Culture

New double-contrast technique picks up small tumors on MRI

image: A new technique developed by researchers at UC Davis offers a significant advance in using magnetic resonance imaging to pick out even very small tumors from normal tissue. The team created a probe that generates two magnetic resonance signals that suppress each other until they reach the target, at which point they both increase contrast between the tumor and surrounding tissue.

Image: 
Xiandoing Xue, UC Davis

researchers at the University of California, Davis offers a significant advance in using magnetic resonance imaging to pick out even very small tumors from normal tissue. The work is published May 25 in the journal Nature Nanotechnology.

Chemical probes that produce a signal on magnetic resonance imaging (MRI) can be used to target and image tumors. The new research is based on a phenomenon called magnetic resonance tuning that occurs between two nanoscale magnetic elements. One acts to enhance the signal, and the other quenches it. Previous studies have shown that quenching depends on the distance between the magnetic elements. This opens new possibilities for non-invasive and sensitive investigation of a variety of biological processes by MRI.

The UC Davis team created a probe that generates two magnetic resonance signals that suppress each other until they reach the target, at which point they both increase contrast between the tumor and surrounding tissue. They call this two-way magnetic resonance tuning (TMRET).

Combined with specially developed imaging analysis software, the double signal enabled researchers to pick out brain tumors in a mouse model with greatly increased sensitivity.

"It's a significant advance," said senior author Yuanpei Li, Associate Professor of biochemistry and molecular medicine at the UC Davis School of Medicine and Comprehensive Cancer Center. "This could help detect very small early-stage tumors."

Two magnetic components

The probe developed by the UC Davis team contains two components: nanoparticles of superparamagnetic iron oxide (SPIO), and pheophorbide a-paramagnetic manganese (P-Mn), packaged together in a lipid envelope. SPIO and P-Mn both give strong, separate signals on MRI, but as long as they are physically close together those signals tend to cancel each other out, or quench. When the particles enter tumor tissue, the fatty envelope breaks down, SPIO and P-Mn separate, and both signals appear.

Li's laboratory focuses on the chemistry of MRI probes and developed a method to process the data and reconstruct images, which they call double-contrast enhanced subtraction imaging or DESI. But for expertise in the physical mechanisms, they reached out to Professors Kai Liu and Nicholas Curro at the UC Davis Department of Physics (Liu is now at Georgetown University). The physicists helped elucidate the mechanism of the TMRET method and refine the technique.

The researchers tested the method in cultures of brain and prostate cancer cells and in mice. For most MRI probes, the signal from the tumor is up to twice as strong as from normal tissue - a "tumor to normal ratio" of 2 or less. Using the new dual-contrast nanoprobe, Li and colleagues could get a tumor-to-normal ratio as high as 10.

Li said the team is interested in translating the research into clinical use, although that will require extensive work including toxicology testing and scaling up production before they could apply for investigational new drug approval.

Credit: 
University of California - Davis

Study reveals first evidence inherited genetics can drive cancer's spread

image: When researchers analyzed the immune cells in the tumors and grouped them by type, they found more cancer-fighting cells in mice with ApoE4.

Image: 
Elizabeth and Vincent Meyer Laboratory of Systems Cancer Biology at The Rockefeller University

Sometimes cancer stays put, but often it metastasizes, spreading to new locations in the body. It has long been suspected that genetic mutations arising inside tumor cells drive this potentially devastating turn of events.

Now researchers have shown for the first time that our own pre-existing genetics can promote metastasis.

A new study, published May 25 in Nature Medicine, suggests that differences in a single gene, carried within someone's genome from birth, can alter progression of melanoma, a type of skin cancer. The researchers suspect these inherited variations may have the same effect on other types of cancer as well.

"Patients often ask 'Why am I so unlucky? Why did my cancer spread?' As doctors, we never had an answer," says lead investigator Sohail Tavazoie, Leon Hess Professor and senior attending physician. "This research provides an explanation."

The discovery may transform how scientists think about cancer metastasis, and lead to a better understanding patients' risks in order to inform treatment decisions, Tavazoie says.

The mystery of metastasis

Metastasis occurs when cancer cells escape the original tissue to establish new tumors elsewhere, a phenomenon that leads to the majority of cancer deaths. Scientists have suspected that cancer cells, which initially emerge due to mutations inside normal cells, gain their travelling ability following further mutations. But after decades of searching, they have yet to find such a genetic change that could be proven to encourage metastasis.

Previous research in Tavazoie's lab had identified a gene called APOE, present in the DNA of all of the body's cells before any cancer arises, that can impact the spread of melanoma. The gene produces a protein that appears to interfere with a number of processes used by cancer cells to metastasize, such as forming blood vessels, growing deeper into healthy tissue, and withstanding assault from tumor-fighting immune cells.

Humans, however, carry one of three different versions of ApoE: ApoE2, ApoE3, and ApoE4. Benjamin Ostendorf, a physician scientist in the lab, hypothesized that these variants could explain why melanoma progresses differently in different people.

In experiments with mice possessing one of each of the versions of the gene, he and colleagues found tumors in those with ApoE4 grew the smallest and spread the least.

A closer look revealed that ApoE4 is the most effective version of ApoE in terms of enhancing the immune response to tumor cells. Compared to animals with other variants, the mice carrying ApoE4 showed a greater abundance of tumor-fighting T cells recruited into the melanoma tumor, as well as reduced blood vessels.

"We think that a major impact of the variations in ApoE arises from differences in how they modulate the immune system's attack," Ostendorf says.

Toward better treatment

Genetic data from more than 300 human melanoma patients echoed the mouse experiments: On average, people with ApoE4 survived the longest, while those with ApoE2 lived the shortest. This connection to outcomes suggests that doctors could look at patients' genetics to assess the risk of their cancer progressing.

It could also influence the course of treatment. Melanoma patients are sometimes given therapy that encourages their own immune systems to better fight the cancer. The team's analysis of information from such patients, as well as experiments with mice, showed that those with ApoE4 respond best to immune-boosting therapies.

Likewise, the researchers showed that an experimental compound that increases production of ApoE, RGX-104, was effective at helping mice with ApoE4 fight off tumors. RGX-104 is currently in clinical trials. (Tavazoie is a scientific cofounder of Rgenix, the company that developed RGX-104.)

Further research is needed to determine how to optimize treatments for patients with other ApoE variants, Tavazoie says. ApoE2, for instance, was associated with an increased risk of metastasis. The researchers evidence so far suggests that ApoE3's metastasis-suppressing ability falls between that of the other two. "We need to find those patients whose genetics put them at risk for poor survival and determine what therapies work best for them," Tavazoie says.

The implications may extend beyond cancer. Other studies have shown that variations in ApoE contribute to Alzheimer's disease: ApoE4 aggravates risk of this neurodegenerative disorder, in contrast to its suppression of cancer progression.

"It's not quite clear what ApoE does in Alzheimer's, but we believe our work in cancer can inform our understanding of this disease as well," Tavazoie says. His lab, normally focused on cancer, has begun investigating the connection to the neurodegenerative disorder.

Credit: 
Rockefeller University

Synthesis of prebiotic peptides gives clues to the origin of life on Earth

image: Time dependencies of the glycylglycine (a, c) and diglycylgly-cine (b, d) concentrations (data obtained by HPLC) and their yields for the glycine-sodium trimetaphosphate-imidazole (1:1:1) system at 75 °C with different pH values (a, b) and at different temperatures with pH 9.5 (c, d); initial concentrations c0 = 0.1 M, reactor residence time τr = 16 min, total volume Vt = 25 ml, reactor volume Vr = 16 ml

Image: 
Kazan Federal University

Coordination Compounds Lab of Kazan Federal University started researching prebiotic peptide synthesis in 2013 with the use of the ASIA-330 flow chemistry system. Many lab projects are devoted to the problem of selectivity and specificity of processes in living nature. This problem is directly related to prebiotic chemistry, whose foundations were laid as a result of the amino acids synthesis by the German chemist Adolph Friedrich Ludwig Strecker (the Strecker reaction, 1851) and of the sugar synthesis by the Russian chemist, the founder of the Kazan Chemical School, Alexander Butlerov (the formose reaction, 1861). Studies on the prebiotic synthesis of sugars and peptides are aimed at a deeper understanding of the most fundamental and intriguing problem of our time - the origin of life.

The kinetics of oligopeptides formation in the flow systems glycine - sodium trimetaphosphate - imidazole/N-methylimidazole at thermocyclic regime was investigated by liquid chromatography (HPLC) and 31P NMR methods in the ranges of temperature from 45 to 90°C and pH from 8.5 to 11.5. Formation of significant amounts of glycylglycine (yield up to 52%) and diglycylglycine was revealed. Better results are obtained at 75°C in slightly alkaline conditions (pH 9.5-10.5), and in the presence of imidazole yields of oligopeptides are bigger than without this heterocycle. It should be mentioned that the used non-equilibrium regime of the glycylglycine and diglycylglycine syntheses turns out to be one of the most effective among all prebiotic syntheses reported so far in the literature, both in the absence and in the presence of imidazole. Earlier, H. Sawai and L.E. Orgel discovered that heterocycles, such as imidazole, can increase yields of peptides in solid state (Sawai H., Orgel L.E. (1975) J. Mol. Evol. 6:185-197. doi:10.1007/bf01732355). However, the proposed explanation of the catalytic effect of imidazole due to initial formation of N-triphosphoryl imidazole as a key intermediate is not working in the reactions studied by us because in the imidazole - trimetaphosphate mixture signals of any imidazole N-phosphates are absent in 31P NMR spectra. In this situation, a new imidazole catalysis mechanism by which imidazole reacts with cyclic N,O-phosphoryl glycine giving N-imidazolyl-O-glycyl phosphate as a key intermediate was proposed and validated in the present investigation. Detailed reaction mechanisms were proposed and justified by quantum chemical calculations using density functional theory (DFT) method at the high level (CAM-B3LYP/TZVP) with accounting solvent effect by the polarized continuum model (?-PCM). It is emphasized that while in the absence of imidazoles, prebiotic activation of amino acids occurs at the N-terminus, and in the presence of imidazoles it shifts to the O-terminus. This means that in the peptide elongation N-imidazolyl-O-aminoacyl phosphates play in prebiotic systems the outstanding role similar to that of aminoacyl adenylates formed at the ATP and aminoacyl-tRNA synthetases presence in biosystems. This seems to be a key pathway for prebiotic evolution in terms of peptide synthesis. So, the new crucial role of imidazoles in prebiotic evolution was discovered. The systems used and modes of their conversion can be good models for prebiotic peptide syntheses in a flow thermocyclic regime, including prebiotic peptide syntheses under conditions of various hydrothermal systems, particulary in Kamchatka, where temperature and pressure fluctuations are detected and pH varies from 2.0 to 9.5 while temperature ranges from 55 to 98oC in hot springs.

The work is of importance for the development of the problem of prebiotic peptide synthesis. The results can be used in the synthesis of small oligopeptides. In addition, the used experimental setup in combination with mathematical modeling and quantum-chemical calculations can be used to study other processes in the thermocyclic mode. The fact that N-methylimidazole has catalytic effect on the prebiotic peptide synthesis is especially important because similar heterocycles can be formed under shock exposure at prebiotic conditions (Shtyrlin V.G. et al. (2019) Orig. Life Evol. Biosph. 49:1-18. doi:10.1007/s11084-019-09575-8). In the cited work, it was found that upon impact on the water - formamide - bicarbonate - sodium hydroxide system, placed in a stainless steel preservation capsule, 7 imidazole derivatives (out of 21 products) are formed. It was established that the most effective syntheses proceed at pH ~9.5, and ammonia and formaldehyde are formed among many intermediate products. Note that according to the results of the cited study, a new hypothesis about the origin of life was proposed: life could have originated due to the impact of meteorites on alkaline water-formamide lakes located near volcanoes on the early Earth.

Further research can pertain to the synthesis of oligopeptides containing other amino acids and the synthesis of other biopolymers, primarily sugars. Particular attention will be paid to experimental and theoretical studies of mechanisms of heterogeneous catalysis in prebiotic syntheses of biopolymers. The focus will be on the role of coordination and complexation with metals in prebiotic syntheses, since metal complexes could control the stereoselectivity and specificity of many vital processes at the first stages of biochemical evolution.

Credit: 
Kazan Federal University

MetaviralSPAdes -- New assembler for virus genomes

When a new virus emerges, biologists rush to reconstruct its genome - a prerequisite for future diagnostic and vaccine development. The challenge with viral sequencing during an outbreak is that a sample from a patient, like saliva from a COVID-19 patient that was used for the very first SARS-COV-2 coronavirus sequencing effort, contains genomes of many other, often harmless, viruses. Not to mention hundreds of much larger bacterial genomes that live in our mouth and make it difficult to find the viral sequences among them.

It raises the challenge of metagenome sequencing, reading hundreds of genomes at once, a more difficult computational problem than sequencing a single genome. Metagenome sequencing results in 1000s sequences representing pieces of various viral and bacterial genomes and it remains unclear which of these pieces represent the genome of the pathogen. The next task, known as metavirome sequencing, is to identify various viral sequences (hidden among much longer bacterial sequences!) and stitch them together into a complete viral genome of a pathogen that caused the outbreak.

There was no specialized viral metagenome assembler until recently. But the joint team of Russian and US researchers from Saint-Petersburg State University and University of California at San Diego just released the metaviralSPAdes assembler (published in journal Bioinformatics on May 16) that turns the analysis of the metavirome sequencing results into an easy task.

Biologists still cannot read the entire genome in the same way we read a book from the beginning to the end - instead they read small snippets of a genome. Genome assembly is not unlike putting together a puzzle from a million such pieces, and it is often viewed as one of the most difficult algorithmic problems in bioinformatics. Nevertheless, the most widely used genome assembler today, called SPAdes, was used in nearly 9000 papers. It was used to analyze pathogens causing MERS in Saudi Arabia (Cotten et al., Lancet 2013), Ebola in Congo (Maganga et al., New England Journal of Medicine, 2013), gonorrhoea in England (Chisholm et al., Sex Transm Infect, 2016), meningitis in Ghana (Kwambana-Adams et al., BMC Infectious Diseases 2016), dengue in Sumatra (Sasmono et al., Am. J. Trop. Med. Hyg. 2017), and dozens other outbreaks in the last eight years since SPAdes was released.

However, metagenome assembly of a 1000 genomes is much more difficult than assembly of a single genome. It is not unlike putting together a 1000 puzzles (each with a million pieces!) at once, from a huge pile of a billion pieces from all these puzzles, all mixed together in a single bag. However, three years ago, the same Russian-US team that developed SPAdes, also developed metaSPAdes to address these challenges. metaSPAdes has quickly become a leading metagenomic assembler that has already been applied in over 500 metagenomic projects.

However, it is not trivial to extract viral sequences from a huge metaSPAdes output, as a virus genome is hiding among thousands of pieces of reconstructed bacterial genomes.
New metaviralSPAdes assembler not only finds such pieces of viral sequences but also stitches them together into the completed genome.

The COVID-19 pandemic is a wake-up call for biologists studying transmission of viruses from animal to humans. It emphasizes the importance of viral surveillance in various animal hosts such as going to caves where bats live, collecting their fecal samples, and studying the huge repertoire of bat viruses BEFORE rather than AFTER a pandemic strikes. Bats have an unparalleled immune system that allows them to co-exist with a multitude of viruses that can kill humans. However, in addition to the logistics of collecting all such samples, building a census of various viral genomes across various animals is a difficult computational problem.

With metaviralSPAdes at hand, biologists can now reconstruct these viral genomes in bats or any other potential sources of future pandemics.

Credit: 
St. Petersburg State University

COVID-19 should be treated as a thrombotic disease, Brazilian pulmonologist argues

image: Thorax tomography showing pulmonary changes observed in patients with COVID19.

Image: 
Elnara Negri

The hypothesis that blood clotting disorders may explain some of the worst symptoms of COVID-19, including respiratory failure and pulmonary fibrosis, was suggested in mid-April by researchers in Brazil affiliated with the University of São Paulo’s Medical School (FM-USP) via an article accepted for publication by the Journal of Thrombosis.

In less than a month, the topic had been highlighted in articles posted to the websites of Science and Nature, both of which are among the world’s leading scientific publications.

One of the first scientists to report the “thrombotic nature” of the disease caused by the novel coronavirus (SARS-CoV-2) was Elnara Negri, a researcher and pulmonologist at Hospital das Clínicas, the hospital complex run by FM-USP – the largest in Latin America – and Hospital Sírio-Libanês, a leading private hospital also in São Paulo City.

“Around March 25, we were treating a patient whose breathing was rapidly deteriorating,” Negri told Agência FAPESP. “When she was intubated, I observed that her lungs were easy to ventilate. They weren’t hardened and stiff, as you’d expect in someone with acute respiratory distress. Shortly thereafter, I noticed that the patient had an ischemic toe.”

The latter condition has been referred to as COVID-toe and can affect all ten toes. It is caused by the obstruction of the small blood vessels that circulate blood in the feet. Negri observed a similar phenomenon many years ago in patients who underwent open heart surgery with extracorporeal circulation.

“In the old days, a device was used to pump oxygen into the blood, and clots would form inside the blood vessels. I’d seen the condition before and knew how to treat it,” she said.

Negri prescribed heparin, one of the most widely used anti-coagulant drugs worldwide. In under 18 hours, the patient’s oxygen saturation improved, and her angry red toe regained a healthy pink color. The same effect was achieved with other patients treated at the Sírio-Libanês. “Since that day, we’ve treated approximately 80 COVID-19 patients, and so far, none of them has died. Four are currently in the ICU [intensive care unit]. The rest are in the ward or have been discharged,” Negri said.

Most studies show that severe COVID-19 patients require 28 days of mechanical ventilation on average, whereas those treated with heparin typically improve after ten to 14 days of intensive care.

An article by Negri and colleagues describing their clinical experience with the first 27 patients who were treated with the protocol developed at Sírio-Libanês is available on medRxiv as a preprint (not yet peer-reviewed) version.

Pathological evidence

Shortly after the first successful administration of heparin, Negri shared the finding with colleagues Marisa Dolhnikoff and Paulo Saldiva, pathologists at FM-USP who are coordinating the autopsies of patients who die from COVID-19 at Hospital das Clínicas.

Using a minimally invasive technique developed during a project supported by FAPESP, the pathologists observed focal bleeding associated with mini-clots (microthrombi) in the small blood vessels of the lungs due to platelet clumping (more at: agencia.fapesp.br/32955 and agencia.fapesp.br/32810).

Negri, Dolhnikoff, Saldiva and colleagues recently wrote to the editor of the Journal of Thrombosis and Haemostasis, describing their findings. Entitled “Pathological evidence of pulmonary thrombotic phenomena in severe COVID-19”, this is the first article in the scientific literature to report this topic. Fully peer-reviewed and accepted for publication by the journal, the study could potentially revolutionize treatment of the disease.

Paradigm shift

SARS-CoV-2 was not the first coronavirus (CoV) to cause a public health crisis. The 2002-04 global outbreak of severe acute respiratory syndrome (SARS) caused almost 800 deaths, and Middle East respiratory syndrome (MERS) has killed 850 people since 2012. Both are coronavirus diseases. Neither has reached Brazil so far.

“Patients with SARS or MERS develop a strong inflammatory reaction in the lungs, and this can lead to a condition known as acute respiratory distress,” Negri said. “The pulmonary alveoli, the tiny sacs in which carbon dioxide is exchanged for oxygen, fill up with dead cells, pus, and other inflammatory substances, hardening the lung tissue and impairing oxygenation of the organism.”

COVID-19 is different, at least initially, Negri added. SARS-CoV-2 does not cause severe inflammation of the lungs but does cause desquamation of the alveolar epithelial tissue.

“The epithelial cells die after being infected, fall into the alveolar lumen and leave the basement membrane exposed,” she said. “The organism’s defense system thinks the region is raw or ulcerated and assumes there’s a risk of hemorrhage, triggering a storm of interleukins [proteins that act as immune signalers] and what we call a ‘coagulation cascade’. The platelets begin clumping together to form clots and ‘plug the leak’.”

The clots block the lung’s small blood vessels and cause microinfarcts (cellular death or tissue necrosis). The regions of tissue that die due to a lack of blood supply are replaced by scar tissue in a process called fibrosis. In addition, microthrombi at the alveolar-blood vessel interface prevent the passage of oxygen to smaller arteries.

“This explains why COVID-19 patients may not have difficulty breathing even though their oxygen saturation is low. Many come to hospital walking and talking and very soon have to be intubated,” Negri said.

If the intravascular clotting is not rapidly treated, microinfarcts and fibrosis tend to spread throughout the lungs. Opportunistic bacteria and fungi may infect the damaged tissue and cause pneumonia, as SARS-CoV-2 leads to a decrease in the number of immune cells (lymphopenia). The patient may develop acute respiratory distress at the end of this process.

Heparin helps avert this outcome via two mechanisms. Negri found that the drug dissolves the microthrombi that prevent oxygen from flowing from the alveoli to the pulmonary blood vessels and contributes to the regeneration of the vascular endothelium, the layer of epithelial cells that line the interior of blood vessels.

“Damaged endothelium is like a road full of potholes. It hinders the flow of blood and leads to more clotting. This creates a snowball effect,” Negri said.

A third possible mechanism of action of heparin was described by a study recently conducted at the Federal University of São Paulo (UNIFESP) with FAPESP’s support. In vitro experiments by the biomedical scientist Helena Bonciani Nader and colleagues showed that heparin brings about a 70% reduction in cell invasion by SARS-CoV-2 (more at: agencia.fapesp.br/33200).

“There may be an anti-viral effect, which should be investigated in greater depth. As I like to say, we’re changing tires without stopping the car,” Negri said.

In Negri’s opinion, however, many lives may have been lost because patients diagnosed with COVID-19 were treated from the start as cases of acute respiratory syndrome and placed in ICU beds with lower levels of hydration and more intense mechanical ventilation. “These two approaches worsen the thrombotic condition. We need to change the treatment paradigm,” she said.

Negri would like heparin to be administered as soon as the oxygen saturation level falls below 93%, which may happen between the seventh and tenth days after the onset of flu-like symptoms and can be detected by a physician in a private or public clinic.

“It’s pointless to buy the drug from a pharmacy and swallow a pill,” she warned. “That will have no therapeutic effect and could cause bleeding. It must be injected, and a medic must calculate the right dose.”

It should be stressed that heparin has significant effects on various physiological processes, and if the drug is administered without medical supervision, it can endanger the patient’s life. Self-medication and failure to take side effects into account are particularly hazardous in the case of treatment for COVID-19.

Definitive evidence

A randomized clinical trial will be needed to demonstrate the therapeutic efficacy of heparin in COVID-19 patients. This means there need to be two randomly chosen groups with similar characteristics, only one of which receives the drug. The results for this group are then compared with the outcomes for the group not given the drug.

The FM-USP researchers plan to begin this project shortly, in partnership with colleagues at the University of Toronto (Canada) and the University of Amsterdam (Netherlands). They are only waiting for approval from the Ethics Committee at Hospital das Clínicas and Brazil’s National Research Ethics Committee (CONEP).

“The trial will entail giving heparin to patients who come to the outpatient clinic with low oxygen saturation levels and seeing if treatment with the anti-coagulant can avoid the need for mechanical ventilation,” Negri said.

The article “Pathological evidence of pulmonary thrombotic phenomena in severe COVID-19” by Marisa Dolhnikoff, Amaro Nunes Duarte-Neto, Renata Aparecida de Almeida Monteiro, Luiz Fernando Ferraz da Silva, Ellen Pierre de Oliveira, Paulo Hilário Nascimento Saldiva, Thais Mauad, and Elnara Marcia Negri can retrieved from onlinelibrary.wiley.com/doi/epdf/10.1111/jth.14844.

Journal

Journal of Thrombosis and Haemostasis

DOI

10.1111/JTH.14844

Credit: 
Fundação de Amparo à Pesquisa do Estado de São Paulo

The evolutionary history of the Milky Way determined in more detail than ever

video: Simulation showing the drastic episodes of star formation produced by the approach and interaction of the Sagittarius dwarf galaxy with the Milky Way 6,000, 2,000 and 1,000 billion years ago.

Image: 
Sagittarius orbital evolution adapted from David R. Law (Dunlap Institute, University of Toronto). Gabriel Pérez Díaz, SMM (IAC).

The Milky Way, the whiteish strip of light which is prominent in both the summer and the winter skies, is the densest part of the disc of the Galaxy which we are inside. However, over very long periods it has not always looked the same, and its evolution is a challenge to current astrophysics.

To study this evolution, ESA's Gaia mission is measuring the luminosities, positions, motions, and the chemical composition of a large number of individual stars in our Galaxy.

Combining apparent luminosity with measured distance, astronomers at the IAC have found the intrinsic luminosity of 24 million stars within a sphere of 6,500 light years around our Sun. Comparing their luminosities and colours with accurate models of stars they have obtained the most detailed evolutionary history of the Milky Way up to now.

Irregular rate

"We might well have expected that the Milky Way did not form stars at a constant rate throughout its history, but we didn't expect such well defined periods of great activity", comments Tomás Ruiz Lara, an IAC astrophysicist and the first author of the article.

Some 13 billion years ago star formation was violent and sustained, but the rate at which stars formed declined gradually as time passed.

However, superposed on this simple behaviour, there were dramatic episodes of star formation, during which the rate grew to four times the normal value. The first took place some 5-6 billion years ago, followed by others, 2 billion, one billion, and one hundred million years ago. But it wasn't known what could provoke such violent events in a system as massive as our Galaxy.

For an answer to this question we need to know that the Milky Way, although in a relatively empty zone of the universe, is not completely isolated: together with our neighbour the Andromeda galaxy (M31) and tens of much smaller galaxies (called dwarfs) which go round it in orbit, it is part of the so-called Local Group.

Among the nearby dwarf galaxies, the Sagittarius dwarf is prominent, and currently is in full interaction with our Galaxy. But this is not happening only just now, complex simulations suggest that already some 5 to 6 billion years ago Sagittarius made its first approach to the Milky Way. This approach was repeated 2 and 1 billion years ago, coinciding exactly with the star formation events revealed in this study (as well as in the Sagittarius galaxy itself).

"Everything indicates -explains Carme Gallart, an IAC researcher and a member of the team- that these interactions between the two systems were able to stimulate the formation of new stars in our galaxy, drastically affecting its evolution. These results question some of the current models of star formation in galaxies, and put constraints on future theoretical studies".

An unexpected implication of this work is to situate our Solar System in its context. The Solar System formed some 4,700 billion years ago, from the collapse of a large cloud of gas and dust. "It is possible -comments Tomás Ruiz Lara- that our Sun was one of the many stars formed some 5,000 billion years ago as a consequence of the interaction between our Galaxy and the Sagittarius galaxy. It could be that we are witnessing one of the key astronomical events which gave rise to the world as we know it today".

Credit: 
Instituto de Astrofísica de Canarias (IAC)

New method provides unique insight into the development of the human brain

Stem cell researchers at Lund University in Sweden have developed a new research model of the early embryonic brain. The aim of the model is to study the very earliest stages of brain to understand how different regions in the brain are formed during embryonic development. With this new insight, researchers hope to be able to produce different types of neural cells for the treatment of neurological diseases more efficiently. The study is published in the journal Nature Biotechnology.

In order to develop stem cell treatments for neurological diseases such as Parkinson's Disease, epilepsy and stroke, researchers must first understand how the human brain develops in the embryonic stage. With knowledge of how neural cells are formed at different developmental stages, researchers have the opportunity to develop new stem cell therapies more quickly in the laboratory.

"The challenge is that there are thousands of different sub-types of neural cells in the human brain, and for each disease we need to be able to produce exactly the right type of neural cell", says Agnete Kirkeby, researcher at the Wallenberg Centre for Molecular Medicine and the Department of Experimental Medical Science at Lund University.

Studies on how each individual neural cell forms in the embryo during brain development are essential for the researchers to be able to understand how to produce these specific cells in the laboratory.

Research on the early development of the human brain, from five days after the fertilisation of the cell to approximately seven weeks, have so far been difficult as researchers have not had access to human embryonic tissue from these early stages of development. Therefore, nearly all knowledge of the earliest development of the brain is based on studies in flies, chickens and mice.

"However, the composition of the human brain differs greatly from the animals' brains. Therefore, this period in the development of the human brain has long been viewed as the black box of neurology", says Agnete Kirkeby.

Together with colleagues from the University of Copenhagen and bioengineers Thomas Laurell and Marc Isaksson from the Faculty of Engineering at Lund University, Agnete and her team have now created a model that mimics the early developmentalstages of the human brain through the use of stem cells. The stem cells are cultivated in a custom-built cell culture chamber where they are exposed to an environment which resembles the environment in the early embryonic brain.

"In the laboratory model called MiSTR (Microfluidic-controlled Stem cell Regionalisation), we can create tissue that contains different brain regions next to each other, similar to an embryonic brain approximately four to five weeks after fertilisation."

"We start with a small group of cells that will form the brain and instruct the cells by exposing them to a gradient of a specific growth factor (WNT) so that they form different regions of the brain. Our model is better than previously published models because it is much more reproducible and contains more brain regions. We can now use it to study unknown characteristics in the early development of the human brain", explains Agnete Kirkeby.

Agnete Kirkeby believes that the new method may be used to investigate how brain cells in the early embryonic stages react to certain chemicals surrounding us in our daily lives

"This is a significant step forward for stem cell research. For the first time, we now have access to tissue that resembles the early embryonic brain and can therefore study processes behind brain development in a way that has not been possible before. We can for instance use it for testing how chemical substances in our environment might impact on embryonic brain development." explains Kirkeby.

Another aim for the future is to use the model to create a complete map of the development of the human brain. This will help to speed up the development of new stem cell treatments for neurological diseases.

"Once we have the map we will also become better at producing human neural cells in the laboratory that could be used for transplantations, regenerative therapy and to study the brain's function as well as different disease states. . It took us ten years to develop a stem cell treatment for Parkinson's disease because our methods were dependent on trial and error. Our goal is that this process will be much faster in the future for other diseases", concludes Agnete Kirkeby.

Credit: 
Lund University

COVID-19 news from Annals of Internal Medicine

Below please find a summary and link(s) of new coronavirus-related content published today in Annals of Internal Medicine. The summary below is not intended to substitute for the full article as a source of information. A collection of coronavirus-related content is free to the public at http://go.annals.org/coronavirus.

1. Loss of Smell and Taste in 2013 European Patients With Mild to Moderate COVID-19

The COVID-19 pandemic has spread worldwide rapidly. Commonly reported symptoms, such as fever, cough, dyspnea, fatigue, and myalgia, are nonspecific, and the lack of testing in some European countries may make the diagnosis of COVID-19 challenging. However, two distinctive symptoms were identified recently: loss of smell and loss of taste. The authors from University of Mons; Mons, Belgium and Université Libre de Bruxelles; Brussels, Belgium used a standardized online questionnaire to collect clinical and epidemiologic data from 2,153 consecutive hospitalized and ambulatory patients in 18 European hospitals with mild-to-moderate COVID-19 to evaluate the prevalence and features of, as well as recovery from, smell dysfunction. The authors found that the prevalence of self-reported smell and taste dysfunction is higher than previously reported and may be characterized by different clinical forms. Their results suggest that anosmia may not be related to nasal obstruction or inflammation. Read the full text: https://www.acpjournals.org/doi/10.7326/M20-2428.

Media contacts: A PDF for this article is not yet available. Please click the link to read full text. The lead author, Jerome R. Lechien, MD, PhD, MS, can be reached at Jerome.Lechien@umons.ac.be.

Credit: 
American College of Physicians

Epilepsy-related deaths common in young adults and are not reducing, new research shows

image: A new study due to be presented at the European Academy of Neurology (EAN) Virtual Congress shows the burden of potentially avoidable epilepsy-related deaths in young adults remains large, with those aged between 16 and 24 having a six-fold increased risk of epilepsy-related death.

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EAN

(Vienna, Monday, 25 May, 2020) A new study presented today at the European Academy of Neurology (EAN) Virtual Congress shows the burden of potentially avoidable epilepsy-related deaths in young adults remains large, with those aged between 16 and 24 having a six-fold increased risk of epilepsy-related death.

The research found that mortality rates for epilepsy-related deaths did not decrease between 2009 (6.8 per 100,000) and 2015 (9.1 per 100,000), despite advances in treatment during this time. Young adult patients in their early 20s and 30s were found to be at the highest risk, with 78% of epilepsy-related deaths under the age of 55 years classified as potentially avoidable.

The study is being conducted in Scotland and looks to identify the burden of epilepsy-related deaths, what proportion of these are potentially avoidable, and ascertain the factors that may put patients at an increased risk.

The researchers collected anonymous data from healthcare settings for patients that died between 2009 and 2016, identifying 2,149 epilepsy-related deaths. 60% of these patients (1,276) had one or more seizure-related or epilepsy-related hospital admission in the years prior to death, yet less than a quarter (516) were seen in a neurology clinic. The most common causes of death within the study were sudden unexpected death in epilepsy (SUDEP), aspiration pneumonia, cardiac arrest, congenital malformation and alcohol-related deaths. The data will be compared with data from living patients with epilepsy of the same age and gender. These comparisons will focus on the patients' epilepsy type, socio-economic class, standards of care received, and the presence of additional disorders, such as depression.

Dr Gashirai Mbizvo, completing this Scottish Epilepsy Deaths Study (SEDS) at The University of Edinburgh, comments that "Epilepsy patients are at a higher risk of early death than the general population, but reasons for this are unclear. We hope that we can use this data to learn lessons and reduce the burden of epilepsy-related deaths in the future, many of which we believe are likely to be avoidable. Highlighting such risk factors, and identifying those that could be prevented, might lead to changes in epilepsy care and, ultimately, fewer epilepsy-related deaths in the future."

Epilepsy is a chronic noncommunicable disease of the brain that affects around 50 million people globally, making it one of the most common neurological diseases worldwide. It can cause seizures or periods of confusion in patients, which can either occur randomly or from triggers, such as a lack of sleep, stress or drinking alcohol. In many cases, people with epilepsy suffer from negative stigma and discrimination.

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Spink Health

New studies reveal extent and risks of laughing gas & stimulant abuse among young people

(Vienna, Sunday, 24 May, 2020) The extent and risks associated with recreational abuse of laughing gas and psychostimulants by young people have today been revealed in two studies reported at the European Academy of Neurology Virtual Congress.

In one study, researchers from Turkey reported increasing stimulant use among medical students approaching their final exams, despite the substantial risks to their health. In the second study, researchers from the Netherlands detailed the neurological outcomes associated with recreational use of laughing gas (nitrous oxide), suggesting that, for some individuals, permanent neurological damage can occur.

Increasing use of psychostimulants among medical students:

The increasing and widespread use of psychostimulants among medical students as they progress through their training has been revealed by a team of researchers from Istanbul in Turkey.

The team studied 194 medical students who completed an online survey evaluating their stimulant use, side effects, and academic performance grades. First-year students (n=93; control group) were compared with fourth-, fifth-, and sixth-year students (n=101; study group).

"Non-medical use of prescription stimulants has become a growing public health concern on university campuses over the past two decades," explained Dr Suna Ertu?rul from the Demiroglu Bilim University in Istanbul, Turkey, who presented the results of the study. "Medicine is one of the longest and most competitive degrees to study for and many students believe that using stimulants helps to enhance their academic performance and live an active life."

The Turkish researchers found that 16.1% of their study group were using psychostimulants such as methylphenidate and modafinil compared with 6.8% of the control group. Three-quarters of the study group reported experiencing side effects, including insomnia, high heartrates and agitation. No differences were observed in the academic performance between the stimulant users and non-users.

"Our study confirms that stimulant use increases during the course of studying for a medical degree, but that this does not improve academic performance as these students believe," said Dr Ertu?rul.

Recreational use of laughing gas:

The recreational use of laughing gas, which is used as an anaesthetic agent in dental practices and during labour, is on the increase, resulting in growing numbers of patients with neurological problems reporting to specialist outpatient clinics and emergency rooms.

"In our neurologic practice, we are seeing more and more patients with neurological problems resulting from recreational use of laughing gas," explained Dr Anne Bruijnes from the Zuyderland Medical Center in Heerlen, Netherlands, who presented the study findings at the meeting. "We saw our first patient in 2017, and since then the number has increased steadily, so we decided to conduct a retrospective study to describe the clinical features and outcomes of the patients we've seen."

According to the study team, 13 patients with an average age of 21 years were treated at the medical centre between 2017 and 2019. The most common symptoms reported were paresthesias (tingling and numbness in the hands, legs, arms and feet) and lower limb weakness. Eight patients (62%) were given a clinical diagnosis of axonal polyneuropathy, two (15%) showed evidence of spinal cord degeneration, and three (23%) showed clinical symptoms of both polyneuropathy and spinal cord degeneration (myelopolyneuropathy). All patients received vitamin B12 supplementation and were advised to stop using laughing gas.

Laughing gas usage is thought to be on the increase with one in 11 young people aged 16-24 using it annually. Many users are unaware of potential consequences, which can also include paranoia, breathing problems and even death.

"Most of our patients made a full recovery, however, some continued to have minor symptoms and three experienced difficulties with everyday activities and were referred to a rehabilitation physician," she said.

Dr Bruijnes believes the true extent of the laughing gas problem may not be known, with many abusers failing to seek medical help. "This is a major cause for concern," she said. "Whilst this study is on a relatively small sample, we know that laughing gas use is on the increase. We now know that it causes a vitamin B12 deficiency, which can affect the spinal cord and lead to permanent damage if not treated promptly."

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Spink Health

Anti-obesity medications mitigate weight regain in RYGB surgery patients

SILVER SPRING, Md.--Researchers have discovered that anti-obesity medications such as phentermine and topiramate, used individually or in combination, can significantly reduce weight regain in patients after Roux-en-Y gastric bypass surgery, according to a retrospective study published online in Obesity, the flagship journal of The Obesity Society.

"Our study provides evidence that medications can help, especially in situations where the weight gain is occurring at a rapid rate. Characterization of weight regain as a rate is novel and adds to the understanding of this important clinical problem," said Nawfal Istfan, MD, PhD, associate professor of medicine at Boston University School of Medicine and attending physician at Boston Medical Center in Boston, Mass. Istfan is the corresponding author of the study.

Weight regain after gastric bypass surgery is well recognized, normally occurring two years after the surgery and ultimately affecting 25 percent of patients. It is becoming increasingly urgent to mitigate its occurrence and preserve the metabolic and medical benefits of weight loss surgery. The application of pharmacologic agents to deal with this specific problem has been limited in the medical literature.

Researchers used the electronic medical records of nearly 1,200 multi-ethnic patients who underwent Roux-en-Y gastric bypass surgery between 2004 and 2015 at Boston Medical Center. The evaluation of weight regain was made by comparing each patient's weight during subsequent, post-operative office visits to nadir weight (lowest weight after Roux-en-Y gastric bypass surgery), taking into consideration the interval during which weight regain occurred. Seven time intervals were used in the analysis ranging from before surgery to 6 years after surgery. Patients prescribed anti-obesity medications and who came for follow-up visits were classified as adherent users, whereas those who missed follow-up visits were considered non-adherent.

After using three independent statistical models, researchers demonstrated that anti-obesity medications decrease cumulative weight regain by about 10 percent relative to nadir weight and reduce the odds of rapid weight-regain occurrence after Roux-en-Y gastric bypass surgery. Researchers also found that of the 760 patients who achieved nadir weight and are at risk for weight regain, 350 were documented users of anti-obesity medications.

These results take into account that patients typically lost weight when taking anti-obesity medications and regained weight during intervals when the medications were not prescribed. Additionally, patients started anti-obesity medications at different stages and used them at variable and intermittent periods.

The authors noted that the full potential of phentermine and topiramate and newer anti-obesity medications to counter weight recidivism and prevent the reoccurrence of obesity-related comorbidities need to be explored in further prospective clinical trials. Guidelines also need to be established for initiating and monitoring the potential long-term use of anti-obesity medications after bariatric surgery.

"One of the ways to address this particular set of limitations in future study with a prospective clinical trial would be to set specific protocols regarding use of anti-obesity medications by providers. Specifically, providing education for providers on individual anti-obesity medications for them to understand mechanisms of action, then separately creating a clinical workflow to incorporate use of anti-obesity medications, in particular settings of weight recidivism," said Crystal Johnson-Mann, MD, assistant professor, Department of Surgery, Division of Gastrointestinal Surgery, at the University of Florida College of Medicine in Gainesville. "For optimal results in a prospective trial, individual prescribing tendencies (or lack of prescribing) needs to be eliminated and be uniform across all of the providers involved in the care of these patients post-operatively."

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The Obesity Society

Researchers uncover the arks of genetic diversity in terrestrial mammals

Maximizing the protection of life on Earth requires knowledge of the global patterns of biodiversity at multiple dimensions, from genetic diversity within species, to species and ecosystem diversity. Yet, the lack of genetic sequences with geographic information at global scale has so far hindered our ability to map genetic diversity, an important, but hard to detect, biodiversity dimension.

In a new study, researchers from the Universities of Copenhagen and Adelaide have collected and georeferenced a massive amount of genetic data for terrestrial mammals and evaluated long-standing theories that could explain the global distribution of genetic diversity. They found that regions of the world rich in deep evolutionary history, such as Northern Andes, the Eastern Arc Mountains, Amazonia, the Brazilian Atlantic forest, the central America jungles, sub-Saharan Africa and south-eastern Asia are also strongholds of genetic diversity. They also show that the relatively stable climate in these regions during the past 21'000 years contributes significantly to this intraspecific richness.

"Genetic diversity within species is a critical component of biodiversity, playing two important roles at the same time. It reflects species evolutionary history and defines their capacity to adapt under future environmental change. However, and despite the predictions of major biodiversity theories, the actual global distribution of genetic diversity remained, so far, a mystery. Recent collective efforts to populate public databases with genetic sequences and their localities allowed us to evaluate these theories and generate the first global maps of genetic diversity in terrestrial mammal assemblages", says Spyros Theodoridis, Postdoctoral Researcher at the Center for Macroecology, Evolution and Climate, GLOBE Institute, and lead author of the study.

"The tropics, and more specifically tropical mountain regions, host large amounts of the global pool of genetic diversity. These arks of biodiversity are under a high pressure today due to climate and land-use change. The conservation of genetic diversity in these areas should be a priority in on-going conservation efforts", says David Nogues-Bravo, the senior author of the study and Associate Professor at the University of Copenhagen.

The study also evaluated the effects of climate change during the last 21'000 years in shaping current patterns of genetic diversity. Regions of the world that experienced less severe change in temperature and precipitation harbor higher levels of genetic diversity, potentially due to reduced population extinctions. It also suggests that past inter-annual precipitation variability contributes to higher genetic diversity possibly through population adaptive divergence.

"While we show that areas of high genetic diversity tend to occur in regions where climates have remained relatively unchanged during past periods of global-scale climate change, many of these regions are forecast to experience major climate disturbances in the near future. Unfortunately, this is likely to lead to a loss of genetic diversity in many biodiversity hotspots", says Damien Fordham, Associate Professor at The University of Adelaide's Environment Institute and a coauthor of the study.

"The identified correlations of genetic diversity with evolutionary history and past climate change allowed us to develop predictive models at global scale, particularly in regions that lack sufficient data, such as the tropics. These predictions constitute a first step towards filling major gaps of knowledge for genetic diversity, and can inform and be further validated by field-work campaigns in data-poor regions of the Earth", says Carsten Rahbek, head of the Center for Macroecology, Evolution and Climate.

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University of Copenhagen - The Faculty of Health and Medical Sciences

Artificial intelligence can make personality judgments based on our photographs

Russian researchers from HSE University and Open University for the Humanities and Economics have demonstrated that artificial intelligence is able to infer people's personality from 'selfie' photographs better than human raters do. Conscientiousness emerged to be more easily recognizable than the other four traits. Personality predictions based on female faces appeared to be more reliable than those for male faces. The technology can be used to find the 'best matches' in customer service, dating or online tutoring.

The article 'Assessing the Big Five personality traits using real-life static facial images' will be published on May 22 in Scientific Reports.

Physiognomists from Ancient Greece to Cesare Lombroso have tried to link facial appearance to personality, but the majority of their ideas failed to withstand the scrutiny by modern science. The few established associations of specific facial features, such as facial width-to-height ratio, with personality traits are quite weak. Studies asking human raters to make personality judgments based on photographs have produced inconsistent results, suggesting that our judgments are too unreliable to be of any practical importance.

Nevertheless, there are strong theoretical and evolutionary arguments to suggest that some information about personality characteristics, particularly, those essential for social communication, might be conveyed by the human face. After all, face and behaviour are both shaped by genes and hormones, and social experiences resulting from one's appearance may affect one's personality development. However, the recent evidence from neuroscience suggests that instead of looking at specific facial features, the human brain processes images of faces in a holistic manner.

Researchers from two Moscow universities, HSE University (Higher School of Economics) and Open University for the Humanities and Economics, have teamed up with a Russian-British business start-up BestFitMe to train a cascade of artificial neural networks to make reliable personality judgments based on photographs of human faces. The performance of the resulting model was above that discovered in previous studies which used machine learning or human raters. The artificial intelligence was able to make above-chance judgments about conscientiousness, neuroticism, extraversion, agreeableness, and openness based on 'selfies' the volunteers uploaded online. The resulting personality judgments were consistent across different photographs of the same individuals.

The study was done in a sample of 12 thousand volunteers who completed a self-report questionnaire measuring personality traits based on the "Big Five" model and uploaded a total of 31 thousand 'selfies'. The respondents were randomly split into a training and a test group. A series of neural networks were used to preprocess the images to ensure consistent quality and characteristics, and exclude faces with emotional expressions, as well as pictures of celebrities and cats. Next, an image classification neural network was trained to decompose each image into 128 invariant features, followed by a multi-layer perceptron that used image invariants to predict personality traits.

The average effect size of r = .24 indicates that AI can make a correct guess about the relative standing of two randomly chosen individuals on a personality dimension in 58% of cases as opposed to the 50% expected by chance. In comparison with the meta-analytic estimates of correlations between self-reported and observer ratings of personality traits, this indicates that an artificial neural network relying on static facial images outperforms an average human rater who meets the target in person without prior acquaintance. Conscientiousness emerged to be more easily recognizable than the other four traits. Personality predictions based on female faces appeared to be more reliable than those for male faces.

There are a vast number of potential applications to be explored. The recognition of personality from real-life photos can complement the traditional approaches to personality assessment in situations where high speed and low cost are more important than high accuracy. Artificial intelligence can be used to propose products that are the best fit for the customer's personality or to select the possible 'best matches' for individuals in dyadic interactions, such as customer service, dating or online tutoring.

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National Research University Higher School of Economics

Cell reproduction dogma challenged

image: Immunostained proteins SYCP3 (green) and DAZL (red) in embryonic ovaries of a control mouse (left); a mouse with mutant null Aldh1a1, Aldh1a2, and Aldh1a3 alleles (centre); and a mouse with mutant null retinoic acid receptor gene alleles (right). In all three situations, germ cells (red) have entered meiosis, as evidenced by the presence of SYCP3 on meiotic chromosomes (green).

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Anne-Amandine Chassot and Norbert B. Ghyselinck

Meiosis is essential to sexual reproduction. For almost 15 years, it has been commonly held that retinoic acid, a molecule derived from vitamin A, triggers meiosis in mammalian germ cells. Yet, in joint articles published in Science Advances ( 22 May 2020 ), french researchers from the Institut de Biologie Valrose (CNRS / INSERM / Université Côte d'Azur) and the IGBMC (CNRS / INSERM / University of Strasbourg), with their colleagues, demonstrate that meiosis in mice begins and proceeds normally even in the absence of retinoic acid. These findings set the stage for new research in the field of reproductive biology.

Meiosis is an essential process that results in novel assortments of chromosomes for the transmission of unique sets of genes to offspring. Beginning with a diploid[1] germ cell (an oogonium in females or a spermatogonium in males), it yields haploid[2] gametes (oocytes in females or spermatozoa in males). The union of an oocyte and a spermatozoon combines both parental haploid genomes in a single diploid cell destined to give rise to an embryo, marking the start of the next generation.

In mammals, cells found in developing gonads (ovaries in females or testes in males) provide germ cells with structural support, nourishment, and protection. They also emit molecular signals that determine what will become of the germ cells. One of the signalling molecules is retinoic acid, widely thought to trigger germ cell meiosis. Despite the 2011 publication of findings casting doubt on this assumption, the idea that retinoic acid is a switch for meiosis has risen to the status of dogma.

Together with colleagues,[3] scientists from the Institut de Biologie Valrose in Nice and the IGBMC in Strasbourg conducted two complementary studies of the mouse foetal ovary to clarify the role of this molecule, by (i) inhibiting its synthesis and (ii) removing its receptors. Neither approach prevented normal initiation of meiosis in germ cells. Furthermore, viable infant mice were born after fertilization of oocytes lacking retinoic acid receptors, proving that these cells are functionally intact.

These twin studies therefore refute the dogma of a retinoic acid trigger for meiosis in germ cells, ending a debate that has lasted nearly a decade and a half. By dismissing a long-held tenet, these findings invite the scientific community to reconsider its working assumptions and investigate new leads in the search for the real signals controlling initiation of germ cell meiosis.

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CNRS

Past is prologue: Genetic 'memory' of ancestral environments helps organisms readapt

Organisms carry long-term "memories" of their ancestral homelands that help them adapt to environmental change, according to a new study that involved raising chickens on the Tibetan Plateau and an adjacent lowland site.

The study provides new insights into how creatures adapt to changing environments, a topic that's especially relevant today in the context of rapid climate change, which is creating challenges for plants and animals worldwide.

The chicken was domesticated from the red jungle fowl in South Asia and Southeast Asia at least 4,000 to 4,500 years ago. It was brought to the Tibetan Plateau by about 1,200 years ago, where it acquired high-altitude adaptations such as an increase in oxygen-carrying red blood cells.

In a set of experiments by University of Michigan biologists and their Chinese colleagues, researchers hatched and reared hundreds of chickens on the Tibetan Plateau, at an elevation of nearly 11,000 feet, and at an adjacent lowland site in China's Sichuan Province. Some of the eggs from lowland chickens were hatched on the plateau, and some high-altitude eggs were hatched at a site 2,200 feet above sea level.

The goal was to assess the relative contributions of two types of phenotypic change--meaning changes to an organism's observable physical characteristics or traits--to the process of environmental adaptation. "Plastic" phenotypic changes involve altered gene activity but no rewriting of the genetic code in DNA molecules, while mutations cause altered gene activity by modifying the sequence of letters in the code itself.

Evolutionary biologists have debated the relative roles of plastic and mutation-induced changes in adaptation, and whether the former serve as stepping stones to the latter.

In the chicken study, researchers were specifically interested in how organisms readapt when reintroduced to ancestral environments. They found that plastic changes play a more prominent role when organisms return to an ancestral home than when they adapt to new environments.

"These findings reveal a mechanism by which past experience affects future evolution," said Jianzhi Zhang, the study's senior author and a professor in the U-M Department of Ecology and Evolutionary Biology.

"Our findings contribute to the recent debate on the relative roles of plastic and genetic changes in adaptation and reveal the importance of considering whether the environment is changing to a novel or ancestral one."

The findings are scheduled for publication May 22 in the journal Science Advances.

To study the relative roles of plastic and DNA-sequence changes, the researchers looked at gene-expression differences between lowland and Tibetan chickens in five tissue types: brain, liver, lung, heart and muscle. To do that, they analyzed RNA transcriptomes from cells in those tissues.

The genome is made of DNA that contains the instructions needed to build an organism. For those instructions to be carried out, DNA must be read and transcribed into messenger RNA molecules.

By analyzing the entire collection of RNA sequences in a cell, known as the transcriptome, researchers can determine when and where genes are turned on and off. Gene-expression studies provide snapshots of actively expressed genes under various conditions.

Changes in gene activity alter an organism's phenotype, which includes its morphology, behavior and physiology. The term phenotypic plasticity refers to environmentally induced phenotypic changes that do not involve genetic mutations.

In the chicken study, the researchers found that while many mutation-induced phenotypic changes were necessary when the animals first adapted to the Tibetan Plateau, plastic changes largely transformed the transcriptomes to the preferred state when Tibetan chickens were brought back to the lowland.

A similar result was seen with egg "hatchability," the fraction of fertilized chicken eggs that hatched in the study.

When lowland eggs were incubated on the unfamiliar Tibetan Plateau, hatchability was significantly lower than that of Tibetan chicken eggs. But when Tibetan eggs were incubated in the lowland--an environment familiar from the distant past--there was no significant difference in hatchability between the two groups.

The egg result suggests that adaptive mutational changes are needed when an organism is brought to an unfamiliar environment for the first time, while plastic changes will do the trick when those same creatures return to an ancestral home.

Zhang's team also analyzed transcriptomes from previous studies of guppies and E. coli bacteria and found comparable results--regardless of whether the new environment was more stressful or less stressful than the ancestral environment.

"In summary, our work uncovers a phenomenon conserved from bacteria to vertebrates that organisms remember their ancestral environments in the form of phenotypic plasticity," the authors wrote.

Credit: 
University of Michigan