StemCell Therapy

Question: Which genetic syndromes increase the risk of breast cancer?

Many risk factors for breast cancer have been identified, including genetic, environmental, and lifestyle factors. Some are modifiable and others are not. A family history of breast cancer in a first-degree relative is the most widely recognized breast cancer risk factor, but only 5-10% of women diagnosed with breast cancer have a known genetic predisposition. Women with a family history of breast cancer in a mother or sister have a 1.5-3 fold increase in the risk of developing breast cancer.

Multi-panel genetic testing for hereditary breast cancer syndromes is currently not standard for all women diagnosed with breast cancers due to insufficient data regarding interpretation accuracy and its utility. For now, BRCA1/2 testing accounts for half of the detected genetic breast mutations and is recommended in a women with: Personal history of breast cancer diagnosed before the age of 50, multiple female relatives with breast cancer on same side of the family or family history of male breast cancer, multiple breast cancers, both breast and ovarian cancer,with Ashkenazi Jewish heritage.

Those with BRCA mutation are at risk for developing breast cancer (50 to 80%) by age 70 and developing ovarian cancer (40-60%) by age 85. Since 2014, PALB2 (partner and localizer of BRCA2 gene) testing is frequently added to BRCA due to its inherent breast cancer risk of 5 to 9 times the average. Optional genetic panel testing includes PTEN, TP53, ATM, CDH1, CHEK2, NBN, NF1, STK11, and PMS2/MSH2 Lynch syndrome, also known as hereditary non-polyposis colorectal cancer, is a hereditary cancer syndrome, and is associated with multiple types of cancers, particularly colon, ovarian and endometrial/uterine, as well as breast cancers. Women with these mismatch repair genetic mutations (Lynch) may also have a 2-3 fold increase risk of breast cancer compared to the general population.

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Your Cancer Answers: Which genetic syndromes increase the risk of breast cancer? - Lompoc Record

New research published in Nature has revealed important genetic causes of the most severe forms of COVID-19 disease.

Researchers studied over 2,000 severely ill patients with COVID-19, and compared their genomes to those of healthy people from existing population studies in the UK. They found that patients were much more likely to possess variations in a small number of genes that affect anti-viral immune responses and inflammation information that suggests existing drugs could be useful treatments for severe disease.

COVID-19 has been known for almost a year now, but the variation in effects on different people remains baffling: some experience no discernible symptoms at all, others a mild or moderate illness, and some a very distinct, severe and life-threatening illness. Although certain clear risk factors have emerged for the most dangerous forms of the disease, notably older age and certain conditions such as heart disease, diabetes and severe obesity, both within and outside these groups, SARS-CoV-2 infection causes a bewildering and unpredictable range of responses.

Understanding precisely who is and is not at greater risk of dangerous forms of the disease would play a very important role in ongoing efforts to control the disease and prevent the worst effects. It would allow preventative efforts including new vaccines to be directed first towards those at greatest risk. It also offers important clues to the underlying mechanisms that drive the most severe forms of disease, and hence to potential treatments.

It has seemed likely from the beginning that genetic variation between different people accounts for some of the otherwise inexplicable variation in disease severity. It may also account for differing disease susceptibility how likely someone is to become infected; this is the case for many other infectious diseases, though it is less obvious to see and hence to study. Doctors and scientists around the world have thrown themselves into efforts to uncover the genomic factors driving severe disease.

This new paper used DNA samples from over 2,200 patients with severe COVID-19 treated in over 200 intensive care units were obtained from to major research initiatives, the GenOMICC (Genetics Of Mortality In Critical Care) and the ISARIC Coronavirus Clinical Characterisation Consortium 4C studies. Genome sequences were compared with healthy control subject genomes from the UK Biobank to identify areas of the genome where there were significant differences. Findings were checked against samples from a similar number of hospitalised cases from the COVID-19 Host Genetics Initiative.

A handful of important genes involved in severe COVID-19 were identified, of two main types. The first group were genes involved in antiviral defences; the OAS gene helps block replication and spread of the virus, whilst IFNAR2 is involved in the production of an important immune mediator, interferon, which helps to trigger immune responses to viral infections. Weak early responses to infection could help the SARS-CoV-2 virus to spread and grow in the patient.

These discoveries are in line with earlier findings that pinpointed genetic changes that impaired interferon function among severe COVID-19 patients. Whilst giving interferon to critically ill patients has not proved very effective, there is hope that early administration to people with genetic predisposition to poor interferon responses who are infected by the virus might prevent severe disease.

The second group of genes implicated in severe COVID-19 were likely to play a role in the dangerous inflammatory lung damage seen in patients in critical care. These included rare variants in the TYK2, DPP9 and CCR2 genes. TYK2 is involved in controlling immune response; a rare variant that causes excessive inflammation was common among patients. This is a positive finding, since there are already anti-inflammatory drugs that target this particular biological pathway, and could prove to be valuable new treatments. Both DPP9 and CCR2 are also involved in different aspects of inflammatory responses to infection.

The researchers expect that there are other genes that affect the risk of severe disease, and hope to uncover more of these in due course as they analyse genomes additional patients; rarer genetic changes are harder to find and require larger numbers of people in studies. They are particularly interested in additional genetic factors that might account for the increased risk of severe disease seen in certain ethnic groups.

Meanwhile, other researchers continue to employ genome sequencing of the virus itself, rather than human hosts, to aid the battle against COVID-19. The UK government recently announced an additional 12.2 million funding for the COVID-19 Genomics UK (COG-UK) Consortium to continue and expand viral genome sequencing. Combining this information with patient data helps to identify whether the virus is becoming more or less infectious, or dangerous, or amenable to new vaccines all vital information.

Tackling COVID-19 without the insights provided by genomics would be infinitely more difficult like trying to understand the virus and the disease blindfolded and would undoubtedly have hugely slowed the development of vaccines, treatments and other responses to limit the harm caused by the pandemic.

Take a look at our short animation on pandemic in the genomic era

Link:
Further genetic clues to severe COVID-19 - PHG Foundation

Humans come in a variety of heights and genetics play a key role in determining whether you will be short or tall.

Theres much more than just heredity to consider before assuming a person will automatically be the same height as their parents. Medical conditions, hormonal deficiencies, and more can all contribute to how tall you are.

Read on to learn about all of the components that contribute to a persons natural height.

Genetics are among the prominent factors that contribute to how tall youll be.

As a general rule of thumb, your height can be predicted based on how tall your parents are. If they are tall or short, then your own height is said to end up somewhere based on the average heights between your two parents.

Genes arent the sole predictor of a persons height. In some instances, a child might be much taller than their parents and other relatives. Or, perhaps, they may be much shorter.

Such key differences may be explained by other factors outside of your genes that contribute to height.

Aside from genetics, there are other factors to consider that can determine a persons height, especially during childhood and adolescence.

While eating more vegetables wont automatically make you taller, getting adequate nutrition during your growing years is critical in human development, including your height.

A diet based on whole, nutritious foods can ensure you will grow up to the height your genes might dictate. On the flip side, a poor diet could lead to a shorter stature compared to your parents.

Eating healthy isnt so simple for all families. Children of a poor socioeconomic status may be at risk of a lack of access to nutrition, along with poor access to adequate health care. This, in turn, can contribute to a shorter height.

You may notice that boys grow slower than girls at first, due to differences in puberty milestones. Overall though, adult males tend to be an average of 14 centimeters (5.5 inches) taller compared to adult females.

During puberty, hormones are essential for regulating body growth. These include thyroid hormones, human growth hormones, and sex hormones such as testosterone and estrogen.

Any abnormalities in these hormones could alter growth as well as your overall height. Children who develop hypothyroidism (low thyroid) or pituitary gland disorders may experience shorter than average height compared to their parents.

Rarely, hormonal disorders can contribute to being taller than normal. For example, gigantism is caused by too many human growth hormones produced by pituitary gland tumors.

Some conditions present at birth may dictate a persons height. For example, achondroplasia (dwarfism) is a rare bone growth disorder that runs in families.

Another congenital disorder that can cause short stature is known as Turner syndrome. This rare condition causes delays in puberty. Unlike achondroplasia, Turner syndrome doesnt run in families.

Other congenital disorders lead to a taller than normal stature. These include Marfan and Klinefelter syndromes.

Marfan syndrome is caused by connective tissue enlargements, while Klinefelter syndrome occurs when males are born with an additional copy of the X chromosome.

Overall, theres no way you can increase your height. Each person is born with genes that will help dictate how tall they become, but other factors such as inadequate nutrition or medical conditions may alter this outlook.

Hormonal conditions may be the few exceptions. If a lack of thyroid or human growth hormones is detected during childhood, then taking medications may help reverse the effects on height.

However, once you reach adulthood, taking hormonal replacements wont make you taller. At this point, your full height has already been achieved, and taking any medications or supplements wont make a difference.

Its important to focus on good nutrition during childhood, but sticking with these habits will also contribute to your overall health into adulthood and beyond regardless of your height.

Poor posture and lack of exercise can also contribute to poor stature, so correcting these items may help increase your height (or the appearance of it).

Its widely regarded that your genes will dictate how tall you become. However, there are other exceptions to this rule, including your gender, access to nutrition, and any underlying medical or congenital conditions you may have.

See a doctor if you have any concerns about your height, or if you have a child who isnt reaching their growth milestones. They can discuss nutritional issues with you, and they may help rule out the possibility of any hormonal issues.

Continue reading here:
Is Height Genetic? Why and Why Not? - Healthline

A dedicated University of WisconsinMadison clinician, educator, advocate and researcher, Renata Laxova, professor emerita of medical genetics and pediatrics, passed away recently after a brief illness. She was 89.

Laxovas lifelong interests focused on the causes of intellectual and developmental disabilities, prenatal diagnosis of genetic disorders and birth defects, cancer genetics, and above all the relationships between medical professionals and the patients and families they serve. She was especially interested in coping strategies for families in difficult situations.

Renata Laxova

Laxova obtained MD and PhD degrees from the University Medical School in Brno, in what is now the Czech Republic. Initially trained in pediatrics, she later specialized in medical genetics at University College and Guys Hospital in London. She came to the United States in 1975 and joined the UWMadison departments of Pediatrics and Medical Genetics, where she served until she retired in 2000.

A skilled educator, Laxova loved teaching and stressed the importance of making clinical care personal. Understanding that genetics could be an extremely complicated discipline, Laxova worked to build awareness and accessibility through education and experiences. She underscored the importance of the patient perspective and was one of the first on campus to invite parents and families to share with her students their experiences caring for children with genetic conditions or disabilities.

David Wargowski, a clinical geneticist in the Waisman Center Medical Genetic Clinic a clinic and program Laxova helped build says Laxova inspired him to pursue a career in genetics. He first met Laxova as a medical student at UWMadison.

I found human genetics fascinating in college and was excited to have an opportunity to learn about how it applied to the medical care of people with genetic conditions, Wargowski says.

In the mid-1980s, medical genetics was still a field which primarily addressed rare disorders that were off the radar of most physicians.I learned about many of those, but more important to my medical training was learning from Laxovas example that being a good doctor is about more than being knowledgeable. It also means being compassionate and devoted to patients.

Patient care was primary for Laxova. Her innate ability to make connections with patients and learn their story set her apart. She is remembered for asking families during clinical visits, How can we most help you? a sentiment that embodied her commitment to patient advocacy and care that also led to her work on resources and supports for families throughout the state.

Responding to concern that many genetic disorders were going unnoticed and undiagnosed, Laxova helped establish the Genetic Contact Network. Within the network, professionals throughout the state identify people in need of genetic counseling and make referrals. These efforts led to the corresponding Genetic Services Network of outreach clinics and Laxova was a driving force behind the service sites in Green Bay, La Crosse and Eau Claire, among others.

At the Waisman Center, Laxova was in charge of the medical genetics program and clinic program and all of its elements clinical, education and research long before there was a program director, says Wargowski.

In 1976, Laxova was also instrumental in establishing the masters in genetic counseling training program with founding director Joan Burns. The training program was among the first of its kind in the United States and Laxova served as its first medical director, a position she held for more than 20 years. During that time, she helped train hundreds of genetic counselors while treating patients and their families in the Waisman Medical Genetics Clinic.

Casey Reiser, director of the Genetic Counselor Training Program, was herself a student in the third class of genetic counselors. Like Wargowski, Reiser had the opportunity to work with Laxova both as a student and colleague.

She was always animated and enthusiastic when she shared her knowledge with students, says Reiser. Renata was an inspiration, a wonderful mentor, and a beloved friend. She will be missed by many.

While known for the successes of her career, Laxova is also remembered for her experiences escaping both the Holocaust and communism. Laxova twice fled her homeland of the Czech Republic (then known as Czechoslovakia). In the days leading up to World War II, she escaped from the Nazis through safe passage to Britain on the last Kindertransport, which rescued thousands of children from the Holocaust. She returned in 1946.

In the late 1960s, married to her husband Tibor, and as a young mother, doctor and researcher, she once again made her way to Britain to avoid the encroaching Russian communist regime. The couple later moved to Wisconsin, where Tibor, a veterinarian, opened a practice. She joined the faculty of UWMadison in 1975. Her lifes story is chronicled in a poignant memoir dedicated to her grandson titled Letter to Alexander.

Wargowski describes the sentiment felt by many who knew and worked with Laxova.

If you didnt know her, Im sorry you didnt have that chance, he says. She was a remarkably gracious person with an amazing life story. She was absolutely devoted to her patients, her craft and her colleagues, especially those who asked for the opportunity to learn from her. She was a remarkably compassionate person and physician who taught more than genetics. She practiced a love for her patients to which most of us can only aspire, and an intolerance of disparity and discrimination that challenges the most motivated among us.

University Archives has two oral interviews with Renata Laxova from 2004 and 2008. You can access them here: https://search.library.wisc.edu/digital/AMGNC3S2LPJZPN83

More:
Holocaust survivor, geneticist, patient advocate remembered for inspiring others - University of Wisconsin-Madison

The US Food and Drug Administration granted approval yesterday (December 14) for a genetically modified line of pigs that marks the first time a GM animal has been given the regulatory greenlight for both therapeutic development and food consumption, the agency says in a statement. The alteration knocks out alpha-gal, a sugar molecule on the surface of cells, and could help minimize allergic reactions to pork and reduce the risk of organ rejection in transplant patients.

The move represents a a tremendous milestone for scientific innovation, FDA Commissioner Stephen Hahn says in the statement. The FDA strongly supports advancing innovative animal biotechnology products that are safe for animals, safe for people, and achieve their intended results.

Pigs with the genetic modification are known as GalSafe pigs and are made by Revivicor Inc, a subsidiary of the US biotech United Therapeutics. Research in the mid-2010s indicated that the knockout made transplants from the pigs less likely to be rejected by primate recipients.

The director of the FDAs Center for Veterinary Medicine, Steven Solomon, told reporters in a conference call yesterday that developers who want to use GalSafe pigs for therapeutic purposes will still have to seek approval for their applications. I think that people need to be careful, Solomon said, STATreports. Thats why in part, its going to require further evaluation for xenotransplantation, xenograft, or the other activities by the medical products centers and FDA.

As far as food production is concerned, the statement notes that the meat is safe for consumption by the general population, adding that Revivicor intends to sell meat from GalSafe pigs by mail order, rather than in supermarkets.

The agencys evaluation also concluded that GalSafe pigs presented low risk to the environment, with an impact that is no greater than from conventional pigs. It adds that no animal safety concerns were noted for GalSafe pigs beyond those that would be expected in well-managed, commercial swine populations.

Multiple other efforts to develop genetically engineered pigs are underway around the world, including some alterations designed to make pigs grow faster, and others aimed at making the animals more resistant to lethal viruses such as porcine reproductive and respiratory syndrome virus (PRRSV).

See original here:
FDA Clears Genetic Modification in Pigs for Biomedicine and Food - The Scientist

CiBER-seq dissects genetic networks

Cells integrate environmental signals and internal states to dynamically control gene expression. Muller et al. developed a technique to dissect this cellular logic by linking targeted, genome-wide genetic perturbations with a deep-sequencing readout that quantitatively measured the expression phenotype induced by each perturbation. The method, dubbed CiBER-seq, was able to recapitulate known regulatory pathways linking protein synthesis with nutrient availability in budding yeast cells. Unexpectedly, the authors found that the cellular logic also appears to consider protein production machinery in this decision. By uncovering additional facets of this deeply conserved pathway, the findings demonstrate the utility of comprehensive and quantitative CiBER-seq profiling in mapping the gene networks underlying cellular decisions.

Science, this issue p. eabb9662

Systematically profiling the effects of genetic perturbations is a powerful approach that has revealed the molecular basis for a wide range of biological phenomena. The simple, programmable DNA recognition of CRISPR-Cas9 enables genome-wide genetic analysis in human cells and many other systems. Cas9 is guided by a short RNA to a complementary sequence in the genome, where it can introduce mutations or alter gene expression. Pooled libraries of guide RNAs (gRNAs) that individually target each gene in the genome allow us to introduce genetic perturbations systematically into a population of cells. A key challenge is measuring the phenotypic effects caused by individual guides in these pooled libraries and linking these phenotypes back to the associated gRNA, thereby finding the gene that is responsible.

Molecular phenotypes such as gene expression changes provide a clear and sensitive measure for many cellular processes. We sought a general approach to profile how the expression of a particular gene of interest changed when other genes were perturbed. We began with a library of gRNAs, each disrupting one gene, and linked these guides with an expression reporter containing a guide-specific nucleotide barcode. gRNAs that alter reporter expression will change the abundance of the expressed RNA barcode specifically associated with that guide. Deep sequencing of these expressed barcodes quantifies each of these guide-specific reporter expression effects individually within a pooled, complex population. We have implemented this strategy by combining CRISPR interference (CRISPRi) with barcoded expression reporter sequencing (CiBER-seq).

We used CiBER-seq to profile the responses of several yeast promoters tied to a range of biological functions. Each promoter yielded a distinct pattern of responses that could be understood in terms of its known function and regulation. For example, we rediscover the control of MET6 expression by regulatory ubiquitylation and connect the bud scar protein Cwp1 to other genes required for budding and cytokinesis. Our analysis of the HIS4 promoter, a well-characterized target of the integrated stress response, yielded a range of genetic perturbations that activate this pathway by causing the accumulation of uncharged transfer RNAs (tRNAs). We also uncovered a notable role for tRNA depletion in this response, as impaired tRNA biogenesis activated HIS4 expression through a distinct pathway. In order to understand this regulation, we carried out genetic interaction analysis and looked for quantitative deviations in CiBER-seq profiles caused by the introduction of a second genetic perturbation. We also developed an indirect CiBER-seq approach to measure translational and posttranslational regulation, which both play roles in the signaling pathways upstream of HIS4.

CiBER-seq produces comprehensive phenotypic profiles that offer insights into gene function and regulation. These high-throughput and quantitative phenotypic measurements are also well suited for the systematic measurement of genetic interactions, which contain rich information about the operation of biological processes. This approach can be applied to study a wide range of transcriptional, translational, and posttranslational regulatory responses, and it has the potential to shed light on many areas of biology.

CRISPR-Cas9 gRNA cassettes are linked with transcriptional reporters containing specific barcodes. The RNA-to-DNA ratio for each barcode, measured by deep sequencing, reveals the reporter expression phenotype induced by each gRNA.

To realize the promise of CRISPR-Cas9based genetics, approaches are needed to quantify a specific, molecular phenotype across genome-wide libraries of genetic perturbations. We addressed this challenge by profiling transcriptional, translational, and posttranslational reporters using CRISPR interference (CRISPRi) with barcoded expression reporter sequencing (CiBER-seq). Our barcoding approach allowed us to connect an entire library of guides to their individual phenotypic consequences using pooled sequencing. CiBER-seq profiling fully recapitulated the integrated stress response (ISR) pathway in yeast. Genetic perturbations causing uncharged transfer RNA (tRNA) accumulation activated ISR reporter transcription. Notably, tRNA insufficiency also activated the reporter, independent of the uncharged tRNA sensor. By uncovering alternate triggers for ISR activation, we illustrate how precise, comprehensive CiBER-seq profiling provides a powerful and broadly applicable tool for dissecting genetic networks.

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CiBER-seq dissects genetic networks by quantitative CRISPRi profiling of expression phenotypes - Science Magazine

Genetic Testing to Establish Strong Foothold in Current and Future Healthcare System

The notable rise in the demand for hereditary genetic testing over the past few years is one of the major factors that is expected to fuel the growth of the global genetic analysis services market in the upcoming decade. Technological advancements coupled with the drive to discover new and innovative genetic analysis techniques are set to shape the overall growth trajectory of the global genetic analysis services market during the forecast period. Over the past decade, the genome testing sector has witnessed consistent developments due to which, the global genetic analysis services market is anticipated to expand at an impressive rate during the assessment period.

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Hereditary genetic testing has emerged as ideal, and a rapidly evolving technology within the genetic analysis services market. This is likely to continue, owing to advancements in technology and findings of research activities. The increasing demand for improved and cutting-edge prediction and diagnostic tools and services coupled with surge in demand for disease monitoring is anticipated to play a key role in the overall growth of the global genetic analysis services market during the assessment period.

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Healthcare experts and credible researchers around the world are of the opinion that genetic testing is expected to be the future of the healthcare ecosystem. Advancements in the biomedical field coupled with the notable rise in the number of companies that are developing new genetic-testing kits are expected to augment the global genetic analysis services market during the forecast period. Moreover, as interest levels for precision medicine continues to witness sizeable growth around the world, as a result of which the demand for genetic analysis services is projected to grow at an impressive pace.

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Uptake of Next-generation Sequencing and Multi-gene Tests to Drive Market

Advancements in the genetic technology are likely to play an instrumental role in shaping the growth trajectory of the global genetic analysis services market during the forecast period. Furthermore, due to advancements in technology, the scope of genetic testing has widened by a considerable margin due to which, the demand for genetic analysis services is increasing. While genetic analysis services in the past were largely time-consuming and cumbersome, at present, increasing speed and availability of genomic testing are anticipated to present a plethora of opportunities to the players involved in the current market landscape for genetic analysis services.

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In addition, the gradual shift in the point of access to testing is evolving, as more number of consumers can avail genetic analysis services outside the healthcare setting. Advancements in genetic medicine at the back of advancements in technology are likely to bolster the growth of the global genetic analysis services market during the assessment period.

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Research and Development Activities in Full Swing amid COVID-19 Pandemic

Research and development activities are expected to continue in full swing amid the ongoing COVID-19 pandemic. The significant rise in the demand for genetic counseling services during the ongoing COVID-19 crisis is anticipated to generate consistent revenue for the players involved in the genetic analysis services market. Furthermore, researchers and scientists are increasingly focusing on discovering genetic mechanisms that are required to prevent the spread and transmission of the novel coronavirus disease. Genetic research is estimated to unlock various intricate details of the novel coronavirus, thereby opening up new opportunities for mitigation. The ongoing research pertaining to genetics and its correlation with the ongoing pandemic is expected to provide a detailed and microscopic understanding of the overall cellular mechanisms of the virus.

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Genetic Analysis Services Market: Uptake of Next-generation Sequencing and Multi-gene Tests to Drive Market - BioSpace

From phenotype to structure

Much insight has come from structures of macromolecular complexes determined by methods such as crystallography or cryoelectron microscopy. However, looking at transient complexes remains challenging, as does determining structures in the context of the cellular environment. Braberg et al. used an integrative approach in which they mapped the phenotypic profiles of a comprehensive set of mutants in a protein complex in the context of gene deletions or environmental perturbations (see the Perspective by Wang). By associating the similarity between phenotypic profiles with the distance between residues, they determined structures for the yeast histone H3-H4 complex, subunits Rpb1-Rpb2 of yeast RNA polymerase II, and subunits RpoB-RpoC of bacterial RNA polymerase. Comparison with known structures shows that the accuracy is comparable to structures determined based on chemical cross-links.

Science, this issue p. eaaz4910; see also p. 1269

Determining the structures of protein complexes is crucial for understanding cellular functions. Here, we describe an integrative structure determination approach that relies on in vivo quantitative measurements of genetic interactions. Genetic interactions report on how the effect of one mutation is altered by the presence of a second mutation and have proven effective for identifying groups of genes or residues that function in the same pathway. The point mutant epistatic miniarray profile (pE-MAP) platform allows for rapid measurement of genetic interactions between sets of point mutations and deletion libraries. A pE-MAP is made up of phenotypic profiles, each of which contains all genetic interactions between a single point mutant and the entire deletion library.

We observe a statistical association between the distance spanned by two mutated residues in a protein complex and the similarity of their phenotypic profiles (phenotypic similarity) in a pE-MAP. This observation is in agreement with the expectation that mutations within the same functional region (e.g., active, allosteric, and binding sites) are likely to share more similar phenotypes than those that are distant in space. Here, we explore how to use these associations for determining in vivo structures of protein complexes using integrative modeling.

We generated a large pE-MAP by crossing 350 mutations in yeast histones H3 and H4 against 1370 gene deletions (or hypomorphic alleles of essential genes). The phenotypic similarities were then used to generate spatial restraints for integrative modeling of the H3-H4 complex structure. The resulting ensemble of H3-H4 configurations is accurate and precise, as evidenced by its close similarity to the crystal structure. This finding indicates the utility of the pE-MAP data for integrative structure determination. Furthermore, we show that the pE-MAP provides a wealth of biological insight into the function of the nucleosome and can connect individual histone residues and regions to associated complexes and processes. For example, we observe very high phenotypic similarities between modifiable histone residues and their cognate enzymes, such as H3K4 and COMPASS, or H3K36 and members of the Set2 pathway. Furthermore, the pE-MAP reveals several residues involved in DNA repair and others that function in cryptic transcription.

We demonstrate that the approach is transferable to other complexes and other types of phenotypic profiles by determining the structures of two complexes of known structure: (i) subunits Rpb1 and Rpb2 of yeast RNA polymerase II, using a pE-MAP of 53 point mutants crossed against 1200 deletions and hypomorphic alleles; and (ii) subunits RpoB and RpoC of bacterial RNA polymerase, using a chemical genetics map of 44 point mutants subjected to 83 environmental stresses. The accuracy and precision of the models are comparable to those based on chemical cross-linking, which is commonly used to determine protein complex structures. Moreover, the accuracy and precision improve when using pE-MAP and cross-linking data together, indicating complementarity between these methods and demonstrating a premise of integrative structure determination.

We show that the architectures of protein complexes can be determined using quantitative genetic interaction maps. Because pE-MAPs contain purely phenotypic measurements, collected in living cells, they generate spatial restraints that are orthogonal to other commonly used data for integrative modeling. The pE-MAP data may also enable the characterization of complexes that are difficult to isolate and purify, or those that are only transiently stable. Recent advances in CRISPR-Cas9 genome editing provide a means for extending our platform to human cells, allowing for identification and characterization of functionally relevant structural changes that take place in disease alleles. Expanding this analysis to look at structural changes in host-pathogen complexes and how they affect infection will also be feasible by introducing specific mutations into the pathogenic genome and studying the phenotypic consequences using genetic interaction profiling of relevant host genes.

pE-MAPs are generated by measuring the growth of yeast colonies (left) and visualized as a heatmap (background). We present an application of pE-MAPs to determine protein complex structures, using integrative modeling, and apply it to histones H3 and H4 (right) and other complexes. H3 (purple) and H4 (teal) are highlighted in the context of the nucleosome [gray, modified Protein Data Bank (PDB) 1ID3].

Determining structures of protein complexes is crucial for understanding cellular functions. Here, we describe an integrative structure determination approach that relies on in vivo measurements of genetic interactions. We construct phenotypic profiles for point mutations crossed against gene deletions or exposed to environmental perturbations, followed by converting similarities between two profiles into an upper bound on the distance between the mutated residues. We determine the structure of the yeast histone H3-H4 complex based on ~500,000 genetic interactions of 350 mutants. We then apply the method to subunits Rpb1-Rpb2 of yeast RNA polymerase II and subunits RpoB-RpoC of bacterial RNA polymerase. The accuracy is comparable to that based on chemical cross-links; using restraints from both genetic interactions and cross-links further improves model accuracy and precision. The approach provides an efficient means to augment integrative structure determination with in vivo observations.

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Genetic interaction mapping informs integrative structure determination of protein complexes - Science Magazine

Otto von Habsburg never got to be emperor. Born in 1912, he watched as his familys grasp on political power slipped, and the dynasty that once dominated central Europe and beyond became just another surname that whispered of a greater history. A vocal participant in Europes postwar politics, he couldnt forget the legacy hed been born into: once, on being asked if he planned to watch an Austria-Hungary football match, he is said to have responded Perhaps who are we playing?

Otto, who spoke seven languages and whose heart was buried in Hungary while the rest of him reposed in Austria, was among the last of a line that can be traced at least to the 10th century, to the first Habsburg we can speak of with any certainty: Kanzelin (or possibly Lanzelin) of Altenburg, a small-time magnate in what today is Switzerland. Martyn Radys panoramic history narrates how Kanzelin and his descendants made money, territorial gains and enemies: the monks of a monastery they themselves had founded spread the idea that the earliest Habsburgs were no more than robber barons.

The family took their name from the Habichtsburg or Hawks Castle, from which heartlands they fitfully expanded their influence, until by the 15th century they were rulers of the Holy Roman empire, a great patchwork of princedoms and territories and the premier power in Europe next to France. Charles V, who became King of Spain in 1516 and was elected emperor in 1519, had as his motto plus ultra, meaning still further. In the 16th and 17th centuries Habsburg power spread across the globe, with the dynasty establishing a presence in sites from Brazil, Mexico and Peru to Goa, the Philippines and Taiwan, at the same time as their forces fought for dominance against those of the Ottoman sultans to the east. In 1700 Habsburg power came to an end in Spain and its associated territories, but the central European branch of the family would remain a pre-eminent force for two centuries yet.

The Habsburgs are often remembered for their dogged insistence on keeping power within the family. Between the 15th and the 18th century, the family branches assiduously married their young off to each other (after receiving papal permission for these incestuous unions). Rady notes that between 1450 and 1750, there were four uncle-niece marriages, 11 marriages between first cousins, four marriages between first cousins-once-removed, eight between second cousins, and many other marriages with more remote kinship. This genetic feedback loop contributed to a high incidence of mental illness, epilepsy, birth defects and other illnesses among Habsburg children, as well as the notorious Habsburg jaw, which even sympathetic portraitists struggled to conceal.

In telling a family history that spans a thousand years and almost every continent, Rady sets himself an almost impossible task. The Mbius strip of their family tree and the extent and variety of the lands and peoples they ruled over make writing any Habsburg history a kind of choose-your-own-adventure exercise, where the historians own interests and expertise will always shape the broader story. The backbone of Radys narrative is a fairly traditional chronological account, sketching the character of rulers and reigns since the end of the 10th century. Some chapters pause the action, leaving high politics to one side to allow time to discuss cultural and social questions, from the Peruvian baroque to an early 18th-century Serbian vampire craze. The effect is that of a well-polished lecture course, offering a digestible narrative of the familys rise and fall, leavened with some material that sets the central political story in its wider context. Whats missing is a sustained sense of what life was like for the millions who lived under the Habsburgs: how their wars, reforms, assassinations, and peccadilloes made themselves felt (when they did) among their subjects. What did the Habsburg story mean to those they ruled over?

Maybe its natural that historians would struggle to pin down the experience of life under the Habsburgs, since the breadth and sprawl of their lands meant that they themselves often felt as if they reigned over a paper empire. Great swathes of their lands would not see a rulers physical presence for decades or centuries, but a great central mechanism of chanceries, secretaries and civil servants toiled to record and regulate affairs. In the earliest days of the dynasty, they bolstered their power by drawing up histories and genealogies that boasted of their noble origins. When a little more was needed, they werent above faking the necessary evidence: in the 14th century, Rudolf of Habsburg had his scribes draw up fake charters that helped seal his familys claims to political power and regional control. Their paper empire would only grow, with Philip II of Spain a 16th-century royal micromanager who tried in vain to follow a global empire from his desk in Madrid. By the 1850s, about 50,000 civil servants came to work every day to track and tweak the operations of empire in a bewildering variety of languages.

From 19th-century censored texts to the royal propaganda of 400 years previously, Rady has managed to make sense of an empire and its archives in a way that its own rulers often struggled to. A real strength of this account is its attention to Habsburg stories outside Europe, from attempts to meddle in the 17th-century kingdom of Kongo, and the brief period in which emperor Franz Joseph became the colonial ruler of the Chinese port of Tianjin, to the role of Austrian ships in transporting hundreds of thousands of enslaved Africans into the eastern Mediterranean and beyond in the 19th century.

But all glory fades and when it did, the Habsburgs were a family who knew how to die. The posthumous journey of Otto von Habsburgs heart was part of a family tradition: from 1619 onwards, Habsburg rulers bodies would be divided in three, with the heart going to the Loreto chapel of the Augustinian church in Vienna, and much of the rest of the body going to the crypt of the nearby Capuchin church, while the citys imposing Stephansdom housed a growing collection of Habsburg intestines deep in its own sacred bowels. Their death throes were felt around the world, with early modern royal deaths plunging communities from Madrid to Mexico City into mourning, and inspiring the construction of towering catafalques which memorialised dead monarchs and their achievements.

Grief and loss were a part of the Habsburg experience, not least for the emperor Franz Joseph, who lost his son Rudolf to suicide, his wife Sisi to assassination by an Italian anarchist, and his brother, Maximilian, at the hands of a Mexican firing squad after four years as the countrys unlikely emperor he died with the words Viva Mexico! Viva independencia! on his lips. Maximilians nephew, the Archduke Franz Ferdinand, would be gunned down in Sarajevo in 1914: the dynastys dying days had begun. When the last emperor, Karl I, was ushered out of Viennas Schnbrunn Palace by the socialist leader Karl Renner, it was with the words: Herr Habsburg the taxi is waiting.

The Habsburgs: The Rise and Fall of a World Power is published by Allen Lane (30). To order a copy go to guardianbookshop.com. Delivery charges may apply.

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The Habsburgs by Martyn Rady review negative genetic feedback loop - The Guardian

The 1997 science fiction film Gattaca is set in a dystopic future in which the practice of eugenics selective breeding designed to pass on desired genetic traits is the norm.

In this society, couples who want to have children pursue technological reproduction rather than natural procreation. This allows them to pick which of their embryonic children they want to bear after surveying their genomes.

The moral imperative is for parents to conceive and bear the best possible child, not only with preferred physical traits or predispositions for particular talents, but also free from hereditary disease and disability.

To roll the dice and welcome whatever child you get is seen as irresponsible: Not only would you be knowingly disadvantaging your child, you would also be risking reintroducing undesirable genes back into the gene pool.

Sadly, what was science fiction just a few years ago has become a reality.

In the cover story of the December issue of The Atlantic, reporter Sarah Zhang visits Denmark, a country considered moral pioneers in the field of prenatal genetic testing, diagnosis, and decision-making.

In her conversations with families and experts, Zhang uncovers a devastating trend: more than 95% of pregnancies that have a test result showing a likelihood of Trisomy 21, known more commonly as Down syndrome, end in abortion. The phenomenon of selective abortion is gaining traction despite the fact that some results are false positives, and the fact that persons with Trisomy 21 have excellent survival rates and life expectancies.

Persons with Trisomy 21 have varying symptoms (and varying degrees of severity of symptoms), including intellectual disabilities and muscular-skeletal issues. They are more susceptible to heart problems, gastrointestinal abnormalities, and speech issues. Severe cases require significant intervention, therapy, and resources.

Yet others with Down syndrome go to college, find employment, live independently, and get married. Just like any person, their particular challenges and strengths become evident over time, in part due to their genetic makeup as well as the environment in which they develop.

Within hours of the 8,000-word articles publication online, some were praising Zhangs reporting for humanizing and giving a voice to people with Down syndrome. Others, including pro-lifers, expressed outrage: For instance, one writer at The Federalist accused the author of seeking to create sympathy and understanding for eugenics and a modern-day genocide.

But beyond the pieces implications for the pro-life and pro-choice movements, Zhang identifies an uncomfortable, telling paradox one that signals the dawn of what has been called the genetic information age. She writes:

In wealthy countries, it seems to be at once the best and the worst time for Down syndrome. Better health care has more than doubled life expectancy. Better access to education means most children with Down syndrome will learn to read and write. Few people speak publicly about wanting to eliminate Down syndrome. Yet individual choices are adding up to something very close to that.

Put in other words, the article is an invitation for the world to ask itself: How can a society that celebrates diversity, inclusion, and tolerance allow its members who have genetic differences to be systematically, surgically extracted from its population?

During an amniocentesis, a doctor punctures the abdominal wall of a pregnant woman to withdraw the fluid. The fluid is then analyzed for various chromosomal abnormalities. Today, that information can be gleaned from a mothers blood sample by the 10th week of pregnancy. (Shutterstock)

Three overlapping factors have created new moral questions around child-bearing: 1) reproductive technologies, originally designed to assist couples struggling with infertility, have proliferated in type and availability; 2) the project to map the human genome, completed in 2003, has given scientists and doctors a window into the genes of their patients as well as their patients gametes; and 3) prenatal genetic testing has become a routine part of obstetric care.

While originally developed to assist couples who were unable to conceive children through natural procreation, artificial reproductive technologies (ART) now comprise a booming fertility industry. Services like in vitro fertilization are now cheaper, less riskier to women, and more likely to be covered by insurance and thus more widely available.

Because marriage and child-bearing are increasingly delayed in wealthier nations, both infertility and the risk of chromosomal abnormalities are on the rise. This makes in vitro fertilization, now paired with genetic testing, a more desirable method of reproduction: From a consumer standpoint, getting the healthiest possible child is the best investment in terms of time, cost, and risk.

But even if a woman gets pregnant naturally, she is likely to be offered prenatal screening for major chromosomal abnormalities. In the U.S., prenatal testing was generally offered to women over 35 or those with high-risk pregnancies. As of 2019, more than 60% of OBGYNs had offered it as part of their standard care to all patients.

In Denmark, nearly all pregnant women choose to have their developing children screened for genetic abnormalities.

Prenatal testing used to be done later in the second trimester if an ultrasound revealed atypical development, or if parents knew they were carriers for genetic conditions. Today, that information as well as the sex of the baby can be gleaned from a mothers blood sample by the 10th week of pregnancy.

Genetic counselors are supposed to present findings with value neutrality, meaning their language and affect is not supposed to sway patients decision-making. But Zhang spoke to advocates for persons with Down syndrome who were actively lobbying health care providers to change their language, for fear that the increase in selective abortion was correlated to language that increased parental fear.

Even shifting language from risk to probability could help open parents up to choosing life, they argued.

In many of the cases Zhang learned about, the children were originally wanted sometimes desperately so but in one catastrophic moment, they became unwanted. Parental fears about their childs quality of life as well as disappointment over losing the family that they had hoped for swayed them toward abortion.

Suddenly, Zhang writes, a new power was thrust into the hands of ordinary people the power to decide what kind of life is worth bringing into the world.

The world that The Atlantic article describes is one shaped by what Notre Dame law and political science professor O. Carter Snead calls expressive individualism in his new book What It Means to Be Human: The Case for the Body in Public Bioethics (Harvard University Press, $39.95).

This philosophy equates being fully human with finding the unique truth within ourselves and freely constructing our individual lives to reflect it, writes Snead. It considers human relationships as transactional, formed by agreements, promises, and consent for the mutual benefits of the parties involved.

Such a philosophy, he argues, leaves us without a coherent vision of our moral obligations to one another, especially the most vulnerable. This is illustrated in Zhangs piece by a series of moral quandaries that selective abortion poses.

Pope Francis kisses Peter Lombardi, 12, of Columbus, Ohio, after the boy rode in the popemobile during his general audience in St. Peter's Square at the Vatican in 2018. (Catholic News Service/Vatican Media)

If reproductive decision-making is an individual choice, what should a society do when thousands (or millions) of individual choices result in massive demographic or sociological changes?

Is a eugenic movement brought about by a societys own choosing any less problematic than one which is forced on a people, such as the campaign to eradicate persons with disabilities designed by the Nazis or the current campaign by the Chinese government to eliminate its Uyghurs population?

Zhang uncovers what she calls the most perverse moral problem in an exchange with a Danish woman who heads the National Down Syndrome Association. The woman, who is also a mother to 18-year-old son with Down syndrome, educates expectant parents about the condition.

During one of their conversations, the teenage boy leans over and looks at his mothers phone. The title of a controversial documentary called Death to Down Syndrome was displayed on the screen, and he immediately recoiled.

The reporter realized that he was cognizant of the fact that there are people who dont want people like him to be born. Moreover, his mother supports the right to abortion, even in cases like his.

The scene illustrates the ultimate conundrum for a society that supports the unrestricted right to abortion while claiming to uphold the equality of all human beings as a foundational moral principle: A woman must convince her child that his life is valuable, dignified, and worthy of living, while also supporting the rights of others to end the life of their child with his same genetic markers.

The response of a Catholic reader to the article would seem clear-cut: Because abortion is the taking of human life in its most vulnerable stage, it violates the fundamental right of all human beings to continue their life until natural death. Abortion, as well as any reproductive technology involving the creation, testing, and destruction of embryos, must be rejected.

But Catholic teaching does not stop at the moral evaluation of the technology or the act of abortion. The Gospel goes deeper it speaks to the heart of parents who receive a devastating diagnosis. It speaks to the vocation of health care workers and geneticists to heal when they can and offer comfort when they cannot. And it speaks to families about what it means to be open to the mystery of Gods design for family life.

In a 2019 speech, Pope Francis lamented the fact that thanks to modern prenatal testing techniques, even the suspicion of an illness, and especially the certainty of a disease, changes the experience of pregnancy and causes deep distress to women and couples.

The isolation and worry about the suffering that lies ahead, the pope said, is like a silent cry, a call for help in the darkness, when faced with an illness whose outcome cannot be foreseen with certainty.

In the face of fear and isolation, parents need support from a larger community, whether through their extended family, the parish, or others who have been in their situation. Support from a community is the first antidote to the individualism and isolation of reproductive choice.

When it comes to the issue of medical language, The Atlantic article notes that while genetic counselors and obstetricians are trained and required to present genetic information in as neutral a way as possible to patients, that doesnt always happen.

Pope Francis has admonished clinicians who use the phrase incompatible with life to describe genetic conditions that correspond with short lifespans or severe physical and cognitive impairments. For one thing, where there is a living human being, there is life.

Second, he says:

No human being can ever be unfit for life, whether due to age, state of health or quality of existence. Every child who appears in a womans womb is a gift that changes a familys history, the life of fathers and mothers, grandparents and of brothers and sisters. That child needs to be welcomed, loved and nurtured.

The fact that so many parents, when faced with a diagnosis of Down syndrome or other genetic anomalies, choose abortion tells Catholics a few things about why and where the Gospel is needed.

A society that reveres health and wellness is one that will have trouble in the face of sickness, aging, and death. It needs to hear the good news that suffering has been redeemed, and that it stretches the hearts of patients, caregivers, and the people they encounter.

A scene from the movie Gattaca. (IMDB)

Being mortals, bodily decay or dysfunction will come to all of us; some members of our human family experience it more acutely or earlier than others. They should receive more care, not more marginalization, because of it.

A materialist society that reduces people to their bodies and even microscopically, to their genetic material needs to know the truth that human beings have a body and a soul. The most important quality that children have and develop is their capacity to love, something that does not depend on their physical or cognitive ability.

A consumer-driven society, one that has become accustomed to customizable, curated lifestyles, is one that considers parenthood as a fulfillment of desires or a way to construct meaning and identity. Such a society which does not pause at the ways it commodifies its children needs to be reminded to protect the little ones. And a society that has unlimited access to information desperately needs wisdom.

The opening credits of Gattaca include a cautionary line from the Book of Ecclesiastes: Consider what God has done: Who can straighten what He has made crooked?

The answer to this rhetorical question should humble us. It should also help us to see all children not as something owed, but as gifts to be received as is, with all of their challenges and strengths.

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The Genetic Information Age is here. Are we ready? - Angelus News

The lynx-hare predator-prey cycle that has existed for thousands of years in North America is increasingly under threat from climate change.

The lynx are specialist predators that rely almost exclusively on snowshoe hare for food. This has led to a tight link between the populations of the two species; as the snowshoe hare populations rise and fall over a roughly 10-year cycle, lynx populations follow suit, says Dr. Jamie Gorrell, a VIU Biology Professor. When hare abundance is at its peak, lynx have plenty of food and have high survival rates, causing population booms that match, but lag slightly behind, those of the hare.

As snowshoe hare populations begin to decline, some lynx change their behaviour and begin to travel long distances, sometimes more than 1,000 kilometres, in search of food.

To understand how this cycle, which helps maintain the biodiversity of more than a dozen species in the boreal forest, could be impacted by climate change Gorrell and Dr. Evan Hersh, a VIU post-doctoral fellow, are studying the genetics of Canada lynx.

The genetic information will help researchers and conservationists understand lynx movements and connectivity among populations to identify potential habitat corridors that are essential to ensuring lynx populations remain genetically diverse.

Genetically mixed lynx populations will in turn help lessen the impact climate change may have on the stability of the lynx-hare cycle, a process vital to the functioning of boreal and sub-boreal ecosystems, says Gorrell.

Hersh is using genomic analyses and bioinformatics to analyze DNA samples that were collected with the help of Yukon residents, fur trappers and the Yukon Community Ecological Monitoring Program. The samples were collected at multiple phases during a 10-year cycle in hare abundance.

Hersh recently finished his PhD in plant ecology and evolution at the University of British Columbia and has extensive experience in genomic techniques. He says biologists now also need to be computer programmers to be able to crunch the huge amounts of data being generated in the genomic era.

Hersh will be comparing the genetic differences between Canada lynx from different areas. He said with newer techniques, instead of comparing a few hundred genetic markers, researchers can now compare tens of thousands of genetic markers.

Were hoping this thousandfold increase in the amount of data will give us the ability to figure out what is going on with their population structure. To date, no one has really applied these cutting-edge genomic techniques that produce huge amounts of data to analyze the population structure of Canada lynx within a conservation and management context, says Hersh.

The lynx needs these huge chunks of boreal forest that are continuous, not broken into little patches. If something happens in the southern portion of the boreal region, due to human use or climate change, and the area starts getting fragmented, then lynx movement can potentially be impacted, says Hersh.

They could have trouble passing over certain regions where there isnt enough boreal forest for them to travel through, which could have cascading effects on hare populations and potentially disrupt the cycle.

Hersh said if lynx and hare populations no longer follow predictable cycles, this can have tremendous impacts on the biodiversity of Boreal forests. It is estimated that the abundances of over 25 vertebrates are also regulated by this cycle. While the exact consequences of a disruption are difficult to predict, it could alter the natural patterns of genetic variation in all species that fluctuate with the cycle, which could ultimately reduce their ability to respond to future changes in their habitat and climate.

The concern is if climate change reduces the continuity of the forest and lynx cant move as far anymore, then this could disrupt that 10-year cycle.

This relationship between predator and prey could start to fall apart, so thats a potential consequence of climate change that we might not expect to happen. No one knows whats going to happen to the lynx and hare populations, says Gorrell. Most predator-prey relationships are generally stable over time and the abundance of predators and prey will stay relatively constant, but the lynx and hare have these huge peaks and crashes that happen like clockwork and its amazing how that cyclical relationship has maintained over time.

Gorrell and Hersh will be completing their research over the next two years thanks to an Accelerate Fellowship grant for $90,000 awarded jointly from Mitacs and Bill Harrower, principal biologist at High-Country Wildlife.

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MEDIA CONTACT:

Rachel Stern, Communications Officer, Vancouver Island University

C: 250.618.0373 lE: Rachel.Stern@viu.ca | T: @VIUNews

List of Project Supports/Partners

Research will be completed thanks to a grant from Mitacs and Bill Harrower, principal biologist at High-Country Wildlife.

This project is also being supported by:

The Community Ecological Monitoring project includes collaboration among researchers from:

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VIU Researchers Examining Genetics of Canada Lynx | News | Vancouver Island University | Canada - Vancouver Island University News

1.

Hold on to your crowns, royal devotees: This one's a doozy. Prince Louis, whose mother is Kate Middleton, happens to look like Michael Middleton, who is get this Kate's father. I know, we were shocked, too. In a rare public appearance over the weekend, the 2-year-old prince was photographed alongside his family, and royal fans were quick to point out the striking physical similarities between Louis and his maternal grandfather. It's unclear why commenters thought the resemblance was particularly noteworthy, although it wasn't the first time Grandpa Middleton and the royal children have proven genetics do, in fact, exist. At least we now know there's hope for a non-bald King of the United Kingdom sometime in the next century. [Daily Express]

Despite the global pandemic, Cody Simpson has been pretty busy this year. He wasn't just singing, writing poetry, working as a United Nations Ocean Advocate, and falling in and out of love with Miley Cyrus. A "silent fire" in his stomach fueled his return to competitive swimming, and after five months of training, the Australian singer secured a spot in the 2021 Australian Olympic trials for the 100-meter butterfly event. "It is my greatest ambition to expand the limit and perceived notion of what's possible for someone to achieve in a single lifetime," Simpson wrote, "and I'm here to tell you can do absolutely ANYTHING if you are willing to work for it." H/T to Simpson for inspiring us while simultaneously putting us all to shame. [People]

The accolades start coming and they don't stop coming. Nearly 20 years after Shrek was released, we can breathe a sigh of relief knowing that our favorite ogre will be remembered for a long time to come. The Library of Congress announced this year's additions to the National Film Registry (which works to "ensure the survival, conservation, and increased public availability of America's film heritage"), and Shrek made the cut, getting praise for being "entertaining and emotionally impactful at levels to be appreciated by both children and their adults." The 25 selected films also include a record number of films directed by women and people of color. "We are not trying to set records but rather to set the record straight," Librarian of Congress Carla Hayden said. Hallelujah. [Variety, Library of Congress]

Story continues

Less than three weeks until The Office leaves Netflix? No, God, please no! The classic NBC show will be removed from Netflix at the end of the year and head to NBCUniversal's streaming service Peacock, and on Monday, it was announced that users will need a paid subscription to stream most of the episodes. Starting on Jan. 1, the first two seasons of The Office will stream on Peacock for free with ads, but seasons three through nine will require a $4.99 a month Peacock Premium subscription. That's yet another streaming service fans are being asked to pay for alongside Netflix, Hulu, Disney+, HBO Max, and more enough to make you want to shout, "I declare bankruptcy!" [The Wrap, Variety]

Taylor Swift released Evermore less than a month after Netflix released season four of The Crown, so it's not entirely unreasonable to suggest every song on Swift's surprise album is actually about the monarchy. However, one song in particular seems like it really fits the narrative, leading many fans to speculate the album's fifth track, "Tolerate it," is based on the relationship between Princess Diana and Prince Charles. The song, which distressingly details a broken relationship, references themes of infidelity and mental health that are also explored on The Crown. Swift also sings about using "fancy" tableware, and we all know the monarchy is very fancy. If that weren't enough, one of the song's lyrics is "You're so much older," which, hello, Charles was 12 years Diana's senior! Wake up, America the writing is quite literally on the wall. [Insider]

More stories from theweek.comJoe Biden still doesn't get itThe Trump campaign is asking its email list if Trump should run for president in 2024Washington National Cathedral rings funeral bell for 30 minutes to mourn 300,000 COVID-19 deaths

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The daily gossip: A T-Swift lyric theory, royal genetics, and the future of The Office - Yahoo News

Thousands of years ago, people in South America began domesticating Solanum pimpinellifolium, a weedy plant with small, intensely flavored fruit. Over time, the plant evolved into S. lycopersicum - the modern cultivated tomato.

Although today's tomatoes are larger and easier to farm compared with their wild ancestor, they also are less resistant to disease and environmental stresses like drought and salty soil.

Researchers from Boyce Thompson Institute, led byZhangjun Fei, created a high-quality reference genome for S. pimpinellifolium and discovered sections of the genome that underlie fruit flavor, size and ripening, stress tolerance and disease resistance.The results were publishedinNature Communicationson November 16.

"This reference genome will allow researchers and plant breeders to improve traits like fruit quality and stress tolerance in the tomato," said Fei, "for example, by helping them discover new genes in the modern tomato as well as by reintroducing genes from S. pimpinellifolium that were lost over time as S. lycopersicum was domesticated."

Fei is a BTI faculty member and co-corresponding author on the paper, as well as an adjunct professor in Cornell University's School of Integrative Plant Science (SIPS).

Although other groups had previously sequenced S. pimpinellifolium, Fei said this reference genome is more complete and accurate, thanks in part to cutting-edge sequencing technologies that are able to read very long pieces of DNA.

"Older sequencing technologies that read short pieces of DNA can identify mutations at the single-base level," said Shan Wu, a postdoctoral scientist in Fei's lab and co-corresponding author on the paper. "But they aren't good at finding structural variants, like insertions, deletions, inversions or duplications of large chunks of DNA."

"Many known traits of the tomato are caused by structural variants, so that is why we focused on them," Fei said. "Structural variants also are understudied because they are more difficult to identify."

Fei's group compared their S. pimpinellifolium reference genome to that of the cultivated tomato, called Heinz 1706, and found more than 92,000 structural variants.

The researchers then combed thetomato pan-genome, a database with the genomes of more than 725 cultivated and closely related wild tomatoes, and discovered structural variants related to many important traits. For example, the modern cultivated tomato has some genomic deletions that reduce their levels of lycopene, a red pigment with nutritional value, and an insertion that reduces their sucrose content.

Jim Giovannoni, BTI faculty member and co-author of the study, notes that many consumers are disappointed in the quality and flavor of modern production tomatoes because past breeding efforts ignored those traits in favor of performance and yield.

"Identification of the additional genetic diversity captured in the S. pimpinellifolium genome provides breeders with opportunities to bring some of these important features back to store-bought tomatoes," said Giovannoni, who is also an adjunct professor in SIPS and a scientist with the U.S. Department of Agriculture's Agricultural Research Service.

The researchers found many other structural variants that could be of interest to plant breeders, including variants in numerous disease-resistance genes and in genes involved in fruit size, ripening, hormonal regulation, metabolism, and the development of flowers, seeds and leaves.

The group also found structural variants associated with regulating the expression of genes involved in the biosynthesis of lipids in fruit skin, which could help improve the fruit's post-harvest performance.

"So much genetic diversity was lost during tomato domestication," Fei said. "These data could help bring some of that diversity back and result in tomatoes that taste better, are more nutritious and more resilient."

Reference: Wang X, Gao L, Jiao C, et al. Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding. Nature Communications. 2020;11(1):5817. doi:10.1038/s41467-020-19682-0.

This article has been republished from the following materials. Note: material may have been edited for length and content. For further information, please contact the cited source.

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Bringing Back Tomato's Genetic Diversity That Was Lost in Domestication - Technology Networks

Genes are by no means a crystal ball, but they can be used to forecast susceptibility to a variety of conditions, from cancers and heart disease to chronic inflammatory conditions. As such, they can help healthcare professionals and patients make better care decisions.

Generally speaking, whenpeople today think about genetic predispositions, theythink about their parents and family trees.However, those inherited genetic variationsbequeathed by ourparents and grandparents are only a portion ofacomplete genetic picture and often not the most revealing one.Thegenetic variationsmost commonly linked to disease are actually?not?the ones from your parents; rather, they areacquiredas one ages.

Mom and Dad Cant Take All the Heat forAll Health ChallengesUnlike inheritedgenetic predispositions,accumulatedgenetic changes(otherwise known as somatic)are the result ofenvironmental influences, such as smoking, chemicals or ultra-violet radiation. They can also stem from common errorscells make as they duplicate themselves over time.The expansion of these detrimental variations cause damage to DNA within blood cells,aphenomenon known as clonal hematopoiesis (CH), whichincreases susceptibility to many diseases, including many types of cancer.

Germline variations in genes still indicate potential vulnerabilities, with one in five healthy adults estimated to carry an inherited marker. However, these genetic abnormalities represent a static metric. Once individuals are tested for inherited variations, they will never need to do so again. Whats more, many of the predispositions that surfaced through this testing can be addressed through lifestyle and medical interventions. It boils down to being aware of them.

Somatic changes, on the other hand, can happen at any stage of life. While many of these changes have no clinical ramifications, some of them can exacerbate predispositions inherited from our parents because the disease is often the result of multiple genetic variations banding together, inherited or acquired.

The chances of an acquired variation accumulating and accelerating within the body increase significantly as we age, generally after the age of 40 and growing each decade. This could drastically change a patients health profile, casting inherited vulnerabilities into a new light without any warning or symptoms.

Understanding Accumulated VariationsA growing body of research links somatic changes to an increased likelihood of blood cancers and cardiovascular disease, both heart disease and stroke. The same research reveals that these accumulated genetic variations contribute to infection and severe inflammatory reactions, some of which are associated with severe cases of Covid-19.

A study conducted byJAMA Cardiologyexplores theconnectionbetween accumulated genetic change anda pro-inflammatory immune response that resembles the exaggerated cytokine release syndrome (CRS)experienced by patients with severeCovid-19.Notably,the researchfoundthat patients who experienced the most extreme inflammatory response carried variationsTET2 and DMNT3A, both of which accumulate in genes over time.

Another research report published inCancersanalyzingpatients hospitalized with severe Covid-19disease found a much higher frequency of clonal hematopoiesis (CH) of indeterminate potential (sometimes called clonal hematopoiesis of indeterminate potential or CHIP) ),an age-associated condition in cells,in all age groups.

Additionally,accumulatedDNA damage to the JAK2 gene has been found in alargeproportion of cancer-free patients with venous thrombosis, a known complicationof Covid-19.While preliminary,the findingsdemonstratecompellingcorrelations betweensomaticgenetic change andCovid-19 severity that could be used to identify patients prone to complications early, intervene soonerand inform treatment strategies.

It is believed thatproviders can applythese correlations to other areas of care toassess an individuals susceptibilityto a wide range of diseases, and ultimately improve and extend quality of life.

Improving Care Decisions with Somatic insightsAugmenting currenthealth assessmentsand care strategies with accumulated geneticdatacan open new pathways for disease detection, response and prevention.The scientificand medicalcommunitieshaveonly scratched the surface ofwhat we can learn from these insights. Even so,understanding somatic damage showsgreatpromise for helping individualsstay ahead of their health concerns and respond in a more informed way.

Photo: Andy, Getty Images

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Accumulated genetic variations: What they are and why they matter to a complete health picture - MedCity News

Getting to the guts of local evolution

The microbiota of mammals is a product of coevolution. However, humans exhibit a range of adaptive peculiarities that can be quite geographically specific. The human microbiota also displays a variety of community compositions and a range of overlapping and redundant metabolic characteristics that can alter host physiology. For example, lactase persistence is a genetic characteristic of European populations, but in populations lacking the lactase gene, milk sugar digestion is endowed by the microbiota instead. Suzuki and Ley review the evidence for the role that the microbiota plays in local adaptation to new and changing human circumstances.

Science, this issue p. eaaz6827

When human populations expanded across the globe, they adapted genetically to local environments in response to novel selection pressures. Drivers of selection include exposure to new diets, climates, or pathogens. Humans harbor microbiotas that also respond to changes in local conditions and changes in their hosts. As a result, microbiotas may alter the adaptive landscape of the host through modification of the environment. Examples include changes to a foods nutritional value, the hosts tolerance to cold or low amounts of oxygen, or susceptibility to invading pathogens. By buffering or altering drivers of selection, the microbiota may change host phenotypes without coevolution between host and microbiota. Functions of the microbiota that are beneficial to the host may arise randomly or be acquired from the environment. These beneficial functions can be selected without the host exerting genetic control over them. Hosts may evolve the means to maintain beneficial microbes or to pass them to offspring, which will affect the heritability and transmission modes of these microbes. Examples in humans include the digestion of lactose via lactase activity (encoded by the LCT gene region) in adults and the digestion of starch by salivary amylase (encoded by the AMY1 gene)both are adaptations resulting from shifts in diet. The allelic variation of these genes also predicts compositional and functional variation of the gut microbiota. Such feedback between host alleles and microbiota function has the potential to influence variation in the same adaptive trait in the host. How the microbiota modifies host genetic adaptation remains to be fully explored.

In this paper, we review examples of human adaptations to new environments that indicate an interplay between host genes and the microbiota, and we examine in detail the LCTBifidobacterium and the AMY1Ruminococcus interactions. In these examples, the adaptive host allele and adaptive microbial functions are linked. We propose host mechanisms that can replace or recruit beneficial microbiota functions during local adaptation. Finally, we search for additional examples where microbiotas are implicated in human genetic adaptations, in which the genetic basis of adaptation is well described. These range from dietary adaptations, where host and microbial enzymes can metabolize the same dietary components (e.g., fatty acid and alcohol metabolism), through climate-related adaptations, where host and microbes can induce the same physiological pathway (e.g., cold-induced thermogenesis, skin pigmentation, and blood pressure regulation), to adaptations where hosts and microbes defend against the same local pathogens (e.g., resistance to malaria, cholera, and others). These examples suggest that microbiota has the potential to affect host evolution by modifying the adaptive landscape without requiring coevolution.

Well-studied examples of local adaptation across diverse host species can be revisited to elucidate previously unappreciated roles for the microbiota in host-adaptive evolution. In the context of human adaptation, knowledge of microbial functions and host genemicrobe associations is heavily biased toward observations made in Western populations, as these have been the most intensively studied to date. Testing many of the interactions proposed in this Review between host genes under selection and the microbiota will require a wider geographic scope of populations in their local contexts. Because genes under strong selection in humans are often involved in metabolic and other disorders and can vary between populations, future investigations of host genemicrobe interactions that relate to human adaptation may contribute to a deeper understanding of microbiota-related diseases in specific populations. Investigating host genemicrobe interactions in a wider variety of human populations will also help researchers go beyond collections of anecdotes to form the basis of a theory that takes microbial contributions to host adaptation into account in a formal framework. A better understanding of reciprocal interactions between the host genome and microbiota in the context of adaptive evolution will add another dimension to our understanding of human evolution as we moved with our microbes through time and space.

When human populations adapt genetically to new environments, their microbiotas may also participate in the process. Microbes can evolve faster than their host, which allows them to respond quickly to environmental change. They also filter the hosts environment, thereby altering selective pressures on the host. Illustrated here are examples of interactions between adaptive host alleles and adaptive microbiota functions where the microbiota likely modified the adaptive landscape in response to changes in diet (e.g., changes in levels of starch and milk consumption), exposure to local pathogens (e.g., malaria parasites and Plasmodium spp.), and changes in local climate (e.g., cold stress and hypoxia). In this paper, we discuss the resulting relationships between host-adaptive alleles and microbiota functions.

As human populations spread across the world, they adapted genetically to local conditions. So too did the resident microorganism communities that everyone carries with them. However, the collective influence of the diverse and dynamic community of resident microbes on host evolution is poorly understood. The taxonomic composition of the microbiota varies among individuals and displays a range of sometimes redundant functions that modify the physicochemical environment of the host and may alter selection pressures. Here we review known human traits and genes for which the microbiota may have contributed or responded to changes in host diet, climate, or pathogen exposure. Integrating hostmicrobiota interactions in human adaptation could offer new approaches to improve our understanding of human health and evolution.

Continue reading here:
The role of the microbiota in human genetic adaptation - Science

When applying genetics to the study of COVID-19, scientists are learning a lot. Our DNA codes for proteins, some of which are required for SARS-CoV-2 to interact with and infect a host cell, others that are implicated in the downstream effects of viral infection, such as inflammatory responses. But how do scientists choose which genes to study?A new study by Dr Thomas Stoeger, a postdoc at North Western University, suggests there is a historical bias involved; scientists are studying human genes that have already been heavily investigated, independent of COVID-19.

In this installment of Teach Me in 10, Stoeger expands on the key points of this study and the implications of bias in scientific research.

Full research publication: Meta-Research: COVID-19 research risks ignoring important host genes due to pre-established research patterns.

For more Teach Me in 10 videos, check out our hub page.

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Teach Me in 10 Why COVID-19 Genetics Research May Be Biased With Dr Thomas Stoeger - Technology Networks

Scientists at Boyce Thompson Institute have produced a high-quality chromosome-scale genome sequence for the currant tomato Solanum pimpinellifolium, the wild progenitor of the modern cultivated tomato Solanum lycopersicum.

Solanum pimpinellifolium in Botanisk tidsskrift, 1872.

Tomato is the worlds leading vegetable crop with a total production of 182 million tons and a worth over US $60 billion in 2018.

Solanum pimpinellifolium carrying red, small, and round fruits is the wild progenitor of the cultivated tomato.

It was domesticated in South America to give rise to Solanum lycopersicum var. cerasiforme, which was later improved into the big-fruited tomato Solanum lycopersicum var. lycopersicum in Mesoamerica.

Although other groups had previously sequenced Solanum pimpinellifolium, the new reference genome is more complete and accurate, thanks in part to cutting-edge sequencing technologies that are able to read very long pieces of DNA, said co-lead author Dr. Zhangjun Fei, a researcher at Boyce Thompson Institute and Robert W. Holley Center for Agriculture and Health at the U.S. Department of Agricultures Agricultural Research Service.

Older sequencing technologies that read short pieces of DNA can identify mutations at the single-base level, said co-lead author Dr. Shan Wu, a postdoctoral scientist at Boyce Thompson Institute.

But they arent good at finding structural variants, like insertions, deletions, inversions or duplications of large chunks of DNA.

Many known traits of the tomato are caused by structural variants, so that is why we focused on them, Dr. Fei said.

Structural variants also are understudied because they are more difficult to identify.

The scientists compared their reference genome of Solanum pimpinellifolium to that of the cultivated tomato, called Heinz 1706, and found more than 92,000 structural genetic variants.

They then combed the tomato pan-genome, a database with the genomes of more than 725 cultivated and closely related wild tomatoes, and discovered structural variants related to many important traits.

For example, the modern cultivated tomato has some genomic deletions that reduce their levels of lycopene, a red pigment with nutritional value, and an insertion that reduces their sucrose content.

Identification of the additional genetic diversity captured in the Solanum pimpinellifolium genome provides breeders with opportunities to bring some of these important features back to store-bought tomatoes, said co-author Dr. Jim Giovannoni, a researcher at Boyce Thompson Institute and Robert W. Holley Center for Agriculture and Health at the U.S. Department of Agricultures Agricultural Research Service.

The authors found many other structural variants that could be of interest to plant breeders, including variants in numerous disease-resistance genes and in genes involved in fruit size, ripening, hormonal regulation, metabolism, and the development of flowers, seeds and leaves.

They also found structural variants associated with regulating the expression of genes involved in the biosynthesis of lipids in fruit skin, which could help improve the fruits post-harvest performance.

So much genetic diversity was lost during tomato domestication, Dr. Fei said.

These data could help bring some of that diversity back and result in tomatoes that taste better, are more nutritious and more resilient.

The results appear in the journal Nature Communications.

_____

X. Wang et al. 2020. Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding. Nat Commun 11, 5817; doi: 10.1038/s41467-020-19682-0

This article is based on a press-release provided by Boyce Thompson Institute.

Continued here:
Researchers Sequence Genome of Tomato's Wild Ancestor | Genetics - Sci-News.com

Researchers based at the Neuroscience Institute at the University of Sheffield in the UK have identified a new genetic risk factor for Motor Neurone Disease (MND) in so-called 'junk DNA'.

The newly discovered genetic changes are present in up to 1% of MND patients.

The research, published in the journal Cell Reports, focused on genetic mutations in non-coding DNA, often known as junk DNA because it does not directly encode protein sequences. Non-coding DNA makes up more than 99% of the human genome, but currently is relatively unexplored.This research also includes new methods for studying mutations in non-coding DNA which could be applied to other diseases.

The authors of the study reported that they determined an existing neuroprotective drug developed at the University of California San Diego (UCSD) called SynCav1 could help MND patients carrying the newly discovered genetic mutation.

An experimental gene therapy for the treatment of neurological disorders such as MND and Alzheimers disease, SynCav1 has been licensed to CavoGene LifeSciences.

MND or Amyotrophic Lateral Sclerosis (ALS), as it is also known, affects motor neurons in the brain and spinal cord that form the connection between the nervous system and muscles to enable movement of the body. The progressive disease affects a patient's ability to walk, talk, use their arms and hands, eat and breathe.

Around 5,000 people in the UK and 30,000 people in the US are currently living with MND, with numbers expected to rise.

High-income countries currently have the highest rates of motor neuron diseases worldwide, and the burden is increasing with the ageing population, shows an analysis of the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2016.

Dr Jonathan Cooper-Knock, lead author of the study and NIHR clinical lecturer in Neurology at the Neuroscience Institute at the University of Sheffield, said: "Until now scientists have never systematically examined non-coding or junk DNA in relation to the development of MND.

"Not only have we identified a mutation in junk DNA which puts people at risk of developing a certain form of the MND, but we have also found that by targeting the mutated gene with the established neuroprotective drug called SynCav1, it might be possible to halt or potentially prevent the disease progressing in those patients.

"This is a significant breakthrough in terms of genetic risk factors driving personalized medicine for MND patients."

Link:
An experimental gene therapy may be effective for MND patients with a newly discovered genetic mutation - BioPharma-Reporter.com

New genetic differences have been discovered to play a vital role in regulating blood pressure, according to research part funded by us and published in Nature Genetics.

Researchers based at the University of Cambridge and round the world studied the genetic make-up of 1.3 million people with diverse ancestries. They found 106 new regions of DNA and 87 new rare genetic variations associated with blood pressure.

The rare genetic variants had an eight times greater effect on blood pressure compared to more common variants. Thirty-two of the rare variants were located within newly identified sections of DNA linked to blood pressure, and 55 were located within genes already known to be associated with its regulation.

The importance of the work is illustrated by the finding that six of the genes identified in this study, four of which contain rare variants, are already drug targets for heart and circulatory conditions. This suggests that the other genes identified may also be good targets for developing new drugs.

The researchers therefore hope that these findings will lead to new ways to prevent and treat high blood pressure.

Professor Sir Nilesh Samani, our Medical Director, said:

This major study has revealed new underlying genetic factors which add to the blueprint of what dictates our blood pressure.

High blood pressure is a major risk factor for heart and circulatory diseases. These new discoveries should shed light on potential new ways to prevent and treat high blood pressure and ensure its in a healthy range, ultimately to reduce deadly heart attacks and strokes.

Read more about high blood pressure

Read more:
Rare genetic differences play vital role in blood pressure - British Heart Foundation

A new report added by Research Dive offers insights and puts forth the impact of COVID-19 catastrophe on the global human genetics market. According to the report, the human genetics market is estimated to grow at a significant rate and generate robust revenue share by 2027 during the forecast period from 2020 to 2027.

The report provides brief summary and an in-depth information of the market by collecting data from industry experts and different sources prevalent in the market. The statistics presented in the report are extensive, reliable, and the outcome of an exhaustive analytical research. The report offers qualitative and quantitative trend analysis for the period of 2020-2027 to assist stakeholders to understand the overall market scenario. Comprehensive analysis of the key segments validates the types of products used in the industry and their applications.

MARKET SEGMENTATION

On the basis of type, the global human genetics market is segmented into:

Product Type Segmentation Prenatal Genetics Cytogenetics Molecular Genetics & Symptom Genetics

For More Detail Insights, Download Sample Copy of the Report at: https://www.researchdive.com/request-toc-and-sample/2137

On the basis of application, the global human genetics market is segmented into:

Cytogenetics Molecular Genetics Prenatal Genetics Symptom Genetics Research Center Industry Segmentation Forensic Laboratories Hospital

On the basis of region, the global human genetics market is segmented into:

North America U.S. Canada Mexico

Europe Germany UK France Spain Italy Rest of Europe

Asia-Pacific Japan China India Australia South Korea Rest of Asia-Pacific

LAMEA Brazil Argentina Saudi Arabia South Africa UAE Rest of LAMEA

Connect with Our Analyst to Contextualize Our Insights for Your Business: https://www.researchdive.com/connect-to-analyst/2137

KEY COMPANIES COVERED

The research report summarizes and outlines several aspects of the key players operating in the global human genetics market such as company snapshot, business performance, product portfolio, recent developments & strategies, SWOT analysis, and many more. The key players listed are:

LGC Forensics Agilent Technologies QIAGEN N.V. Bode Technology Illumina Thermo Fisher Scientific Inc. Promega Corporation Orchid Cellmark Inc. NextOmics GE Healthcare Takara Bio Inc. Oxford Nanopore Pacific Biosciences

RECENT DEVELOPMENTS

The key players of the market are adopting several strategies to obtain a leading position in the global industry. For instance, in August 2020, Ancestry launched AncestryHealth, a product that features next-generation sequencing with an ability to screen the genes associated with blood disorders, breast cancer, colon cancer, and heart disease.

Contact Us:

Mr. Abhishek PaliwalResearch Dive30 Wall St. 8th Floor, New YorkNY 10005 (P)+ 91 (788) 802-9103 (India)+1 (917) 444-1262 (US) TollFree : +1 -888-961-4454Email:support@researchdive.comLinkedIn:https://www.linkedin.com/company/research-diveTwitter:https://twitter.com/ResearchDiveFacebook:https://www.facebook.com/Research-DiveBlog:https://www.researchdive.com/blogFollow us on:https://covid-19-market-insights.blogspot.com

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Insights on Human Genetics Market 2020 to 2027: COVID-19 Impact Analysis, Drivers, Opportunity Analysis, Restraints, and Forecast - The Courier