Signal Injection Attack on Time-to-Digital Converter and Its Application to Physically Unclonable Function

Physically unclonable function (PUF) is a technology to generate a device-unique identifier using process variation. PUF enables a cryptographic key that appears only when the chip is active, providing an efficient countermeasure against reverse-engineering attacks. In this paper, we explore the data conversion that digitizes a physical quantity representing PUF’s uniqueness into a numerical value as a new attack surface. We focus on time-to-digital converter (TDC) that converts time duration into a numerical value. We show the first signal injection attack on a TDC by manipulating its clock, and verify it through experiments on an off-the-shelf TDC chip. Then, we show how to leverage the attack to reveal a secret key protected by a PUF that uses a TDC for digitization

Hybrid mode atomic force microscopy of phase modulation and frequency modulation

This is a pre-copyedited, author-produced version of an article accepted for publication in Microscopy following peer review. The version of record Yamamoto T., Miyazaki M., Nomura H., et al. Hybrid mode atomic force microscopy of phase modulation and frequency modulation. 72(3), 236-242 1 June 2023 is available online at: https://doi.org/10.1093/jmicro/dfac057.We propose hybrid phase modulation (PM)/frequency modulation (FM) atomic force microscopy (AFM) to increase the imaging speed of AFM in high-Q environments. We derive the relationship between the phase shift, the frequency shift and the tip-sample interaction force from the equation of motion for the cantilever in high-Q environments. The tip-sample conservative force is approximately given by the sum of the conservative force with respect to the phase shift in the PM mode and that with respect to the frequency shift in the FM mode. We preliminarily demonstrate that the hybrid PM/FM-AFM is a new and very promising AFM operation mode that can increase imaging speed

Optical Imaging of a Single Molecule with Subnanometer Resolution by Photoinduced Force Microscopy

Yamamoto T., Yamane H., Yokoshi N., et al. Optical Imaging of a Single Molecule with Subnanometer Resolution by Photoinduced Force Microscopy. ACS Nano 18, 1724 (2024); https://doi.org/10.1021/acsnano.3c10924.Visualizing the optical response of individual molecules is a long-standing goal in catalysis, molecular nanotechnology, and biotechnology. The molecular response is dominated not only by the electronic states in their isolated environment but also by neighboring molecules and the substrate. Information about the transfer of energy and charge in real environments is essential for the design of the desired molecular functions. However, visualizing these factors with spatial resolution beyond the molecular scale has been challenging. Here, by combining photoinduced force microscopy and Kelvin probe force microscopy, we have mapped the photoinduced force in a pentacene bilayer with a spatial resolution of 0.6 nm and observed its “multipole excitation”. We identified the excitation as the result of energy and charge transfer between the molecules and to the Ag substrate. These findings can be achieved only by combining microscopy techniques to simultaneously visualize the optical response of the molecules and the charge transfer between the neighboring environments. Our approach and findings provide insights into designing molecular functions by considering the optical response at each step of layering molecules

Anti-angiogenic effect of siphonaxanthin from green alga, Codium fragile.

Since anti-angiogenic therapy has becoming a promising approach in the prevention of cancer and related diseases, the present study was aimed to examine the anti-angiogenic effect of siphonaxanthin from green alga (Codium fragile) in cell culture model systems and ex vivo approaches using human umbilical vein endothelial cells (HUVECs) and rat aortic ring, respectively. Siphonaxanthin significantly suppressed HUVEC proliferation (p<0.05) at the concentration of 2.5 μM (50% as compared with control) and above, while the effect on chemotaxis was not significant. Siphonaxanthin exhibited strong inhibitory effect on HUVEC tube formation. It suppressed the formation of tube length by 44% at the concentration of 10 μM, while no tube formation was observed at 25 μM, suggesting that it could be due to the suppression of angiogenic mediators. The ex vivo angiogenesis assay exhibited reduced microvessel outgrowth in a dose dependent manner and the reduction was significant at more than 2.5 μM. Our results imply a new insight on the novel function of siphonaxanthin in preventing angiogenesis related diseases

Roles of Phosphatidic Acid in Virus RNA Replication

Eukaryotic positive-strand RNA [(+)RNA] viruses are intracellular obligate parasites replicate using the membrane-bound replicase complexes that contain multiple viral and host components. To replicate, (+)RNA viruses exploit host resources and modify host metabolism and membrane organization. Phospholipase D (PLD) is a phosphatidylcholine- and phosphatidylethanolamine-hydrolyzing enzyme that catalyzes the production of phosphatidic acid (PA), a lipid second messenger that modulates diverse intracellular signaling in various organisms. PA is normally present in small amounts (less than 1% of total phospholipids), but rapidly and transiently accumulates in lipid bilayers in response to different environmental cues such as biotic and abiotic stresses in plants. However, the precise functions of PLD and PA remain unknown. Here, we report the roles of PLD and PA in genomic RNA replication of a plant (+)RNA virus, Red clover necrotic mosaic virus (RCNMV). We found that RCNMV RNA replication complexes formed in Nicotiana benthamiana contained PLDα and PLDβ. Gene-silencing and pharmacological inhibition approaches showed that PLDs and PLDs-derived PA are required for viral RNA replication. Consistent with this, exogenous application of PA enhanced viral RNA replication in plant cells and plant-derived cell-free extracts. We also found that a viral auxiliary replication protein bound to PA in vitro, and that the amount of PA increased in RCNMV-infected plant leaves. Together, our findings suggest that RCNMV hijacks host PA-producing enzymes to replicate

The absence of SOX2 in the anterior foregut alters the esophagus into trachea and bronchi in both epithelial and mesenchymal components

In the anterior foregut (AFG) of mouse embryos, the transcription factor SOX2 is expressed in the epithelia of the esophagus and proximal branches of respiratory organs comprising the trachea and bronchi, whereas NKX2.1 is expressed only in the epithelia of respiratory organs. Previous studies using hypomorphic Sox2 alleles have indicated that reduced SOX2 expression causes the esophageal epithelium to display some respiratory organ characteristics. In the present study, we produced mouse embryos with AFG-specific SOX2 deficiency. In the absence of SOX2 expression, a single NKX2.1-expressing epithelial tube connected the pharynx and the stomach, and a pair of bronchi developed in the middle of the tube. Expression patterns of NKX2.1 and SOX9 revealed that the anterior and posterior halves of SOX2-deficient AFG epithelial tubes assumed the characteristics of the trachea and bronchus, respectively. In addition, we found that mesenchymal tissues surrounding the SOX2-deficient NKX2.1-expressing epithelial tube changed to those surrounding the trachea and bronchi in the anterior and posterior halves, as indicated by the arrangement of smooth muscle cells and SOX9-expressing cells and by the expression of Wnt4 (esophagus specific), Tbx4 (respiratory organ specific), and Hoxb6 (distal bronchus specific). The impact of mesenchyme-derived signaling on the early stage of AFG epithelial specification has been indicated. Our study demonstrated an opposite trend where epithelial tissue specification causes concordant changes in mesenchymal tissues, indicating a reciprocity of epithelial-mesenchymal interactions

Crystal structure of the hemolytic lectin CEL-III isolated from the marine invertebrate Cucumaria echinata : Implications of domain structure for its membrane pore-formation mechanism

CEL-III is a Ca^＋ -dependent and galactose-specific lectin purified from the sea cucumber, Cucumaria echinata, which exhibits hemolytic and hemagglutinating activities. Six molecules of CEL-III are assumed to oligomerize to form an ion-permeable pore in the cell membrane. We have determined the crystal structure of CEL-III by using single isomorphous replacement aided by anomalous scattering in lead at 1.7 Å resolution. CEL-III consists of three distinct domains as follows: the N-terminal two carbohydrate-binding domains (1 and 2), which adopt β-trefoil folds such as the B-chain of ricin and are members of the (QXW)_3 motif family; and domain 3, which is a novel fold composed of two α-helices and one β-sandwich. CEL-III is the first Ca^ -dependent lectin structure with two β-trefoil folds. Despite sharing the structure of the B-chain of ricin, CEL-III binds five Ca^ ions at five of the six subdomains in both domains 1 and 2. Considering the relatively high similarity among the five subdomains, they are putative binding sites for galactose-related carbohydrates, although it remains to be elucidated whether bound Ca^ is directly involved in interaction with carbohydrates. The paucity of hydrophobic interactions in the interfaces between the domains and biochemical data suggest that these domains rearrange upon carbohydrate binding in the erythrocyte membrane. This conformational change may be responsible for oligomerization of CEL-III molecules and hemolysis in the erythrocyte membranes.This research was originally published in Journal of Biological Chemistry. Tatsuya Uchida, Takayuki Yamasaki, Seiichiro Eto, Hajime Sugawara, Genji Kurisu, Atsushi Nakagawa, Masami Kusunoki and Tomomitsu Hatakeyama. Crystal structure of the hemolytic lectin CEL-III isolated from the marine invertebrate Cucumaria echinata : Implications of domain structure for its membrane pore-formation mechanism. Journal of Biological Chemistry. 2004; 279, 37133-37141. © the American Society for Biochemistry and Molecular Biology

Self-Assembly of Elastin–Mimetic Double Hydrophobic Polypeptides

We have constructed a novel class of “double-hydrophobic” block polypeptides based on the hydrophobic domains found in native elastin, an extracellular matrix protein responsible for the elasticity and resilience of tissues. The block polypeptides comprise proline-rich poly(VPGXG) and glycine-rich poly(VGGVG), both of which dehydrate at higher temperature but form distinct secondary structures, β-turn and β-sheet respectively. In water at 45 °C, the block polypeptides initially assemble into nanoparticles rich in β-turn structures, which further connect into long (>10 μm), beaded nanofibers along with the increase in the β-sheet content. The nanofibers obtained are well-dispersed in water, and show thermoresponsive properties. Polypeptides comprising each block component assemble into different morphologies, showing that the conjugation of poly(VPGXG) and poly(VGGVG) plays a role for beaded fiber formation. These results may provide innovative ideas for designing peptide-based materials but also opportunities for developing novel materials useful for tissue engineering and drug delivery systems

Evaluation of the Pichia pastoris expression system for the production of GPCRs for structural analysis

<p>Abstract</p> <p>Background</p> <p>Various protein expression systems, such as <it>Escherichia coli </it>(<it>E. coli</it>), <it>Saccharomyces cerevisiae </it>(<it>S. cerevisiae</it>), <it>Pichia pastoris </it>(<it>P. pastoris</it>), insect cells and mammalian cell lines, have been developed for the synthesis of G protein-coupled receptors (GPCRs) for structural studies. Recently, the crystal structures of four recombinant human GPCRs, namely β₂adrenergic receptor, adenosine A_2areceptor, CXCR4 and dopamine D3 receptor, were successfully determined using an insect cell expression system. GPCRs expressed in insect cells are believed to undergo mammalian-like posttranscriptional modifications and have similar functional properties than in mammals. Crystal structures of GPCRs have not yet been solved using yeast expression systems. In the present study, <it>P. pastoris </it>and insect cell expression systems for the human muscarinic acetylcholine receptor M2 subtype (CHRM2) were developed and the quantity and quality of CHRM2 synthesized by both expression systems were compared for the application in structural studies.</p> <p>Results</p> <p>The ideal conditions for the expression of CHRM2 in <it>P. pastoris </it>were 60 hr at 20°C in a buffer of pH 7.0. The specific activity of the expressed CHRM2 was 28.9 pmol/mg of membrane protein as determined by binding assays using [³H]-quinuclidinyl benzilate (QNB). Although the specific activity of the protein produced by <it>P. pastoris </it>was lower than that of Sf9 insect cells, CHRM2 yield in <it>P. pastoris </it>was 2-fold higher than in Sf9 insect cells because <it>P. pastoris </it>was cultured at high cell density. The dissociation constant (Kd) for QNB in <it>P. pastoris </it>was 101.14 ± 15.07 pM, which was similar to that in Sf9 insect cells (86.23 ± 8.57 pM). There were no differences in the binding affinity of CHRM2 for QNB between <it>P. pastoris </it>and Sf9 insect cells.</p> <p>Conclusion</p> <p>Compared to insect cells, <it>P. pastoris </it>is easier to handle, can be grown at lower cost, and can be expressed quicker at a large scale. Yeast, <it>P. pastoris</it>, and insect cells are all effective expression systems for GPCRs. The results of the present study strongly suggested that protein expression in <it>P. pastoris </it>can be applied to the structural and biochemical studies of GPCRs.</p

Burning Mouth Syndrome and Atypical Odontalgia

Objective: This study aimed (1) to investigate the differences in clinical characteristics of patients between 2 groups, those who have atypical odontalgia (AO) only and those who have AO with burning mouth syndrome (BMS), and (2) to assess the influence of psychiatric comorbidity factors on patients' experiences. Method: Medical records and psychiatric referral forms of patients visiting the Psychosomatic Dentistry Clinic of Tokyo Medical and Dental University between 2013 and 2016 were reviewed. The final sample included 2 groups of 355 patients: those who have AO only (n = 272) and those who have AO with BMS (AO-BMS; n = 83). Clinicodemographic variables (gender, age, comorbid psychiatric disorders, and history of headache or sleep disturbances) and pain variables (duration of illness, pain intensity, and severity of accompanying depression) were collected. Initial pain assessment was done using the Short-Form McGill Pain Questionnaire, and depressive state was determined using the Zung Self-Rating Depression Scale. Results: The average age, female ratio, and sleep disturbance prevalence in the AO-only group were significantly lower than those in AO-BMS group. AO-BMS patients rated overall pain score and present pain intensity significantly higher than did the AO-only patients (P = 0.033 and P = 0.034, respectively), emphasizing sharp (P = 0.049), hot-burning (P = 0.000), and splitting (P = 0.003) characteristics of pain. Patients having comorbid psychiatric disorders had a higher proportion of sleep disturbance in both groups and a higher proportion of depressive state in the AO-only group. Conclusions: AO-BMS patients have different epidemiological characteristics, sleep quality, and pain experiences compared to AO-only patients. The presence of psychiatric comorbidities in both groups may exacerbate sleep quality. We suggest that BMS as a comorbid oral disorder in AO patients contributes to a more intensively painful experience