Category Archives: Genetics

Genetics

DNA Markers Uncovered in Grape Genetics Research Reveal What Makes the Perfect Flower – SciTechDaily

Flower sex is an important factor when breeding for quality cultivars.

Wines and table grapes exist thanks to a genetic exchange so rare that its only happened twice in nature in the last 6 million years. And since the domestication of the grapevine 8,000 years ago, breeding has continued to be a gamble.

When todays growers cultivate new varieties trying to produce better-tasting and more disease-resistant grapes it takes two to four years for breeders to learn whether they have the genetic ingredients for the perfect flower.

Females set fruit, but produce sterile pollen. Males have stamens for pollen, but lack fruit. The perfect flower, however, carries both sex genes and can self-pollinate. These hermaphroditic varieties generally yield bigger and better-tasting berry clusters, and theyre the ones researchers use for additional cross-breeding.

Now, Cornell scientists have worked with the University of California, Davis, to identify the DNA markers that determine grape flower sex. In the process, they also pinpointed the genetic origins of the perfect flower. Their paper, Multiple Independent Recombinations Led to Hermaphroditism in Grapevine, published on April 13, 2021, in the Proceedings of the National Academy of Science.

This is the first genomic evidence that grapevine flower sex has multiple independent origins, said Jason Londo, corresponding author on the paper and a research geneticist in the USDA-Agricultural Research Service (USDA-ARS) Grape Genetics Unit, located at Cornell AgriTech. Londo is also an adjunct associate professor of horticulture in the School of Integrative Plant Science (SIPS), part of the College of Agriculture and Life Sciences.

This study is important to breeding and production because we designed genetic markers to tell you what exact flower sex signature every vine has, Londo said, so breeders can choose to keep only the combinations they want for the future.

Today, most cultivated grapevines are hermaphroditic, whereas all wild members of the Vitis genus have only male or female flowers. As breeders try to incorporate disease-resistance genes from wild species into new breeding lines, the ability to screen seedlings for flower sex has become increasingly important. And since grape sex cant be determined from seeds alone, breeders spend a lot of time and resources raising vines, only to discard them several years down the line upon learning theyre single-sex varieties.

In the study, the team examined the DNA sequences of hundreds of wild and domesticated grapevine genomes to identify the unique sex-determining regions for male, female and hermaphroditic species. They traced the existing hermaphroditic DNA back to two separate recombination events, occurring somewhere between 6 million and 8,000 years ago.

Londo theorizes that ancient viticulturists stumbled upon these high-yielding vines and collected seeds or cuttings for their own needs freezing the hermaphroditic flower trait in domesticated grapevines that are used today.

Many wine grapes can be traced back to either the first or second event gene pool. Cultivars such as cabernet franc, cabernet sauvignon, merlot, and Thompson seedless are all from the first gene pool. The pinot family, sauvignon blanc, and gamay noir originate from the second gene pool.

What makes chardonnay and riesling unique is that they carry genes from both events. Londo said this indicates that ancient viticulturalists crossed grapes between the two gene pools, which created some of todays most important cultivars.

Documenting the genetic markers for identifying male, female and perfect flower types will ultimately help speed cultivar development and reduce the costs of breeding programs.

The more grape DNA markers are identified, the more breeders can advance the wine and grape industry, said Bruce Reisch, co-author and professor in both the Horticulture and the Plant Breeding and Genetics sections of SIPS. Modern genetic sequencing technologies and multi-institutional research collaborations are key to making better grapes available to growers.

Reference: Multiple independent recombinations led to hermaphroditism in grapevine by Cheng Zou, Mlanie Massonnet, Andrea Minio, Sagar Patel, Victor Llaca, Avinash Karn, Fred Gouker, Lance Cadle-Davidson, Bruce Reisch, Anne Fennell, Dario Cantu, Qi Sun and Jason P. Londo, 9 April 2021, Proceedings of the National Academy of Sciences.DOI: 10.1073/pnas.2023548118

Funding for this study was provided by a Specialty Crop Research Initiative Competitive Grant from the USDA National Institute of Food and Agriculture.

Co-authors on the paper also include Cheng Zou and Qi Sun at the Cornell Institute of Biotechnology; Melnie Massonnet, Andrea Minio and Dario Cantu at UC Davis; Lance Cadle-Davidson at the USDA-ARS Grape Genetics Unit; Victor Llaca at Corteva Agriscience; Avinash Karn and Fred Gouker in the Horticulture Section of SIPS; and Sagar Patel and Anne Fennell of South Dakota State University.

Erin Rodger is the senior manager of marketing and communications for Cornell AgriTech.

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DNA Markers Uncovered in Grape Genetics Research Reveal What Makes the Perfect Flower - SciTechDaily

Genetics

Research on Bizarre Rodent Genetics Solves a Mystery And Then Things Got Even Stranger – SciTechDaily

A Taiwan vole, closely related to the creeping vole described in the study. Credit: Lai Wagtail / Flickr (CC BY-NC-ND 2.0)

Open up Scott Roys Twitter bio and youll see a simple but revealing sentence: The more I learn the more Im confused. Now the rest of the scientific world can share in his confusion. The San Francisco State University associate professor of Biologys most recent research, published earlier this month in one of the scientific worlds most prestigious journals, catalogues a strange and confounding system of genes in a tiny rodent that scientists have ignored for decades.

This is basically the weirdest sex chromosome system known to science, Roy said. Nobody ordered this. But hes serving it anyway.

The owner of those chromosomes is the creeping vole, a burrowing rodent native to the Pacific Northwest. Scientists have known since the 60s that the species had some odd genes: Their number of X and Y chromosomes (bundles of DNA that play a large role in determining sex) is off from whats expected in male and female mammals.

That finding caught Roys eye when presented by a guest speaker at a San Francisco State seminar, and he realized that modern technology might be able to shed new light on the mysteries hiding in the voles DNA. After working with collaborators to disentangle the voles genetic history resulting in one of the most completely sequenced mammal genomes that exists, according to Roy the story only got stranger.

The team found that the X and Y chromosomes had fused somewhere in the rodents past, and that the X chromosome in males started looking and acting like a Y chromosome. The numbers of X chromosomes in male and female voles changed too, along with smaller pieces of DNA getting swapped between them. The researchers published their results in Science on May 7, 2021.

Drastic genetic changes like these are exceptionally rare: The way genes determine sex in mammals has stayed mostly the same for about 180 million years, Roy explains. Mammals, with few exceptions, are kind of boring, he said. Previously we would have thought something like this is impossible.

So how did the genes of this unassuming rodent end up so jumbled? Its not an easy question to answer, especially since evolution is bound to produce some strangeness simply by chance. Roy, however, is determined to figure out the why. He suspects that what the team found in the voles genome is something like the aftermath of an evolutionary battle for dominance between the X and Y chromosome.

The research couldnt have happened, Roy says, without collaborations with Oregon fish and wildlife biologists who had a creeping vole sample sitting in a lab freezer. He also teamed up with a group from Oklahoma State University when the two groups started chatting about creeping vole DNA sequences that were posted on the internet and both realized they were working on the same question.

Another key was working at a teaching-focused institution. Roy says he has the time to develop ideas with colleagues and students at SF State, and he can do research where he doesnt quite know what hell find. This is a great example of non-hypothesis-based biology, Roy explained. The hypothesis was, This system is interesting. I bet if you looked into it some more, thered be other interesting things.

It wont be the last time Roys lab goes out on a limb. He and his collaborators plan to look into the genomes of other species related to the voles to chart the evolutionary path that led to this strange system. Hell also continue DNA sequencing curiosities across the tree of life.

These bizarre systems give us a handhold to start to understand why the more common systems are the way they are and why our biology works as it does, he explained. By delving into the weirdest that nature has to offer, maybe we can come to understand ourselves better, too.

Reference: Sex chromosome transformation and the origin of a male-specific X chromosome in the creeping vole by Matthew B. Couger, Scott W. Roy, Noelle Anderson, Landen Gozashti, Stacy Pirro, Lindsay S. Millward, Michelle Kim, Duncan Kilburn, Kelvin J. Liu, Todd M. Wilson, Clinton W. Epps, Laurie Dizney, Luis A. Ruedas and Polly Campbell, 7 May 2021, Science.DOI: 10.1126/science.abg7019

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Research on Bizarre Rodent Genetics Solves a Mystery And Then Things Got Even Stranger - SciTechDaily

Genetics

New peanut has a wild past and domesticated present – Johnson City Press (subscription)

ATHENS The wild relatives of modern peanut plants have the ability to withstand disease in ways that modern peanut plants cant. The genetic diversity of these wild relatives means that they can shrug off the diseases that kill farmers peanut crops, but they also produce tiny nuts that are difficult to harvest because they burrow deep in the soil.

Consider it a genetic trade-off during its evolution, the modern peanut lost its genetic diversity and much of the ability to fight off fungus and viruses, but gained qualities that make peanuts so affordable, sustainable and tasty that people all over the world grow and eat them.

Modern peanut plants were created 5,000 to 10,000 years ago, when two diploid ancestors plants with two sets of chromosomes came together by chance, and became tetraploids plants with four sets of chromosomes. While domesticated peanuts traveled around the world and show up in cuisine from Asia to Africa to the Americas, their wild relatives stayed close to home in South America.

Over the past several years, researchers at the University of Georgia, particularly at the Wild Peanut Lab in Athens, have been homing in on the genetics of those wild relatives and detailing where those resiliency traits lie in their genomes. The goal has always been to understand wild peanut varieties well enough to make use of the advantageous ancient genes the ones the wild relatives have, but modern peanuts lost while holding onto the modern traits that farmers need and consumers want.

Most of the wild species still grow in South America, said Soraya Leal-Bertioli, who runs the Wild Peanut Lab with her husband, David Bertioli. They are present in many places, but you dont just come across them on the streets. One has to have the collectors eye to spot them in the undergrowth.

Those wild plants cant breed with other peanuts in nature any longer because they have only two sets of chromosomes.

The wilds are ugly distant relatives that peanut does not want to mix with, Leal-Bertioli said, but we do the match making.

Researchers in Athens and Tifton have successfully crossed some of those wild species together to create tetraploid lines that can be bred with peanuts. Those new lines will give plant breeders genetic resources that will lead to a bumper crop of new varieties with disease resistance and increased sustainability. The newly released lines wont produce the peanuts that go into your PB&J tomorrow, but they are the parents of the plants that farmers will grow in coming years.

The Journal of Plant Registrations published the details about the first of these germplasm lines this month. The lines were created by a team led by the Bertiolis, who conduct peanut research through the College of Agricultural and Environmental Sciences Institute for Plant Breeding, Genetics and Genomics. They also manage separate global research projects for the Feed the Future Innovation Lab for Peanut, a U.S. Agency for International Development project to increase the global food supply by improving peanuts.

The new lines developed by the Bertiolis are resistant to early and late leaf spot, diseases that cost Georgia peanut producers $20 million a year, and root-knot nematode, a problem that few approved chemicals can fight. Called GA-BatSten1 and GA-MagSten1, they are induced allotetraploids, meaning they are made through a complex hybridization that converts the wild diploid species into tetraploids.

The second set of new varieties comes from work done in Tifton and led by Ye Juliet Chu, a researchers in Peggy Ozias-Akins lab within the CAES Department of Horticulture. These three varieties are made from five peanut relatives and show resistance to leaf spot. One is also resistant to tomato spotted wilt virus, a disease that almost wiped out peanut cultivation in the U.S. in the 1990s.

Creating the first fertile allotetraploids is a challenge, but then scientists can cross them with peanuts and, through generations, select for the right traits. Plant breeders will be able to take these lines made from peanuts wild relatives and cross them with modern domesticated peanuts to get the best of both a plant that looks like peanuts and produces nuts with the size and taste of modern varieties, but that has the disease-fighting ability of the wild species.

In Tifton, for example, the team has crossed the wild species with cultivated peanuts to get a line thats 25% wild and 75% cultivated. Randomly breeding the two together will create some plants with small seeds, weak pegs, sprawling growth pattern and low yield, but by using genetic mapping, breeders can find the plants that carry disease-fighting genes and also have attractive market traits.

We plan to perform genetic mapping with these materials and define the beneficial wild genomic regions for molecular breeding, Chu said. We still need to define the genomic regions in the synthetic allotetraploids conferring desirable traits and specifically integrate those regions into cultivated peanuts.

While plant breeders have known the value of the diversity in wild peanut species for decades, they couldnt keep track of those valuable wild genes until recently. The peanut industry in Georgia and other states has invested in work to sequence peanuts and the two ancestor species, knowing that the work to understand the peanut genome would pay off. With genetic markers developed using the genome, breeders not only can tell that a plant has a desirable trait, they know what genome regions are responsible for that trait and can combine DNA profiling with traditional field selection to speed the complex process of developing a new variety.

It streamlines everything, David Bertioli said. You can make a cross, which produces 1,000 seeds, but before planting them, their DNA can be profiled. That way you can see that only 20 of those plants are ideal for further breeding. Forty years ago, youd have to plant them all, making the process much more cumbersome.

Marker-assisted selection for peanut breeding has been implemented in Ozias-Akins lab in Tifton for the past decade. Applying genetic markers associated with resistance from wild peanuts using this selection platform will accelerate the deliverance of peanut varieties pyramided with superior agronomic performance and strong disease resistance.

With ongoing work, the Journal of Plant Registration will document the release of other peanut germplasm with resistance to important diseases. Releasing the lines, along with the molecular markers for their advantageous traits, provides the peanut-breeding community with genetic resources to produce more resilient crops.

In the past, we knew where we were going, but it was like everyone drew their own map, David Bertioli said. Now, its like we have GPS. (Scientists) can tell each other, Here are my coordinates. What are yours? And all the data is published.

Breeders can access the seeds of the wild species crosses through the USDA-ARS National Plant Germplasm System in Fort Collins, Col., or in the U.S. Department of Agricultures Plant Genetic Resources and Conservation Unit in Griffin.

For more information about peanut research being performed at UGA, visit peanuts.caes.uga.edu.

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New peanut has a wild past and domesticated present - Johnson City Press (subscription)

Genetics

Variety is the spice of life… and key to saving wildlife – Pursuit

In the critical battle against extinction, conservationists use a variety of tactics to try to save species.

One of the most fundamental tools is maintaining the amount of variation of genetic material (DNA) in a group of animals - this is described as their genetic diversity. In general, the greater the genetic diversity, the higher chance of long-term survival.

This technique works because a wider range of genes and gene variants is more likely to enable a species to adapt to unexpected conditions, including new diseases and warmer climates.

Just like having a small pack of playing cards, if we dont have many to choose from, our options are limited.

The Tasmanian Devil has faced this issue, persisting as populations that have in the past been small, with reducing genetic diversity.

This limited genetic variation has meant the Devils immune system has reduced genetic options to adapt and fight off the contagious cancer known as the Devil Facial Tumour Disease.

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The field of conservation, genetics deals mainly with strategies to conserve or enhance genetic diversity within species populations to promote their capacity to adapt, reduce the negative effects of inbreeding and random genetic drift, and ultimately, decrease their extinction risk.

So, from a conservation genetic perspective, a high level of genetic diversity within a species population (compared with other populations from the same species) generally reflects a healthy viable population.

A recent perspective has challenged this school of thought, arguing that the amount of genetic variation present in a population is not an important consideration for their conservation.

Because this view is not supported by the literature and ignores well-established evolutionary principles, its concerning that it may affect how conservation genetic strategies are applied in future.

Genetic variation is measured by heterozygosity which is the presence of different versions of the same gene known as alleles at a number of locations across the genome of individuals.

The process of inbreeding leads to increased sameness or homozygosity that is the same versions of a gene are the same allele through mating between related individuals.

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Deleterious alleles (versions that negatively affect health) reduce the likelihood of reproducing for an individual, and are typically expressed when homozygous.

This results in a decrease the individual and population chance of survival, known as fitness, and has been seen in the Helmeted Honeyeater.

For an accurate estimation of the health of a population from a genetic viewpoint, both the diversity and sameness of genetic makeup need to be considered.

In making their arguments, the authors of the recent perspective separate the effects of genetic variation that influences traits important for survival the so-called adaptive or functional variation from genetic variation that does not, or neutral variation.

Variation in genes that directly affect disease susceptibility or drought tolerance would be regarded as adaptive, whereas variation in genes that do not affect these traits or any other traits would be regarded as neutral.

However, its not usually possible to distinguish these types of variation, so conservation genetics typically assesses variation without reference to whether it is neutral or adaptive.

In a recent publication, we discuss the difficulty associated with identifying adaptive diversity, particularly in relation to how genomic information can be used to predict the future vulnerability of species under climate change.

Within this paper, we highlight that while genomics is providing valuable insights into processes like inbreeding, theres a need to further develop approaches based on functional genes before we can use genomics to predict how species may genetically evolve to deal with future climate change.

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Increasingly, variation in conservation genetics is now being characterised based on DNA sequence variation thats scattered throughout the thousands of nucleotides that make up an organisms genome - so-called single nucleotide polymorphism or SNP markers.

This variation is regarded as a reasonable approximation of adaptive potential, particularly as adaptation involving traits like growth ability, stress tolerance and even disease tolerance are also scattered throughout the genome.

Any sign of variation in the genome is taken as a signal of variation more generally.

Research shows that when flies, birds and other organisms adapt to new environments, hundreds or even thousands of genes throughout the genome can be part of the adaptation process and that these are often inconsistent between evolutionary events, making it hard to identify specific genes involved in adaptation.

There is plenty of evidence that overall levels of genetic variation, regardless of whether its adaptive or neutral, affects the rate of adaptation of populations and high levels reduce the probability of populations becoming extinct.

The best studies come from careful laboratory experiments where a large number of populations derived from the same source, but differing in genetic variation, are compared.

Results from these experiments show that larger and genetically diverse populations have much lower extinction rates in experimental systems like flies and crustaceans.

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Under field conditions, theres also a lot of evidence that an injection of new genetic variants boosts the fitness of threatened species. This includes the genetic rescue strategy used successfully to prevent the extinction of the Mount Buller Mountain Pygmy-possum in Victoria.

The initial recovery of genetic health in these populations is partly associated with decreasing inbreeding but, in the longer term, the increase in genetic variation will be important for adaptation.

But these genetic strategies cannot succeed, without addressing threats like habitat destruction and invasive predators both of which went hand-in-hand with the genetic rescue of the Mountain Pygmy-possum.

There is no doubt that many species lacking genetic variation can still be highly successful. This includes many weedy species of animals and plants that do not have much genetic variation including pest species that reproduce clonally like many aphids.

There are also some highly invasive species in Australia that have limited diversity, including foxes, carp, and deer and more. But these species can often reproduce quickly, are freed from natural predators and competitors, and are often generalists, resulting in the quick expansion of populations and range in non-native environments.

Conservation genetics does not focus on such comparisons between species instead, it tends to focus on native species of conservation concern where the relative fitness of populations is linked directly to their relative levels of genetic variation.

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As we head into an uncertain world, it is important to ensure that threatened species have the best chance of surviving changes to their environment.

There are different ways of boosting genetic variation in populations that have become genetically vulnerable, including the deliberate introduction of individuals from other populations and the re-establishment of habitat corridors.

All of these efforts should coincide with restoration programs that help conservation-dependent species maintain large population sizes, which will in turn enable the maintenance of high levels of genetic diversity, increasing resilience and adaptive capacity.

These are key principles that must be followed given that adaptive changes to environmental stressors remain unpredictable at the genetic level, are complex involving many genes and are likely to depend on biological as well as environmental factors.

When it comes to conservation efforts in the immediate future, assessing genetic variation across a species entire genome must be pivotal in our decision making.

Banner: Mountain Pygmy Possum/ Andrew Weeks

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Variety is the spice of life... and key to saving wildlife - Pursuit

Genetics

Geisinger contracted to study links between genetic variations and cancer – NorthcentralPa.com

Danville, Pa. - Researchers from Geisinger have received a five-year, $3.6 million contract to study the role of genetic variation in cancer from the National Cancer Institute (NCI).

Geisinger will work together with NCI's Division of Cancer Epidemiology and Genetics (DCEG) to analyze data from Geisinger's MyCode Community Health Initiative, a project with over 276,000 voluntary participants.

The work will be led by David J. Carey, Ph.D., professor and chair of the Department of Molecular and Functional Genomics at Geisinger and a MyCode principal investigator, and Douglas Stewart, M.D., a senior investigator at DCEG.

The investigative team will use a genome-first approach, analyzing data from MyCode participants to identify specific gene variants and then linking that information to the participants electronic health records.

This approach will allow investigators to determine the effect of these gene variants on cancer risk.

The size and scope of the MyCode project provides an opportunity to investigate the relationship between multiple genes and cancers to develop a better understanding of genetic cancer risk in a large clinical population, expanding the list of relevant genes to investigate during genetic cancer screenings.

The project builds on a history of successful collaboration between Drs. Carey and Stewart in investigating the role of gene variants in specific cancers, including a recent study of DICER1 syndrome, which is linked to lung, thyroid, and other kinds of tumors, published in JAMA Network Open.

This partnership allows Geisinger and NCI investigators to combine our expertise in cancer diagnosis, epidemiology, cancer biology, and genetics, Dr. Carey said.

The data available through MyCode provides us with a unique opportunity to investigate the genetic risk of cancer in a large regional population," Dr. Carey continued.

Since 2007, MyCode has enrolled more than 276,000 participants in Pennsylvania. With DNA sequence and health data currently available on nearly 175,000 of these participants, MyCode is one of the largest studies of its kind in the world.

The project is funded with federal funding from the National Cancer Institute, National Institutes of Health, and Department of Health and Human Services.

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Geisinger contracted to study links between genetic variations and cancer - NorthcentralPa.com

Genetics

Genetics of the fetus and placenta control developmental abnormalities – BioNews

10 May 2021

Developmental abnormalities, including those leading to miscarriage and autism, are primarily controlled by the genetics of the fetus and placenta.

Abnormalities of the placental trophoblast bilayer the primary barrier between maternal and fetal tissues are known as trophoblast inclusions. These abnormalities are linked with aneuploidy and miscarriage. However, it has not been known whether they occur due to the mother's uterine environment or the genetics of the fetus.

'Mothers often feel that they are responsible for these defects. But it's not their fault,' said Dr Harvey Kliman, senior author and researcher at Yale School of Medicine, Connecticut. 'This new research points to the genetics of these children as being the most important cause.'

In a study publishedin Placenta, the scientists examined placental data from 48 sets of identical and non-identical twins. They discovered that trophoblast inclusions were present with similar frequency in identical twins, yet non-identical twins showed a significantly different number of trophoblast inclusions.

Identical twins share the same DNA sequence, whereas non-identical twins share an average of half of their DNA sequence the same as non-twin siblings.

As a non-identical twin, lead author Julia Katz, a former Yale undergraduate who is now a medical student at Hofstra University, New York, included her own placental slides from birth in the study.

Katz's twin brother was born underweight and with several congenital abnormalities, 'I had a lot of guilt, growing up, about why my twin had certain conditions that I didn't,' Katz explained. 'I think mothers also tend to blame themselves.'

The authors concluded that developmental abnormalities are influenced by the genetic makeup of the fetus and that the resulting trophoblast inclusions can serve as a marker of genetic abnormality.

'This work suggests that developmental abnormalities are much more likely to be due to the genetics of the child, and not the mother's fault,' Dr Kliman concluded.

According to the Centres for Disease Control and Prevention, birth defects affect one in every 33 babies born in the USA each year and are the leading cause of infant deaths, accounting for 20 percent of all infant deaths.

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Genetics of the fetus and placenta control developmental abnormalities - BioNews

Genetics

COVID-19 one year into the pandemic: from genetics and genomics to therapy, vaccination, and policy – DocWire News

This article was originally published here

Hum Genomics. 2021 May 10;15(1):27. doi: 10.1186/s40246-021-00326-3.

ABSTRACT

COVID-19 has engulfed the world and it will accompany us all for some time to come. Here, we review the current state at the milestone of 1 year into the pandemic, as declared by the WHO (World Health Organization). We review several aspects of the on-going pandemic, focusing first on two major topics: viral variants and the human genetic susceptibility to disease severity. We then consider recent and exciting new developments in therapeutics, such as monoclonal antibodies, and in prevention strategies, such as vaccines. We also briefly discuss how advances in basic science and in biotechnology, under the threat of a worldwide emergency, have accelerated to an unprecedented degree of the transition from the laboratory to clinical applications. While every day we acquire more and more tools to deal with the on-going pandemic, we are aware that the path will be arduous and it will require all of us being community-minded. In this respect, we lament past delays in timely full investigations, and we call for bypassing local politics in the interest of humankind on all continents.

PMID:33966626 | DOI:10.1186/s40246-021-00326-3

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COVID-19 one year into the pandemic: from genetics and genomics to therapy, vaccination, and policy - DocWire News

Genetics

The Genetics of Asthma – News-Medical.net

Asthma is a chronic condition characterized by lung airway inflammation that is caused by both genetic and environmental factors.

Asthma is a chronic inflammatory condition affecting the airways of the lungs that is caused by increased airway responsiveness and reversible airway obstruction. This leads to symptoms of chest tightness, wheezing, coughing, and shortness of breath.

When these symptoms occur (usually suddenly), it is known as an asthma attack. Reliever inhalers (normally blue) can be used as effective and quick emergency treatments to combat asthma attacks. However, if emergency inhalers are not available, or medical attention is not immediately sought, asthma attacks can be life-threatening and 3 people die every day in the UK due to untreated asthma attacks.

The worldwide prevalence of asthma has been increasing and continues to rise across the world. More specifically, asthma rates in urban areas are increasing more than in rural areas. Many of the causes of asthma may be attributed to environmental factors such as smoking, air pollution, climate change, but also increasing evidence points towards specific genetic factors that may directly cause asthma in families or predispose individuals to later-onset asthma especially in combination with environmental factors.

Image Credit: Lightspring/Shutterstock.com

Almost half of all people affected by asthma have a genetic susceptibility either inherited genetic mutations or single nucleotide polymorphisms (SNPs) which increase the risk of developing asthma especially in combination with certain environmental factors.

For example, people with no family history of asthma have a 5% risk of developing asthma. Having a sibling or a parent with asthma increases this risk to 25%, having both parents with asthma increases this risk to 50%, and having a monozygotic twin increases the risk to 75%. This clearly illustrates a strong genetic basis for asthma risk. The latter also highlights that asthma is not a purely genetic disease and the environment plays an important role in determining asthma risk too (otherwise the risk would be 100% with a monozygotic twin).

Where genes play a strong role as compared to the environment would be primarily in early-onset asthma. Having a family history of asthma usually results in earlier onset disease thus genes may be implicated in the age at onset of disease. Furthermore, the severity of the disease may also be uniform in families e.g., more severe asthmatic parent leading to a severely asthmatic child. Specific genes may increase the risk of allergic asthma (most common) whereas others are involved in non-allergic asthma (rarer but tends to be more severe and usually occurs later in life).

Most genes implicated in asthma are related to inflammation/modulation of the immune system, or to do with lung physiology. To date, over 100 such genes have been identified with more being identified each year. These genes include specific cytokines (inflammation/immunity), Toll-like receptors, major histocompatibility complexes (MHC), receptors, cysteine leukotriene metabolic pathway, airway hyperresponsiveness, lung function as well as some other genes.

Specific genes commonly implicated in asthma include:

Many of these genes are involved in inflammation, immunity, and lung function. Mutations or polymorphisms to any of these genes compromise their normal function thus leading to dysregulated immune/inflammatory responses (i.e., exaggerated response), or remodeling of the airways decreasing lung function, or increasing hyperresponsiveness.

Collectively they contribute either to causing earlier-onset asthma, or predisposing adults to developing asthma later in life in combination with certain environmental factors (such as smoking, air pollution, dust mites, or pollen) or combination with other conditions such as dermatitis.

In summary, asthma is a complex multifactorial condition that has many causes both environmental and genetic. Having a family history of asthma increases the risk of asthma thus suggesting a strong genetic basis. Certain genes may only predispose individuals to asthma (later-onset/environmentally triggered), however, other genes may be directly causative of asthma particularly early-onset or that which is more severe (typically running in families). Knowing what genes cause asthma or increase the risk of asthma is important in the development of novel therapies and treatments.

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The Genetics of Asthma - News-Medical.net

Genetics

The Science of Aliens, Part 2: What Kind of Genetic Code Would Extraterrestrials Have? – Air & Space Magazine

All cellular life on Earth is based on DNA, which transfers informationabout everything from hair color to personality traitsfrom one generation to the next. The four chemical bases that convey this information are adenine (A), cytosine (C), guanine (G), and thymine (T).

The other essential information molecule on Earth is RNA, in which thymine (T) is replaced by uracil (U). RNA has a one-string structure rather than a double-string structure like DNA. The first cellular life on our planet is thought to have relied exclusively on this means of transferring genetic informationin the so-called RNA worldand even today there are viruses (like the one that causes COVID) that only use RNA.

In a paper recently published in Science, a research group led by Dona Sleiman from the Institute Pasteur in Paris has discovered that some viruses show more variation in their genetic coding than was previously known. In the RNA of these viruses, adenine (A) is replaced with Z, where Z stands for diaminopurine.

This follows an earlier study by Zunyi Yang and colleagues at the Foundation for Applied Molecular Evolution in Gainesville, Florida, showing that an artificial genetic system could be created by adding two additional non-standard bases to ordinary DNA. Amazingly, the artificial six-base system continued to evolve rather than reverting back to the natural four-base system. This implies that the DNA we take as standardmade of A, C, G, and Tis just one of many viable solutions to the challenge of biological information transfer.

The variability does not stop here. Strings of DNA are organized in base triplets that determine which of the standard 20 amino acids are assigned to synthesize proteins. However, these triplet assignments are not universal. For example, CUG, which usually codes for the amino acid serine, instead codes for the amino acid leucine in some types of fungi. Also, some organisms naturally encode for two additional amino acids instead of the standard 20 amino acids.

What does this brief excursion into genetics have to do with alien life? While it is believed that all life on our planet derives from one common ancestor, the genetic code is much more flexible and diverse than usually appreciated. The biochemistry of information transfer in an alien species would almost certainly use different building blocks and encodings, and perhaps even a different number of bases. Our genetic code is surely highly optimized for life on Earth, but I feel certain that there are many optimal solutionsperhaps some that are even betterfor transferring information chemically from one generation to the next.

We, of course, cannot say what type of genetic code an alien species would use. But given that it would most likely be biochemically different, it would mostly likely be easily distinguishable from life on Earth. It may even be more different than we expect. A fascinating out-of-the-box genetic system has been suggested by Gerald Feinberg and Robert Shapiro, based on magnetic orientations rather than chemistry. They showed how magnetized particles, when approaching a magnetic chain, will align with the chain. As a result, the chain is duplicated, and this method could in principle be used to convey information in a binary code.

So, while alien life may well transmit genetic information using structures similar to RNA and DNA, we should always be prepared to expect the unexpected.

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Excerpt from:
The Science of Aliens, Part 2: What Kind of Genetic Code Would Extraterrestrials Have? - Air & Space Magazine

Genetics

Genes and metastatic breast cancer: What role do they play? – Medical News Today

Metastatic breast cancer (MBC) refers to breast cancer that has spread beyond the breasts and nearby lymph nodes to other organs in the body. MBC is also known as advanced or stage 4 cancer.

MBC can develop after an initial diagnosis of earlier stage breast cancer. It is also possible for MBC to be a persons first diagnosis.

There is currently no cure for MBC, but there are many treatment options available that can slow the cancers growth.

This article explores the role that genes play in the development of MBC and how genetic testing is leading researchers to newer targeted treatments.

Mutations in genes can affect a persons susceptibility to breast cancer. Specifically, two categories of mutations germline mutations and somatic mutations may increase an individuals risk of developing breast cancer.

Germline mutations are present in every cell of the body. These mutations run in families, and a person may inherit them from a parent. About 510% of breast cancer cases develop because a person has a hereditary predisposition to breast cancer.

On the other hand, somatic mutations are changes that develop after birth. These changes occur in a single cell and in any cells that derive from that single cell if it divides. A person cannot inherit somatic mutations.

Some specific germline and somatic gene mutations may increase a persons risk of developing breast cancer that progresses to MBC.

We know about several germline mutations, like BRCA1 and BRCA2, that increase our risk [of] cancer. Often, the cancers that these mutations cause are more aggressive, so are at higher risk of metastasizing, explained Dr. Natasha B. Hunter, a board certified oncologist at Seattle Cancer Care Alliance in Washington.

We also know that tumors develop somatic mutations, some of which can increase their ability to evade immune detection or make them resistant to therapies, Dr. Hunter added.

Genetic testing does not yet play a role in the diagnosis or detection of MBC.

A doctor diagnoses MBC the same way they do other stages of breast cancer with laboratory tests, imaging tests, and biopsies.

However, research is ongoing into how genetic testing can help oncologists catch breast cancer just as it starts to spread beyond the affected breast.

We dont use genetic testing for the diagnosis or detection of MBC currently, said Dr. Hunter, but we hope that at some point we may be able to use highly sensitive detection methods that use DNA or other substances in the blood to detect early metastatic disease so that we could intervene and treat before the development of incurable MBC.

Genetic testing is useful for determining a persons risk of developing breast cancer in the first place.

There are strict criteria set forth by the National Comprehensive Cancer Network (NCCN) for breast cancer genetic testing, and they are generally the criteria the insurance companies use to establish testing guidelines, explained Dr. Susan Klugman.

Dr. Klugman is the director of reproductive and medical genetics with the Montefiore Health System and a professor at the Albert Einstein College of Medicine, both in New York City, NY.

The NCCN indicates genetic testing when a person:

The NCCN also states that doctors may consider genetic testing when a person has had multiple primary breast cancers and first received a diagnosis between the ages of 50 and 65 years.

They may also consider genetic testing when a person does not meet any of the other criteria but has a 2.5% to 5% chance of having a BRCA1 or BRCA2 cancer-causing gene mutation based on probability models.

[Individuals] found to have mutations or changes in certain genes pathogenic variants can opt for surveillance and medical therapy or prophylactic surgery prior to the onset of cancer, Dr. Klugman told Medical News Today.

The results of genetic testing can be valuable to family members as well.

Relatives who are of reproductive age [who] are planning to have a family, and have a genetic mutation, could consider preimplantation genetic testing after in vitro fertilization to avoid passing down the genetic mutation to offspring, Dr. Klugman added.

Standard treatments for MBC are drug therapies such as chemotherapy, immunotherapy, hormone therapy, and targeted drugs. Sometimes, doctors use a combination of these therapies. In other situations, a person may need to undergo surgery or radiation therapy.

The results of genetic testing influence treatment plans for MBC. Certain mutations make a person eligible to receive particular therapies. The detection of genetic mutations can help doctors design more tailored and effective treatment plans.

The tumors of patients with germline BRCA mutations can be particularly responsive to PARP inhibitors, which take advantage of the DNA repair issues that the BRCA mutation causes, said Dr. Hunter.

Patients with certain mutations in the tumor itself (somatic mutations) can also receive targeted therapies. For instance, patients whose tumors harbor PIK3CA mutations can receive a medication called alpelisib, Dr. Hunter added.

Genetic testing results can also qualify individuals for clinical trials in which they can access newer treatment options that they would not typically have access to in traditional clinical settings.

Current treatments for MBC can help slow the growth of tumors, improve symptoms, and extend survival, but the condition remains incurable. However, ongoing research into genetics may hold the key to a brighter outlook.

I think we are only seeing the tip of the iceberg in terms of our understanding of genetics, gene expression, and other molecular-level interactions in breast cancer, Dr. Hunter told MNT.

Right now, added Dr. Hunter, I think were seeing the most potential in continuous monitoring to detect early metastatic disease so that we could intervene and treat before the development of incurable MBC holding the potential for cure with early detection. But I think theres much more thats exciting on the horizon.

Original post:
Genes and metastatic breast cancer: What role do they play? - Medical News Today