Genetics Genetics For Dummies Cheat Sheet Cheat Sheet / Updated 11-21-2023 Genetics is a complex field with lots of details to keep straight. But when you get a handle on some key terms and concepts, including the structure of DNA and the laws of inheritance, you can start putting the pieces together for a better understanding of genetics. View Cheat Sheet

Genetics Gene Editing Article / Updated 01-30-2020 One of the hottest topics these days is gene editing (also known as genome editing). Gene editing is a group of genetic engineering technologies that allow scientists to change a specific sequence within the genome. Each of these technologies involves an engineered enzyme called a nuclease, which can cut DNA, along with some kind of guide to lead the enzyme to the right place in the genome. Subsequently, the cell’s own DNA repair machinery can repair the break, inserting a new segment of DNA if a fragment of DNA with the desired sequence is provided. Gene editing could be used in a couple of different ways. First, it could be used to replace a sequence with a disease-causing mutation with the normal sequence, thereby correcting the underlying cause of a patient’s condition. Another use could be to disrupt a gene that is being expressed and turn it off. This would be helpful for conditions in which there is an excess of expression that contributes to the disorder, such as oncogenes in cancer. Technologies to perform gene editing have been around for more than 20 years; however, the different tools vary with respect to how well they work. Gene editing tools that have been developed include the following: Zinc finger nucleases (ZFNs): ZFNs use a specific type of DNA binding domain (referred to as a zinc finger domain) to recognize the target sequence. While they have been successfully used to modify various plants, they are not really used anymore because they frequently affected the wrong sequence. Transcription activator-like effector nucleases (TALENs): TALENs use a transcription activator-like effector DNA binding domain that can be customized to target a specific sequence. TALENs have a higher efficiency than ZFNs and have been used to alter the genomes of a variety of different organisms. It has also been used experimentally to correct mutations that cause human disease. CRISPR-Cas9 (pronounced “crisper cass 9”): The CRISPR-Cas9 system is the most recently introduced and appears to have the highest accuracy of any of the methods. The system uses a customizable RNA guide to target the sequence to be edited, along with a CRISPR-associated protein (Cas). Because of its efficiency and accuracy, this method is rapidly becoming the most widely used approach for performing gene editing. The CRISPR-Cas9 gene editing system is also the method that has been hitting the headlines. The basics of this system are described in the following section. In addition, since the system could be used in either somatic cells (the cells of the body other than the eggs or sperm) or in the germline (the sex cells – eggs and sperm), the importance of this distinction is discussed. The promise that the CRISPR-Cas9 system holds for the future treatment of genetic diseases has also raised some significant concerns. CRISPR-Cas9 gene editing CRISPR stands for clustered regularly interspersed short palindromic repeats. Cas9 is the CRISPR-associated protein number 9. CRISPR-Cas9 is based on a defense system that occurs naturally in some bacteria. Scientists discovered that the DNA in these bacteria contained many short palindromic sequences. Palindromes are words or sequences that are the same both forward and backward, such as the word racecar or the DNA sequence CATAATAC. In the bacteria, these short palindromic sequences flanked segments of DNA from a virus that had previously infected the cell. Basically, every time a bacterium was infected with a virus (and survived the infection), the bacterium saved a bit of the viral DNA by inserting it between the palindromic DNA sequences (see the following figure). It would then make a small piece of RNA from this sequence, which would then be attached to a Cas protein that is able to cut DNA into pieces. If the bacterium was infected again by the same virus, the armed Cas protein would recognize the viral DNA and destroy it immediately. The CRISPR-Cas9 system for gene editing uses a short RNA guide sequence that can bind to a specific target sequence in the genome. This guide RNA also binds to the Cas9 protein. To use this system for correcting a gene known to carry a mutation, the Cas9 protein with the guide RNA attached could be introduced into a cell with the defective gene, along with fragments containing the normal gene sequence. Once the guide RNA-Cas9 complex binds to its target sequence in the genome, the Cas9 protein would cut the DNA at the target location. The cells own DNA repair machinery could then be used to replace the defective copy of the gene with a correctly functioning version (without any mutation). Another potential use for this system would be to disrupt genes that are causing problems. For example, if a gene is producing a growth factor that is contributing to cancer cell division and proliferation, the guide sequence could target the gene and the attached Cas9 protein could cut it and stop it from making the growth factor. Germline versus somatic gene editing Gene editing could be performed in a somatic cell (a body cell other than an egg or sperm), such that the edited sequence ends up only in the tissue of interest. In this case, the genetic change would not be passed on to subsequent generations. Alternatively, gene editing could be performed in a manner that results in the altered sequence being in all the cells of the body. In this case, the editing would need to occur in a germ cell (such as an egg or sperm) or in a one-cell zygote (fertilized egg). This would also lead to a genome alteration what would be passed onto future generations, something associated with a unique set of ethical issues. The ethics of gene editing Both germline and somatic gene editing raise significant ethical concerns. In both cases, there are concerns about off-target editing (that is, when the wrong sequence gets changed, perhaps with devastating consequences). And like any new technology, there are definite concerns regarding the overall safety of such a procedure and the health implications for the organism in which the editing was performed (and potentially future offspring if germline editing is carried out). In addition, like all other genetic engineering technologies and some genetic testing approaches, there are worries regarding the potential to use these techniques to enhance one’s genetics, as opposed to treating a genetic condition. Informed consent also triggers some very real apprehensions, since modifying someone’s germline involves performing the change before the person is born and before they can provide consent. From a societal perspective, concerns have been raised regarding the equal access to such technologies and concerns related to how genetic diseases or traits are viewed. If therapies based on gene editing become clinically available, will everyone be able to afford them? Will this lead to a negative view of certain genetic disorders or traits, and an attempt to remove them from society? Most of these concerns have been brought to the forefront since the first report demonstrating that genome editing in a human embryo is possible, which was published by a Chinese research group in 2015. This study, however, utilized an embryo that was not capable of developing to term. Later in 2015, there was a call for a voluntary worldwide moratorium on using CRISPR-Cas9 to alter the germline genome in humans. Despite this, a later report from China in 2018 described the use of gene editing to make twins who were immune to HIV infection. However, the genetic status of these individuals has not been verified. At the time this article was written, a search on the clinicaltrials.gov website (which lists future, ongoing, and completed clinical trials) identified 19 different trials designed to study gene editing in somatic cells using CRISPR-Cas9. This included studies for the treatment of sickle cell disease, beta-thalassemia, and blood cell cancers (such as leukemia), and at least three of these trials have study sites in the United States. Little has been reported from these studies, but one researcher has stated that the first beta-thalassemia patient he treated hadn’t needed a blood transfusion in the four months since treatment was initiated. No trials were identified that involved modification of the human germline. View Article

Genetics Genetically Modified Organisms: Animals, Plants, Bacteria Article / Updated 01-30-2020 Transgenic critters (genetically modified organisms) are all over the place. Animals, insects, and bacteria have all gotten in on the fun. In this article, you take a trip to the transgenic zoo to learn a little bit about the menagerie. Transgenic animals Mice were the organisms of choice in the development of transgenic methods. One of the ways that transgenic mice can be created is by inserting a transgene into a mouse’s genome during the process of fertilization. When a sperm enters an egg, there’s a brief period before the two sets of DNA (maternal and paternal) fuse to become one. The two sets of DNA existing during this intermission are called pronuclei. Geneticists discovered that by injecting many copies of the transgene (with its promoter and sometimes with a marker gene, too) directly into the paternal pronucleus (see the following figure), the transgene was sometimes integrated into the embryo’s chromosomes. If the transgene integrates into one of the mouse chromosomes when still at the one-cell stage, it will end up in all the cells of the mouse’s body. If it integrates after several rounds of cell division, then not all the embryo’s cells will contain the transgene. The cells that do have the transgene often have multiple copies (oddly, these end up together in a head-to-tail arrangement), and the transgenes are inserted into the mouse’s chromosomes at random. The resulting, partly transgenic mouse is mosaic. Mosaicism is when there are two population of cells in the animal. In this case, there is one that contains and expresses the transgene and one that does not. To get a fully transgenic animal, many mosaic animals are mated in the hope that non-mosaic transgenic offspring will be produced from one or more matings. One of the first applications of the highly successful mouse transgenesis method used growth hormone genes. When introduced into the mouse genome, rat, human, and bovine growth hormone genes all produced mice that were much larger than normal. The result encouraged the idea that growth hormone genes engineered into meat animals would allow faster production of larger, leaner animals. However, transgenic pigs with the human growth hormone gene didn’t fare very well; in studies, they grew faster than their nontransgenic counterparts but only when fed large amounts of protein. And female transgenic pigs turned out to be sterile. All the pigs showed muscle weakness, and many developed arthritis and ulcers. Unfortunately, cows didn’t fare any better. In contrast, fish do swimmingly with transgenes and transgenic salmon with the growth hormone gene grow six times faster than their nontransgenic cousins and convert their food to body weight much more efficiently, meaning that less food makes a bigger fish. Primates have also been targeted for transgenesis as a way to study human disorders including aging, neurological diseases, and immune disorders. The first transgenic monkey was born in 2000. This rhesus monkey was endowed with a simple marker gene because the purpose of the study was simply to determine whether transgenesis in monkeys was possible. Since then, transgenic primates that model human disease, such as a transgenic monkey that can be used to model Huntington disease have been created and are showing great promise as a tool for studying treatments for these conditions. Transgenic pets: Glow-in-dark fish Ever have one of those groovy posters that glows under a black light? Well, move that black light over to the aquarium — there’s a new fish in town. Originally derived from zebrafish, a tiny, black-and-white–striped native of India’s Ganges River, these glowing versions bear a gene that makes them fluorescent. The little, red, glow-in-the-dark wonders (referred to as GloFish) are the first commercially available transgenic pets. Zebrafish are tried-and-true laboratory veterans — they even have their own scientific journal! Developmental biologists love zebrafish because their transparent eggs make it simple to observe development. Geneticists use zebrafish to study the functions of all sorts of genes, many of which have direct counterparts in other organisms, including humans. And genetic engineers have taken advantage of these easy-to-keep fish, too; scientists in Singapore saw the potential to use zebrafish as little pollution indicators. The Singapore geneticists used a gene from jellyfish to make their zebrafish glow in the dark. The action of the fluorescent gene is set up to respond to cues in the environment (like hormones, toxins, or temperature). The transgenic zebrafish then provide a quick and easy to read signal: If they glow, a pollutant is present. Of course, glowing fish are so unique that some enterprising soul couldn’t let lab scientists have all the fun. Thus, these made-over zebrafish have hit the market. Currently, GloFish are available in more than 10 different colors, including green, red, orange, pink, purple, or blue! Initially, when GloFish were introduced in 2003, the state of California banned their sale outright. However, they changed their decision in 2015, after GloFish sales were approved by the FDA, the U.S. Fish and Wildlife Service, and a variety of state-level regulators. Transgenic insects A number of uses for transgenic insects appear to be on the horizon. Malaria and other mosquito-borne diseases are a major health problem worldwide, but the use of pesticides to combat mosquito populations is problematic because resistant populations rapidly replace susceptible ones. And in fact, the problem isn’t really the mosquitoes themselves (despite what you may think when you’re being buzzed and bitten). The problem is the parasites and viruses the mosquitoes carry and transmit through their bites. In response to these problems, at least one research group has developed a transgenic mosquito in which expression of the transgene results in an early death. Research trials with these mosquitos in Brazil were designed to see if they may help decrease the population of mosquitoes that spreads dengue fever or the Zika virus. However, it is still unclear whether the release of these transgenic mosquitos is decreasing the population without the unintended consequence of creating hybrid mosquitos. Another potential use for transgenic insects would be to release of millions of transgenically infertile bugs that attract the mating attentions of fertile ones. The matings result in infertile eggs, reducing the reproduction of the target insect population. This is an especially appealing idea when used to combat invasive species that can sweep through crops with economically devastating results. Transgenic bacteria Bacteria are extremely amenable to transgenesis. Unlike other transgenic organisms, genes can be inserted into bacteria with great precision, making expression far easier to control. As a result, many products can be produced using bacteria, which can be grown under highly controlled conditions, essentially eliminating the danger of transgene escape. Many important drugs are produced by recombinant bacteria, such as insulin for treatment of diabetes, clotting factors for the treatment of hemophilia, and human growth hormone for the treatment of some forms of short stature. These sorts of medical advances can have important side benefits as well: Transgenic bacteria can produce much greater volumes of proteins than traditional methods. Transgenic bacteria are safer than animal substitutes, such as pig insulin, which are slightly different from the human version and may therefore cause allergic reactions. To use bacteria to make human proteins for the treatment of disease, the gene for the human protein must be isolated. For example, to make human insulin, DNA is obtained from an insulin-producing pancreatic cell (see the following figure). The insulin gene is isolated and inserted into a bacterial plasmid. The plasmid containing the human gene is then introduced into E. coli, which then acts as a factory for making the insulin protein. Transgenic bacteria are used to produce large quantities of insulin, which can then be purified and used to treat patients with diabetes. Transgenic plants Plants are really different from animals, but not in the way you may think. Plant cells are totipotent, meaning that practically any plant cell can eventually give rise to every sort of plant tissue: roots, leaves, and seeds. When animal cells differentiate during embryo development, they lose their totipotency forever (but the DNA in every cell retains the potential to be totipotent). For genetic engineers, the totipotency of plant cells reveals vast possibilities for genetic manipulation. Much of the transgenic revolution in plants has focused on moving genes from one plant to another, from bacteria to plants, or even from animals to plants. Like all transgenic organisms, transgenic plants are created to achieve various ends, including nutritionally enhancing certain foods (such as rice) or altering crops to resist either herbicides used against unwanted competitor plants or the attack of plant-eating insects. Getting new genes into the plant To put new genes into plants, genetic engineers can either: Use a vector system from a common soil bacterium called Agrobacterium. Agrobacterium is a plant pathogen that causes galls — big, ugly, tumor-like growths — to form on infected plants. In the figure, you can see what a gall looks like. Gall formation results from integration of bacterial genes directly into the infected plant’s chromosomes. The bacteria enters the plant from a wound such as a break in the plant’s stem that allows bacteria to get past the woody defense cells that protect the plant from pathogens (just as your skin protects you). The bacterial cells move into the plant cells, and once inside, DNA from the bacteria’s plasmids — the circular DNAs that are separate from the bacterial chromosome — integrate into the host plant’s DNA. The bacterial DNA pops itself in more or less randomly and then hijacks the plant cell to allow it to replicate. Like the geneticists using virus vectors for gene therapy, genetic engineers snip out gall-forming genes from the Agrobacterium plasmids and replace them with transgenes. Host plant cells are grown in the lab and infected with the Agrobacterium. Because these cells are totipotent, they can be used to grow an entire plant — roots, leaves, and all — and every cell contains the transgene. When the plant forms seeds, those contain the transgene, too, ensuring that the transgene is passed to the offspring. Shoot plants with a gene gun so that microscopic particles of gold or other metals carry the transgene unit into the plant nucleus by brute force. Gene guns are a bit less dependable than Agrobacterium as a method for getting transgenes into plant cells. However, some plants are resistant to Agrobacterium, thus making the gene gun a viable alternative. With gene guns, the idea is to coat microscopic pellets with many copies of a transgene and by brute force (provided by compressed air) shove the pellets directly into the cell nuclei. By chance, some of the transgenes are inserted into the plant chromosomes. Commercial applications Transgenic plants have made quite a splash in the world of agriculture. So far, the main applications of this technology have addressed two primary threats to crops: Weeds: The addition of herbicide-resistant genes make crop plants immune to the effects of weed-killing chemicals, allowing farmers to spread herbicides over their entire fields without worrying about killing their crops. Weeds compete with crop plants for water and nutrients, reducing yields considerably. Soybeans, cotton, and canola (a seed that produces cooking oil) are only a few of the crop plants that have been genetically altered to tolerate certain herbicides. Bugs: The addition of transgenes that confer pest-killing properties to plants effectively reduces crop losses to plant-eating bugs. Geneticists provide pest-protection traits using the genes from Bacillus thuringiensis (otherwise known as Bt). Organic gardeners discovered the pesticide qualities of Bt, a soil bacterium, years ago. Bt produces a protein called Cry. When an insect eats the soil bacteria, digestion of Cry releases a toxin that kills the insect shortly after its meal. However, the Cry toxin is not toxic to animals and has been deemed safe for consumption by the FDA. Transgenic corn and cotton were the first to carry the Bt Cry Others now include potatoes, eggplants, soybeans, and tomatoes, although not all are commercially available yet. Points of contention about GMOs Few genetic issues have excited the almost frenzied response met by transgenic crop plants. Opposition to transgenic plants generally falls into four basic categories, including food safety issues, transgene escape, the development of resistance, and harming unintended targets. Food safety issues Normally, gene expression is highly regulated and tissue-specific, meaning that proteins produced in a plant’s leaves, for example, don’t necessarily show up in its fruits. Because of the way transgenes are inserted, however, their expression isn’t under tight control. Opponents to transgenics worry that proteins produced by transgenes may prove toxic, making foods produced by those crop plants unsafe to eat. Safety evaluations of transgenic crops rely on a concept called substantial equivalence. Substantial equivalence is a detailed comparison of transgenic crop products with their nontransgenic equivalents. This comparison involves chemical and nutritional analyses, including tests for toxic substances. If the transgenic product has some detectable difference, that trait is targeted for further evaluation. Thus, substantial equivalence is based on the assumptions that any ingredient or component of the nontransgenic product is already deemed safe and that only new differences found in the transgenic version are worth investigating. For example, in the case of transgenic potatoes, unmodified potatoes are thought to be safe, so only the Bt that had been introduced was slated for further tests. Escaped transgenes The escape of transgenes into other hosts is a widely reported fear of transgenics opponents. Canola, a common oil-seed crop, provides one good example of how quickly transgenes can get around. Herbicide-resistant canola was marketed in Canada in 1996 or so. By 1998, wild canola plants in fields where no transgenic crop had ever been grown already had not one but two different transgenes for herbicide resistance. This finding was quite a surprise because no commercially available transgenic canola came equipped with both transgenes. It’s likely that the accidental transgenic acquired its new genes via pollination. In 2002, several companies in the United States failed to take adequate precautions mandated by law to prevent the escape of corn transgenes via pollination or the accidental germination of untended transgenic seeds. These lapses resulted in fines — and the release of transgenes into unintended crops. Developing resistance The third major point of opposition to transgenics — the development of resistance to transgene effects — is connected to the widespread movement of transgenes. The point of developing most of these transgenic crops is to make controlling weeds or insect pests easier. Additionally, transgenic crops (particularly transgenic cotton) have the potential to significantly reduce chemical use, which is a huge environmental plus. However, when weeds or insects acquire resistance to transgene effects, the chemicals that transgenics are designed to replace are rendered obsolete. Full-blown resistance development depends on artificial selection supplied by the herbicide or the plant itself. Resistance develops and spreads when insects that are susceptible to the pesticide transgene being used are all killed. The only insects that survive and reproduce are, you guessed it, able to tolerate the pesticide transgene. Insects produce hundreds of thousands of offspring, so it doesn’t take long to replace susceptible populations with resistant ones. Damaging unintended targets The argument against transgenic plants is that nontarget organisms may suffer ill effects. For example, when Bt corn was introduced, controversy arose surrounding the corn’s toxicity to beneficial insects (that is, bugs that eat other bugs) and desirable creatures like butterflies. Indeed, Bt is toxic to some of these insects, but it’s unclear how much damage these natural populations sustain from Bt plants. The biggest threat to migratory monarch butterflies is likely habitat destruction in their overwintering sites in Mexico, not Bt corn. View Article

Genetics What are Transgenic Organisms? Article / Updated 01-30-2020 If genetic modification is so ubiquitous, what’s the problem with transgenic organisms? After all, humans have been at this whole genetic modification thing for centuries, right? Well, historically, humans have modified organisms by controlling matings between animals and plants with preexisting genetic compatibility, not by introducing sequences from different species. Transgenics are often endowed with genes from very different species. (The bacterial gene that’s been popped into corn to make it resistant to attack by plant-eating insects is a good example.) Therefore, transgenic organisms wind up with genes that never could have moved from one organism to another without considerable help. After these “foreign” genes get into an organism, they don’t necessarily stay put. One of the biggest issues with transgenic plants, for example, is uncontrolled gene transfer to other, unintended species. Another controversial aspect of transgenic organisms has to do with gene expression; many people worry that transgenes will be expressed in agricultural products in unwanted or unexpected ways, making food harmful to eat. To understand the promises and pitfalls of transgenics, you first need to know how transgenes are transferred and why. Recombinant DNA technology is the set of methods used for all transgenic applications. This set of techniques also falls under the classification of genetic engineering. Genetic engineering refers to the directed manipulation of genes to alter phenotype in a particular way. Thus, genetic engineering is also used in gene therapy to bring in healthy genes to counteract the effects of mutations. While different vectors, different source DNA, and different cell populations can be used, this basic process that underlies the creation of transgenes is essentially the same in the different types of organisms – animals, insects, bacteria, or plants. Follow the transgenesis process In general, developing transgenic organisms involves three major steps: Find (and potentially alter) the gene that controls trait(s) of interest. Slip the transgene into an appropriate delivery vehicle (a vector). Create fully transgenic organisms that pass on the new gene on to future generations. The process of finding and mapping genes is pretty similar from one organism to another and has been made much easier now that so many different organisms have had their genomes sequenced. After scientists identify the gene they want to transfer, they many need to alter the gene so that it works properly outside the original organism. Make a transgene using recombinant DNA technology Recombinant DNA technology involves taking DNA from two different sources, cutting it, and then putting the pieces back together in different combinations. This process has been used for decades in order to clone genes or other segments of DNA. When we say “clone genes,” we mean to isolate the gene (various methods exist for doing this), insert it into a vector (such as a bacterial plasmid — a circular piece of DNA from a bacterium), and replicate in appropriate host cells, in order to create exact copies of the gene. In order to clone a gene, the DNA first needs to be cut. To do this, scientists use restriction enzymes. Restriction enzymes are naturally made by bacteria, which use these proteins as a defense for viral infection. More than 3000 restriction enzymes have been characterized, with each one cutting DNA at a very specific sequence. For example, a common restriction enzyme known as EcoRI (which is made by the bacterium E. coli) cuts specifically at the sequence 5'-GAATTC-3'. EcoRI is also known to cut DNA so that sticky ends results — that is, it leaves short single-stranded DNA sequences at the ends of the cut fragments. The following figure shows how a restriction enzyme can cut DNA to leave sticky ends. The AATT overhang allows another fragment with a complementary end to come in and bind here. So, if you cut a fragment of human DNA with EcoRI and you cut a bacterial plasmid with EcoRI, both would end up having the same sticky ends. When you combined them, the fragment of human DNA can then be inserted between the two sticky ends of the bacterial plasmid. The plasmid can then be introduced into bacterial cells, which are grown in culture. In every new bacterial cell, there will be a copy of the plasmid vector containing the gene of interest. The gene is considered cloned after it is placed in the vector and the vector has been reproduced. Modify the gene to reside in its new home All genes must have promoter sequences, the genetic landmarks that identify the start of a gene, to allow transcription to occur. When it comes to creating a transgenic organism, the promoter sequence in the original organism may not be very useful in the new host; as a result, a new promoter sequence is needed to make sure the gene gets turned on when and where it’s wanted. Using the same recombinant DNA techniques used in cloning a gene, an appropriate promoter can be inserted upstream of the gene to introduced, such that the gene would now be under the control of the designated promoter. Some promoters that are used are set to keep the gene on continually in all the cells of the organism. Other promoters are used because they only turn on (express the gene) in certain cell types or at a certain point in development. When more precise regulation is needed, genetic engineers can use promoters that respond to conditions in the environment. In addition to the promoter, genetic engineers must also find a good companion gene — called a marker gene — to accompany the transgene. The marker gene provides a strong and reliable signal indicating that the whole unit (marker and transgene) is in place and working. Common markers include genes that convey resistance to antibiotics. With these kinds of markers, geneticists grow transgenic cells in a medium that contains the antibiotic. Only those that have resistance (conveyed by the marker gene) survive, providing a quick and easy way to tell which cells have the transgene (alive) and which don’t (dead). Other markers or reported genes that can be used are those that allow for visualization of transgene expression, such as the gene for green fluorescent protein. View Article

Genetics 10 Defining Events in Genetics Article / Updated 01-30-2020 Many milestones define the history of genetics. The events in the world of genetics are listed here roughly in order of historical occurrence. The publication of Darwin’s The Origin of Species Earthquakes have aftershocks — little mini-earthquakes that rattle around after the main quake. Events in history sometimes cause aftershocks, too. The publication of one man’s life’s work is such an event. From the moment it hit the shelves in 1856, Charles Darwin’s The Origin of Species was deeply controversial (and still is). The basis of evolution is elegantly simple: Individual organisms vary in their ability to survive and reproduce. For example, a sudden cold snap occurs, and most individuals of a certain bird species die because they can’t tolerate the rapid drop in temperature. But individuals of the same species that can tolerate the unexpected freeze survive and reproduce. As long as the ability to deal with rapid temperature drops is heritable, the trait is passed to future generations, and more and more individuals inherit it. When groups of individuals are isolated from each other, they wind up being subjected to different sorts of events (such as weather patterns). After many, many years, stepwise changes in the kinds of traits that individuals inherit based on events like a sudden freeze accumulate to the point that populations with common ancestors become separate species. Darwin concluded that all life on earth is related by inheritance in this fashion and, thus, has a common origin. Darwin arrived at his conclusions after years of studying plants and animals all over the world. What he lacked was a convincing explanation for how individuals inherit advantageous traits. Yet the explanation was literally at his fingertips. Gregor Mendel figured out the laws of inheritance at about the same time that Darwin was working on his book. Apparently, Darwin failed to read Mendel’s paper — he scrawled notes on the papers immediately preceding and following Mendel’s paper but left Mendel’s unmarked. Darwin’s copious notes show no evidence that he was even aware of Mendel’s work. Even without knowledge of how inheritance works, Darwin accurately summarized three principles that are confirmed by genetics: Variation is random and unpredictable. Studies of mutation confirm this principle. Variation is heritable (it can be passed on from one generation to the next). Mendel’s own research — and thousands of studies over the past century — confirms heritability. Variation changes in frequency over the course of time. For decades, genetic studies have confirmed that genetic variation within populations changes because of things like mutation, accidents, and geographic isolation (to name only a few causes). Regardless of how you view it, the publication of Darwin’s The Origin of Species is pivotal in the history of genetics. If no genetic variation existed, all life on earth would be precisely identical. Variation gives the world its rich texture and complexity, and it’s what makes you wonderfully unique. The rediscovery of Mendel’s work In 1866, Gregor Mendel wrote a summary of the results of his gardening experiments with peas. His work was published in the scientific journal Versuche Pflanzen Hybriden, where it gathered dust for nearly 40 years. Although Mendel wasn’t big on self-promotion, he sent copies of his paper to two well-known scientists of his time. One copy remains missing; the other was found in what amounts to an unopened envelope — the pages were never cut. (Old printing practices resulted in pages being folded together; the only way to read the paper was to cut the pages apart.) Thus, despite the fact that his findings were published and distributed (though limitedly), his peers didn’t grasp the magnitude of Mendel’s discovery. Mendel’s work went unnoticed until three botanists — Hugo de Vries, Erich von Tschermak, and Carl Correns — all reinvented Mendel’s wheel, so to speak. These three men conducted experiments that were very similar to Mendel’s. Their conclusions were identical — all three “discovered” the laws of heredity. De Vries found Mendel’s work referenced in a paper published in 1881. (De Vries coined the term mutation, by the way.) The author of the 1881 paper, a man by the name of Focke, summarized Mendel’s findings but didn’t have a clue as to their significance. De Vries correctly interpreted Mendel’s work and cited it in his own paper, which was published in 1900. Shortly thereafter, Tschermak and Correns also discovered Mendel’s publication through de Vries’s published works and indicated that their own independent findings confirmed Mendel’s conclusions as well. William Bateson is perhaps the great hero of this story. He was already incredibly influential by the time he read de Vries’s paper citing Mendel, and unlike many around him, he recognized that Mendel’s laws of inheritance were revolutionary and absolutely correct. Bateson became an ardent voice spreading the word. He coined the terms genetics, allele (shortened from the original allelomorph), homozygote, and heterozygote. Bateson was also responsible for the discovery of linkage, which was experimentally confirmed later by Morgan and Bridges. DNA transformation Frederick Griffith wasn’t working to discover DNA. The year was 1928, and the memory of the deadly flu epidemic of 1918 was still fresh in everyone’s mind. Griffith was studying pneumonia in an effort to prevent future epidemics. He was particularly interested in why some strains of bacteria cause illness and other seemingly identical strains do not. To get to the bottom of the issue, he conducted a series of experiments using two strains of the same species of bacteria, Streptococcus pneumonia. The two strains looked very different when grown in a Petri dish, because one grew a smooth carpet and the other a lumpy one (he called it “rough”). When Griffith injected smooth bacteria into mice, they died; rough bacteria, on the other hand, were harmless. To figure out why one strain of bacteria was deadly and the other wasn’t, Griffith conducted a series of experiments. He injected some mice with heat-killed smooth bacteria (which turned out to be harmless) and others with heat-killed smooth in combination with living rough bacteria. This combo proved deadly to the mice. Griffith quickly figured out that something in the smooth bacteria transformed rough bacteria into a killer. But what? For lack of anything better, he called the responsible factor the transforming principle. Oswald Avery, Maclyn McCarty, and Colin MacLeod teamed up in the 1940s to discover that Griffith’s transforming principle was actually DNA. This trio made the discovery by a dogged process of elimination. They showed that fats and proteins don’t do the trick; only the DNA of smooth bacteria provides live rough bacteria with the needed ingredient to become a killer. Their results were published in 1944, and like Mendel’s work nearly a century before, their findings were largely rejected. It wasn’t until Erwin Chargaff came along that the transforming principle started to get the appreciation it deserved. Chargaff was so impressed that he changed his entire research focus to DNA. Chargaff eventually determined the ratios of bases in DNA that helped lead to Watson and Crick’s momentous discovery of DNA’s double helix structure. The discovery of jumping genes By all accounts, Barbara McClintock was both brilliant and a little odd; a friend once described her as “not fooled or foolable.” McClintock was unorthodox in both her research and her outlook, as she lived and worked alone for most of her life. Her career began in the early 1930s and took her into a man’s world — very few women worked in the sciences in her day. In 1931, McClintock collaborated with another woman, Harriet Creighton, to demonstrate that genes are located on chromosomes. This fact sounds so self-evident now, but back then, it was a revolutionary idea. McClintock’s contribution to genetics goes beyond locating genes on chromosomes, though. She also discovered traveling bits of DNA, sometimes known as jumping genes. In 1948, McClintock, working independently, published her results demonstrating that certain genes in corn could hop around from one chromosome to another without translocation. Her announcement triggered little reaction at first. It’s not that people thought McClintock was wrong; she was just so far ahead of the curve that her fellow geneticists couldn’t comprehend her findings. Alfred Sturtevant (who was responsible for the discovery of gene mapping) once said, “I didn’t understand one word she said, but if she says it is so, it must be so!” Now referred to as transposable elements or transposons, scientists have since discovered that there are many different types. It is also now known that up to half of the human genome contains sequences from transposable elements. However, many of these are basically ancient relics that are no longer able to jump. And many others are rendered silent by certain genetic mechanisms. For those that are still active and able to move, the effect depends on where they land. If they land within a gene, they can cause a mutation that results in disease. In other cases, their movement can contribute to genetic diversity and evolution of the species. The frequency with which transposons move depends on the species and the type of transposon. It took nearly 40 years before the genetics world caught up with Barbara McClintock and awarded her the Nobel Prize in Physiology or Medicine in 1983. By then, jumping genes had been discovered in many organisms. Feisty to the end, this grand dame of genetics passed away in 1992 at the age of 90. The birth of DNA sequencing So many events in the history of genetics lay a foundation for other events to follow. Frederick Sanger’s invention of chain-reaction DNA sequencing is one of those foundational events. In 1980, Sanger shared the Nobel Prize in Chemistry with Walter Gilbert for their work on DNA. Sanger figured out how to use the characteristics of DNA and of DNA replication to determine the sequence of DNA. Chain-termination sequencing, as Sanger’s method is called, uses the same mechanics as replication in your cells. Sanger figured out that he could control the DNA building process by snipping off one oxygen molecule from the building blocks of DNA. The resulting method allowed identification of every base, in order, along a DNA strand, sparking a revolution in the understanding of how your genes work. This process is responsible for the Human Genome Project, DNA fingerprinting, genetic engineering, and gene therapy. The invention of PCR In 1985, while driving along a California highway in the middle of the night, Kary Mullis had a brainstorm about how to carry out DNA replication in a tube. His idea led to the invention of polymerase chain reaction (PCR), a pivotal point in the history of genetics. In essence, PCR acts like a copier for DNA. Even the tiniest snippet of DNA can be copied. Scientists need many copies of a DNA molecule before enough is present for them to examine. Without PCR, large amounts of DNA are needed to generate a DNA fingerprint. However, at many crime scenes, only tiny amounts of DNA are present. PCR is the powerful tool that every crime lab in the country now uses to detect the DNA left behind at crime scenes and to generate DNA fingerprints. Mullis’s bright idea turned into a billion-dollar industry. Although he reportedly was paid a paltry $10,000 for his invention (from the lab where he worked), he received the Nobel Prize for Chemistry in 1993 (a sort of consolation prize). The development of recombinant DNA technology In 1970, Hamilton O. Smith discovered restriction enzymes, which act as chemical cleavers to chop DNA into pieces at very specific sequences. As part of other research, Smith put bacteria and a bacteria-attacking virus together. The bacteria didn’t go down without a fight — instead, it produced an enzyme that chopped the viral DNA into pieces, effectively destroying the invading virus altogether. Smith determined that the enzyme, now known as HindII (named for the bacteria Haemophilus influenzae Rd), cuts DNA every time it finds certain bases all in a row and cuts between the same two bases every time. This fortuitous (and completely accidental!) discovery was just what was needed to spark a revolution in the study of DNA. Some restriction enzymes make offset cuts in DNA, leaving single-stranded ends. The single-strand bits of DNA allow geneticists to “cut-and-paste” pieces of DNA together in novel ways, forming the entire basis of what’s now known as recombinant DNA technology. Gene therapy, the creation of genetically engineered organisms, and practically every other advance in the field of genetics these days all depend on the ability to cut DNA into pieces without disabling the genes and then to put the genes into new places — a feat made possible thanks to restriction enzymes. Researchers have used thousands of restriction enzymes to help map genes on chromosomes, study gene function, and manipulate DNA for diagnosis and treatment of disease. Smith shared the Nobel Prize in Physiology or Medicine in 1978 with two other geneticists, Dan Nathans and Werner Arber, for their joint contributions to the discovery of restriction enzymes. The invention of DNA fingerprinting Sir Alec Jeffreys has put thousands of wrongdoers behind bars. Almost single-handedly, he’s also set hundreds of innocent people free from prison. Not bad for a guy who spent most of his time in the genetics lab. Jeffreys invented DNA fingerprinting in 1985. By examining the patterns made by human DNA after it was diced up by restriction enzymes, Jeffreys realized that every person’s DNA produces a slightly different number of various sized fragments (which number in the thousands). Jeffreys’s invention has seen a number of refinements since its inception. PCR and the use of STRs (short tandem repeats) have replaced the use of restriction enzymes. Modern methods of DNA fingerprinting are highly repeatable and extremely accurate, meaning that a DNA fingerprint can be stored much like a fingerprint impression from your fingertip. Crime laboratories all over the United States make use of the methods that Jeffreys pioneered, and the information that these labs generate is housed in a huge database hosted by the FBI. This data can then be accessed by police departments in order to help match criminals to crimes. In 1994, Queen Elizabeth II knighted Jeffreys for his contributions to law enforcement and his accomplishments in genetics. The birth of developmental genetics Every cell in your body has a full set of genetic instructions to make all of you. The master plan of how an entire organism is built from genetic instructions remained a mystery until 1980, when Christiane Nüsslein-Volhard and Eric Wieschaus identified the genes that control the whole body during fly development. Fruit flies and other insects are constructed of interlocking pieces, or segments. A group of genes (collectively called segmentation genes) tells the cells which body segments go where. These genes, along with others, give directions like top and bottom and front and back, as well as the order of body regions in between. Nüsslein-Volhard and Wieschaus made their discovery by mutating genes and looking for the effects of the “broken” genes. When segmentation genes get mutated, the fly ends up lacking whole sections of important body parts or certain pairs of organs. A different set of genes (called homeotic genes) controls the placement of all the fly’s organs and appendages, such as wings, legs, eyes, and so on. One such gene is eyeless. Contrary to what would seem logical, eyeless actually codes for normal eye development. Using the same recombinant DNA techniques made possible by restriction enzymes, Nüsslein-Volhard and Wieschaus moved eyeless to different chromosomes where it could be turned on in cells in which it was normally turned off. The resulting flies grew eyes in all sorts of strange locations — on their wings, legs, butts, you name it. This research showed that, working together, segmentation and homeotic genes put all the parts in all the right places. Humans have versions of these genes, too; your body-plan genes were discovered by comparing fruit fly genes to human DNA. The work of Francis Collins and the Human Genome Project In 1989, Francis Collins and Lap-Chee Tsui identified the single gene responsible for cystic fibrosis. The very next year, the Human Genome Project (HGP) officially got underway. Collins, who has both a medical degree and a PhD in physical chemistry, later replaced James Watson as the head of the National Human Genome Research Institute in the United States and supervised the race to sequence the entire human genome from start to finish. In 2009, Collins became the director of the U.S. National Institutes of Health. Collins is one of the true heroes of modern genetics. He kept the HGP ahead of schedule and under budget. He continues to champion the right to free access to all the HGP data, making him a courageous opponent of gene patents and other practices that restrict access to discovery and healthcare, and he’s a staunch defender of genetic privacy. Although the human genome is still bits and pieces away from being completely sequenced, the project wouldn’t have been a success without the tireless work of Collins. View Article

Genetics 10 Hot Issues in Genetics Article / Updated 01-30-2020 Genetics is a field that grows and changes with every passing day. This list shines the spotlight on ten of the hottest topics and next big things in this ever-changing scientific landscape. Direct-to-consumer genetic testing Not too long ago, genetic testing was uncommon and was reserved for visits to a geneticist, genetic counselor, or other specialized healthcare provider. Now, a trip to the drug store, a little spit in a tube that you put in the mail, and that’s it. A few weeks or months later and you get to learn all about yourself! Of course, it’s not really that straightforward. Direct-to-consumer tests come in several varieties. The most common of these tests is genetic ancestry testing. Genetic ancestry testing involves testing individuals for sequence variations throughout the genome. The frequency of certain variants differs among different ancestral populations. Therefore, an analysis of the variants that a person carries and a comparison with previously tested individuals of known ancestry can give us an idea of where that person’s ancestors came from. Popular direct-to-consumer genetic tests also include testing for health risks and common traits. The companies that offer these tests provide risk assessments for certain health conditions based on the particular sequence variants a person carries. For example, a specific variant in the gene for apoliprotein E (APOE) has been associated with an increased risk for developing late-onset Alzheimer disease (AD). Carrying the APOE e4 allele appears to increase one’s risk for developing AD late in life. Carrying two copies of the allele raises the risk even higher. It is important to note that this is not a predictive test. It cannot tell you if you will develop AD or not, only whether you have an increased risk based on the versions of the APOE gene that you carry. Similar testing can tell you about your risk for conditions such as celiac disease, Parkinson’s disease, and diabetes, among others, but it cannot tell you whether or not you will get them. At least one company offers testing for three variants in the breast cancer genes BRCA1 and BRCA2 (. The three variants that are a part of this test are found much more often in individuals of Ashkenazi (Eastern European) Jewish ancestry. Carriers of one of these three gene changes have a significantly increased risk for breast and ovarian cancer. One of the things that is hard for many patients to understand about the BRCA1 and BRCA2 testing that is performed is that they will not be tested for the vast majority of mutations in these genes (thousands have been reported). So, if the person tested does not carry one of the three mutations included in the test, it does not rule out the possibility that they carry another mutation in one of these genes. And if the person is not of Ashkenazi Jewish ancestry, this portion of the test is of little value, since it is unlikely they would carry one of the three mutations anyway. Whole exome sequencing The genome is a complete set of chromosomes from an organism, including all coding and noncoding DNA. The exome contains all of the coding sequences found in the genome — all the exons in all of the genes. The exome, which is estimated to account for less than two percent of the genome, provides the instructions for creating the proteins in the body. Most mutations that cause genetic disorders are found in the exome. With advances in DNA sequencing technologies, it is now relatively straightforward (and not crazy expensive) to sequence the exomes of individuals in search of a genetic diagnosis. Consequently, whole exome sequencing has now entered mainstream genetics and is increasingly being used for patients who are suspected of having a genetic syndrome that has yet to be diagnosed. In many cases, patients have been on a long diagnostic odyssey with numerous medical evaluations, chromosome studies, and single gene tests, with no success. Whole exome sequencing allows for the testing of all known genes at the same time, regardless of the specific clinical features the person demonstrates. Not only is whole exome sequencing providing diagnoses for those who were previously diagnosed with an “unknown genetic syndrome” (and many answers to the many questions of frustrated parents), it is providing a lot of information about the spectrum of features that can be associated with any particular disorder. We are finding out that the symptoms of genetic disorders can be quite varied. This means that someone may have a condition that would not have been suspected previously because they show features that are quite different than what is typically seen in individuals who have been diagnosed with the disorder. One of the limitations of whole exome sequencing is the identification of incidental findings or genetic changes of unclear consequence. Incidental findings are those that are unrelated to why the testing was performed, such as identifying a gene changes that increases the risk for Alzheimer disease in a child who was tested because of intellectual disabilities. Genetic changes for which the effect is unclear typically are referred to as variants of unknown significance. It’s possible these changes could be the cause of some disorder, but it is also possible that they are completely harmless. The problem is there is not enough information about them yet to know which is true, and it is not always clear whether someone’s medical care should be altered based on the finding of a variant for which the effect is uncertain. Whole exome sequencing is also being performed in large groups of individuals without genetic syndromes in order to determine how common different variants are in the population. The Exome Aggregation Consortium (ExAC) and the 100,000 Genomes Project are two collaborations that are collecting exome and/or genome data from a large number of individuals from a variety of ethnic backgrounds. Because of data like this, variants that were once classified as pathogenic (that is, as a disease-causing mutation) are now being reclassified as benign because we now know these variants are quite common in the general population (and, therefore, highly unlikely to cause any problems). Whole genome sequencing While whole exome sequencing involves determining the order of the nucleotides in all the exons in the genome, whole genome sequencing involves determining the sequence of the nucleotides in the entire genome. Whole genome sequencing was what was done during the Human Genome Project. And in the time since the Human Genome Project was completed, the ease with which sequencing can be performed and the significantly lowered cost have led to whole genome sequencing entering the clinic (just as with whole exome sequencing). The idea with whole genome sequencing is that it should theoretically be able to identify of the cause of rare genetic conditions that cannot be diagnosed using more traditional methods, or even whole exome sequencing. Scientists estimate that about 85 percent of disease-causing mutations involve the coding sequences of the genome. The remaining 15 percent or are expected to be located in noncoding sequences that are not covered in other types of tests. Whole genome sequencing could identify the previously unidentifiable mutations in those with undiagnosed genetic syndrome. Indeed, a project in the United Kingdom is allowing all children with serious illnesses to have whole genome testing. So far, the program has found that about 1 in 4 seriously ill kids had an underlying genetic syndrome. One case was a girl with a rare and severe form of epilepsy, and once her diagnosis was made, it was realized that the child had been taking medication that was known to aggravate that type of epilepsy. The mutation that caused this condition could have been found using more traditional approaches, but whole genome sequencing was able to provide a result in several weeks without having to undergo a diagnostic odyssey. As with whole exome sequencing, two of the main concerns with whole genome sequencing are incidental findings and the identification of variants of unknown clinical significance. Stem cell research Stem cells may hold the key to curing brain and spinal cord injuries. They may be part of the cure for cancer. These little wonders may be the magic bullet to solving all sorts of medical problems, but they’re at the center of controversies so big that their potential remains unknown. You’ve probably guessed (or already knew) that one of the sources of stem cells for research is embryonic tissue — and therein lies the rub. However, in 2006, scientists figured out a way to turn multipotent stem cells (cells that can give rise to just a few, related cell types) from an adult organism into pluripotent stem cells (cells that can give rise to any of the cell types in the body of an organism). These stem cells are referred to as induced pluripotent stem cells. This discovery meant that it was now possible to collect stem cells from a patient, modify them, and return them to the patient, eliminating the chance of tissue rejection. Currently, the most common use of stem cells is in hematopoietic stem cell therapy, which can be used to treat certain types of cancer and immune conditions. In hematopoietic stem cell therapy, the stem cells can be obtained from bone marrow, from the bloodstream, or from blood in the umbilical cord. This type of stem cell is a multipotent stem cell, which can give rise to any of the blood-related cell types (such as red blood cells and white blood cells). Other uses of stem cells are being evaluated, with hopes that stem cell therapy will be able to help those with a number of different conditions, including neurodegenerative disorders and blindness. In fact, in 2018, researchers from England reported the results of a phase I clinical trial in which two patients with age-related macular degeneration were treated with stem cells. In age-related macular degeneration, specific light-sensitive cells in the retina die off, resulting in a progressive loss of central vision. In the trial, the eyes of both patients were injected with a patch of stem cells. Over the course of the following year, both patients showed dramatic improvement in their eyesight. While stem cells in one form or another have yet to find their way into everyday medicine, ongoing studies are promising and it is likely just a matter of time. When considering new or experimental medical therapies, it is important that the patient is aware of the history and experience of the provider and medical practice offering the treatment. Anyone considering medical treatment for a chronic condition should consult with a licensed and reputable healthcare provider. The ENCODE Project The goal of the Human Genome Project was to sequence the entire human genome. In 2001, a draft of the human genome sequence was published. And after about 13 years from start to finish (2 years ahead of schedule), the project was deemed complete. As a result of the project, we now know that there are approximately 22,000 genes (compared to the original prediction of 100,000 genes) and that coding sequences (the sequences that actually code for the protein products made by the genes) account for less than 2 percent of the entire human genome. We also have many new and improved tools for the analysis of genetic data. What we didn’t know is the function of the more than 98 percent of sequences — noncoding sequences that were once referred to as junk DNA. The Encyclopedia of DNA Elements (ENCODE) Project is a follow-up to the Human Genome Project. This project involves more than 30 research groups and more than 400 scientists from across the globe. The main goal of this project is to explore and determine the function of the noncoding sequences in the human genome. Research to date suggests that more than 80 percent of the noncoding sequences play a role in the regulation of gene expression. Research also is attempting to determine whether differences in the expression of certain genes (as opposed to difference in gene sequence) can be linked with the development of specific genetic disorders. While most disease-causing mutations are found in the protein-coding portions of gene (the exons), some are found in non-coding regions of the genes (such as in the promoters or introns). Scientists also expect that sequence variants located in other noncoding regions, including regions located distant to the gene itself (such as in enhancers or silencers), could affect gene expression and result in the development of genetic conditions. Proteomics Genomics is the study of whole genomes. Proteomics is the study of all the proteins an organism makes. Proteins do all the work in your body. They carry out all the functions that genes encode, so when a gene mutation occurs, the protein is what winds up being altered (or goes missing altogether). Given the link between genes and proteins, the study of proteins may end up telling researchers more about genes than the genes themselves! Proteins are three-dimensional. Proteins not only get folded into complex shapes but also get hooked up with other proteins and decorated with other elements such as metals. Scientist can’t just look at a protein and tell what its function is. However, if researchers can better understand each protein and what role it may play, proteins may be a big deal in the development of medicines and other treatments, because medications act upon the proteins in your system. Cataloging all the proteins in your proteome isn’t easy, because researchers have to sample every tissue to find them all. Nonetheless, the rewards of discovering new drugs and treatments for previously untreatable diseases may make the effort worthwhile. Proteomics hasn’t made a big splash in clinical settings just yet — complexities and technological setbacks have slowed progress. However, like most things in genetics, it’s likely just a matter of time. Gene chips Technology is at the heart of modern genetics, and one of the most useful developments in genetic technology is the gene chip. Also known as microarrays, gene chips allow researchers to quickly determine which genes are at work (that is, being expressed) in a given cell. Gene expression depends on messenger RNA (mRNA), which is produced through transcription. The mRNAs get tidied up and sent out into the cell cytoplasm to be translated into proteins. The various mRNAs in each cell tell exactly which of the thousands of genes are at work at any given moment. In addition, the number of copies of each mRNA conveys an index of the strength of gene expression. The more copies of a particular mRNA, the stronger the action of the gene that produced it. Gene chips are grids composed of bits of DNA that are complementary to the mRNAs the geneticist expects to find in a cell. It works like this: The bits of DNA are attached to a glass slide. All the mRNAs from a cell are passed over the gene chip, and the mRNAs bind to their DNA complements on the slide. Geneticists measure how many copies of a given mRNA attach themselves to any given spot on the slide to determine which genes are active and what their strength is. Gene chips are relatively inexpensive to make and can each test hundreds of different mRNAs, making them a valuable tool. One thing this screening can be used for is to compare mRNAs from normal cells to those from diseased cells (such as cancer). By comparing the genes that are turned on or off in the two cell types, geneticists can determine what’s gone wrong and how the disease may be treated. Scientists are also using microarrays to screen thousands of genes rapidly to identify specific mutations that cause disease, or to test patients for certain types of chromosome abnormalities. Evolution of antibiotic resistance Unfortunately, not all “next big things” are good. Antibiotics are used to fight diseases caused by bacteria. When penicillin (a common antibiotic) was developed, it was a wonder drug that saved many, many of lives. However, many antibiotics are nearly useless now because of the evolution of antibiotic resistance. Bacteria don’t have sex, but they still pass their genes around. They achieve this feat by passing around little circular bits of DNA called plasmids. Almost any species of bacteria can pass its plasmids on to any other species. Thus, when bacteria that are resistant to a particular antibiotic run into bacteria that aren’t resistant, the exchange of DNA endows the formerly susceptible bacteria with antibiotic resistance. Antibacterial soaps and the overprescribing of antibiotics make the situation worse by killing off all the nonresistant bacteria, leaving only the resistant kind behind. This can make illnesses that result from bacterial infections very difficult to treat. Consequently, scientists must continually work to develop new, more powerful antibiotics in an effort to stay one step ahead of the bacteria. Circumventing Mother Nature While you get your nuclear DNA (your autosomes and sex chromosomes) from both your mother and your father, your mitochondrial DNA (mtDNA) comes solely from your mother. So, conditions that are the result of changes in the mtDNA can only be inherited from mom. And if mom carries a mutation in her mtDNA, each of her children have a risk of inheriting it and developing a mitochondrial disorder, many of which are quite severe and potentially lethal. Well, a relatively new technique for preventing the inheritance of a mitochrondrial disorders is mitochondrial transfer (or mitochondrial replacement therapy). To minimize the chance of a child inheriting his mother’s mtDNA mutation and developing a mitochondrial disorder, scientists developed a procedure where the mother’s mitochondria could be replaced with the mitochondria from a donor, so the child would inherit someone else’s mitochondrial DNA but her mother’s nuclear DNA. In 2016, the birth of a child that resulted from this procedure was reported. The family had already had two children who had died from the mitochondrial disorder Leigh syndrome. The nucleus of one of the mother’s eggs (containing the nuclear DNA) was transferred into a donor egg that had the nucleus removed. The egg was then fertilized by sperm from the father and implanted in the mother. The couple had a healthy son who had very low levels of the mother’s mtDNA mutation and no clinical symptoms of Leigh syndrome. Genetics from afar For many, a referral to a geneticist or genetic counselor means traveling several hours (potentially to another state) and often having to navigate a large, unfamiliar city. It may also mean a very long wait, from the time of referral to the time of the actual appointment. In the entire state of Alaska, there is currently a single genetics clinic with a single clinical geneticist. And in some states, the demand far exceeds the availability; consequently, the wait for an appointment can be as long as 12 to 18 months. To improve access to genetics services, there has been a significant increase in the use of telegenetics. Telegenetics involves using either the telephone or videoconferencing to connect a patient with a genetics provider. In a virtual patient visit with a clinical geneticist, the patient attends a clinic at a local physician’s office. The visit requires a computer, high-speed internet, a good camera, a few specialized medical tools, and a provider onsite (such as a nurse or genetic counselor) to assist. The geneticist can perform a thorough evaluation while being hundreds of miles away. Even more common these days are telephone genetic counseling sessions. Genetic counselors can provide all aspects of genetic counseling (including pre-test and post-test counseling) while the patient enjoys the comforts of home. View Article

Genetics DNA Technology: Copying a Gene with PCR Article / Updated 04-23-2019 The polymerase chain reaction (PCR) is a process that can turn a single copy of a gene into more than a billion copies in just a few hours. It gives medical researchers the ability to make many copies of a gene whenever they want to genetically engineer something. For years, the very structure of DNA made studying it rather challenging. After all, DNA is incredibly long and very tiny. Fortunately, the advent of DNA technology, the tools and techniques used for reading and manipulating the DNA code, has made working with DNA much easier. In 1983, Kary Mullis discovered the PCR process, which allows scientists to make numerous copies of DNA molecules that they can then study. Today, PCR is used for Making lots of DNA for sequencing Finding and analyzing DNA from very small samples for use in forensics Detecting the presence of disease-causing microbes in human samples Producing numerous copies of genes for genetic engineering Scientists can even combine DNA from different organisms to artificially create materials such as human proteins or to give crop plants new characteristics. They can also compare different versions of the same gene to see exactly where disease-causing variations occur. PCR targets the gene to be copied with primers, single-stranded DNA sequences that are complementary to sequences next to the gene to be copied. To begin PCR, the DNA sample that contains the gene to be copied is combined with thousands of copies of primers that frame the gene on both sides. DNA polymerase uses the primers to begin DNA replication and copy the gene. The basic steps of PCR are repeated over and over until you have billions of copies of the DNA sequence between the two primers. The polymerase chain reaction. PCR works a little like chain e-mails. If you get a chain e-mail and send it on to two friends, who each send it on to two of their friends, and so on, pretty soon everyone has seen the same e-mail. In PCR, first a DNA molecule is copied, then the copies are copied, and so on, until you have 30 billion copies in just a few hours. View Article

Genetics Exploring Genetics Research Article / Updated 03-26-2016 People have been wondering why they look like their parents for centuries. Observations of nature over the past few millenia have led people to ask "Why?" and "How?" repeatedly. The search for answers has led to fascinating findings. Genetic pioneering Mendel's pea plant experiments jumpstarted the field of modern genetics. Once it was known that heredity was based in the cells and that genes carried the hereditary information, scientists built upon each other's work, adding more and more knowledge to the base. Tiny animals that didn't take up too much laboratory space, didn't eat much, and that could create successive generations quickly were used to try out theories and learn more. Fruit flies (the genus and species name is Drosophila melanogaster) and mice or rats are most often used. To produce a new generation, which is the only way to see whether a mutation or trait is passed on, you must wait for the parental generation to mature to the point where they can reproduce. Then, you must wait through the gestation period once the parents have mated. Mice and fruit flies mature quickly and have short gestation periods. Humans, though, are not capable of reproducing until after puberty occurs during the teenage years, and then the gestation period is nine months. That's quite a wait for results! Since Mendel's days in the monastery garden, DNA was found, and its structure was figured out. When James Watson and Francis Crick figured out that DNA was a double helix, scientists were able to determine that it split apart to be replicated. Once scientists knew how DNA was copied within the cell, they could figure out the genetic code. Knowing the genetic code allowed them to determine what amino acids and proteins were produced. And that led them to the Human Genome Project. Mapping ourselves: The Human Genome Project You've probably heard about this project on the news, even if you didn't know what a genome was at the time. (By the way, a genome is the total collection of genes in a species.) In 1988, laboratories all across the world began determining the DNA sequences of human DNA. If you are wondering why the Human Genome Project is a big deal, think of it this way. If you were a researcher and you wanted to study a specific human gene, first you would have to know what chromosome it "lived" on. To provide the "address" of each human gene, researchers set out to build a map of the nucleotide sequences in the DNA of each human chromosome. Sounds like a daunting task, doesn't it? Well, the process of DNA sequencing became automated, and with several laboratories around the country all working toward the same goal and sequencing different pieces of DNA using really sophisticated computer programs, the project was largely completed several years ahead of schedule — how often does that happen? Now armed with a roadmap of where every gene is located, researchers can turn their attention toward making good use of that information. Knowing where each gene resides in the chromosomes, the "bad" genes — the ones that cause disease or cancer or other undesirable traits — can be sought out. Gene therapy research is trying to prevent the bad genes from having their undesirable effect or to convert them to good genes. It is predicted that the future of medicine will heavily use gene therapy to prevent the occurrence of diseases rather than medicines to treat diseases that have already taken hold. However, now that research is dealing with human genes, plenty of controversy is peppering the positive results. An uproar in the 1980s occurred when a genetically engineered strawberry was created. As geneticists, biochemists, and molecular cell biologists discover more about what can be done with genetic information, others are worried about the implications of such technology. Even after gene therapy has been successfully used, people just are not sure how to approach the future. Should gene therapy and cloning be regulated by the government? What would happen if genes being inserted into a patient went to the wrong chromosome? If plants and animals are altered, will the balance of nature be disrupted? Will "designer" babies be created? What do you call your mother if she's your clone, and therefore also your twin sister? These questions have been asked not only by researchers, but also by government officials, journalists, and people sitting around their dining room tables. But, with so much promise in developing genetic techniques, it is hard to contain enthusiasm. Researchers know that they can help people now. Why wait? Table 1 gives you just a few examples of what is being done now with genetically engineered products. Table 2 shows you what is on the laboratory benches now. But before you know it, these tables will grow much longer. Any takers? Table 1: Genetically Engineered Products Product Benefit Alpha-interferon Normally produced in small amounts in the body, has very important immune function. Genetically engineered bacteria can cause the body to create lots of alpha-interferon. Now used to shrink tumors, as well as treat hepatitis B and hepatitis C. Beta-interferon Also a naturally occurring protective protein that is produced in small quantities. The genetically engineered variety is used to treat multiple sclerosis, a serious autoimmune disorder in which the body attacks its own nerve fibers, eventually causing an inability to move. Humulin (human insulin) In the past, pigs were used to create insulin that was used in humans with diabetes. However, because it was pig insulin, and not human insulin, some serious side effects could occur. Now, Escherichia coli, a very common intestinal bacteria, can be inserted with the gene for human insulin and turned into little human insulin factories. The insulin they make causes much fewer side effects and is much safer. Monoclonal antibodies Antibodies are cells in the immune system that fight off invading organisms. Monoclonal antibodies are made by combining B lymphocytes (cells from the immune system) from mice with cancer-causing cells. These hybrid (mixed) cells start to produce antibodies against the cancerous cells. Monoclonal antibodies are used instead of chemotherapy in patients with a form of bone cancer. Tissue plasminogen activator (tPA) This protein is the body's clot buster. It occurs naturally in the body to keep blood flow moving. What scientists did was genetically engineer the substance so that it could be produced outside of the body and in larger quantities. The genetically engineered product is given to patients who just had a heart attack or stroke to dissolve blockage that was the culprit. Table 2: Genetics in the Works Product/Research Area Expected Effect Functional genomics Study of certain DNA sequences in an organism and how they function, taking into consideration all the DNA of the organism. Microarray analysis Instead of studying one gene in one organism, the techniques associated with microarray analysis may allow thousands of genes to be studied at one time or in many different organisms at once. Antisense therapy Hopes to stop bad genes from functioning, which would prevent the protein they produce from having a negative effect. Creating new chromosomes Could possibly create entire human chromosomes that would contain genes to cure certain diseases. These could be inserted into people with a disease so that their body would replicate the good genes instead of the bad ones. View Article

Genetics Genetics: Examining the Basics of Chromosomes Article / Updated 03-26-2016 Chromosomes are threadlike strands that are composed of DNA. To pass genetic traits from one generation to the next, the chromosomes must be copied, and then the copies must be divvied up. Most prokaryotes have only one circular chromosome that, when copied, is passed on to the daughter cells (new cells created by cell division) during mitosis. Eukaryotes have more complex problems to solve (like divvying up half of the chromosomes to make sex cells), and their chromosomes behave differently during mitosis and meiosis. Additionally, there are various terms to describe the anatomy, shapes, the number of copies, and situations that eukaryotic chromosomes find themselves in. This article gets into the intricacies of chromosomes in the eukaryotic cells, because they're so complex. Counting out chromosome numbers Each eukaryotic organism has a very specific number of chromosomes per cell — ranging from one to many. For example, humans have 46 total chromosomes. These chromosomes come in two varieties: Sex chromosomes: These chromosomes determine gender. Human cells contain two sex chromosomes. If you're female, you have two X chromosomes, and if you're male, you have an X and a Y chromosome. Autosomal chromosomes: Autosomal simply refers to non-sex chromosomes. So, sticking with the human example, do the math, and you can see that humans have 44 autosomal chromosomes. Ah, but there's more. In humans, chromosomes come in pairs. That means you have 22 pairs of uniquely shaped autosomal chromosomes plus 1 pair of sex chromosomes, for a total of 23 chromosome pairs. Your autosomal chromosomes are identified by numbers — 1 through 22. So, you have two chromosome 1s, two 2s, and so on. When chromosomes are divided into pairs, the individual chromosomes in each pair are considered homologous, meaning that the paired chromosomes are identical to one another in shape and size. For example, your two single chromosome 2s are paired up because they're identical in shape and size. These homologous chromosomes are sometimes referred to as homologs for short. Chromosome numbers can get a bit confusing. Humans are diploid, meaning we have two copies of each chromosome. Some organisms (like bees and wasps) have only one set of chromosomes (cells with one set of chromosomes are referred to as haploid); others have three, four, or as many as sixteen copies of each chromosome! The number of chromosome sets held by a particular organism is called the ploidy. The total number of chromosomes doesn't tell you what the ploidy of an organism is. For that reason, the number of chromosomes an organism has is often listed as some multiple of n. Thus, humans are 2n = 46 (indicating that humans are diploid and the total number of chromosomes is 46). A single set of chromosomes referred to by the n is the haploid number. Human sex cells such as eggs or sperm are haploid. Examining chromosome anatomy Chromosomes are often depicted in stick-like forms. Chromosomes don't look like sticks, though. In fact, most of the time they're loose and string-like. Chromosomes only take on this distinctive shape and form when cell division is about to take place (during metaphase either through meiosis or mitosis). They're often drawn in this very distinctive shape and form because the special characteristics of eukaryotic chromosomes are easier to see. The part of the chromosome that appears pinched together (located in the middle of the chromosome) is called the centromere. The placement of the centromere (whether it's closer to the top, middle, or bottom of the chromosome) is what gives each chromosome its unique shape. The ends of the chromosomes are called telomeres. Telomeres are made of densely packed DNA and serve to protect the DNA message carried by the chromosome. The differences in shapes and sizes of chromosomes are easy to see, but the most important differences between chromosomes are hidden deep inside the DNA. Chromosomes carry genes. Genes are sections of DNA that make up the building plans for physical traits. The genes tell the body how, when, and where to make all the structures that are necessary for the processes of living. Each pair of homologous chromosomes carries the same — but not necessarily identical — genes. For example, both chromosomes of a particular homologous pair might contain the gene for hair color, but one can be a "brown hair" version of the gene — alternative versions of genes are called alleles — and the other can be a "blond hair" allele. Any given gene can have one or more alleles. The alleles code for the different physical traits (phenotypes) you see in animals and plants like hair color or flower shape. Each point along the chromosome is called a locus (Latin for "place"). The plural of locus is loci (pronounced low-sigh). Most of the phenotypes that you see are produced by multiple genes (that is, genes occurring at different loci and often on different chromosomes) acting together. For instance, human eye color is determined by at least three different genes that reside on two different chromosomes. View Article

Genetics How Cells Work: Prokaryotes and Eukaryotes Article / Updated 03-26-2016 Knowing how cells work is critical in the genetics field. All living things consist of one or both of two cell types: prokaryotes and eukaryotes. The basic biologies of prokaryotes and eukaryotes are similar but not identical, so understanding the differences and similarities between them is important. The process of passing genetic material from one generation to the next depends completely on how cells grow and divide. To reproduce, a simple organism such as bacteria or yeast simply copies its DNA (through a process called replication) and splits in two. But organisms that reproduce sexually go through a complicated dance that includes mixing and matching strands of DNA (a process called recombination) and then reducing the amount of DNA in special sex cells to arrive at completely new genetic combinations for their offspring. There are two basic kinds of organisms — ones with a nucleus and those without a nucleus (a compartment filled with DNA surrounded by a membrane called a nuclear envelope): Prokaryotes: Organisms whose cells lack a nucleus and therefore have DNA floating loosely in the liquid center of the cell. Prokaryotes divide, and thus reproduce, by simple mitosis. Eukaryotes: Organisms that have a well-defined nucleus to house and protect the DNA. Eukaryotes divide by meiosis for sexual reproduction. Prokaryotes: Cells without a nucleus Organisms composed of cells without nuclei are classified as prokaryotes, which means "before nucleus." Prokaryotes are the most common forms of life on earth. You are, at this very moment, covered in and inhabited by millions of prokaryotic cells: bacteria. Much of your life and your body's processes depend on these arrangements; for example, the digestion going on in your intestines is partially powered by bacteria that break down the food you eat. Most of the bacteria in your body are completely harmless to you. Other species of bacteria, however, can be vicious and deadly, causing rapidly transmitted diseases such as cholera. All bacteria, regardless of temperament, are simple, one-celled prokaryotic organisms. None have cell nuclei, and all are small cells with relatively small amounts of DNA. The exterior of a prokaryotic cell is encapsulated by a cell wall that serves as the bacteria's only protection from the outside world. A plasma membrane (membranes are thin sheets or layers) regulates the exchange of nutrients, water, and gases that nourish the bacterial cell. DNA, usually in the form of a single hoop-shaped piece (segments of DNA like this one are called chromosomes), floats around inside the cell. The liquid interior of the cell is called the cytoplasm. The cytoplasm provides a cushiony, watery home for the DNA and other cell machinery that carries out the business of living. Prokaryotes divide, and thus reproduce, by simple mitosis. Eukaryotes: Cells with a nucleus Organisms that have cells with nuclei are classified as eukaryotes (meaning "true nucleus"). Eukaryotes range in complexity from simple one-celled animals and plants all the way to complex multicellular organisms like you. Eukaryotic cells are fairly complicated and have numerous parts to keep track of. Like prokaryotes, eukaryotic cells are held together by a plasma membrane, and sometimes a cell wall surrounds the membrane (plants, for example have cell walls). But that's where the similarities end. The most important feature of the eukaryotic cell is the nucleus — the membrane-surrounded compartment that houses the DNA that's divided into one or more chromosomes. The nucleus protects the DNA from damage during day-to-day living. Eukaryotic chromosomes are usually long, string-like segments of DNA instead of the hoop-shaped ones found in prokaryotes. Another hallmark of eukaryotes is the way the DNA is packaged: Eukaryotes usually have much larger amounts of DNA than prokaryotes, so to fit all that DNA into the tiny cell nucleus, it must be tightly wound around special proteins. Unlike prokaryotes, eukaryotes have all sorts of cell parts, called organelles, that help carry out the business of living. The organelles are found floating around in the watery cytoplasm outside the nucleus. Two of the most important organelles are the following: Mitochondria: The powerhouses of the eukaryotic cell, mitochondria pump out energy by converting glucose to ATP (adenosine triphosphate). ATP acts like a battery of sorts, storing energy until it's needed for day-to-day living. Both animals and plants have mitochondria. Chloroplasts: These organelles are unique to plants. They process the energy of sunlight into sugars that then are used by plant mitochondria to generate the energy that nourishes the living cells. Eukaryotic cells are able to carry out behaviors that prokaryotes can't. For example, one-celled eukaryotes often have appendages, such as long tails (called flagella) or hair-like projections (called cilia) that work like hundreds of tiny paddles, to help them move around. Also, only eukaryotic cells are capable of ingesting fluids and particles for nutrition; prokaryotes must transport materials through their cell walls, a process that severely limits their culinary options. In most multicellular eukaryotes, cells come in two basic varieties: body cells (called somatic cells) and sex cells (or gametes). The two cell types have very different functions and are produced in very different ways. Multicellular eukaryotes: Somatic cells Somatic cells are produced by simple cell division called mitosis. Somatic cells of multicellular organisms like you are differentiated into special cell types. Skin cells and muscle cells are both somatic cells, for instance, but if you were to examine your skin cells under a microscope and compare them with your muscle cells, you'd see their structures are very different. The various cells that make up your body all have the same basic components (membrane, organelles, and so on), but the arrangements of the elements change from one cell type to the next so that they can carry out various jobs such as digestion (intestinal cells), energy storage (fat cells), or oxygen transport to your tissues (blood cells). Multicellular eukaryotes: Sex cells (gametes) Sex cells are specialized cells that are used for reproduction. Only eukaryotic organisms engage in sexual reproduction. Sexual reproduction combines genetic material from two organisms and requires special preparation in the form of a reduction in the amount of genetic material allocated to sex cells — a process called meiosi. In humans, the two types of sex cells are eggs and sperm. 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