AI-based search for convergently expanding, advantageous mutations in SARS-CoV-2 by focusing on oligonucleotide frequencies

Among mutations that occur in SARS-CoV-2, efficient identification of mutations advantageous for viral replication and transmission is important to characterize and defeat this rampant virus. Mutations rapidly expanding frequency in a viral population are candidates for advantageous mutations, but neutral mutations hitchhiking with advantageous mutations are also likely to be included. To distinguish these, we focus on mutations that appear to occur independently in different lineages and expand in frequency in a convergent evolutionary manner. Batch-learning SOM (BLSOM) can separate SARS-CoV-2 genome sequences according by lineage from only providing the oligonucleotide composition. Focusing on remarkably expanding 20-mers, each of which is only represented by one copy in the viral genome, allows us to correlate the expanding 20-mers to mutations. Using visualization functions in BLSOM, we can efficiently identify mutations that have expanded remarkably both in the Omicron lineage, which is phylogenetically distinct from other lineages, and in other lineages. Most of these mutations involved changes in amino acids, but there were a few that did not, such as an intergenic mutation.

Genomic Surveillance in Japan of AY.29--A New Sub-lineage of SARS-CoV-2 Delta Variant with C5239T and T5514C Mutations

In the present study, we report a new sub-lineage of the SARS-CoV-2 Delta variant called AY.29, which has C5239T and T5514C mutations. We investigated the monthly trend of AY.29 in Japan within 37,737 Delta variants downloaded on October 2, 2021. Among the total Japanese Delta variants, the AY.29 sub-lineage accounted for 95.1%. In terms of monthly trends, the sequences became predominant in June, and accounted for 95.4%, 97.6% and 90.5% of the reported sequences in July, August and September, respectively. Furthermore, the number of Delta variants imported from abroad during the Tokyo 2020 Olympics and Paralympics (held in August 2021) was extremely low during the fifth wave in Japan. Therefore, the epidemic of the new Delta variant is attributable to a newly occurring mutation in Japan.

Unsupervised explainable AI for the collective analysis of a massive number of genome sequences: various examples from the small genome of pandemic SARS-CoV-2 to the human genome

In genetics and related fields, huge amounts of data, such as genome sequences, are accumulating, and the use of artificial intelligence (AI) suitable for big data analysis has become increasingly important. Unsupervised AI that can reveal novel knowledge from big data without prior knowledge or particular models is highly desirable for analyses of genome sequences, particularly for obtaining unexpected insights. We have developed a batch-learning self-organizing map (BLSOM) for oligonucleotide compositions that can reveal various novel genome characteristics. Here, we explain the data mining by the BLSOM: unsupervised and explainable AI. As a specific target, we first selected SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) because a large number of the viral genome sequences have been accumulated via worldwide efforts. We analyzed more than 0.6 million sequences collected primarily in the first year of the pandemic. BLSOMs for short oligonucleotides (e.g., 4~6-mers) allowed separation into known clades, but longer oligonucleotides further increased the separation ability and revealed subgrouping within known clades. In the case of 15-mers, there is mostly one copy in the genome; thus, 15-mers appeared after the epidemic start could be connected to mutations. Because BLSOM is an explainable AI, BLSOM for 15-mers revealed the mutations that contributed to separation into known clades and their subgroups. After introducing the detailed methodological strategies, we explained BLSOMs for various topics. The tetranucleotide BLSOM for over 5 million 5-kb fragment sequences derived from almost all microorganisms currently available and its use in metagenome studies. We also explained BLSOMs for various eukaryotes, such as fishes, frogs and Drosophila species, and found a high separation ability among closely related species. When analyzing the human genome, we found evident enrichments in transcription factor-binding sequences (TFBSs) in centromeric and pericentromeric heterochromatin regions. The tDNAs (tRNA genes) were separated by the corresponding amino acid.

Time-series trend of pandemic SARS-CoV-2 variants visualized using batch-learning self-organizing map for oligonucleotide compositions

To confront the global threat of coronavirus disease 2019, a massive number of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequences have been decoded, with the results promptly released through the GISAID database. Based on variant types, eight clades have already been defined in GISAID, but the diversity can be far greater. Owing to the explosive increase in available sequences, it is important to develop new technologies that can easily grasp the whole picture of the big-sequence data and support efficient knowledge discovery. An ability to efficiently clarify the detailed time-series changes in genome-wide mutation patterns will enable us to promptly identify and characterize dangerous variants that rapidly increase their population frequency. Here, we collectively analyzed over 150,000 SARS-CoV-2 genomes to understand their overall features and time-dependent changes using a batch-learning self-organizing map (BLSOM) for oligonucleotide composition, which is an unsupervised machine learning method. BLSOM can separate clades defined by GISAID with high precision, and each clade is subdivided into clusters, which shows a differential increase/decrease pattern based on geographic region and time. This allowed us to identify prevalent strains in each region and to show the commonality and diversity of the prevalent strains. Comprehensive characterization of the oligonucleotide composition of SARS-CoV-2 and elucidation of time-series trends of the population frequency of variants can clarify the viral adaptation processes after invasion into the human population and the time-dependent trend of prevalent epidemic strains across various regions, such as continents.

Human cell-dependent, directional, time-dependent changes in the mono- and oligonucleotide compositions of SARS-CoV-2 genomes

BackgroundWhen a virus that has grown in a nonhuman host starts an epidemic in the human population, human cells may not provide growth conditions ideal for the virus. Therefore, the invasion of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which is usually prevalent in the bat population, into the human population is thought to have necessitated changes in the viral genome for efficient growth in the new environment. In the present study, to understand host-dependent changes in coronavirus genomes, we focused on the mono- and oligonucleotide compositions of SARS-CoV-2 genomes and investigated how these compositions changed time-dependently in the human cellular environment. We also compared the oligonucleotide compositions of SARS-CoV-2 and other coronaviruses prevalent in humans or bats to investigate the causes of changes in the host environment. ResultsTime-series analyses of changes in the nucleotide compositions of SARS-CoV-2 genomes revealed a group of mono- and oligonucleotides whose compositions changed in a common direction for all clades, even though viruses belonging to different clades should evolve independently. Interestingly, the compositions of these oligonucleotides changed towards those of coronaviruses that have been prevalent in humans for a long period and away from those of bat coronaviruses. ConclusionsClade-independent, time-dependent changes are thought to have biological significance and should relate to viral adaptation to a new host environment, providing important clues for understanding viral host adaptation mechanisms.

Unsupervised explainable AI for simultaneous molecular evolutionary study of forty thousand SARS-CoV-2 genomes

Unsupervised AI (artificial intelligence) can obtain novel knowledge from big data without particular models or prior knowledge and is highly desirable for unveiling hidden features in big data. SARS-CoV-2 poses a serious threat to public health and one important issue in characterizing this fast-evolving virus is to elucidate various aspects of their genome sequence changes. We previously established unsupervised AI, a BLSOM (batch-learning SOM), which can analyze five million genomic sequences simultaneously. The present study applied the BLSOM to the oligonucleotide compositions of forty thousand SARS-CoV-2 genomes. While only the oligonucleotide composition was given, the obtained clusters of genomes corresponded primarily to known main clades and internal divisions in the main clades. Since the BLSOM is explainable AI, it reveals which features of the oligonucleotide composition are responsible for clade clustering. The BLSOM has powerful image display capabilities and enables efficient knowledge discovery about viral evolutionary processes.

Human muscle gene expression following resistance exercise and blood flow restriction.

INTRODUCTION: Blood flow restriction in combination with low-intensity resistance exercise (REFR) increases skeletal muscle size to a similar extent as compared with traditional high-intensity resistance exercise training. However, there are limited data describing the molecular adaptations that occur after REFR. PURPOSE: To determine whether hypoxia inducible factor-1 alpha (HIF-1alpha) and REDD1 mRNA are expressed differently in REFR compared with low-intensity resistance exercise with no blood flow restriction (CONTROL). Secondly, to determine whether low-intensity resistance exercise is able to induce changes in mRNA expression of several anabolic and catabolic genes as typically seen with high-intensity resistance exercise. METHODS: Six subjects were studied at baseline and 3 h after a bout of leg resistance exercise (20% 1RM) in REFR and CONTROL subjects. Each subject participated in both groups, with 3 wk separating each visit. Muscle biopsy samples were analyzed for mRNA expression, using qRT-PCR. RESULT: Our primary finding was that there were no differences between CONTROL and REFR for any of the selected genes at 3 h after exercise (P > 0.05). However, low-intensity resistance exercise increased HIF-1alpha, p21, MyoD, and muscle RING finger 1 (MuRF1) mRNA expression and decreased REDD1 and myostatin mRNA expression in both groups (P < 0.05). CONCLUSION: Low-intensity resistance exercise can alter skeletal muscle mRNA expression of several genes associated with muscle growth and remodeling, such as REDD1, HIF-1alpha, MyoD, MuRF1, and myostatin. Further, the results from REFR and CONTROL were similar, indicating that the changes in early postexercise gene expression were attributable to the low-intensity resistance exercise bout, and not blood flow restriction.

Relationships between muscle mass or power and bone mineral density in postmenopausal women / 体力科学

The purpose of this study was to investigate the relationships between muscle mass or muscle power and bone mineral density in 43 postmenopausal women. Single photon absorptiometry was used to measure the bone mineral density and bone width of the calcaneuse. Isotonic muscle power of knee extensions (KE), knee flexions and incline squats (ISQ) were measured, using the power processor (VINE Co., Ltd.) . Statistical analysis demonstrated a significant positive correlation (p<0.05) between bone mineral density and lean body mass or muscle thickness. Although, bone mineral density was not significantly correlated with body mass index or fat mass, it was significantly corre-lated with leg muscle power. Further, the bone mineral density was also positively correlated with muscle contraction speed in the motion of KE (p<0.01) and ISQ (p<0.05), but not with muscle strength. This data suggest that the bone mineral density is closely related to the muscle power and/or speed rather than the muscle strength in postmenopausal women.

Effects of <I>Vespa</I> Amino Acid Mixture (VAAM) lsolated from Hornet Larval Saliva and Modified VAAM Nutrients on Endurance Exercise in Swimming Mice / 体力科学

For endurance exercise in swimming mice, 1.8% VAAM (<I>Vespa</I>amino acid mixtiure) which has the same amino acid components as hornet (<I>Vespa</I>mandarinia) larval saliva, 1.8% casein amino acid mixture (CAAM), 10% glucose, or amino acid mixtures in which the amino acids were varied while maintaining the same molar ratio as VAAM were administered orally to mice. Mice recieving 1.8% VAAM showed significantly longer maximum swimming times than mice receiving other nutrients. Among these nutrients, mixtures of proline, glycine, and essential amino acid mixture (EAAM) from the VAAM component, showed maximum times near those with VAAM. In swimming exercise in mice earring of 0.3g tail weight, mice administered 1.8% VAAM showed lower blood lactate concentrations and higher blood glucose concentrations than mice recieving other nutrients. Mice recieving 1.8% VAAM also had lower lactate concentrations in muscle as well as blood. This suggests that VAAM suppresses lactate production and glucose catabolism during exercise. The effects of hornet larval saliva were stronger than those of VAAM. VAAM therefore showed the major effect of the saliva. The results suggest that VAAM improves physiological condition during endurance exercise. A positive correlation was observed between the blood concentrations of lactate and glucose in exercising mice administered various nutrients (r=0.779) . This suggests metabolic equilibration between glucose and lactate during exercise. A positive correlation (r=0.507) was also found between the maximum swimming time and blood glucose concentration. Maximum swimming times were highest at low (Ca. 2.5 mMol) and high (Ca. 4.0 mMol) blood lactate concentrations in high blood glucose concentrations. These facts support that glucose homeostasis is important in prolonged exercise.

Effects of Vespa Amino Acid Mixture(VAAM) Isolated from Hornet Larval Saliva and Modified VAAM Nutrients on Endurance Exercise in Swimming Mice. Improvement in Performance and Changes of Blood Lactate and Glucose / 体力科学

For endurance exercise in swimming mice, 1.8% VAAM (<I>Vespa</I>amino acid mixtiure) which has the same amino acid components as hornet (<I>Vespa</I>mandarinia) larval saliva, 1.8% casein amino acid mixture (CAAM), 10% glucose, or amino acid mixtures in which the amino acids were varied while maintaining the same molar ratio as VAAM were administered orally to mice. Mice recieving 1.8% VAAM showed significantly longer maximum swimming times than mice receiving other nutrients. Among these nutrients, mixtures of proline, glycine, and essential amino acid mixture (EAAM) from the VAAM component, showed maximum times near those with VAAM. In swimming exercise in mice earring of 0.3g tail weight, mice administered 1.8% VAAM showed lower blood lactate concentrations and higher blood glucose concentrations than mice recieving other nutrients. Mice recieving 1.8% VAAM also had lower lactate concentrations in muscle as well as blood. This suggests that VAAM suppresses lactate production and glucose catabolism during exercise. The effects of hornet larval saliva were stronger than those of VAAM. VAAM therefore showed the major effect of the saliva. The results suggest that VAAM improves physiological condition during endurance exercise. A positive correlation was observed between the blood concentrations of lactate and glucose in exercising mice administered various nutrients (r=0.779) . This suggests metabolic equilibration between glucose and lactate during exercise. A positive correlation (r=0.507) was also found between the maximum swimming time and blood glucose concentration. Maximum swimming times were highest at low (Ca. 2.5 mMol) and high (Ca. 4.0 mMol) blood lactate concentrations in high blood glucose concentrations. These facts support that glucose homeostasis is important in prolonged exercise.

The effect of voluntary exercise and the influence of saline loading on systolic blood pressure and vascular lesions in stroke-prone SHR / 体力科学

The effects of voluntary exercise on resting systolic blood pressure and vascular lesions of stroke-prone spontaneously hypertensive rats (stroke-prone SHR) were investigated with and without 1 % saline loading. Forty male stroke-prone SHR aged 7 weeks were assigned to one of 4 experimental groups. Each consisted 10 animals ; sedentary control (S), sedentary with 1 % saline loading (SS), exercised control (E), and exercised with 1 % saline loading (ES) . Animals were sacrificed at the 5 th week. In the prehypertensive phase, resting caudal arterial systolic blood pressure was significantly lower in the E group than in the S group. However, after being loaded with 1 % saline, the ES group showed higher resting systolic blood pressure than those of the SS group. In addition, the ES group revealed severer renal, myocardial, and cerebrovascular lesions than those of the rest of the groups.

Cholesterol metabolism in rat after two intensities of treadmill exercise training / 体力科学

In this study, we investigated the effect of exercise training on serum and liver chblesterol levels and on biosynthesis of liver cholesterol in rats. The training was carried out at low [Low-Ex, 60% max O<SUB>2</SUB> consumption (VO<SUB>2</SUB>) ] and high (High-Ex, 75% max VO<SUB>2</SUB>) intensities for 16 weeks. The energy expenditure was adjusted to be equivalent. The succinate dehydrogenase activities of gastrocnemius muscle in the Low-Ex group and High-Ex group were higher than that of control, 36% and 109% (p<0.05) respectively. The levels of total and high density lipoprotein cholesterol in serum were 14-26% lower than those of control, but no difference was detected between the trained groups. The activity of HMG-CoA reductase in liver microsome was significantly higher than that of control for both trained groups. However, the stimulation of this enzyme activity was not changed by training intensity.

Effect of exercise training and influence of saline loading on cholesterol metabolism in rats / 体力科学

The effect of voluntary exercise training and influence of saline loading on blood pressure and cholesterol metabolism in rats were investigated in this study. Experimental animals used were male Wistar strain rats, aged 7 weeks old. These rats were allocated respectively into four groups, each of which consisted of 10 rats; sedentary control (SC), sedentary with 1 % saline loading (SS), training control (TC), and training with 1 % saline loading (TS) . In each of groups rats were sacrificed at the 10 th week.<BR>Following results were obtained in this study.<BR>1) The mean values of systolic blood pressure remained unchanged in all four groups, 2) serum and hepatic cholesterol levels were lowered by 10 weeks of exercise training, 3) the ratio of HDL-cholesterol to total cholesterol increased significantly in the training groups compared to that in the sedentary groups, 4) the incorporation of <SUP>14</SUP>C-acetate into liver cholesterol was significantly lower in the SS group than in the SC group, and 5) a direct correlationship was found between the increased exercise level and the incorporation of acetate into liver cholesterol in both TC and TS groups.