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Archive for the ‘genetics’ category: Page 7

Sep 15, 2021

An observational and Mendelian randomisation study on vitamin D and COVID-19 risk in UK Biobank

Posted by in categories: biotech/medical, energy, genetics

The discriminatory power of the UVB variable is somewhat limited in this study, because UVB radiation is low at this time of the year, particularly at the high northern latitude of UK—larger effects might be observed if variation in UVB is greater. We only used ambient UVB, and did not capture individual behavioural differences that would determine the actual level of vitamin D synthesis in the skin, such as duration and time of day spent outside, clothing, etc. It is important to note that time of year is the strongest predictor of vitD-UVB. To avoid bias control dates were assigned to follow the same distribution as case dates, which might have led to artificially diminished differences in vitD-UVB between cases and controls, however analysis relating to hospitalisation and death are not affected by this. We also conducted an analysis of the genetically-predicted vitamin D and a number of state-of-the-art MR analyses. However, the main limitation is the lack of power. Given the small number of COVID-19 patients and the relatively small percentage of variance (4.2%) explained by vitamin D-related genetic variants, this MR study was not adequately powered to detect small causal effect and negative results should be interpreted with caution. Additionally, MR studies only consider linear effects between 25-OHD levels and COVID-19 risk, which do not capture what happens at the extremes of vitamin D deficiency. Therefore, it cannot rule out the possibility that seriously ill patients (due to an underlying pathology) with extremely low vitamin D levels could be predisposed to COVID-19 infection and increased COVID-19 severity and mortality. Furthermore, 25-OHD levels are the used biomarker of vitamin D status in the study population, nevertheless, they correlate poorly with the active form of vitamin D (1,25-OH2D), which exerts the effects of vitamin D on a cellular level. Thus, this study cannot exclude effects of 1,25-OH2D on COVID-19 risk.

Another limitation of this cohort relates to the fact that not all participants have been tested for present (or past) COVID-19 infection; consequentially, taking participants who were not tested as controls could be a potential source of bias, given that misclassification of controls might be substantial due to the presence of asymptomatic infected individuals, further driving our findings to the null. This is evident from the 1:2 ratio between outpatient vs. inpatient cases. It should be acknowledged that the COVID-19 cases in UK biobank have a high rate of hospitalisation due to the very limited and targeted testing at this stage of the pandemic in the UK, so this study reflects mainly those with more severe COVID-19 and gives less information about true infection risk, or risk of milder disease. In addition, we excluded individuals with a negative COVID-19 testing result from the controls due to the risk of those being false negatives. Although there is a risk of introducing selection bias, we believe that the risk of introducing misclassification bias if we included them in the analysis could be higher22,23. Additionally, given the presence of asymptomatic infected individuals, taking participants who were not tested as controls could also be another potential source of bias. Our study assessed the effect of genetically predicted vitamin D levels on COVID-19 risk while taking into consideration of ambient UVB radiation during the pandemic. We show an indication of an inverse association between genetically predicted vitamin D levels and severe COVID-19. Findings from our study are consistent with a recent randomised controlled trial (RCT) that found protective effect of vitamin D supplementation among those hospitalised with COVID-1924. However, other clinical trials did not show an effect. For instance, a randomised trial of 240 patients showed that supplementation with a single very large dose of 200,000 IU of vitamin D3 that increased serum vitamin D levels (21–44 ng/ml) was nonetheless ineffective in decreasing the length of hospital stay or any other clinical outcomes among hospitalized patients with severe COVID-1925. It has been estimated that one SD change in standardized natural-log transformed 25-OHD levels corresponds to a change in 25-OHD levels of 29.2 nmol/l in vitamin D insufficient individuals (serum 25-OHD levels 50 nmol/l), which is comparable to the 21.2 nmol/l mean increase in 25-OHD levels conferred by taking daily 400 IU of cholecalciferol, the amount of vitamin D most often found in vitamin D supplements26. This estimation has clinical implication on the dose of vitamin D supplement for disease prevention. Given the lack of highly effective therapies against COVID-19, it is important to remain open-minded to emerging results from rigorously conducted studies of vitamin D.

In conclusion, we found no significant associations between COVID-19 risk and measured 25-OHD levels after adjusted for covariates, but this finding is limited by the fact that the vitamin D levels were measured on average 11 years before the pandemic. Ambient UVB was strongly and inversely associated with COVID-19 hospitalization and death. The main MR analysis did not show that genetically-predicted vitamin D levels were causally associated with COVID-19 risk, although MR sensitivity analyses indicated a potential causal effect. Overall, the effect of vitamin D levels on the risk or severity of COVID-19 remains controversial, further studies are needed to validate vitamin D supplementation as a means of protecting against worsened COVID-19.

Sep 14, 2021

Scientists Say They Could Bring Back Woolly Mammoths. But Maybe They Shouldn’t

Posted by in categories: bioengineering, biotech/medical, genetics

A company formed by Harvard genetics professor George Church, known for his pioneering work in genome sequencing and gene splicing, hopes to genetically resurrect woolly mammoths.

Sep 14, 2021

Study Finds Evidence of Possible Link Between Herpes Simplex and Neurogenerative Diseases

Posted by in categories: biotech/medical, genetics, life extension, neuroscience

Because the herpesvirus sits in neurons forever, there is speculation it is connected to neurodegenerative diseases. The immune system requires inflammation to constantly fight off the virus, and neurons have some degree of damage because of this continuous immune response, according to Dr. Tibor Valyi-Nagy, professor of pathology, director of neuropathology at UIC and research collaborator on the study.


Summary: Researchers discovered mutations of the OPTN gene resulted in increased herpesvirus 1 growth in the brains of mice, leading to the death of local neurons. This resulted in accelerated neurodegeneration. OPTN deficiency was also associated with impairments in immune response. While these findings are specific to the HSV-1 virus, researchers believe the findings may apply to up to eight herpesvirus infections.

Source: University of Illinois at Chicago

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Sep 13, 2021

A fountain of youth for ageing stem cells in bone marrow

Posted by in categories: biotech/medical, genetics, life extension

As we age, our bones become thinner, we suffer fractures more often, and bone-diseases such as osteoporosis are more likely to occur. One responsible mechanism involves the impaired function of the bone-marrow stem cells, which are required for the maintenance of bone integrity. Researchers from the Max Planck Institute for Biology of Ageing and CECAD Cluster of Excellence for Ageing Research at the University of Cologne have now shown that the reduced stem cell function upon aging is due to changes in their epigenome. They were able to reverse these changes in isolated stem cells by adding acetate. This fountain of youth for the epigenome could become important for the treatment of diseases such as osteoporosis.

Aging Researchers have been looking at epigenetics as a cause of aging processes for some time. Epigenetics looks at changes in and chromosomes that do not alter the sequence of the genes themselves, but do affect their activity. One possibility is changes in proteins called histones, which package the DNA in our cells and thus control access to DNA. The Cologne research group of Peter Tessarz has now studied the epigenome of mesenchymal . These stem cells are found in marrow and can give rise to different types of cells such as cartilage, bone and fat cells.

Sep 13, 2021

A Clever ‘Gene Silencing’ Injection Has Been Approved For Treating High Cholesterol

Posted by in categories: biotech/medical, genetics

This is an emerging therapeutic technique that works by targeting the underlying causes of a disease, rather than the symptoms it causes. It does this by targeting a particular gene, and preventing it from making the protein that it produces.


The United Kingdom’s NHS has very recently approved a new cholesterol-lowering jab which will be offered to 300,000 people over the next three years.

The drug – inclisiran – will be administered twice a year as an injection.

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Sep 12, 2021

New programmable gene editing proteins found outside of CRISPR systems

Posted by in categories: bioengineering, biotech/medical, genetics

Within the last decade, scientists have adapted CRISPR systems from microbes into gene editing technology, a precise and programmable system for modifying DNA. Now, scientists at MIT’s McGovern Institute and the Broad Institute of MIT and Harvard have discovered a new class of programmable DNA modifying systems called OMEGAs (Obligate Mobile Element Guided Activity), which may naturally be involved in shuffling small bits of DNA throughout bacterial genomes.

These ancient DNA-cutting enzymes are guided to their targets by small pieces of RNA. While they originated in bacteria, they have now been engineered to work in human cells, suggesting they could be useful in the development of gene editing therapies, particularly as they are small (~30% the size of Cas9), making them easier to deliver to cells than bulkier enzymes. The discovery, reported in the journal Science, provides evidence that natural RNA-guided enzymes are among the most abundant proteins on earth, pointing toward a vast new area of biology that is poised to drive the next revolution in genome editing technology.

The research was led by McGovern investigator Feng Zhang, who is James and Patricia Poitras Professor of Neuroscience at MIT, a Howard Hughes Medical Institute investigator, and a core institute member of the Broad Institute. Zhang’s team has been exploring natural diversity in search of new molecular systems that can be rationally programmed.

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Sep 10, 2021

Researchers decipher genetic mechanism that makes the midge invulnerable to harsh conditions

Posted by in categories: biotech/medical, evolution, genetics

Circa 2014


New collaborative research published in the journal Nature Communications by scientists from Japan, Russia and the US contains the genetic analysis on a species of African midge, which can survive a wide array of extreme conditions including large variations in temperature, extreme drought and even airless vacuums such as space. The team successfully deciphered the genetic mechanism that makes the midge invulnerable to these harsh conditions. Prof. Noriyuki Satoh and Dr. Takeshi Kawashima of Prof. Satoh’s Marine Genomics Unit, as well as Prof. Alexander Mikeyhev of the Ecology and Evolution Unit, and Mr. Manabu Fujie and Dr. Ryo Koyanagi of the DNA Sequencing Section at the Okinawa Institute of Science and Technology Graduate University have contributed to the collaboration.

The midge, Polypedilum vanderplanki, is capable of anhydrobiosis, a unique state that allows an organism to survive even after losing 97% of its body water. Anhydrobiotic organisms are also able to survive other severe conditions such as extreme temperatures ranging from 90°C to-270°C, vacuums and high doses of radiation; all of which would be lethal to most other life forms.

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Sep 10, 2021

New tool reveals genetic influence of some sex-biased diseases, including lupus

Posted by in categories: biotech/medical, genetics, neuroscience, sex

Many human diseases can differ between males and females in their prevalence, manifestation, severity or age of onset. Examples include Lupus, where more than 80% of patients are females; Alzheimer’s disease, where females have higher incidence and tend to suffer quicker cognitive decline; and COVID-19 infections that are frequently more severe in males.

These sex differences may have a that is attributable to the sex . The X chromosome—one of the two sex chromosomes—is known to play an important role in human development and disease. New research led by Penn State College of Medicine reveals for the first time that sex-biased diseases can be attributable to that escape X chromosome inactivation (XCI), a process that ensures that females do not overexpress genes on their X-chromosomes.

The team developed a that can identify these XCI escape genes, and it may also help in determining whether a female will develop a sex-biased disease and if the disease will become progressively worse over time. The tool may even be useful in understanding the in immune responses to COVID-19, as the disease is thought to produce more severe symptoms and higher mortality in men than in women.

Sep 9, 2021

The Big Bang and the genetic code

Posted by in categories: chemistry, cosmology, genetics, humor, particle physics

Circa 2000


A 1940 paper by Gamow and Mario Schoenberg was the first in a subject we now call particle astrophysics. The two authors presciently speculated that neutrinos could play a role in the cooling of massive collapsing stars. They named the neutrino reaction the Urca process, after a well known Rio de Janeiro casino. This name might seem a strange choice, but not to Gamow, a legendary prankster who once submitted a paper to Nature in which he suggested that the Coriolis force might account for his observation that cows chewed clockwise in the Northern Hemisphere and counterclockwise in the Southern Hemisphere.

In the 1940s Gamow began to attack, with his colleague Ralph Alpher, the problem of the origin of the chemical elements. Their first paper on the subject appeared in a 1948 issue of the Physical Review. At the last minute Gamow, liking the sound of ‘alpha, beta, gamma’, added his old friend Hans Bethe as middle author in absentia (Bethe went along with the joke, but the editors did not). Gamow and Alpher, with Robert Herman, then pursued the idea of an extremely hot neutron-dominated environment. They envisioned the neutrons decaying into protons, electrons and anti-neutrinos and, when the universe had cooled sufficiently, the neutrons and protons assembling heavier nuclei. They even estimated the photon background that would be necessary to account for nuclear abundances, suggesting a residual five-degree background radiation.

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Sep 9, 2021

Gene self-correction in ‘chromosome caps’ can beat mutations, help prevent blood cancers

Posted by in categories: biotech/medical, genetics, life extension

Mentions telomeres.

~~~


People with rare disorders that cause shortened telomeres—protective caps that sit at the end of chromosomes—may be more likely to have blood cancers such as leukemia or myelodyplastic syndrome. Now, Johns Hopkins Medicine scientists have discovered several “self-correcting” genetic mutations in bone marrow that may protect such patients from these cancers.

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