The impact of rare cancer and early-line treatments on the benefit of comprehensive genome profiling-based precision oncology

BACKGROUND

Comprehensive genome profiling (CGP) serves as a guide for suitable genomically matched therapies for patients with cancer. However, little is known about the impact of the timing and types of cancer on the therapeutic benefit of CGP.

MATERIALS AND METHODS

A single hospital-based pan-cancer prospective study (TOP-GEAR; UMIN000011141) was conducted to examine the benefit of CGP with respect to the timing and types of cancer. Patients with advanced solid tumors (>30 types) who either progressed with or without standard treatments were genotyped using a single CGP test. The subjects were followed up for a median duration of 590 days to examine therapeutic response, using progression-free survival (PFS), PFS ratio, and factors associated with therapeutic response.

RESULTS

Among the 507 patients, 62 (12.2%) received matched therapies with an overall response rate (ORR) of 32.3%. The PFS ratios (≥1.3) were observed in 46.3% (19/41) of the evaluated patients. The proportion of subjects receiving such therapies in the rare cancer cohort was lower than that in the non-rare cancer cohort (9.6% and 17.4%, respectively; P = 0.010). However, ORR of the rare cancer patients was higher than that in the non-rare cancer cohort (43.8% and 20.0%, respectively; P = 0.046). Moreover, ORR of matched therapies in the first or second line after receiving the CGP test was higher than that in the third or later lines (62.5% and 21.7%, respectively; P = 0.003). Rare cancer and early-line treatment were significantly and independently associated with ORR of matched therapies in multivariable analysis (P = 0.017 and 0.004, respectively).

CONCLUSION

Patients with rare cancer preferentially benefited from tumor mutation profiling by increasing the chances of therapeutic response to matched therapies. Early-line treatments after profiling increase the therapeutic benefit, irrespective of tumor types.

The structure of PSI-LHCI from Cyanidium caldarium provides evolutionary insights into conservation and diversity of red-lineage LHCs

Light-harvesting complexes (LHCs) are diversified among photosynthetic organisms, and the structure of the photosystem I-LHC (PSI-LHCI) supercomplex has been shown to be variable depending on the species of organisms. However, the structural and evolutionary correlations of red-lineage LHCs are unknown. Here, we determined a 1.92-Å resolution cryoelectron microscopic structure of a PSI-LHCI supercomplex isolated from the red alga Cyanidium caldarium RK-1 (NIES-2137), which is an important taxon in the Cyanidiophyceae. We subsequently investigated the correlations of PSI-LHCIs from different organisms through structural comparisons and phylogenetic analysis. The PSI-LHCI structure obtained shows five LHCI subunits surrounding a PSI-monomer core. The five LHCIs are composed of two Lhcr1s, two Lhcr2s, and one Lhcr3. Phylogenetic analysis of LHCs bound to PSI in the red-lineage algae showed clear orthology of LHCs between C. caldarium and Cyanidioschyzon merolae, whereas no orthologous relationships were found between C. caldarium Lhcr1-3 and LHCs in other red-lineage PSI-LHCI structures. These findings provide evolutionary insights into conservation and diversity of red-lineage LHCs associated with PSI.

Formation of Polyion Complex Aggregate Formed from a Cationic Block Copolymer and Anionic Polysaccharide

Block copolymers (PmMn; P20M101 and P100M98) comprising poly(2-(methacryloyloxy)ethylphosphorylcholine) (PMPC, P) containing biocompatible phosphorylcholin pendants and cationic poly((3-acryloylaminopropyl) trimethylammonium chloride) (PMAPTAC, M) were synthesized via a controlled radical polymerization method. The degrees of polymerization of the PMPC and PMAPTAC segments are denoted by subscripts (PmMn). The mixture of cationic PmMn and anionic sodium chondroitin sulfate C (CS) with the pendant anionic carboxylate and sulfonate groups formed polyion complex (PIC) aggregates in phosphate-buffered saline. A charge-neutralized mixture of P20M101 with CS formed P20M101/CS PIC vesicles with a hydrodynamic radius (Rh) of 97.2 nm, zeta potential of ca. 0 mV, and aggregation number (Nagg) of 23,044. PMPC shells covered the surface of the PIC vesicles. The mixture of P100M98 and CS formed PIC spherical micelles with the PIC core and hydrophilic PMPC shells. The Rh, zeta potential, and Nagg of the PIC micelles were 26.4 nm, ca. 0 mV, and 404, respectively. At pH < 4, the carboxylate anions in CS were protonated. Thus, the charge balance in the PIC micelles shifted to decrease the core density owing to the electrostatic repulsions of the excess cations in the core. The PIC micelles dissociated at a NaCl concentration ≥0.6 M owing to the charge screening effect. The positively charged PIC micelles with excess P100M98 can encapsulate anionic dyes owing to electrostatic interaction.

Enantioselectivity of discretized helical supramolecule consisting of achiral cobalt phthalocyanines via chiral-induced spin selectivity effect

Enantioselectivity of helical aggregation is conventionally directed either by its homochiral ingredients or by introduction of chiral catalysis. The fundamental question, then, is whether helical aggregation that consists only of achiral components can obtain enantioselectivity in the absence of chiral catalysis. Here, by exploiting enantiospecific interaction due to chiral-induced spin selectivity (CISS) that has been known to work to enantio-separate a racemic mixture of chiral molecules, we demonstrate the enantioselectivity in the assembly of mesoscale helical supramolecules consisting of achiral cobalt phthalocyanines. The helical nature in our supramolecules is revealed to be mesoscopically incorporated by dislocation-induced discretized twists, unlike the case of chiral molecules whose chirality are determined microscopically by chemical bond. The relevance of CISS effect in the discretized helical supramolecules is further confirmed by the appearance of spin-polarized current through the system. These observations mean that the application of CISS-based enantioselectivity is no longer limited to systems with microscopic chirality but is expanded to the one with mesoscopic chirality.

Measurement of charges and chemical bonding in a cryo-EM structure

Hydrogen bonding, bond polarity, and charges in protein molecules play critical roles in the stabilization of protein structures, as well as affecting their functions such as enzymatic catalysis, electron transfer, and ligand binding. These effects can potentially be measured in Coulomb potentials using cryogenic electron microscopy (cryo-EM). We here present charges and bond properties of hydrogen in a sub-1.2 Å resolution structure of a protein complex, apoferritin, by single-particle cryo-EM. A weighted difference map reveals positive densities for most hydrogen atoms in the core region of the complex, while negative densities around acidic amino-acid side chains are likely related to negative charges. The former positive densities identify the amino- and oxo-termini of asparagine and glutamine side chains. The latter observations were verified by spatial-resolution selection and a dose-dependent frame series. The average position of the hydrogen densities depends on the parent bonded-atom type, and this is validated by the estimated level of the standard uncertainties in the bond lengths.

Structural resolution of a small organic molecule by serial X-ray free-electron laser and electron crystallography

Structure analysis of small crystals is important in areas ranging from synthetic organic chemistry to pharmaceutical and material sciences, as many compounds do not yield large crystals. Here we present the detailed characterization of the structure of an organic molecule, rhodamine-6G, determined at a resolution of 0.82 Å by an X-ray free-electron laser (XFEL). Direct comparison of this structure with that obtained by electron crystallography from the same sample batch of microcrystals shows that both methods can accurately distinguish the position of some of the hydrogen atoms, depending on the type of chemical bond in which they are involved. Variations in the distances measured by XFEL and electron diffraction reflect the expected differences in X-ray and electron scatterings. The reliability for atomic coordinates was found to be better with XFEL, but the electron beam showed a higher sensitivity to charges.

Structure and Function of Gli123 Involved in Mycoplasma mobile Gliding

Mycoplasma mobile is a fish pathogen that glides on solid surfaces by means of its own gliding machinery composed of internal and surface structures. In the present study, we focused on the function and structure of Gli123, a surface protein that is essential for the localization of other surface proteins. The amino acid sequence of Gli123, which is 1,128 amino acids long, contains lipoprotein-specific repeats. We isolated the native Gli123 protein from M. mobile cells and a recombinant protein, rGli123, from Escherichia coli. The isolated rGli123 complemented a nonbinding and nongliding mutant of M. mobile that lacked Gli123. Circular dichroism and rotary-shadowing electron microscopy (EM) showed that rGli123 has a structure that is not significantly different from that of the native protein. Rotary-shadowing EM suggested that Gli123 adopts two distinct globular and rod-like structures, depending on the ionic strength of the solution. Negative-staining EM coupled with single-particle analysis revealed that Gli123 forms a globular structure featuring a small protrusion with dimensions of approximately 15.7, 14.7, and 14.1 nm for the "height," major axis and minor axis, respectively. Small-angle X-ray scattering analyses indicated a rod-like structure composed of several tandem globular domains with total dimensions of approximately 34 nm in length and 6 nm in width. Both molecular structures were suggested to be dimers, based on the predicted molecular size and structure. Gli123 may have evolved by multiplication of repeating lipoprotein units and acquired a role for Gli521 and Gli349 assembly. IMPORTANCE Mycoplasmas are pathogenic bacteria that are widespread in animals. They are characterized by small cell and genome sizes but are equipped with unique abilities for infection, such as surface variation and gliding. Here, we focused on a surface-localizing protein named Gli123 that is essential for Mycoplasma mobile gliding. This study suggested that Gli123 undergoes drastic conformational changes between its rod-like and globular structures. These changes may be caused by a repetitive structure common in the surface proteins that is responsible for the modulation of the cell surface structure and related to the assembly process for the surface gliding machinery. An evolutionary process for surface proteins essential for this mycoplasma gliding was also suggested in the present study.

Unnaturally Distorted Hexagonal Protein Ring Alternatingly Reorganized from Two Distinct Chemically Modified Proteins

In this study, we constructed a semiartificial protein assembly of alternating ring type, which was modified from the natural assembly state via incorporation of a synthetic component at the protein interface. For the redesign of a natural protein assembly, a scrap-and-build approach employing chemical modification was used. Two different protein dimer units were designed based on peroxiredoxin from Thermococcus kodakaraensis, which originally forms a dodecameric hexagonal ring with six homodimers. The two dimeric mutants were reorganized into a ring by reconstructing the protein-protein interactions via synthetic naphthalene moieties introduced by chemical modification. Cryo-electron microscopy revealed the formation of a uniquely shaped dodecameric hexagonal protein ring with broken symmetry, distorted from the regular hexagon of the wild-type protein. The artificially installed naphthalene moieties were arranged at the interfaces of dimer units, forming two distinct protein-protein interactions, one of which is highly unnatural. This study deciphered the potential of the chemical modification technique that constructs semiartificial protein structures and assembly hardly accessible by conventional amino acid mutations.

Structure of a monomeric photosystem I core associated with iron-stress-induced-A proteins from Anabaena sp. PCC 7120

Iron-stress-induced-A proteins (IsiAs) are expressed in cyanobacteria under iron-deficient conditions. The cyanobacterium Anabaena sp. PCC 7120 has four isiA genes; however, their binding property and functional roles in PSI are still missing. We analyzed a cryo-electron microscopy structure of a PSI-IsiA supercomplex isolated from Anabaena grown under an iron-deficient condition. The PSI-IsiA structure contains six IsiA subunits associated with the PsaA side of a PSI core monomer. Three of the six IsiA subunits were identified as IsiA1 and IsiA2. The PSI-IsiA structure lacks a PsaL subunit; instead, a C-terminal domain of IsiA2 occupies the position of PsaL, which inhibits the oligomerization of PSI, leading to the formation of a PSI monomer. Furthermore, excitation-energy transfer from IsiAs to PSI appeared with a time constant of 55 ps. These findings provide insights into both the molecular assembly of the Anabaena IsiA family and the functional roles of IsiAs.

Theoretical Model of the Far-Red-Light-Adapted Photosystem I Reaction Center of Cyanobacterium Acaryochloris marina Using Chlorophyll d and the Effect of Chlorophyll Exchange

A theoretical model of the far-red-light-adapted photosystem I (PSI) reaction center (RC) complex of a cyanobacterium, Acaryochloris marina (AmPSI), was constructed based on the exciton theory and the recently identified molecular structure of AmPSI by Hamaguchi et al. (Nat. Commun., 2021, 12, 2333). A. marina performs photosynthesis under the visible to far-red light (400-750 nm), which is absorbed by chlorophyll d (Chl-d). It is in contrast to the situation of all the other oxygenic photosynthetic processes of cyanobacteria and plants, which contains chlorophyll a (Chl-a) that absorbs only 400-700 nm visible light. AmPSI contains 70 Chl-d, 1 Chl-d^', 2 pheophytin a (Pheo-a), and 12 carotenoids in the currently available structure. A special pair of Chl-d/Chl-d^' acts as the electron donor (P740) and two Pheo-a act as the primary electron acceptor A₀ as the counterparts of P700 and Chl-a, respectively, of Chl-a-type PSIs. The exciton Hamiltonian of AmPSI was constructed considering the excitonic coupling strength and site energy shift of individual pigments using the Poisson-TrESP (P-TrESP) and charge density coupling (CDC) methods. The model was constructed to fit the experimentally measured spectra of absorption and circular dichroism (CD) spectra during downhill/uphill excitation energy transfer processes. The constructed theoretical model of AmPSI was further compared with the Chl-a-type PSI of Thermosynechococcus elongatus (TePSI), which contains only Chl-a and Chl-a^'. The functional properties of AmPSI and TePSI were further examined by the in silico exchange of Chl-d by Chl-a in the models.

Structural basis for the absence of low-energy chlorophylls in a photosystem I trimer from Gloeobacter violaceus

Photosystem I (PSI) is a multi-subunit pigment-protein complex that functions in light-harvesting and photochemical charge-separation reactions, followed by reduction of NADP to NADPH required for CO₂ fixation in photosynthetic organisms. PSI from different photosynthetic organisms has a variety of chlorophylls (Chls), some of which are at lower-energy levels than its reaction center P700, a special pair of Chls, and are called low-energy Chls. However, the sites of low-energy Chls are still under debate. Here, we solved a 2.04-Å resolution structure of a PSI trimer by cryo-electron microscopy from a primordial cyanobacterium Gloeobacter violaceus PCC 7421, which has no low-energy Chls. The structure shows the absence of some subunits commonly found in other cyanobacteria, confirming the primordial nature of this cyanobacterium. Comparison with the known structures of PSI from other cyanobacteria and eukaryotic organisms reveals that one dimeric and one trimeric Chls are lacking in the Gloeobacter PSI. The dimeric and trimeric Chls are named Low1 and Low2, respectively. Low2 is missing in some cyanobacterial and eukaryotic PSIs, whereas Low1 is absent only in Gloeobacter. These findings provide insights into not only the identity of low-energy Chls in PSI, but also the evolutionary changes of low-energy Chls in oxyphototrophs.

Cryo-EM structure of monomeric photosystem II at 2.78 Å resolution reveals factors important for the formation of dimer

Photosystem II (PSII) functions mainly as a dimer to catalyze the light energy conversion and water oxidation reactions. However, monomeric PSII also exists and functions in vivo in some cases. The crystal structure of monomeric PSII has been solved at 3.6 Å resolution, but it is still not clear which factors contribute to the formation of the dimer. Here, we solved the structure of PSII monomer at a resolution of 2.78 Å using cryo-electron microscopy (cryo-EM). From our cryo-EM density map, we observed apparent differences in pigments and lipids in the monomer-monomer interface between the PSII monomer and dimer. One β-carotene and two sulfoquinovosyl diacylglycerol (SQDG) molecules are found in the monomer-monomer interface of the dimer structure but not in the present monomer structure, although some SQDG and other lipid molecules are found in the analogous region of the low-resolution crystal structure of the monomer, or cryo-EM structure of an apo-PSII monomer lacking the extrinsic proteins from Synechocystis sp. PCC 6803. In the current monomer structure, a large part of the PsbO subunit was also found to be disordered. These results indicate the importance of the β-carotene, SQDG and PsbO in formation of the PSII dimer.

Structural insights into the targeting specificity of ubiquitin ligase for S. cerevisiae isocitrate lyase but not C. albicans isocitrate lyase

In Saccharomyces cerevisiae, the glyoxylate cycle is controlled through the posttranslational regulation of its component enzymes, such as isocitrate lyase (ICL), which catalyzes the first unique step of the cycle. The ICL of S.cerevisiae (ScIcl1) is tagged for proteasomal degradation through ubiquitination by a multisubunit ubiquitin ligase (the glucose-induced degradation-deficient (GID) complex), whereas that of the pathogenic yeast Candida albicans (CaIcl1) escapes this process. However, the reason for the ubiquitin targeting specificity of the GID complex for ScIcl1 and not for CaIcl1 is unclear. To gain some insight into this, in this study, the crystal structures of apo ScIcl1 and CaIcl1 in complex with formate and the cryogenic electron microscopy structure of apo CaIcl1 were determined at a resolution of 2.3, 2.7, and 2.6 Å, respectively. A comparison of the various structures suggests that the orientation of N-terminal helix α1 in S.cerevisiae is likely key to repositioning of ubiquitination sites and contributes to the distinction found in C. albicans ubiquitin evasion mechanism. This finding gives us a better understanding of the molecular mechanism of ubiquitin-dependent ScIcl1 degradation and could serve as a theoretical basis for the research and development of anti-C. albicans drugs based on the concept of CaIcl1 ubiquitination.

Structure of the far-red light utilizing photosystem I of Acaryochloris marina

Acaryochloris marina is one of the cyanobacterial species that can use far-red light to drive photochemical reactions for oxygenic photosynthesis. Here, we report the structure of A. marina photosystem I (PSI) reaction center, determined by cryo-electron microscopy at 2.58 Å resolution. The structure reveals an arrangement of electron carriers and light-harvesting pigments distinct from other type I reaction centers. The paired chlorophyll, or special pair (also referred to as P740 in this case), is a dimer of chlorophyll d and its epimer chlorophyll d'. The primary electron acceptor is pheophytin a, a metal-less chlorin. We show the architecture of this PSI reaction center is composed of 11 subunits and we identify key components that help explain how the low energy yield from far-red light is efficiently utilized for driving oxygenic photosynthesis.

Advances in cryo-EM and ED with a cold-field emission beam and energy filtration -Refinements of the CRYO ARM 300 system in RIKEN SPring-8 center

We have designed and evaluated a cryo-electron microscopy (cryo-EM) system for higher-resolution single particle analysis and high-precision electron 3D crystallography. The system comprises a JEOL CRYO ARM 300 electron microscope-the first machine of this model-and a direct detection device camera, a scintillator-coupled camera, GPU clusters connected with a camera control computer and software for automated-data collection and efficient and accurate operation. The microscope provides parallel illumination of a highly coherent 300-kV electron beam to a sample from a cold-field emission gun and filters out energy-loss electrons through the sample with an in-column energy filter. The gun and filter are highly effective in improving imaging and diffraction, respectively, and have provided high quality data since July 2018. We here report on the characteristics of the cryo-EM system, updates, our progress and future plan for running such cryo-EM machines in RIKEN SPring-8 Center.

High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams

Photosystem II (PSII) plays a key role in water-splitting and oxygen evolution. X-ray crystallography has revealed its atomic structure and some intermediate structures. However, these structures are in the crystalline state and its final state structure has not been solved. Here we analyzed the structure of PSII in solution at 1.95 Å resolution by single-particle cryo-electron microscopy (cryo-EM). The structure obtained is similar to the crystal structure, but a PsbY subunit was visible in the cryo-EM structure, indicating that it represents its physiological state more closely. Electron beam damage was observed at a high-dose in the regions that were easily affected by redox states, and reducing the beam dosage by reducing frames from 50 to 2 yielded a similar resolution but reduced the damage remarkably. This study will serve as a good indicator for determining damage-free cryo-EM structures of not only PSII but also all biological samples, especially redox-active metalloproteins.

Coffee consumption and mortality in Japan with 18 years of follow-up: the Jichi Medical School Cohort Study

OBJECTIVE

Coffee consumption can be expected to reduce mortality due to cardiovascular diseases and cancer. This study tested the hypothesis of an inverse association between coffee intake and all-cause mortality and mortality due to cancer, coronary heart disease, or stroke.

STUDY DESIGN

Prospective cohort study.

METHODS

We analyzed data from the Jichi Medical School Cohort Study, Japan, enrolling 9946 subjects (men/women: 3870/6,076, age: 19-93 years) from 12 communities. A food frequency questionnaire assessing the subjects' daily coffee consumption was used.

RESULTS

During an average follow-up of 18.4 years, the total number of deaths was 2024, including 677 for cancer, 238 for coronary heart disease, and 244 for stroke. Cox proportional hazards models were used to calculate hazard ratios (HRs) and 95% confidence intervals (CIs) of all-cause mortality and cause-specific mortality due to cancer, coronary heart disease, and stroke. Overall, no significant association was shown between coffee consumption and all-cause mortality. In the cause-specific mortality analyses, stroke mortality was significantly lower in those who consumed 1-2 cups of coffee daily (HR [95% CI]: 0.63 [0.42-0.95]) than in those who do not consume coffee, and this association occurred only in men.

CONCLUSION

This study showed no significant association between coffee consumption and all-cause mortality. A U-shaped association between coffee consumption and stroke mortality with a 37% lower stroke mortality, only significant in men who consume 1-2 cups of coffee daily was observed. It is necessary to examine the possibility of intervention studies to reduce stroke mortality through coffee consumption.

Extent of self-adjustment to AF in exercise capacity evaluates significance of sinus maintenance and determines suitability of sinus maintenance therapy in patients with persistent AF

 

Atrial fibrillation (AF) causes hemodynamic inefficiency and possibly deteriorates to heart failure (HF). However, we have experienced drastic variances in the extent of HF deterioration in persistent AF (PeAF) patients. Some studies showed that newly developed PeAF (New AF), not preexisting PeAF adversely impacted HF patients in two years. These issues suggest that most PeAF patients gradually adjust to AF-induced hemodynamic inefficiency, however the extent of self-adjustment to PeAF differs among patients. We hypothesized that the extent of the self-adjustment might determine the adverse impact of New AF on patients. We proposed that especially New AF patients with poor adjustment to PeAF should be targeted for aggressive sinus rhythm (SR) maintenance through catheter ablation (RFCA). We considered exercise capacity (EC) of PeAF patients as the extent of the self-adjustment to PeAF. Consequently, we sought to investigate whether EC testing (CPX) in PeAF patients could be used as a determinant for suitability of aggressive SR maintenance therapy in PeAF patients.

Subjects & Method: We performed CPX to evaluate Peak VO2 intake (PVO2) at baseline for 196 consecutive PeAF patients undergoing RFCA (male: 151, female: 45). After &gt;6 months SR-maintenance, CPX was repeated. %PVO was calculated by standardizing PVO to age and gender. During RFCA, Swan-Ganz catheter study was done to monitor changes in hemodynamics before and after RFCA. Echocardiography was done at baseline, 6 months after SR maintenance.

Results

%PVO varied from 38 to 175% before RFCA. %POV2 of NYHA 3 class patients was 76.8±17.7%. PeAF patients with 80% and more of %PVO2 seemed adjusted to AF in terms of exercise capacity. In this study we defined PeAF patients below 80% PVO2 as Non-adjusted. Out of 196 patients, 149 undertook CPX again. Changes in %PVO2 ranged from −38% to 48% (median: 7.0%). According to multi-regression analysis of changes in %PVO, PeAF patients with Non-adjustment (β=0.31), greater increase in HR during repeated CPX (β=0.40), larger reduction in E/e (β=−0.21) after SR maintenance, obtained larger improvement in EC. Particularly, Non-AF adjustment in PeAF patients was the sole predictor of improvement in EC after RFCA.

Furthermore, we sought to identify the determinants of Non-AF adjustment in PeAF patients. Multivariate logistic analysis demonstrated that female patients became Non-adjusted significantly more easily than male (p&lt;0.001). Increase in HR during CPX was the most important factor for adjustment to PeAF. In males, poor LV diastolic function, higher Pulmonary vascular resistance were also negative predictors for adjustment to PeAF. However, there is concern about deterioration in EC for patients with chronotropic incompetence revealed after RFCA.

Conclusion

The extent to which PeAF patients could adjust to AF helps in evaluating the significance of SR-maintenance and determining the suitability of aggressive SR-maintenance therapy.

Funding Acknowledgement

Type of funding source: None

Apple latent spherical virus structure with stable capsid frame supports quasi-stable protrusions expediting genome release

Picorna-like plant viruses are non-enveloped RNA spherical viruses of ~30 nm. Part of the survival of these viruses depends on their capsid being stable enough to harbour the viral genome and yet malleable enough to allow its release. However, molecular mechanisms remain obscure. Here, we report a structure of a picorna-like plant virus, apple latent spherical virus, at 2.87 Å resolution by single-particle cryo-electron microscopy (cryo-EM) with a cold-field emission beam. The cryo-EM map reveals a unique structure composed of three capsid proteins Vp25, Vp20, and Vp24. Strikingly Vp25 has a long N-terminal extension, which substantially stabilises the capsid frame of Vp25 and Vp20 subunits. Cryo-EM images also resolve RNA genome leaking from a pentameric protrusion of Vp24 subunits. The structures and observations suggest that genome release occurs through occasional opening of the Vp24 subunits, possibly suppressed to a low frequency by the rigid frame of the other subunits.

Identification of novel protein domain for sialyloligosaccharide binding essential to Mycoplasma mobile gliding

Sialic acids, terminal structures of sialylated glycoconjugates, are widely distributed in animal tissues and are often involved in intercellular recognitions, including some bacteria and viruses. Mycoplasma mobile, a fish pathogenic bacterium, binds to sialyloligosaccharide (SO) through adhesin Gli349 and glides on host cell surfaces. The amino acid sequence of Gli349 shows no similarity to known SO-binding proteins. In the present study, we predicted the binding part of Gli349, produced it in Escherichia coli and proved its binding activity to SOs of fetuin using atomic force microscopy. Binding was detected with a frequency of 10.3% under retraction speed of 400 nm/s and was shown to be specific for SO, as binding events were competitively inhibited by the addition of free 3'-sialyllactose. The histogram of the unbinding forces showed 24 pN and additional peaks. These results suggested that the distal end of Gli349 constitutes a novel sialoadhesin domain and is directly involved in the gliding mechanism of M. mobile.

P924Prognostic significance of moderate primary mitral regurgitation and atrial fibrillation

Background

Severe primary mitral regurgitation [degenerativeMR (DMR)] is associated with poor outcome, including cardiac death and admission due to worsening heart failure. Whereas little information is available regarding the characteristics of moderate DMR and their impact on prognostic outcome.

The aim of the present study was to investigate the prognosis and its determinant in patients with moderate DMR.

Methods

From 13,700 consecutive patients who underwent transthoracic echocardiography. We selected moderate DMR but without other underlying cardiac diseases. Characteristics and event free rate as compared with age- and gender-matched patients with none to mild MR.

Results

Of a total of our cohort, 185 (1%) patients had moderate DMR, and we compared with 185 age- and gender-matched patients with none to mild MR. During the follow-up period of 1372±655 days, 30 patients (8%) met the composite endpoint defined as cardiac death and admission due to worsening heart failure. Kaplan-Meier analysis showed patients with moderate DMR was significantly associated with a poor outcome compared to patients with none to mild MR (log-ranktest P<0.0001). Cox proportional hazard ratio revealed thatmoderate MR and atrial fibrillation (AF) were the independent predictors of the composite endpoint.

Prgnostic outcome: AF and moderate DMR

Conclusions

Patients withmoderate DMR and concomitant AF had a significant poor outcome. An activesurveillance and some intervention for AF and moderate MR may be required.

Effect of attention bias modification on event-related potentials in patients with irritable bowel syndrome: A preliminary brain function and psycho-behavioral study

BACKGROUND

Attention bias modification normalizes electroencephalographic abnormalities in alpha and beta power percentages related to attention in patients with irritable bowel syndrome (IBS). Yet, it is unknown whether ABM contributes to the normalization of event-related potentials (ERP) in these patients. We hypothesized that ERP related to attention deficit would be normalized after ABM implementation in individuals with IBS.

METHODS

Thirteen patients with IBS and 10 control subjects completed a 2-month intervention that included five ABM sessions. Each session included 128 trials, resulting in a total of 640 trials during the study period. Event-related potentials were measured at the first and fifth sessions. As per the international 10-20 system for electroencephalographic electrode placement, right parietal P4 was evaluated to measure the attention component of facial expression processing.

KEY RESULTS

A group comparison of P100 latency at P4 revealed that latencies were significantly different between groups in session 1 (IBS vs control, 108 ± 8 vs 97 ± 14; t = -2.51, P = .0203). This difference was absent in session 5 (94 ± 11 vs 93 ± 11, respectively; t = -0.397, P = .6954, r = .09), indicating an effect of ABM in the IBS group.

CONCLUSIONS AND INFERENCES

Attention bias modification may have clinical utility for normalizing brain function and specifically attentional abnormalities in patients with IBS.

Optimization of DARTEL Settings for the Detection of Alzheimer Disease

BACKGROUND AND PURPOSE

Although Diffeomorphic Anatomical Registration Through Exponentiated Lie Algebra (DARTEL) has been introduced as an alternative to conventional voxel-based morphometry, there are scant data available regarding the optimal image-processing settings. The aim of this study was to optimize image-processing and ROI settings for the diagnosis of Alzheimer disease using DARTEL.

MATERIALS AND METHODS

Between May 2002 and August 2014, we selected 158 patients with Alzheimer disease and 198 age-matched healthy subjects; 158 healthy subjects served as the control group against the patients with Alzheimer disease, and the remaining 40 served as the healthy data base. Structural MR images were obtained in all the participants and were processed using DARTEL-based voxel-based morphometry with a variety of settings. These included modulated or nonmodulated, nonsmoothed or smoothed settings with a 4-, 8-, 12-, 16-, or 20-mm kernel size. A z score was calculated for each ROI, and univariate and multivariate logistic regression analyses were performed to determine the optimal ROI settings for each dataset. The optimal settings were defined as those demonstrating the highest χ² test statistics in the multivariate logistic regression analyses. Finally, using the optimal settings, we obtained receiver operating characteristic curves. The models were verified using 10-fold cross-validation.

RESULTS

The optimal settings were obtained using the hippocampus and precuneus as ROIs without modulation and smoothing. The average area under the curve was 0.845 (95% confidence interval, 0.788-0.902).

CONCLUSIONS

We recommend using the precuneus and hippocampus as ROIs without modulation and smoothing for DARTEL-based voxel-based morphometry as a tool for diagnosing Alzheimer disease.

Effect of attention bias modification on brain function and anxiety in patients with irritable bowel syndrome: A preliminary electroencephalogram and psycho-behavioral study

BACKGROUND

Gastrointestinal symptoms of irritable bowel syndrome (IBS) show a reciprocal relationship with anxiety. In this intervention-based study, we investigated the utility of attention bias modification (ABM) therapy in patients with IBS. We hypothesized that IBS-related electroencephalographic abnormalities would be normalized after ABM therapy.

METHODS

Seventeen patients with IBS and 13 healthy subjects completed five ABM intervention sessions over a 2-month period. Each session included 128 ABM trials, resulting in a total of 640 trials across the intervention period. For each trial, subjects viewed a pair of facial expression images and were instructed to indicate the position of the neutral face as quickly and accurately as possible by pressing one of two buttons on a button box. Electroencephalography data (alpha and beta power percentages) were collected during the 1st and 5th sessions.

KEY RESULTS

Generalized estimating equations of relative alpha power revealed a significant effect of period was identified at O2 (P=.036). Paired t tests revealed that ABM significantly increased relative alpha power at O2 in patients with IBS. Generalized estimating equation of relative beta power revealed a significant effect of the group × period interaction was identified at Pz (P=.035). Paired t tests revealed that ABM significantly decreased relative beta power at Pz in patients with IBS.

CONCLUSIONS & INFERENCES

Attention bias modification may normalize brain function related to attention and anxiety in patients with IBS.

Integrated Information and Prospects for Gliding Mechanism of the Pathogenic Bacterium Mycoplasma pneumoniae

Mycoplasma pneumoniae forms a membrane protrusion at a cell pole and is known to adhere to solid surfaces, including animal cells, and can glide on these surfaces with a speed up to 1 μm per second. Notably, gliding appears to be involved in the infectious process in addition to providing the bacteria with a means of escaping the host's immune systems. However, the genome of M. pneumoniae does not encode any of the known genes found in other bacterial motility systems or any conventional motor proteins that are responsible for eukaryotic motility. Thus, further analysis of the mechanism underlying M. pneumoniae gliding is warranted. The gliding machinery formed as the membrane protrusion can be divided into the surface and internal structures. On the surface, P1 adhesin, a 170 kDa transmembrane protein forms an adhesin complex with other two proteins. The internal structure features a terminal button, paired plates, and a bowl (wheel) complex. In total, the organelle is composed of more than 15 proteins. By integrating the currently available information by genetics, microscopy, and structural analyses, we have suggested a working model for the architecture of the organelle. Furthermore, in this article, we suggest and discuss a possible mechanism of gliding based on the structural model, in which the force generated around the bowl complex transmits through the paired plates, reaching the adhesin complex, resulting in the repeated catch of sialylated oligosaccharides on the host surface by the adhesin complex.

Prospects for the gliding mechanism of Mycoplasma mobile

Mycoplasma mobile forms gliding machinery at a cell pole and glides continuously in the direction of the cell pole at up to 4.5μm per second on solid surfaces such as animal cells. This motility system is not related to those of any other bacteria or eukaryotes. M. mobile uses ATP energy to repeatedly catch, pull, and release sialylated oligosaccharides on host cells with its approximately 50-nm long legs. The gliding machinery is a large structure composed of huge surface proteins and internal jellyfish-like structure. This system may have developed from an accidental combination between an adhesin and a rotary ATPase, both of which are essential for the adhesive parasitic life of Mycoplasmas.