Publications by authors named "Yusuke Nakai"

The potencies of domestic influenza virus reference antigens were initially calibrated using a single radial immunodiffusion (SRID) assay using primarily prepared international reference antigens. The SRID potency should not be affected when using another reference antigen calibrated with the same international antigen. However, the SRID potency of the test antigens can vary, although the causes of these discrepancies remain unclear.

View Article and Find Full Text PDF

Biomolecules preserved in dental pulp are increasingly being used to identify individuals in the context of forensics and archaeology. Despite the vast amount of research into host and pathogen DNA, the potential use of physiologically informative proteins preserved in dental pulp has rarely been studied. Here, we hypothesized that pregnancy-specific proteins circulating in the blood could be identified from the dental pulp of postpartum individuals and this was investigated using eight human third molars extracted from four postpartum and three control individuals during clinical treatment.

View Article and Find Full Text PDF

In this study, we developed the autonomous lab (ANL), which is a system based on robotics and artificial intelligence (AI) to conduct biotechnology experiments and formulate scientific hypotheses. This system was designed with modular devices and Bayesian optimization algorithms, allowing it to effectively run a closed loop from culturing to preprocessing, measurement, analysis, and hypothesis formulation. As a case study, we used the ANL to optimize medium conditions for a recombinant Escherichia coli strain, which overproduces glutamic acid.

View Article and Find Full Text PDF

Numerous host factors function as intrinsic antiviral effectors to attenuate viral replication. MARCH8 is an E3 ubiquitin ligase that has been identified as a host restriction factor that inhibits the replication of various viruses. This study elucidated the mechanism by which MARCH8 restricts respiratory syncytial virus (RSV) replication through selective degradation of the viral small hydrophobic (SH) protein.

View Article and Find Full Text PDF
Article Synopsis
  • * A study analyzed serum samples from patients with osteoporosis without fractures and those with osteopenia and fragility fractures, identifying six serum proteins that changed similarly between the two groups.
  • * One significant protein, ECM1, showed elevated levels in both groups and could potentially indicate the need for treatment; however, further larger studies are required to validate its effectiveness for early intervention.
View Article and Find Full Text PDF

Physical inactivity associated with gravity unloading, such as microgravity during spaceflight and hindlimb unloading (HU), can cause various physiological changes. In this study, we attempted to identify serum proteins whose levels fluctuated in response to gravity unloading. First, we quantitatively assessed changes in the serum proteome profiles of spaceflight mice using mass spectrometry with data-independent acquisition.

View Article and Find Full Text PDF
Article Synopsis
  • The study investigates how spaceflight impacts healthy tissue functions through changes in the serum proteome of six astronauts during a 6-month mission.
  • Researchers used data-independent acquisition mass spectrometry (DIA-MS) to identify 624 proteins related to bone metabolism, revealing a decrease in T-scores in dual-energy X-ray scans over time.
  • Findings suggest that specific proteins like ALPL, COL1A1, SPP1, and POSTN could serve as indicators of bone metabolism changes in space, advancing our understanding of biological adaptations to long-duration spaceflight.
View Article and Find Full Text PDF

Primary central nervous system lymphoma (PCNSL) is a malignant neoplasm of the central nervous system that is refractory to treatment and has extremely poor prognosis. One factor hindering the development of therapeutic options for PCNSL is its molecular heterogeneity and the extreme difficulty in establishing cell lines that permit intensive research on this disease. In the present study, we developed a method to propagate PCNSL cells using a contacting transwell cell culture system involving brain vascular pericytes.

View Article and Find Full Text PDF
Article Synopsis
  • Gravity impacts the musculoskeletal health of elderly individuals by preventing muscle loss and improving bone density, which enhances quality of life.
  • Researchers analyzed the soleus muscle in mice under various gravity conditions, identifying specific proteins (Myl6b, Gpd1, Fbp2, Pvalb, Actn3) that respond to these gravity changes, indicating a shift towards slow-twitch muscle fibers.
  • Higher levels of Pvalb were found in the blood of mice and osteoporosis patients with muscle atrophy, suggesting it could be a key marker for evaluating muscle and bone health in seniors.
View Article and Find Full Text PDF

Psoriasis is classically regarded as a T-helper 1 (Th1) response-dominant disease believed to be antagonized by the Th2 response, which is responsible for allergic diseases, such as atopic dermatitis. The roles of these responses in psoriasis and the relationship between psoriasis and atopic dermatitis have received increasing attention because it is estimated that more than one million patients are concomitantly affected by psoriasis and atopic dermatitis. To address this, we attempted to determine the characteristics of imiquimod-induced psoriasiform lesions in mice with a concomitant allergic response after co-application of the unrelated allergen ovalbumin onto the skin.

View Article and Find Full Text PDF
Article Synopsis
  • Astronauts experience significant bone loss in microgravity, but the exact molecular mechanisms behind this are still not fully understood.
  • Researchers developed a sensitive mass spectrometry analysis system to study proteomic changes in mouse bones, successfully identifying 40 proteins with varying abundance due to the absence of gravity and 22 proteins unaltered by mechanical stimuli.
  • Notably, one protein, SPARCL1, may stimulate bone degradation processes, potentially revealing new insights into bone metabolism and the impact of mechanical forces on bones in space.
View Article and Find Full Text PDF

Some cultivars of lettuce accumulate anthocyanins, which act as functional food ingredients. Leaf lettuce has been known to be erratic in exhibiting red color when grown under artificial light, and there is a need for cultivars that more stably exhibit red color in artificial light cultivation. In this study, we aimed to dissect the genetic architecture for red coloring in various leaf lettuce cultivars grown under artificial light.

View Article and Find Full Text PDF

The stability of active pharmaceutical ingredients (APIs) and formulations has become a major chemistry, manufacturing, and control (CMC) concern in the pharmaceutical industry because it can determine the feasibility of research and development, the development period, and the development costs of a certain formulation. To streamline the research and development of pharmaceutical products and create useful pharmaceutical products at an early stage, a technology that predicts the stability of formulations at an early stage and with a high degree of accuracy is needed. When predicting the stability of a substance, highly reliable data are required; however, the stability data are affected by analytical variations that depend on the experimenter, measurement device, and conditions used.

View Article and Find Full Text PDF

Dirac fermion systems form a unique Landau level at the Fermi level-the so-called zero mode-whose observation itself will provide strong evidence of the presence of Dirac dispersions. Here, we report the study of semimetallic black phosphorus under pressure by ^{31}P-nuclear magnetic resonance measurements in a wide range of magnetic field up to 24.0 T.

View Article and Find Full Text PDF

Hepatitis B virus (HBV) core antigen (HBc) is a structural protein that forms the viral nucleocapsid and is involved in various steps of the viral replication cycle, but its role in the pathogenesis of HBV infection is still elusive. In this study, we generated a mouse monoclonal antibody (mAb) against HBc and used it in antibody-based in situ biotinylation analysis in order to identify host proteins that interact with HBc. HBc antigen was produced with a wheat germ cell-free protein synthesis system and used to immunize mice.

View Article and Find Full Text PDF
Article Synopsis
  • Human Norwalk viruses (HuNoVs) are the leading cause of gastroenteritis, known for causing food poisoning outbreaks worldwide.
  • This study introduces a new high-throughput proteomic assay to detect a key viral protein (VP1) in HuNoVs, using mass spectrometry for improved diagnosis and surveillance.
  • The method allows for simultaneous genotyping and quantification of VP1 in stool samples, potentially advancing molecular epidemiology studies and clinical applications for HuNoV detection.
View Article and Find Full Text PDF
Article Synopsis
  • Phosphorylation status is important for understanding biological processes in cells, and various analytical methods exist to identify phosphopeptides.
  • The study evaluated four different strategies for enriching phosphopeptides using titanium dioxide (TiO) and Phos-tag ligand particles from digests before mass spectrometry analysis.
  • The results showed that while TiO and Phos-tag methods were effective in enriching phosphopeptides, the Phos-tag agarose beads provided the highest number of identified phosphopeptides, highlighting the value of using multiple enrichment strategies in phosphoproteomic studies.
View Article and Find Full Text PDF
Article Synopsis
  • * Researchers used a proteomic method called data-independent acquisition mass spectrometry (DIA-MS) to identify 27 serum proteins related to the prognosis of severe COVID-19 cases.
  • * Analysis showed that specific proteins might be influenced by cytokine signaling and could help predict patient outcomes, with CHI3L1 and IGFALS identified as potential reliable prognostic markers.
View Article and Find Full Text PDF
Article Synopsis
  • Short-chain fatty acids from non-digestible carbs like fructo-oligosaccharide (FOS) help maintain muscle mass and metabolism in the body.
  • A study on mice in microgravity (μ-g) showed that both soleus (Sol) and extensor digitorum longus muscles lost weight, with a shift in the Sol muscles toward faster-twitch fibers.
  • Despite some muscle loss, FOS ingestion appeared to lessen the impacts of μ-g by slowing down metabolic changes and reducing oxidative stress in Sol muscles.
View Article and Find Full Text PDF

Investigating protein abundance profiles is important to understand the differences in the slow and fast skeletal muscle characteristics. The profiles in soleus (Sol) and extensor digitorum longus (EDL) muscles in mice exposed to 1 g or 3 g for 28 d were compared. The biological implications of the profiles revealed that hypergravity exposure activated a larger number of pathways involved in protein synthesis in Sol.

View Article and Find Full Text PDF

In a tight host-guest complex assembled solely by nondirectional van der Waals forces, unique motions of the guest, such as solid-state inertial rotations, emerge. The regulation of dynamic motions is an important element to be explored for novel functions of such complexes, which may be seemingly difficult to achieve because of the nondirectionality of the assembling forces. A regulated, single-axis rotation was made possible by choosing an appropriate shape of the guest in the tubular host.

View Article and Find Full Text PDF

Jasmonic acid (JA) plays an important role in the induction of herbivore resistance in many plants. However, JA-independent herbivore resistance has been suggested. An herbivore-resistance-inducing substance was isolated from -infected tobacco () leaves in which a hypersensitive response (HR) was induced and identified as loliolide, which has been identified as a β-carotene metabolite.

View Article and Find Full Text PDF

Dynamics of molecules in the solid state holds promise for connecting molecular behaviors with properties of bulk materials. Solid-state dynamics of [60]fullerene (C) is controlled by intimate intermolecular contacts and results in restricted motions of a ratchet phase at low temperatures. Manipulation of the solid-state dynamics of fullerene molecules is thus an interesting yet challenging problem.

View Article and Find Full Text PDF

Water in a nanoconfined geometry has attracted great interest from the viewpoint of not only basic science but also nanofluidic applications. Here, the rotational dynamics of water inside single-walled carbon nanotubes (SWCNTs) with mean diameters larger than ca. 1.

View Article and Find Full Text PDF

VAMP-associated proteins (VAPs) are highly conserved among eukaryotes. Here, we report a functional analysis of one of the VAPs, PVA31, and demonstrate its novel function on leaf senescence in Arabidopsis. The expression of PVA31 is highly induced in senescence leaves, and localizes to the plasma membrane as well as the ARA7-positive endosomes.

View Article and Find Full Text PDF