Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes.

Fruiting bodies (sporocarps, sporophores or basidiomata) of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates their growth, tissue differentiation and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is still limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim at a comprehensive identification of conserved genes related to fruiting body morphogenesis and distil novel functional hypotheses for functionally poorly characterised ones. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported to be involved in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defence, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1 480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10 % of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Citation: Nagy LG, Vonk PJ, Künzler M, Földi C, Virágh M, Ohm RA, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu XB, Nan S, M. Pareek M, Sahu N, Szathmári B, Varga T, Wu W, Yang X, Merényi Z (2023). Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Studies in Mycology 104: 1-85. doi: 10.3114/sim.2022.104.01.

Analysing the genomes of two tick-borne encephalitis viruses isolated in Hungary in 1952 and 2019.

The genomes of two Tick-borne encephalitis virus (TBEV) strains were fully sequenced and compared to those of known Hungarian strains. One was a laboratory strain (KEM-1) isolated in 1952, which had gone through hundreds of passages both on Vero cell cultures and in laboratory mice, while the other was a recent isolate (2019) from questing female ticks. The laboratory strain formed a monophyletic group with the already published 4 Hungarian strains on the evolutionary tree, located relatively close to Finnish (Kumlinge) and Russian (Absettarov) strains. This KEM-1 strain was phylogenetically distantly related both to the geographically close reference strain Neudörfl and the chronologically close Czech isolates from 1953. The 2019 isolate, KEM-195 was related to TBEV isolates from Southern Slovakia and Styria, and had the longest (328 nucleotides) deletion in its 3'-non-coding region among published sequences of strains of European subtype. Our results show that decades of laboratory passage have not altered the viral genome too much and that at least two distinct branches of TBEV strains circulate in Hungary.

Dark Energy Survey Year 1 Results: Cosmological Constraints from Cluster Abundances, Weak Lensing, and Galaxy Correlations.

We present the first joint analysis of cluster abundances and auto or cross-correlations of three cosmic tracer fields: galaxy density, weak gravitational lensing shear, and cluster density split by optical richness. From a joint analysis (4×2pt+N) of cluster abundances, three cluster cross-correlations, and the auto correlations of the galaxy density measured from the first year data of the Dark Energy Survey, we obtain Ω_{m}=0.305_{-0.038}^{+0.055} and σ_{8}=0.783_{-0.054}^{+0.064}. This result is consistent with constraints from the DES-Y1 galaxy clustering and weak lensing two-point correlation functions for the flat νΛCDM model. Consequently, we combine cluster abundances and all two-point correlations from across all three cosmic tracer fields (6×2pt+N) and find improved constraints on cosmological parameters as well as on the cluster observable-mass scaling relation. This analysis is an important advance in both optical cluster cosmology and multiprobe analyses of upcoming wide imaging surveys.

Detection of CMB-Cluster Lensing using Polarization Data from SPTpol.

We report the first detection of gravitational lensing due to galaxy clusters using only the polarization of the cosmic microwave background (CMB). The lensing signal is obtained using a new estimator that extracts the lensing dipole signature from stacked images formed by rotating the cluster-centered Stokes QU map cutouts along the direction of the locally measured background CMB polarization gradient. Using data from the SPTpol 500 deg^{2} survey at the locations of roughly 18 000 clusters with richness λ≥10 from the Dark Energy Survey (DES) Year-3 full galaxy cluster catalog, we detect lensing at 4.8σ. The mean stacked mass of the selected sample is found to be (1.43±0.40)×10^{14}M_{⊙} which is in good agreement with optical weak lensing based estimates using DES data and CMB-lensing based estimates using SPTpol temperature data. This measurement is a key first step for cluster cosmology with future low-noise CMB surveys, like CMB-S4, for which CMB polarization will be the primary channel for cluster lensing measurements.

Observation of a new channel, the production of CH3, in the abstraction reaction of OH radicals with acetaldehyde.

Using laser flash photolysis coupled to photo-ionization time-of-flight mass spectrometry (PIMS), methyl radicals (CH3) have been detected as primary products from the reaction of OH radicals with acetaldehyde (ethanal, CH3CHO) with a yield of ∼15% at 1-2 Torr of helium bath gas. Supporting measurements based on laser induced fluorescence studies of OH recycling in the OH/CH3CHO/O2 system are consistent with the PIMS study. Master equation calculations suggest that the origin of the methyl radicals is from prompt dissociation of chemically activated acetyl products and hence is consistent with previous studies which have shown that abstraction, rather than addition/elimination, is the sole route for the OH + acetaldehyde reaction. However, the observation of a significant methyl product yield suggests that energy partitioning in the reaction is different from the typical early barrier mechanism where reaction exothermicity is channeled preferentially into the newly formed bond. The master equation calculations predict atmospheric yields of methyl radicals of ∼9%. The implications of the observations in atmospheric and combustion chemistry are briefly discussed.

Endometrioid adenocarcinoma arising from adenomyosis: a case report.

BACKGROUND: Endometriosis is most commonly found in the peritoneum of the lesser pelvis and in the genital tract (in the ovaries). Its malignant transformation is quite rare, which usually appears in patients who previously underwent surgical procedures aimed at treating endometriosis. Years of hormone substitution (unopposed estrogen therapy) is also considered to have a role. According to the present authors' current knowledge, these are mostly well-differentiated tumors with low malignancy, which are primarily treated surgically. CASE: In the present case the authors present a 73-year-old female patient who underwent a laparotomy due to abdominal pain and a mass in the lesser pelvis. The authors performed hysterectomy along with bilateral adnexectomy and omental resection. The histological examination of the specimens verified an endometrial adenocarcinoma formed on the ground of adenomyosis and the endometrial adenocarcinoma of the left ovary. CONCLUSION: The malignant transformation of endometriosis is rare, and the mechanisms how it develops on the grounds of adenomyosis is currently unclear.

Subsurface synthesis and characterization of Ag nanoparticles embedded in MgO.

Metal nanoparticles exhibit a localized surface plasmon resonance (LSPR) which is very sensitive to the size and shape of the nanoparticle and the surrounding dielectric medium. The coupling between the electromagnetic radiation and the localized surface plasmon in metallic nanoparticles results in a sizable enhancement of the incident fields, making them possible candidates for plasmonic applications. In particular, partially exposed metallic nanoparticles distributed in a dielectric matrix can provide prime locations for LSPR spectroscopy and sensing. We report the synthesis and characterization of a plasmonic substrate consisting of Ag nanoparticles partially buried in MgO. Ag nanoparticles of different shapes and size distributions were synthesized below the surface of MgO by implanting 200 keV Ag(+) ions followed by annealing at 1000 °C for 10 and 30 h. A detailed optical and structural characterization was carried out to understand the evolution of the Ag nanoparticle and size distribution inside the MgO matrix. Micro x-ray diffraction (Micro-XRD) was employed to investigate the structural properties and estimate the crystallite size. The nanoparticles evolved from a spherical to a faceted morphology with annealing time, assuming an octahedral shape truncated at the (001) planes, as visualized from aberration-corrected transmission electron microscopy (TEM) images. The nanoparticles embedded in MgO were shown to be pure metallic Ag using atom probe tomography (APT). The nanoparticles were partially exposed to the surface by employing plasma etch techniques to remove the overlaying MgO. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) were employed to study the surface morphology and obtain a height distribution for the partially exposed nanoparticles.

Structural characterization of epitaxial Cr(x)Mo(1-x) alloy thin films.

To develop a model system containing regularly spaced misfit dislocations for studies of the radiation resistance of nanoscale defects, epitaxial thin films of Cr, Mo, and Cr(x)Mo(1-x) alloys were deposited on MgO(001) by molecular beam epitaxy. Film compositions were chosen to vary the lattice mismatch with MgO. The film structure was investigated by x-ray diffraction (XRD), Rutherford backscattering spectrometry (RBS) and scanning transmission electron microscopy (STEM). Epitaxial films with reasonably high crystalline quality and abrupt interfaces were achieved at a relatively low deposition temperature, as confirmed by STEM. However, it was found by XRD and RBS in the channeling geometry that increasing the Mo content of the CrMo alloy films degraded the crystalline quality, despite the improved lattice match with MgO. XRD rocking curve data indicated that regions of different crystalline order may be present within the films with higher Mo content. This is tentatively ascribed to spinodal decomposition into Cr-rich and Mo-rich regions, as predicted by the Cr(x)Mo(1-x) phase diagram.

Changes in the expression of pituitary adenylate cyclase-activating polypeptide in the human placenta during pregnancy and its effects on the survival of JAR choriocarcinoma cells.

Pituitary adenylate cyclase-activating polypeptide (PACAP), a neuropeptide with survival-promoting actions, has been observed in endocrine organs and is thought to play a role in reproductive functions, including pregnancy. PACAP occurs in two forms, 27 and 38 amino acid residues, with PACAP38 being the predominant form in human tissues. In the present study, we determined the concentrations of PACAP38 and PACAP27 in first-trimester and full-term human placentas using radioimmunoassay. We found high levels of PACAP38 and lower levels of PACAP27 in different parts of the full-term human placenta. PACAP38 content increased in the placenta during pregnancy, both on the maternal side and on the fetal side. The effects of PACAP on the survival of JAR human choriocarcinoma cells were investigated using flow cytometry and MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide) cell viability assay in cells exposed to the widely used chemotherapeutic agent methotrexate (MTX). It was found that PACAP neither influenced the survival of JAR cytotrophoblast cells nor affected cellular response to the death-inducing effect of the chemotherapeutic agent MTX. The present observations further support the significance of PACAP in the human placenta. The observation that PACAP did not influence the effects of MTX may have future clinical importance, showing that PACAP does not decrease the effects of certain chemotherapeutic agents.

Single- and repeated-dose oral toxicity studies of citicoline free-base (choline cytidine 5'-pyrophosphate) in Sprague-Dawley rats.

The dietary supplement Citicoline free-base (choline cytidine 5'-pyrophosphate) was toxicologically evaluated in Sprague-Dawley rats using oral gavage. In an acute 14-day study, 2000 mg/kg was well tolerated. In a 90-day study, 100, 350, and 1000 mg/kg/day doses resulted in no mortality. In males, slight significant increases in serum creatinine (350 and 1000 mg/kg/day), and decreases in urine volume (all treated groups) were observed. In females, slight significant increases in total white blood cell and absolute lymphocyte counts (1000 mg/kg/day), and blood urea nitrogen (BUN) (100 and 350, but not 1000 mg/kg/day) were noted. A dose-related increase in renal tubular mineralization, without degenerative or inflammatory reaction, was found in females (all treated groups) and two males (1000 mg/kg/day). Renal mineralization in rats (especially females) is influenced by calcium:phosphorus ratios in the diet. A high level of citicoline consumption resulted in increased phosphorus intake in the rats, and likely explains this result.

Coexistence of weak ferromagnetism and ferroelectricity in the high pressure LiNbO3-type phase of FeTiO3.

We report the magnetic and electrical characteristics of polycrystalline FeTiO_{3} synthesized at high pressure that is isostructural with acentric LiNbO_{3} (LBO). Piezoresponse force microscopy, optical second harmonic generation, and magnetometry demonstrate ferroelectricity at and below room temperature and weak ferromagnetism below approximately 120 K. These results validate symmetry-based criteria and first-principles calculations of the coexistence of ferroelectricity and weak ferromagnetism in a series of transition metal titanates crystallizing in the LBO structure.

Nuclear receptors, transcription factors linking lipid metabolism and immunity: the case of peroxisome proliferator-activated receptor gamma.

Exposure to lipids has a major effect on mammalian cells. Naturally, it has a profound impact on their metabolism, but it can also significantly alter their cellular and molecular phenotypes and responses. This latter is via specific signalling pathways leading to alterations in the expression of genes and gene networks. Multicellular organisms utilize a specialized group of proteins to detect and transduce lipid signals to the level of the expression of the genome. These proteins, termed nuclear hormone receptors, are lipid-activated transcription factors regulating gene expression upon binding of small fatty ligands. In this review, we discuss the role and contribution of peroxisome proliferator-activated receptor gamma (PPAR gamma) to macrophage and dendritic cell biology and also to gut epithelial cell function. We discuss how using different experimental systems and approaches the pathways activating the receptor and its target genes can be identified and complex biological processes unravelled. It appears that PPAR gamma is part of the macrophage's response to pathogenic lipoproteins and it coordinately regulates lipid uptake and efflux. Intriguingly, in another cell type of the immune system, dendritic cells, the receptor has overlapping, but distinct functions. In these cells, activation of PPAR gamma leads to altered immune phenotype characterized by increased phagocytic capacity, antigen processing and lipid antigen presenting capacity. This nuclear hormone receptor links lipid metabolism and immune cell function and these links provide unique insights into the regulatory logic of normal physiological responses and certain pathologies, such as atherosclerosis, chronic inflammatory diseases and autoimmunity.

Drugged driving in Hungary 2000-2004.

The authors analyzed the biological samples available in criminal cases that were started because of illicit and prescribed drug-impaired driving between 2000 and 2004. The result of the on-the-spot clinical test is not informative and cannot be evaluated as it is mainly affected by the simultaneous presence of alcohol. Licit or illicit drugs in the urine could be detected in 378 people out of 623 people (60.7%), whereas in 59 cases (9.5%) there was some substance present in the blood. The occurrence multiple drugs was high (36.8%). The joint use of alcohol and drugs has increased in the past few years.

Criminal liability of physicians and other health care professionals in Hungary (review of case law between 1996-2000).

The authors examine the criminal cases involving physicians and other health care workers between January 1996 and December 2000 inclusive. in Hungary. The data are based on the registry of the Criminal Prosecutor's Office. Altogether 94 cases were initiated in this period of time, the accused of the criminal proceeding was a registered nurse in 9 cases, an ambulance paramedic in 5 cases, a pharmacist in 3, and a physician in 77 cases. In cases where registered nurses were involved, the most common act was negligent change of medication or providing inadequate custody of a patient in need, pharmacists were also accused for negligent change of medicinal products. In case of ambulance assistants the most common violation of the professional rules was diagnostic failure or not responding to the call in time. As to physicians, mostly primary care physicians were accused (29%), usually for failing to examine the patient or for diagnostic error, obstetricians-gynecologists (17 %) and traumatologists (12 %) were also frequently accused.

Prenatal and newborn paternity testing with DNA analysis.

In rape against youthful girls which yields pregnancy after the abortion DNA examinations can be performed from the aborted foetal material to provide evidence of paternity of the suspect. In our present work we demonstrate six cases: four of them are rape cases and two where the mother abandoned her newborn baby. These cases proved that DNA-STR profiles can be determined from foetus after the abortion and perpetrator of a rape can be found. Due to our result we suggest that not only placenta but also bloody vernix caseosa is useful tissue for identifying the putative mother because vernix caseosa can be the carrier of the mother's blood.

Acute and subchronic toxicity studies of cryogenically-frozen, cryomilled, Pelodiscus sinensis (Japanese soft-shelled turtle--suppon) powder administered to the rat.

Sprague-Dawley rats received "cryogenically-frozen suppon" (CFS), a cryomilled product derived for the Japanese soft-shelled turtle (Pelodiscus sinensis), widely consumed for its nutritious value and medicinal properties, especially for the maintenance of normal blood pressure and insulin levels, and in women for the treatment of menopausal symptoms. In this acute study, a single limit dose of 2.0 g/kg was given po. common to 10 male and 10 female rats. No adverse effects or mortality were observed during a 14-day period and at gross pathological examination. In the subchronic study, CFS was administered as oral daily doses of 100, 350, and 1000 mg/kg administered for 97 days, resulting in no mortality, no changes in body weight, food and water consumption, hematological and serum chemistry parameters, organ weights, or gross pathology or histopathology. The only treatment related finding was a characteristic excited behavior observed in several male rats from the second or third week of treatment, distributed evenly in all male treatment groups but not affecting all males. The number of excited animals did not change over time, the syndrome occurred in all test item treated male groups with similar incidence. None of the females was so affected.

Temperature effect on the 13C NMR chemical shift of pressurized CO2 containing selected modifiers.

Temperature dependence of 13C NMR chemical shift of pressurized CO2 containing modifiers has been studied. Benzene, C6F6, C6F5OH, (CF3)2CHOH and [(CH3)2N]3PO were used as the modifiers. The 13C chemical shift of CO2 was found to show a different temperature dependence in the presence of selected modifiers.

Protease-elicited TUNEL positivity of non-apoptotic fixed cells.

The appearance of free DNA ends in the chromatin is usually considered an indication of advanced apoptosis. Unexpectedly, the nuclei of non-apoptotic cells derived from mouse thymuses could be specifically labeled by terminal transferase after proteinase K treatment of the fixed, cytocentrifuged samples. Artifactual mechanical or contaminating nucleolytic factors have been ruled out as players in the generation of free DNA ends. The phenomenon was detected in both formaldehyde- and ethanol-fixed specimens, in agarose-embedded fixed cells, and in chromatin spreads. By urea-agarose gel electrophoresis, the average single-strand size of the DNA molecules carrying the free ends was found between 50 and 250 kb. We suggest that ss discontinuities preexisting in the fixed normal cells are unmasked by protease treatment eliciting TUNEL (terminal transferase-mediated nick end-labeling) positivity.

[Competitive polymerase chain reaction: a new method for measuring N-myc amplification]. / Kompetitív polimeráz láncreakció: új lehetöség az N-myc amplifikáció mértékének meghatározására.

The highly variable biological behaviour of neuroblastoma, a neoplasm which belongs to the family of primitive neuroectodermal tumours, is determined by its molecular pathological characteristics. Among them amplification of the N-myc gene is the most important factor in both therapeutic and prognostic points of view. Value of the amplification can be determined by different methods. The latest of them is the competitive polymerase chain reaction (PCR), essence of which is the parallel reaction of the target N-myc gene (exon 3.) and the endogen competitor CF gene (exon 3.) in the same reaction solution. The authors applied the method on 11 neuroblastoma cases diagnosed between 1994 and january of 1999. In three cases the amplification was determined also by fluorescens in situ hybridization (FISH). Six of the 11 cases were detected to have more than 10-fold, two of the six about 100-fold N-myc amplification. Results of the PCR and FISH correlated well. The two methods applied by the authors complete each other and are appropriate for determining the gene amplification which gives valuable prognostic and therapeutic information about the examined tumour.