Evaluation of QSAR models for predicting mutagenicity: outcome of the Second Ames/QSAR international challenge project

Quantitative structure-activity relationship (QSAR) models are powerful in silico tools for predicting the mutagenicity of unstable compounds, impurities and metabolites that are difficult to examine using the Ames test. Ideally, Ames/QSAR models for regulatory use should demonstrate high sensitivity, low false-negative rate and wide coverage of chemical space. To promote superior model development, the Division of Genetics and Mutagenesis, National Institute of Health Sciences, Japan (DGM/NIHS), conducted the Second Ames/QSAR International Challenge Project (2020-2022) as a successor to the First Project (2014-2017), with 21 teams from 11 countries participating. The DGM/NIHS provided a curated training dataset of approximately 12,000 chemicals and a trial dataset of approximately 1,600 chemicals, and each participating team predicted the Ames mutagenicity of each trial chemical using various Ames/QSAR models. The DGM/NIHS then provided the Ames test results for trial chemicals to assist in model improvement. Although overall model performance on the Second Project was not superior to that on the First, models from the eight teams participating in both projects achieved higher sensitivity than models from teams participating in only the Second Project. Thus, these evaluations have facilitated the development of QSAR models.

Precessing jet nozzle connecting to a spinning black hole in M87

The nearby radio galaxy M87 offers a unique opportunity to explore the connections between the central supermassive black hole and relativistic jets. Previous studies of the inner region of M87 revealed a wide opening angle for the jet originating near the black hole1-4. The Event Horizon Telescope resolved the central radio source and found an asymmetric ring structure consistent with expectations from general relativity5. With a baseline of 17 years of observations, there was a shift in the jet's transverse position, possibly arising from an 8- to 10-year quasi-periodicity3. However, the origin of this sideways shift remains unclear. Here we report an analysis of radio observations over 22 years that suggests a period of about 11 years for the variation in the position angle of the jet. We infer that we are seeing a spinning black hole that induces the Lense-Thirring precession of a misaligned accretion disk. Similar jet precession may commonly occur in other active galactic nuclei but has been challenging to detect owing to the small magnitude and long period of the variation.

A ring-like accretion structure in M87 connecting its black hole and jet

The nearby radio galaxy M87 is a prime target for studying black hole accretion and jet formation1,2. Event Horizon Telescope observations of M87 in 2017, at a wavelength of 1.3 mm, revealed a ring-like structure, which was interpreted as gravitationally lensed emission around a central black hole3. Here we report images of M87 obtained in 2018, at a wavelength of 3.5 mm, showing that the compact radio core is spatially resolved. High-resolution imaging shows a ring-like structure of [Formula: see text] Schwarzschild radii in diameter, approximately 50% larger than that seen at 1.3 mm. The outer edge at 3.5 mm is also larger than that at 1.3 mm. This larger and thicker ring indicates a substantial contribution from the accretion flow with absorption effects, in addition to the gravitationally lensed ring-like emission. The images show that the edge-brightened jet connects to the accretion flow of the black hole. Close to the black hole, the emission profile of the jet-launching region is wider than the expected profile of a black-hole-driven jet, suggesting the possible presence of a wind associated with the accretion flow.

Enhanced x-ray emission coinciding with giant radio pulses from the Crab Pulsar

Giant radio pulses (GRPs) are sporadic bursts emitted by some pulsars that last a few microseconds and are hundreds to thousands of times brighter than regular pulses from these sources. The only GRP-associated emission outside of radio wavelengths is from the Crab Pulsar, where optical emission is enhanced by a few percentage points during GRPs. We observed the Crab Pulsar simultaneously at x-ray and radio wavelengths, finding enhancement of the x-ray emission by 3.8 ± 0.7% (a 5.4σ detection) coinciding with GRPs. This implies that the total emitted energy from GRPs is tens to hundreds of times higher than previously known. We discuss the implications for the pulsar emission mechanism and extragalactic fast radio bursts.

Gravitational Test beyond the First Post-Newtonian Order with the Shadow of the M87 Black Hole

The 2017 Event Horizon Telescope (EHT) observations of the central source in M87 have led to the first measurement of the size of a black-hole shadow. This observation offers a new and clean gravitational test of the black-hole metric in the strong-field regime. We show analytically that spacetimes that deviate from the Kerr metric but satisfy weak-field tests can lead to large deviations in the predicted black-hole shadows that are inconsistent with even the current EHT measurements. We use numerical calculations of regular, parametric, non-Kerr metrics to identify the common characteristic among these different parametrizations that control the predicted shadow size. We show that the shadow-size measurements place significant constraints on deviation parameters that control the second post-Newtonian and higher orders of each metric and are, therefore, inaccessible to weak-field tests. The new constraints are complementary to those imposed by observations of gravitational waves from stellar-mass sources.

A large comparison of integrated SAR/QSAR models of the Ames test for mutagenicity$

Results from the Ames test are the first outcome considered to assess the possible mutagenicity of substances. Many QSAR models and structural alerts are available to predict this endpoint. From a regulatory point of view, the recommendation from international authorities is to consider the predictions of more than one model and to combine results in order to develop conclusions about the mutagenicity risk posed by chemicals. However, the results of those models are often conflicting, and the existing inconsistency in the predictions requires intelligent strategies to integrate them. In our study, we evaluated different strategies for combining results of models for Ames mutagenicity, starting from a set of 10 diverse individual models, each built on a dataset of around 6000 compounds. The novelty of our study is that we collected a much larger set of about 18,000 compounds and used the new data to build a family of integrated models. These integrations used probabilistic approaches, decision theory, machine learning, and voting strategies in the integration scheme. Results are discussed considering balanced or conservative perspectives, regarding the possible uses for different purposes, including screening of large collection of substances for prioritization.

Erratum: Large-Scale Shell-Model Analysis of the Neutrinoless ββ Decay of ^{48}Ca [Phys. Rev. Lett. 116, 112502 (2016)]

This corrects the article DOI: 10.1103/PhysRevLett.116.112502.

Standardized cell sources and recommendations for good cell culture practices in genotoxicity testing

Good cell culture practice and characterization of the cell lines used are of critical importance in in vitro genotoxicity testing. The objective of this initiative was to make continuously available stocks of the characterized isolates of the most frequently used mammalian cell lines in genotoxicity testing anywhere in the world ('IVGT' cell lines). This project was organized under the auspices of the International Life Sciences Institute (ILSI) Health and Environmental Sciences Institute (HESI) Project Committee on the Relevance and Follow-up of Positive Results in In Vitro Genetic Toxicity (IVGT) Testing. First, cell isolates were identified that are as close as possible to the isolate described in the initial publications reporting their use in genotoxicity testing. The depositors of these cell lines managed their characterization and their expansion for preparing continuously available stocks of these cells that are stored at the European Collection of Cell Cultures (ECACC, UK) and the Japanese Collection of Research Bioresources (JCRB, Japan). This publication describes how the four 'IVGT' cell lines, i.e. L5178Y TK^+/- 3.7.2C, TK6, CHO-WBL and CHL/IU, were prepared for deposit at the ECACC and JCRB cell banks. Recommendations for handling these cell lines and monitoring their characteristics are also described. The growth characteristics of these cell lines (growth rates and cell cycles), their identity (karyotypes and genetic status) and ranges of background frequencies of select endpoints are also reported to help in the routine practice of genotoxicity testing using these cell lines.

Results of a round-robin exercise on read-across

A round-robin exercise was conducted within the CALEIDOS LIFE project. The participants were invited to assess the hazard posed by a substance, applying in silico methods and read-across approaches. The exercise was based on three endpoints: mutagenicity, bioconcentration factor and fish acute toxicity. Nine chemicals were assigned for each endpoint and the participants were invited to complete a specific questionnaire communicating their conclusions. The interesting aspect of this exercise is the justification behind the answers more than the final prediction in itself. Which tools were used? How did the approach selected affect the final answer?

Large-Scale Shell-Model Analysis of the Neutrinoless ββ Decay of ^{48}Ca

We present the nuclear matrix element for the neutrinoless double-beta decay of ^{48}Ca based on large-scale shell-model calculations including two harmonic oscillator shells (sd and pf shells). The excitation spectra of ^{48}Ca and ^{48}Ti, and the two-neutrino double-beta decay of ^{48}Ca are reproduced in good agreement to the experimental data. We find that the neutrinoless double-beta decay nuclear matrix element is enhanced by about 30% compared to pf-shell calculations. This reduces the decay lifetime by almost a factor of 2. The matrix-element increase is mostly due to pairing correlations associated with cross-shell sd-pf excitations. We also investigate possible implications for heavier neutrinoless double-beta decay candidates.

The host galaxy of a fast radio burst

In recent years, millisecond-duration radio signals originating in distant galaxies appear to have been discovered in the so-called fast radio bursts. These signals are dispersed according to a precise physical law and this dispersion is a key observable quantity, which, in tandem with a redshift measurement, can be used for fundamental physical investigations. Every fast radio burst has a dispersion measurement, but none before now have had a redshift measurement, because of the difficulty in pinpointing their celestial coordinates. Here we report the discovery of a fast radio burst and the identification of a fading radio transient lasting ~6 days after the event, which we use to identify the host galaxy; we measure the galaxy's redshift to be z = 0.492 ± 0.008. The dispersion measure and redshift, in combination, provide a direct measurement of the cosmic density of ionized baryons in the intergalactic medium of ΩIGM = 4.9 ± 1.3 per cent, in agreement with the expectation from the Wilkinson Microwave Anisotropy Probe, and including all of the so-called 'missing baryons'. The ~6-day radio transient is largely consistent with the radio afterglow of a short γ-ray burst, and its existence and timescale do not support progenitor models such as giant pulses from pulsars, and supernovae. This contrasts with the interpretation of another recently discovered fast radio burst, suggesting that there are at least two classes of bursts.

Observation of low- and high-energy Gamow-Teller phonon excitations in nuclei

Gamow-Teller (GT) transitions in atomic nuclei are sensitive to both nuclear shell structure and effective residual interactions. The nuclear GT excitations were studied for the mass number A = 42, 46, 50, and 54 "f-shell" nuclei in ((3)He, t) charge-exchange reactions. In the (42)Ca → (42)Sc reaction, most of the GT strength is concentrated in the lowest excited state at 0.6 MeV, suggesting the existence of a low-energy GT phonon excitation. As A increases, a high-energy GT phonon excitation develops in the 6-11 MeV region. In the (54)Fe → (54)Co reaction, the high-energy GT phonon excitation mainly carries the GT strength. The existence of these two GT phonon excitations are attributed to the 2 fermionic degrees of freedom in nuclei.

Adult orbital xanthogranulomatous disease: adult-onset xanthogranuloma of periorbital location

Adult orbital xanthogranulomatous disease (AOXGD) is a rare granulomatous disorder, which has four subtypes: adult-onset xanthogranuloma (AOX), adult-onset asthma with periocular xanthogranuloma, necrobiotic xanthogranuloma and Erdheim-Chester disease. We report a 42-year-old woman who presented with yellowish nonulcerative nodules on her eyelids. On histopathological examination of a nodule, mild degeneration of collagen fibres was seen, with surrounding infiltration of numerous foam cells and Touton giant cells in the deep dermis. Lymphoid follicles were seen in the reticular dermis. There was no apparent necrobiosis of collagen fibres. There were no clinical symptoms of asthma and no laboratory signs of paraproteinaemia during a follow-up of more than 5 years. We diagnosed this case as AOX, but further long-term follow-up would be required for the differentiation from the other AOXGDs. Dermatologists should be aware of these rare granulomatous disease conditions with ocular/orbital location, because they may cause ophthalmological complications.

The nuclear factor kappa B p50 subunit and cortactin as markers to distinguish between keratoacanthoma and well-differentiated squamous cell carcinoma

BACKGROUND

Distinguishing keratoacanthoma (KA) from well-differentiated squamous cell carcinoma (SCC) is sometimes difficult. Recent evidence indicates that the nuclear factor kappa B p50 subunit (p50) and cortactin might be useful to distinguish between these two conditions.

AIM

To verify whether p50 and cortactin are useful differentiation markers to distinguish between subungual KA and well-differentiated SCC.

METHODS

Immunohistochemistry using p50, cortactin and Ki-67 was performed on 20 patients with KA and 20 patients with facial well-differentiated SC. Ki-67 staining was also evaluated and scored.

RESULTS

Both p50 and cortactin had higher levels of expression in KA than in SCC. Both were localized to the basal-cell layer of KA, whereas they were scattered without polarity throughout the SCC lesions. Although the Ki-67 index was not significantly different between KA and SCC, the staining pattern also showed loss of polarity in SCC.

CONCLUSION

p50 and cortactin might be useful makers to distinguish between KA and well-differentiated SCC.

Recalcitrant facial pemphigus vulgaris: correlation of skin lesions with the ratio of antidesmoglein antibodies 1 and 3

Pemphigus vulgaris (PV) is an autoimmune bullous disease characterized by autoantibodies against desmogleins. We report a case of recalcitrant PV, which progressed from the mucosal to the mucocutaneous type, with a corresponding increase in anti-desmoglein (Dsg)1 and decrease in anti-Dsg3 antibody titres. Thus, the clinical features seemed to correlate with the ratio of anti-Dsg1 and 3. The patient also had anti-Dsg4 antibodies, which might be related to the nonscarring diffuse hair loss and marked facial involvement she also had. The patient did not respond to treatment with systemic steroid, ciclosporin, azathioprine, cyclophosphamide or double filtration plasmapheresis, and eventually died from fulminant thrombotic thrombocytopenic purpura of unknown cause.

Nuclear spins and moments of Ga isotopes reveal sudden structural changes between N=40 and N=50

Collinear laser spectroscopy was performed on Ga (Z=31) isotopes at ISOLDE, CERN. A gas-filled linear Paul trap (ISCOOL) was used to extend measurements towards very neutron-rich isotopes (N=36-50). A ground state (g.s.) spin I=1/2 is measured for 73Ga, being near degenerate with a 3/2{-} isomer (75  eV≲E{ex}≲1  keV). The 79Ga g.s., with I=3/2, is dominated by protons in the πf{5/2} orbital and in 81Ga the 5/2{-} level becomes the g.s. The data are compared to shell-model calculations in the f{5/2}pg{9/2} model space, calling for further theoretical developments and new experiments.

Oral behavior from food intake until terminal swallow

We analyzed oral behavior from food intake until terminal swallow for mastication and swallowing under a freely eating condition with a natural food. Measurements, including movement of the mandible and tongue, the size of the gape, different sequences involved in the oral aspect of the swallowing action, and bolus size and movement were carried out in five "freely eating subjects" using videofluorography. During food intake, the tongue moved forwards and backwards to introduce food into the mouth, to compress the food against the hard palate, and to transport food to the occlusal surface of the molar teeth. Most of the food was swallowed in the first swallow, and any residual food was aggregated by the tongue into a bolus and then swallowed in the last swallow. These findings suggest that 1) tongue manipulation plays an important role in recognizing and evaluating the volume of bite taken, 2) the intra-oral compression of food has a role in the recognition of food texture, 3) stage I transport is closely bound to the texture recognition process, 4) humans need at least two swallows, even with one bite of food, when ingesting food freely, and 5) the duration time of the oral stage of swallowing may depend on the bolus volume and be longer for smaller volumes unlike those measured under the command swallow.

Lowest excitations in 56Ti and the predicted N=34 shell closure

Recent experimental characterization of the subshell closure at N=32 in the Ca, Ti, and Cr isotones has stimulated shell-model calculations that indicated the possibility that the N=34 isotones of these same elements could exhibit characteristics of a shell closure, namely, a high energy for the first excited 2(+) level. To that end, we have studied the decay of 56Sc produced in fragmentation reactions and identified new gamma rays in the daughter N=34 isotone 56Ti. The first 2(+) level is found at an energy of 1127 keV, well below the expected position that would indicate the presence of an N=34 shell closure in 56Ti.

Cellular responses to low dose heavy-ion exposure in human cells

The human lymphoblastoid cell line TK6 was used to study the cellular responses after low-dose (100, 200, 500 mGy) or high-dose (3 Gy) of X rays, C (22 keV.micron-1) and Fe (1000 keV.micron-1) ion exposures. p53 protein induction in individual cells was determined by indirect immunofluorescence staining. Cell-cycle progression after heavy-ion exposure was determined by using a laser scanning cytometer. A characteristic pattern of cell-cycle progression was observed with 3 Gy exposure of Fe ions but not with 100 mGy. Similarly such a pattern with 100 mGy C ion exposure did not match that with 3 Gy. The proportion of p53-induced cells is proportional to the probability of cell being hit by a primary heavy ion. The observed low-dose effect can be reflected in the probability of a hit, although detailed nature about their energy deposition must be considered for more precise estimation of such an effect. New detection methodology must be developed for identification of heavy-ion specific cellular responses.

Mutation induction in human cells after low dose X ray exposure

Mutations induced after low dose ionising radiation exposure have been intensively analysed not only for radiation risk estimation but also for basic understanding of cellular responses. Human lymphoblastoid TK6-20C cells were irradiated with 100 mGy of X rays and mutation at the heterozygous thymidine kinase (TK) locus was selected by trifluorothymidine (TFT) resistance. Although the mutation frequency at the TK locus increased from 5.6 x 10(-6) to 7.4 x 10(-6), this increase was not statistically significant. However, molecular analysis of TK mutants exhibiting loss of heterozygocity (LOH) demonstrated a clear effect of such low dose IR exposure. Exposure to 100 mGy X ray increased the fraction of hemizygous-LOH from 10% to 42%. In previous experiments, a similar tendency in the increase of hemizygous-LOH was also observed in TK6 cells after exposure to a 2 Gy dose of X rays. This type of LOH can be considered as a result of end-joining repair of DNA double strand breaks.

Two starch-branching-enzyme isoforms occur in different fractions of developing seeds of kidney bean

The nature and enzymic properties of starch-branching enzyme (SBE) are two of the dominant factors influencing the fine structure of starch. To understand the role of this enzyme's activity in the formation of starch in kidney bean (Phaseolus vulgaris L.), a study was undertaken to identify the major SBE sequences expressed during seed development and to characterize the enzymic properties of the coded recombinant enzymes. Two SBE cDNA species (designated pvsbe2 and pvsbe1) that displayed significant similarity (more than 70%) to other family A and B SBEs respectively were isolated. Northern blot analysis revealed that pvsbe1 and pvsbe2 were differentially expressed during seed development. pvsbe2 showed maximum steady-state transcript levels at the mid-stage of seed maturation, whereas pvsbe1 reached peak levels at a later stage. Western blot analysis with antisera raised against both recombinant proteins (rPvSBE1 and rPvSBE2) showed that these two SBEs were located in different amyloplast fractions of developing seeds of kidney bean. PvSBE2 was present in the soluble fraction, whereas PvSBE1 was associated with the starch granule fraction. The differences in location suggest that these two SBE isoenzymes have different roles in amylopectin synthesis in kidney bean seeds. rPvSBE1 and rPvSBE2 were purified from Escherichia coli and their kinetic properties were determined. The affinity of rPvSBE2 for amylose (K(m) 1.27 mg/ml) was lower than that of rPvSBE1 (0.46 mg/ml). The activity of rPvSBE2 was stimulated more than 3-fold in the presence of 0.3 M citrate, whereas rPvSBE1 activity was not affected. The implications of the enzymic properties and the distribution of SBEs and amylopectin structure are discussed.

In vitro and in vivo transfer of bcl-2 gene into keratinocytes suppresses UVB-induced apoptosis

Bcl-2 is a member of the large Bcl-2 family and protects cells from apoptosis. Ultraviolet B (UVB) irradiation induces apoptosis of keratinocytes that is known as "sunburn cells." Previously we reported that UVB irradiation induces apoptosis accompanied by sequential activation of caspase 8, 3 and 1 in keratinocytes, and that the process is inhibited by various caspase inhibitors. Using bcl-2-expressing adenovirus vector we investigated the effect of Bcl-2 on UVB-induced apoptosis. Adenovirus vector efficiently introduced bcl-2 gene in cultured normal mouse keratinocytes (NMK cells); almost all NMK cells (1 x 10(6)) were transfected at 1 x 10(8) plaque-forming unit (PFU)/mL. Bcl-2-transfected NMK cells were significantly resistant to UVB-induced apoptosis with the suppressive effect dependent on the Bcl-2 expression level. Following UVB irradiation caspase 8, 3 and 9 activities were stimulated in NMK cells, whereas in bcl-2-transfected cells only caspase 8, but not caspase 3 or 9, activity was stimulated. In order to investigate the effect of Bcl-2 in vivo topical application of Ad-bcl-2 on tape-stripped mouse skin was performed. Following the application Bcl-2 was efficiently overexpressed in almost all viable keratinocytes. The expression was transient with the maximal expression of Bcl-2 on the first day following the application of 1 x 10(9) PFU in 200 microL. The introduced Bcl-2 remained at least for 6 days. UVB irradiation (1250 J/m2) induced apoptosis within 12 h and the maximal effect was observed at 24 h in control mouse skin. Both bcl-2-transfected and topical caspase 3 inhibitor-treated mice skin were resistant to UVB-induced apoptosis. The suppressive effect of Bcl-2 was more potent than that of caspase 3 inhibitor application. Topical application of empty adenovirus vector alone had no effect on Bcl-2 expression or UVB-induced apoptosis. These results indicate that adenovirus vector is an efficient gene delivery system into keratinocytes and that Bcl-2 is a potent inhibitor of UVB-induced apoptosis both in vitro and in vivo.

Expression of human cystatin A by keratinocytes is positively regulated via the Ras/MEKK1/MKK7/JNK signal transduction pathway but negatively regulated via the Ras/Raf-1/MEK1/ERK pathway

Cystatin A, a cysteine proteinase inhibitor, is a cornified cell envelope constituent expressed in the upper epidermis. We previously reported that a potent protein kinase C activator, 12-O-tetradecanoylphorbol-13-acetate, increases human cystatin A expression by the activation of AP-1 proteins. Here, we delineate the signaling cascade responsible for this regulation. Co-transfection of the cystatin A promoter into normal human keratinocytes together with a dominant active form of ras increased the promoter activity by 3-fold. In contrast, a dominant negative form of ras suppressed basal cystatin A promoter activity. Further analyses disclosed that transfection of dominant negative forms of raf-1, MEK1, ERK1, ERK2, or wild-type MEKK1 all increased cystatin A promoter activity in normal human keratinocytes, whereas wild-type raf-1, ERK1, ERK2, or dominant negative forms of MEKK1, MKK7, or JNK1 suppressed the promoter activity. The increased or decreased promoter activity reflected the expression of cystatin A on mRNA and protein levels. These effects were not observed when a cystatin A promoter with a T2 (-272 to -278) deletion was used. In contrast, transfection of dominant negative forms of MKK3, MKK4, or p38 did not affect cystatin A promoter activity. Immunohistochemical analyses revealed that phosphorylated active extracellular signal-regulated kinases and c-Jun N-terminal kinase were expressed in the nuclei of basal cells and cells in the suprabasal-granular cell layer, respectively. These results indicate that the expression of cystatin A is regulated via mitogen-activated protein kinase pathways positively by Ras/MEKK1/MKK7/JNK and negatively by Ras/Raf/MEK1/ERK.

17alpha-hydroxylase deficiency accompanied by adrenal myelolipoma

A 45-year-old woman was admitted because of hypertension and hypokalemia. Primary amenorrhea from birth was noted. Plasma renin activity (PRA), 17alpha-hydroxyprogesterone and androgen levels were low, but progesterone, 11-deoxycorticosterone, corticosterone and adrenocorticotropic hormone (ACTH) were elevated, resulting in a diagnosis of 17alpha-hydroxylase deficiency. Abdominal magnetic resonance imaging revealed a round mass in the left adrenal region, the specimen of which was diagnosed as myelolipoma. After removal of the tumor, the blood pressure, serum potassium and hormone levels were unchanged, indicating an adrenal non-functioning tumor. Excessive ACTH secretion over a long period may stimulate the development of adrenal myelolipoma.

Magic numbers in exotic nuclei and spin-isospin properties of the NN interaction

The magic numbers in exotic nuclei are discussed, and their novel origin is shown to be the spin-isospin dependent part of the nucleon-nucleon interaction in nuclei. The importance and robustness of this mechanism is shown in terms of meson exchange, G-matrix, and QCD theories. In neutron-rich exotic nuclei, magic numbers such as N = 8, 20, etc. can disappear, while N = 6, 16, etc. arise, affecting the structure of the lightest exotic nuclei to nucleosynthesis of heavy elements.