Sunday reading (14.03)
Review of scientific periodicals for March 7-13
Maria Moshareva, PCR.news
Broadcast
1. An international group of scientists has described the mechanism of making substitutions in the amino acid sequence of a protein without changing the mRNA sequence in conditions of tryptophan deficiency in human cells. The replacement takes place without shifting the reading frame. Researchers have shown that in this case, phenylalanine takes the place of tryptophan, and this process is specific. Tryptophan deficiency is often observed in cancer cells due to the increased expression of indolamine-2,3-dioxygenase 1 (IDO1) in them. It turned out that the substitution of tryptophan for phenylalanine in proteins is often observed in cancer cells. They are universal for various types of cancers: specific substitutions of tryptophan for phenylalanine were characteristic of 9 out of 11 analyzed types of cancer. The authors suggest that this phenomenon can be used for cancer immunotherapy, since peptides with such a replacement are included in the repertoire of antigens presented on the surface of a cancer cell and cause a T-cell response.
RNA modifications
2. Scientists from the University of Birmingham and collaborators investigated the role of post—transcriptional modification of mRNA - 2'-O-methylation of ribose on fruit flies. It was previously known that the methyl group in this site can be introduced by the enzymes CMTr1 and CMTr2, which are expressed in neurons. Mice knocked out by CMTr1 and CMTr2 die during embryonic development. But drosophila, knocked out both by one of these genes and by both, were viable. The authors showed that flies knocked out by CMTr1 and CMTr2 have reduced translation in the synapses of neurons. They suggest that 2'-O-methylation of ribose contributes to the localization of transcripts in synapses. However, there is no evidence that this modification increases the stability of transcripts. Flies knocked out by the CMTr1 and CMTr2 genes showed reduced abilities in memory tests.
Cancer diagnosis
3. Scientists from Spain and Germany have proposed a method for diagnosing ductal pancreatic adenocarcinoma based on the composition of the fecal microbiota. They showed that a certain combination of 27 microorganisms in stool samples is a marker of pancreatic cancer. At the same time, the authors excluded non-specific microorganisms from this set, for example, which are markers of inflammation. Metagenomic analysis of stool samples was performed on a Spanish group of patients (it included 57 cases of newly diagnosed cancer, 50 control cases and 29 patients with chronic pancreatitis). Further, the method was validated on a group of 76 patients and healthy controls from Germany and showed that it has a sufficiently high predictive ability. The method was improved by supplementing it with the CA 19-9 marker in blood serum — at the moment it is the only non-invasive marker of pancreatic cancer approved by the FDA.
Structural studies
4. Scientists from the USA have published the structure of the protein capsid of norovirus GII.4 — the most common pathogen of viral gastroenteritis in the world. Previously obtained structures did not have native symmetry. The researchers obtained both a crystal structure with a resolution of 3.0 Å and a structure in solution by cryo—electron microscopy with a resolution of 3.8 Å. A new feature that they were able to identify is the high mobility of the viral protein VP1, which turned out to be able to accept different conformations due to the "hinge". The authors suggest that one of the conformations corresponds to a resting state, and the other, "excited", somehow contributes to the entry of the virus into the cell. The resting state is stabilized by a divalent metal ion, the binding site of which is located in the "hinge" region. Viral gastroenteritis kills more than 200,000 people a year, and the authors hope that their structural studies will optimize the creation of a vaccine.
Artificial parthenogenesis
5. Chinese scientists obtained a mouse by parthenogenesis, making changes in certain parts of the genome in the direction of both methylation and demethylation of DNA. The oocytes were fertilized with polar corpuscles — side cells obtained during meiosis during the formation of oocytes. The polar corpuscles belonged to the same female — this is the way parthenogenesis is carried out in birds and reptiles. Changes in methylation were introduced into seven control imprinting regions by injection of modified Cas9 RNA fused with methyltransferase, or a dCpf1-Tet1 construct aimed at targeted demethylation, as well as guide RNAs. At the blastocyst stage at the age of 3.5 days, the embryos were transplanted to females. From one modified embryo, offspring developed without abnormalities in development.
Predictions of protein structures
6. The AlphaFold2 artificial intelligence program, designed to predict the tertiary structures of proteins, is able to predict the structures of heterodimeric protein complexes. This is reported by scientists from Sweden in Nature Communications. AlphaFold2 also allows us to assess the degree of reliability of the existence of such complexes. About 60% of the complexes in the test trial were identified successfully. The program most accurately determines interactions by means of alpha-helices or beta-sheets, with less efficiency — interactions by means of sprouting sections of polypeptide chains. Also, the effectiveness of detecting bacterial protein complexes was higher than eukaryotic ones. The limitation of the method at present is the impossibility of predicting higher—order structures that include several subunits. The authors estimate that almost 20 thousand out of 64 thousand structures of paired interactions in the human proteome can be predicted by AlphaFold2 with an error rate of 1%, which is an unprecedented result in terms of accuracy and time costs.
HIV
7. The distribution of HIV in the body of infected people was visualized using positron emission tomography. The scientists used a broadly neutralizing antibody specific to the Env protein and labeled with the isotope 89Zr, which has a half-life of 3.2 days and decays with the emission of positrons. The labeled antibody was administered intravenously. The procedure has been approved by the FDA. Previously, the visualization of the immunodeficiency virus was performed only in the body of monkeys. The study involved patients with a high viral load and those patients who had been receiving antiretroviral therapy for a long time, as well as a control group of uninfected people. In infected people, the virus was detected in lymphoid tissue and intestinal tissues, which was previously observed in similar experiments on monkeys. In addition, the accumulation of the virus was observed in the bone marrow and nasal shells, including in patients in whom the virus was suppressed by antiretroviral therapy. The study was conducted on a small sample, and the authors do not exclude possible nonspecific antibody interactions that could distort the results of the study. Studying the reservoirs of HIV accumulation in the body is important for improving the effectiveness of HIV therapy.
Population genomics
8. Mitochondrial DNA is often considered as a neutral genetic marker, but mitochondrial DNA genes play a crucial role in the body and can be subject to selection. An international team of scientists studied the mitochondrial genomes of 62 subantarctic, or Papuan, penguins from nine different locations in the Southern Ocean. They form four separate evolutionary lines. It seems that the genes of complexes I and V of the respiratory chain underwent evolutionary selection in these lines. The authors suggest that such selection is due to the different climatic conditions in which these penguin populations were located, since the energy processes of the cell can affect the peculiarities of warming the body and saving heat. Gene selection of components of the respiratory chain complex I was previously detected in people from Siberia and Atlantic salmon, so the respiratory chain complex I may be involved in adaptation to cold. In addition, the selection of a number of alleles of mitochondrial genes, as previously shown, is due to adaptation to pathogens, and in this case, the discrepancy between the penguin lines is due to their spatial isolation from each other.
9. When a part of the species passes through the "bottleneck", some genetic variants are washed out, and some variants that are not specific to the population as a whole are fixed. During the last glaciation, a group of people found themselves isolated by glaciers in the Bering Strait region, where they remained for several thousand years. Scientists have studied the genomes of modern American populations, the contribution of Native Americans to which is great, in order to identify single-nucleotide substitutions common to them and rare for the rest of humanity. There were 20,424 such replacements. For comparison, the migration event from Africa, when the population also passed through the bottleneck, was marked in modern genomes by 17,490 variants. Interestingly, the isolation events during migration from Africa and isolation in the Bering Strait region were consistent for the Native American population, so they represent a good model of the passage of two "bottlenecks". It turned out that the variants peculiar to the Eurasian population are practically not detected in the descendants of Native Americans, that is, the consequences of the second "bottleneck" erase the consequences of the first. Functionally, the new replacements that have arisen are associated with cardiac function and melanogenesis. It is possible that the selection was aimed at reducing skin pigmentation, which contributed to the formation of vitamin D in conditions of lack of sunlight.
10. Current Biology has published a study of the genomes of the Chabu hunter-gatherer people in Ethiopia and four peoples also descended from ancient hunters and gatherers. The Chabu people are now represented by about two thousand people. The people of the Chabu people turned out to be genetically close to the ancient people who settled Southwestern Ethiopia more than 4,500 years ago. Unlike neighboring peoples, the Chabu people have been undergoing population decline over the past 1400 years. Among the adaptation mechanisms that contribute to the preservation of the hunter-gatherer population in competition with the peoples who have mastered agriculture, scientists call the geographical reduction of the area of residence, moving to areas unattractive for agriculture, adaptation to various cultural practices, including new nutrition practices, the establishment of economic relations in the form of exchange.
The revival of extinct species
11. An international team of scientists turned to the curious topic of the revival of ancient animals. The question they were looking for an answer to — is it possible to change the genome of an animal that exists now so that it turns into a representative of a recently extinct species? As a model animal, the rat from Christmas Island, which became extinct on the border of the XIX–XX centuries, perfectly suited. The genome was able to be read with a high degree of coverage — 60x. However, about 5% of the genome cannot be restored, even using the genome of a modern brown rat as a reference. It included the genes of the immune response and sense of smell. This means that it is impossible to recreate an extinct species from a modern one using genomic editing methods — at best, we will get some kind of hybrid species; probably, the genes that determine the phenotype of this species will not be reproduced. Tom Gilbert from the University of Copenhagen, one of the authors of the study, commented on the possibility of the revival of, for example, a mammoth: "If you want to create a strange elephant with fur that will live in a zoo, it may not matter that you miss some behavioral genes. But it raises a lot of ethical issues."
Hormones
12. The social behavior of Danio rerio fish was studied under conditions of knockout of one of the oxytocin receptors — Oxtr or Oxtrl. The Oxtr knockout had a stronger effect on the social behavior of fish than the Oxtrl knockout. Fish knocked out by the oxytocin receptor were prone to social behavior (approaching their relative behind a transparent partition) at a slightly earlier age than wild-type fish. However, in adulthood, knockout fish gradually lost this tendency, which was not typical of wild-type fish. Curiously, at the peak of their social activity, knockout fish outperformed wild-type fish. In the ability to form a cohesive flock, knockout fish did not differ from wild-type fish at the age of four weeks, but at the age of eight weeks, the flock of knockout fish was less cohesive than from wild-type fish. Knockout of the oxytocin receptor did not affect the aggressiveness of the fish — the frequency of aggressive behavior was not increased. In general, the knockout of the oxytocin receptor does not have a direct pro- or antisocial effect on the behavior of fish, its effect depends on age.
Xenotransplantation
13. The Medical School of the University of Maryland announces the death of the first person in the world to whom the heart of a genetically modified pig was transplanted. He has lived for two months since the operation. David Bennett was 57 years old. A few days before his death, his condition worsened and he was given palliative care. Scientists express their admiration for David's incredible courage and are grateful to him for his historical role in the development of the field of xenotransplantation. For several weeks after transplantation, under conditions of immunosuppression, the heart worked fully, without any signs of rejection, which allows scientists to be optimistic about the future prospects of xenotransplantation. Read more about the operation to transplant the heart of a genetically modified pig to David Bennett here.
Molecular diagnostics
14. A portable device for isothermal amplification with quantitative detection of the product by color change was presented by developers from Greece and the UK. The device is placed in the palm of your hand, and amplification is performed in ordinary plastic test tubes. The built-in camera takes pictures at certain intervals and builds the dependence of the brightness of the image on time according to the parameters of the pixels in the image. The authors claim that the detection limit is comparable to real-time PCR with fluorescent detection. Using the system, it was possible to determine the BRAF V600E mutation both in samples of isolated DNA in the presence of a background from genomic DNA without mutation, and in samples of fixed cancer tissue of patients. The system was also used for the detection of SARS-CoV-2 RNA in a technique combining isothermal amplification with reverse transcription. The sensitivity of the method was 97% with preliminary isolation of RNA and 83% with the formulation of the reaction directly from the smear.
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