicing some of the exons may not be reattached. Since the exons contain coding information for the polypeptide, the removal of some of the exons will produce a slightly different form of the protein. It is important to note that the order of the exons is usually not changed, some of them are just not included in the final mRNA. Alternative splicing is also sometimes called exon shuffling. From an evolutionary perspective, alternative splicing allows a species to produce proteins of related function from a single transcription event. Often these proteins are tissue specific, meaning that the pre-mRNA is edited one way in one tissue, but is alternatively spliced in another. There are many examples of alternative splicing in mammals, and it is believed to play a major role in explaining the size of the proteome.

What Did We Know of Genetics Before Mendel?

There were three major theories on the basis of inheritance that existed prior to Mendel. Each of these periodically gained and lost popularity over time, but remnants of each existed well into the nineteenth century. These included: Pangenesis: Pangenesis is the belief that each part of the body contributed a miniature version of itself to the offspring. For example, each finger would contribute a small version of itself, as would each ear and toe. The inheritance of nonphysical characteristics, such as behavior, presented special problems for the supporters of this theory. Variations of pangenesis were supported by a number of people, including the Greek philosopher Hippocrates, Hugo De Vries, and Charles Darwin. Preformation: The theory that a tiny preformed human, called a homunculus, resided inside of either the egg or sperm cell. This was later adapted to the idea that all parts of the adult are formed early in the development of the zygote, and simply increase in size over time. This theory was supported by seventeenth century scientists such as Anton von Leeuwenhoek, Marcello Malpighi, and Jan Swammerdam. Blending: Under this theory, offspring represented a mixture of the hereditary material. The hereditary material was not a distinct particle, but rather a malleable substance that could be changed over the course of a few generations. This theory was supported by Joseph Kolreuter (1733–1806) and many of the other early researchers of plant hybrids. While Gregor Mendel is considered to be the father of genetics due to his application of the empirical approach to the study of inheritance, he actually represented just one of a long lineage of individuals who were studying inheritance.

DNA MICROARRAYS

One of the newest additions in the arsenal of molecular biology techniques is the use of DNA microarrays, also known as gene chips or DNA chips. One of the main uses of a DNA microarrays is to study patterns of gene expression. Developed in the 1990s, DNA microarrays have provided a more rapid method of screening genomes for genes that are expressed under specific environmental conditions. The technology of a DNA microarray is relatively simple. Using a process called photolithography, which was adapted from a technology used by the electronics industry in the preparation of integrated circuits, a small piece of glass or plastic is spotted with fragments of DNA. These fragments may be genomic DNA that has been fragmented using restriction enzymes. However, most often the DNA is generated using PCR reactions so that the sequence content of each spot on the plate is precisely known. This technology allows researchers to place specific DNA sequences in specific places on the array. Thus, the sequence content of each location on the microarray is known in advance. For example, the first spot on the plate may hold the DNA sequence of an insulin gene, while the next location contains the DNA sequence of a muscle fiber gene. In the early years of development, researchers were able to place several thousand DNA sequences on a single array. To use a DNA microarray a researcher must first prepare a sample of mRNA. When examining patterns of gene expression a researcher willoften prepare mRNA from two different samples. However, some of the newer technologies can spot up to 1 million DNA sequences in a square centimeter area.

What Did We Know of Genetics Before Mendel?

There were three major theories on the basis of inheritance that existed prior to Mendel. Each of these periodically gained and lost popularity over time, but remnants of each existed well into the nineteenth century. These included: Pangenesis - Pangenesis is the belief that each part of the body contributed a miniature version of itself to the offspring. For example, each fingerwould contribute a small version of itself, as would each ear and toe. Preformation - The theory that a tiny preformed human, called a homunucleus, resided inside of either the egg or sperm cell. This was later adapted to the idea that all parts of the adult are formed early in the developmentof the zygote, and simply increase in size over time. Blending - Under this theory, offspring represented a mixture of the hereditary material. The hereditary material was not a distinct particle, but rather a malleable substance that could be changed over the course of a few gen-erationslt are formed early in the developmentof the zygote, and simply increase in size over time.

Why Restriction Map is needed?

Any double-stranded DNA will be cut by a variety of restriction enzymes that have different recognition sequences. By separating the restriction fragments and measuring their sizes by gel electrophoresis, it is possible to deduce where on the DNA molecule each restriction enzyme cuts. A restriction map of the DNA molecule can be drawn showing the location of these cut sites (restriction sites). It is then easy to compare two DNA molecules (for example, to examine the evolutionary relationship between two species) by looking at their restriction maps without the need to determine the nucleotide sequence of each DNA. Restriction maps are also important experimentally during recombinant DNA work, both to plan where individual DNA molecules should best be cut and to monitor the progress of the experiment.