Distinctive features of lipoprotein profiles in stroke patients.

Classes of lipoproteins solubilize lipids in the blood, and their profiles are important for preventing atherosclerotic diseases. These can be identified by gel filtration HPLC, which has been analyzed in a manner that yields the same values as the de facto standard method, i.e.

Theanine, a Tea-Leaf-Specific Amino Acid, Alleviates Stress through Modulation of Npas4 Expression in Group-Housed Older Mice.

Group rearing is a common housing condition, but group-housed older mice show increased adrenal hypertrophy, a marker of stress. However, the ingestion of theanine, an amino acid unique to tea leaves, suppressed stress. We aimed to elucidate the mechanism of theanine's stress-reducing effects using group-reared older mice.

Human lipoproteins comprise at least 12 different classes that are lognormally distributed.

This study presents the results of HPLC, a gentler and rapid separation method in comparison with the conventional ultracentrifugation, for 55 human serum samples. The elution patterns were analysed parametrically, and the attribute of each class was confirmed biochemically. Human samples contained 12 classes of lipoproteins, each of which may consist primarily of proteins.

Mutations in SARS-CoV-2 are on the increase against the acquired immunity.

Monovalent vaccines using mRNA or adenoviruses have provided substantial protection against the COVID-19 pandemic in many countries. However, viral mutations have hampered the efficacy of this approach. The Omicron variant, which appeared in Dec 2021, has caused a pandemic that has exerted pressure on the healthcare system worldwide.

Continuous mutation of SARS-CoV-2 during migration via three routes at the beginning of the pandemic.

Background: It remains unclear how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection started, spread worldwide, and mutated to result in the present variants. This difficulty can be attributed to the limitations associated with the analytical methodology for presenting the differences among genomic sequences. In this study, we critically analysed the early data to explain the start and spread of the pandemic.

Effect of control measures on the pattern of COVID-19 Epidemics in Japan.

Background: COVID-19 has spread worldwide since its emergence in 2019. In contrast to many other countries with epidemics, Japan differed in that it avoided lockdowns and instead asked people for self-control. A travel campaign was conducted with a sizable budget, but the number of PCR tests was severely limited.

SARS-CoV-2 mutations among minks show reduced lethality and infectivity to humans.

SARS-CoV-2 infection in minks has become a serious problem, as the virus may mutate and reinfect humans; some countries have decided to cull minks. Here, the virus sequencing data in minks were analysed and compared to those of human-virus. Although the mink-virus maintained the characteristics of human-virus, some variants rapidly mutated, adapting to minks.

Possible correlated variation of GABA receptor α3 expression with hippocampal cholinergic neurostimulating peptide precursor protein in the hippocampus.

Cholinergic neural activation from the medial septal nucleus to hippocampus plays a crucial role in episodic memory as a regulating system for glutamatergic neural activation in the hippocampus. As a candidate regulating factor for acetylcholine synthesis in the medial septal nucleus, hippocampal cholinergic neurostimulating peptide (HCNP) was purified from the soluble fraction of young adult rat hippocampus. HCNP is released from its precursor protein (HCNP-pp), also referred to as phosphatidylethanolamine-binding protein 1.

Theanine, Antistress Amino Acid in Tea Leaves, Causes Hippocampal Metabolic Changes and Antidepressant Effects in Stress-Loaded Mice.

By comprehensively measuring changes in metabolites in the hippocampus of stress-loaded mice, we investigated the reasons for stress vulnerability and the effect of theanine, i.e., an abundant amino acid in tea leaves, on the metabolism.

Principal component analysis of coronaviruses reveals their diversity and seasonal and pandemic potential.

Coronaviruses and influenza viruses have similarities and differences. In order to comprehensively compare them, their genome sequencing data were examined by principal component analysis. Coronaviruses had fewer variations than a subclass of influenza viruses.

Mutation in Sodium-Glucose Cotransporter 2 Results in Down-Regulation of Amyloid Beta (A4) Precursor-Like Protein 1 in Young Age, Which May Lead to Poor Memory Retention in Old Age.

Senescence-accelerated mouse prone 10 (SAMP10) exhibits cerebral atrophy and depression-like behavior. A line of SAMP10 with spontaneous mutation in the gene encoding the sodium-glucose cotransporter (SGLT) 2 was named SAMP10/TaSlc- (SAMP10-ΔSglt2) and was identified as a renal diabetes model. In contrast, a line of SAMP10 with no mutation in SGLT2 (SAMP10/TaIdrSlc, SAMP10(+)) was recently established under a specific pathogen-free condition.

Green Tea Catechins Trigger Immediate-Early Genes in the Hippocampus and Prevent Cognitive Decline and Lifespan Shortening.

Senescence-accelerated mouse prone 10 (SAMP10) mice, after ingesting green tea catechins (GT-catechin, 60 mg/kg), were found to have suppressed aging-related decline in brain function. The dose dependence of brain function on GT-catechin indicated that intake of 1 mg/kg or more suppressed cognitive decline and a shortened lifespan. Mice that ingested 1 mg/kg GT-catechin had the longest median survival, but the dose was less effective at suppressing cognitive decline.

Re-evaluation of the evolution of influenza H1 viruses using direct PCA.

The history of influenza H1 virus was re-evaluated by applying a new methodology to sequencing data; this objective method enables comparisons among viral types. The approach led to the segregation of all segments of swine and human viruses into three distinct groups: two of them included the pandemic 1977 and 2009 human viruses, and the remaining group may be new in humans. These three groups might have originated from avian viruses and drifted out independently.

Principal Component Analysis applied directly to Sequence Matrix.

Sequence data is now widely used to observe relationships among organisms. However, understanding structure of the qualitative data is challenging. Conventionally, the relationships are analysed using a dendrogram that estimates a tree shape.

Tofu and fish oil independently modulate serum lipid profiles in rats: Analyses of 10 class lipoprotein profiles and the global hepatic transcriptome.

Soy protein and fish oil are food components that decrease the risk of cardiovascular disease. Previous studies demonstrated that these food components reduced serum cholesterol levels and suppressed hepatic lipogenesis. However, the underlying mechanisms of action of these food components remain unclear.

Correction: Lipoproteins comprise at least 10 different classes in rats, each of which contains a unique set of proteins as the primary component.

[This corrects the article DOI: 10.1371/journal.pone.

Lipoproteins comprise at least 10 different classes in rats, each of which contains a unique set of proteins as the primary component.

Although lipoproteins are conventionally separated into a few classes using density gradient centrifugation, there may be a much higher number of physical classes that differ in origin or phase. Comprehensive knowledge of the classes of lipoproteins is rather limited, which hinders both the study of their functions and the identification of the primary causes of related diseases. This study aims to determine the number of classes of lipoproteins that can be practically distinguishable and identify the differences between them.

Sterol regulatory element-binding protein-1c orchestrates metabolic remodeling of white adipose tissue by caloric restriction.

Caloric restriction (CR) can delay onset of several age-related pathophysiologies and extend lifespan in various species, including rodents. CR also induces metabolic remodeling involved in activation of lipid metabolism, enhancement of mitochondrial biogenesis, and reduction of oxidative stress in white adipose tissue (WAT). In studies using genetically modified mice with extended lifespans, WAT characteristics influenced mammalian lifespans.

Sulfur deficiency-induced repressor proteins optimize glucosinolate biosynthesis in plants.

Glucosinolates (GSLs) in the plant order of the Brassicales are sulfur-rich secondary metabolites that harbor antipathogenic and antiherbivory plant-protective functions and have medicinal properties, such as carcinopreventive and antibiotic activities. Plants repress GSL biosynthesis upon sulfur deficiency (-S); hence, field performance and medicinal quality are impaired by inadequate sulfate supply. The molecular mechanism that links -S to GSL biosynthesis has remained understudied.

Parametric analysis of RNA-seq expression data.

Various methods had been introduced for normalization and comparison of RNA-seq count data. However, they lacked objectivity because they based on ad hoc assumptions that were never verified their appropriateness. Here, we introduced a method that assumes parsimony models on data distribution; the assumptions were verified according to exploratory data analysis.

Allantoin, a stress-related purine metabolite, can activate jasmonate signaling in a MYC2-regulated and abscisic acid-dependent manner.

Allantoin is a metabolic intermediate of purine catabolism that often accumulates in stressed plants. Recently, we used Arabidopsis knockout mutants (aln) of ALLANTOINASE to show that this purine metabolite activates abscisic acid (ABA) production, thereby stimulating stress-related gene expression and enhancing seedling tolerance to abiotic stress. A detailed re-examination of the microarray data of an aln mutant (aln-1) confirmed the increased expression of ABA-related genes and also revealed altered expression of genes involved in jasmonic acid (JA) responses, probably under the control of MYC2, a master switch in the JA signaling pathway.

Principal component analysis for designed experiments.

Background: Principal component analysis is used to summarize matrix data, such as found in transcriptome, proteome or metabolome and medical examinations, into fewer dimensions by fitting the matrix to orthogonal axes. Although this methodology is frequently used in multivariate analyses, it has disadvantages when applied to experimental data. First, the identified principal components have poor generality; since the size and directions of the components are dependent on the particular data set, the components are valid only within the data set.