Comprehensive investigations of 2-phenylethanol production by the filamentous fungus Annulohypoxylon stygium.

2-Phenylethanol (2-PE) is an aromatic compound with a rose-like fragrance that is widely used in food and other industries. Yeasts have been implicated in the biosynthesis of 2-PE; however, few studies have reported the involvement of filamentous fungi. In this study, 2-PE was detected in Annulohypoxylon stygium mycelia grown in both potato dextrose broth (PDB) and sawdust medium. Among the 27 A. stygium strains investigated in this study, the strain "Jinjiling" (strain S20) showed the highest production of 2-PE. Under optimal culture conditions, the concentration of 2-PE was 2.33 g/L. Each of the key genes in Saccharomyces cerevisiae shikimate and Ehrlich pathways was found to have homologous genes in A. stygium. Upon the addition of L-phenylalanine to the medium, there was an upregulation of all key genes in the Ehrlich pathway of A. stygium, which was consistent with that of S. cerevisiae. A. stygium as an associated fungus provides nutrition for the growth of Tremella fuciformis and most spent composts of T. fuciformis contain pure A. stygium mycelium. Our study on the high-efficiency biosynthesis of 2-PE in A. stygium offers a sustainable solution by utilizing the spent compost of T. fuciformis and provides an alternative option for the production of natural 2-PE. KEY POINTS: • Annulohypoxylon stygium can produce high concentration of 2-phenylethanol. • The pathways of 2-PE biosynthesis in Annulohypoxylon stygium were analyzed. • Spent compost of Tremella fuciformis is a potential source for 2-phenylethanol.

Finite-size scaling of the high-dimensional Ising model in the loop representation.

Besides its original spin representation, the Ising model is known to have the Fortuin-Kasteleyn (FK) bond and loop representations, of which the former was recently shown to exhibit two upper critical dimensions (d_{c}=4,d_{p}=6). Using a lifted worm algorithm, we determine the critical coupling as K_{c}=0.07770891(4) for d=7, which significantly improves over the previous results, and then study critical geometric properties of the loop Ising clusters on tori for spatial dimensions d=5 to 7. We show that as the spin representation, the loop Ising model has only one upper critical dimension at d_{c}=4. However, sophisticated finite-size scaling (FSS) behaviors, such as two length scales, two configuration sectors, and two scaling windows, still exist as the interplay effect of the Gaussian fixed point and complete-graph asymptotics. Moreover, using the loop-cluster algorithm, we provide an intuitive understanding of the emergence of the percolation-like upper critical dimension d_{p}=6 in the FK-Ising model. As a consequence, a unified physical picture is established for the FSS behaviors in all three representations of the Ising model above d_{c}=4.

Near-gapless genome and transcriptome analyses provide insights into fruiting body development in Lentinula edodes.

Fruiting body development in macrofungi is an intensive research subject. In this study, high-quality genomes were assembled for two sexually compatible monokaryons from a heterokaryotic Lentinula edodes strain WX1, and variations in L. edodes genomes were analyzed. Specifically, differential gene expression and allele-specific expression (ASE) were analyzed using the two monokaryotic genomes and transcriptome data from four different stages of fruiting body development in WX1. Results revealed that after aeration, mycelia sensed cell wall stress, pheromones, and a decrease in CO2 concentration, leading to up-regulated expression in genes related to cell adhesion, cell wall remodeling, proteolysis, and lipid metabolism, which may promote primordium differentiation. Aquaporin genes and those related to proteolysis, mitosis, lipid, and carbohydrate metabolism may play important roles in primordium development, while genes related to tissue differentiation and sexual reproduction were active in fruiting body. Several essential genes for fruiting body development were allele-specifically expressed and the two nuclear types could synergistically regulate fruiting body development by dominantly expressing genes with different functions. ASE was probably induced by long terminal repeat-retrotransposons. Findings here contribute to the further understanding of the mechanism of fruiting body development in macrofungi.

A Comprehensive Assessment of Ultraviolet-Radiation-Induced Mutations in Flammulina filiformis Using Whole-Genome Resequencing.

Nucleotide substitutions have played an important role in molecular evolution, and understanding their dynamics would contribute to genetic studies. Related research with defined DNA sequences lasted for decades until whole-genome sequencing arose. UV radiation (UVR) can generate base changes and other genetic variations in a short period of time, so it would be more meaningful to explore mutations caused by UVR from a genomic perspective. The monokaryon enoki strain WT583 was selected as the experimental material in this study because it can spontaneously produce large amounts of oidia on PDA plates, and the monokaryons originating from oidia have the same genotype as their mother monokaryon. After exposure to UV radiation, 100 randomly selected mutants, with WT583 as the reference genome, were sent for genome sequencing. BWA, samtools, and GATK software were employed for SNP calling, and the R package CMplot was used to visualize the distribution of the SNPs on the contigs of the reference genome. Furthermore, a k-mer-based method was used to detect DNA fragment deletion. Moreover, the non-synonymous genes were functionally annotated. A total of 3707 single-base substitutions and 228 tandem mutations were analyzed. The immediate adjacent bases showed different effects on the mutation frequencies of adenine and cytosine. For adenine, the overall effects of the immediate 5'-side and 3'-side bases were T > A > C > G and A > T > G > C, respectively; for cytosine, the overall effects of the immediate 5'-side and 3'-side bases were T > C > A > G and C > T > A > G, respectively. Regarding tandem mutations, the mutation frequencies of double-transition, double-transversion, 3'-side transition, and 5'-side transition were 131, 8, 72, and 17, respectively. Transitions at the 3'-side with a high mutation frequency shared a common feature, where they held transversions at the 5'-side of A→T or T→A without covalent bond changes, suggesting that the sequence context of tandem motifs might be related to their mutation frequency. In total, 3707 mutation sites were non-randomly distributed on the contigs of the reference genome. In addition, pyrimidines at the 3'-side of adenine promoted its transversion frequency, and UVR generated DNA fragment deletions over 200 bp with a low frequency in the enoki genome. The functional annotation of the genes with non-synonymous mutation indicated that UVR could produce abundant mutations in a short period of time.

Meiosis in an asymmetric dikaryotic genome of Tremella fuciformis Tr01 facilitates new chromosome formation.

BACKGROUND: The dikaryotic stage dominates most of the life cycle in basidiomycetes, and each cell carries two different haploid nuclei. Accurate phasing of these two nuclear genomes and their interactions have long been of interest. RESULTS: We combine PacBio HiFi reads, Nanopore ultra-long reads, and Hi-C data to generate a complete, high-quality asymmetric dikaryotic genome of Tremella fuciformis Tr01, including Haplotypes A and B genomes. We assemble a meiotic haploid DBZ04 genome and detect three recombination events in these two haplotypes. We identify several chromosomal rearrangements that lead to differences in chromosome number, length, content, and sequence arrangement between these two haplotypes. Each nucleus contains a two-speed genome, harboring three accessory chromosomes and two accessory compartments that affect horizontal chromatin transfer between nuclei. We find few basidiospores are ejected from fruiting bodies of Tr01. Most monospore isolates sequenced belong to Tr01-Haplotype A genome architecture. More than one-third of monospore isolates carry one or two extra chromosomes including Chr12B and two new chromosomes ChrN1 and ChrN2. We hypothesize that homologous regions of seven sister chromatids pair into a large complex during meiosis, followed by inter-chromosomal recombination at physical contact sites and formation of new chromosomes. CONCLUSION: We assemble two haplotype genomes of T. fuciformis Tr01 and provide the first overview of basidiomycetous genomes with discrete genomic architecture. Meiotic activities of asymmetric dikaryotic genomes result in formation of new chromosomes, aneuploidy of some daughter cells, and inviability of most other daughter cells. We propose a new approach for breeding of sporeless mushroom.

Extraordinary-log Universality of Critical Phenomena in Plane Defects.

The recent discovery of the extraordinary-log (E-Log) criticality is a celebrated achievement in modern critical theory and calls for generalization. Using large-scale Monte Carlo simulations, we study the critical phenomena of plane defects in three- and four-dimensional O(n) critical systems. In three dimensions, we provide the first numerical proof for the E-Log criticality of plane defects. In particular, for n=2, the critical exponent q[over ^] of two-point correlation and the renormalization-group parameter α of helicity modulus conform to the scaling relation q[over ^]=(n-1)/(2πα), whereas the results for n≥3 violate this scaling relation. In four dimensions, it is strikingly found that the E-Log criticality also emerges in the plane defect. These findings have numerous potential realizations and would boost the ongoing advancement of conformal field theory.

Sweeny dynamics for the random-cluster model with small Q.

The Sweeny algorithm for the Q-state random-cluster model in two dimensions is shown to exhibit a rich mixture of critical dynamical scaling behaviors. As Q decreases, the so-called critical speeding-up for nonlocal quantities becomes more and more pronounced. However, for some quantity of a specific local pattern, e.g., the number of half faces on the square lattice, we observe that, as Q→0, the integrated autocorrelation time τ diverges as Q^{-ζ}, with ζ≃1/2, leading to the nonergodicity of the Sweeny method for Q→0. Such Q-dependent critical slowing-down, attributed to the peculiar form of the critical bond weight v=sqrt[Q], can be eliminated by a combination of the Sweeny and the Kawasaki algorithm. Moreover, by classifying the occupied bonds into bridge bonds and backbone bonds, and the empty bonds into internal-perimeter bonds and external-perimeter bonds, one can formulate an improved version of the Sweeny-Kawasaki method such that the autocorrelation time for any quantity is of order O(1).

Geometric properties of the complete-graph Ising model in the loop representation.

The exact solution of the Ising model on the complete graph (CG) provides an important, though mean-field, insight for the theory of continuous phase transitions. Besides the original spin, the Ising model can be formulated in the Fortuin-Kasteleyn random cluster and the loop representation, in which many geometric quantities have no correspondence in the spin representations. Using a lifted-worm irreversible algorithm, we study the CG-Ising model in the loop representation and, based on theoretical and numerical analyses, obtain a number of exact results including volume fractal dimensions and scaling forms. Moreover, by combining with the loop-cluster algorithm, we demonstrate how the loop representation can provide an intuitive understanding to the recently observed rich geometric phenomena in the random-cluster representation, including the emergence of two configuration sectors, two length scales, and two scaling windows.

Geometric scaling behaviors of the Fortuin-Kasteleyn Ising model in high dimensions.

Recently, we argued [Chin. Phys. Lett. 39, 080502 (2022)0256-307X10.1088/0256-307X/39/8/080502] that the Ising model simultaneously exhibits two upper critical dimensions (d_{c}=4,d_{p}=6) in the Fortuin-Kasteleyn (FK) random-cluster representation. In this paper, we perform a systematic study of the FK Ising model on hypercubic lattices with spatial dimensions d from 5 to 7, and on the complete graph. We provide a detailed data analysis of the critical behaviors of a variety of quantities at and near the critical points. Our results clearly show that many quantities exhibit distinct critical phenomena for 4

Explosive Percolation Obeys Standard Finite-Size Scaling in an Event-Based Ensemble.

Explosive percolation in the Achlioptas process, which has attracted much research attention, is known to exhibit a rich variety of critical phenomena that are anomalous from the perspective of continuous phase transitions. Hereby, we show that, in an event-based ensemble, the critical behaviors in explosive percolation are rather clean and obey the standard finite-size scaling theory, except for the large fluctuation of pseudo-critical points. In the fluctuation window, multiple fractal structures emerge and the values can be derived from a crossover scaling theory. Further, their mixing effects account well for the previously observed anomalous phenomena. Making use of the clean scaling in the event-based ensemble, we determine with a high precision the critical points and exponents for a number of bond-insertion rules and clarify ambiguities about their universalities. Our findings hold true for any spatial dimensions.

Burstiness and information spreading in active particle systems.

We construct a temporal network using the two-dimensional Vicsek model. The bursts of the interevent times for a specific pair of particles are investigated numerically. We found that, for different noise strengths, the distribution of the interevent times of a target edge follows a heavy tail, revealing the burstiness of the signals. To further characterize the nature of the burstiness, we calculate the burstiness parameters and the memory coefficients. The results show that, near the phase transition points of the Vicsek model, the burstiness parameters reach the minimum values for each density, indicating a relationship between the phase transition of the Vicsek model and the bursty nature of the signals. Furthermore, we investigate the spreading dynamics on our temporal network using a susceptible-infected model and observe a positive correlation between them.

Temperature-Dependent Decay of Quasi-Two-Dimensional Vortices across the BCS-BEC Crossover.

We systematically study the decay of quasi-two-dimensional vortices in an oblate strongly interacting Fermi gas over a wide interaction range and observe that, as the system temperature is lowered, the vortex lifetime increases in the Bose-Einstein condensate (BEC) regime but decreases at unitarity and in the Bardeen-Cooper-Schrieffer (BCS) regime. The observations can be qualitatively captured by a phenomenological model simply involving diffusion and two-body collisional loss, in which the vortex lifetime is mostly determined by the slower process of the two. In particular, the counterintuitive vortex decay in the BCS regime can be interpreted by considering the competition between the temperature dependence of the vortex annihilation rate and that of unpaired fermions. Our results suggest a competing mechanism for the complex vortex decay dynamics in the BCS-BEC crossover for the fermionic superfluids.

Monte Carlo study of duality and the Berezinskii-Kosterlitz-Thouless phase transitions of the two-dimensional q-state clock model in flow representations.

The two-dimensional q-state clock model for q≥5 undergoes two Berezinskii-Kosterlitz-Thouless (BKT) phase transitions as temperature decreases. Here we report an extensive worm-type simulation of the square-lattice clock model for q=5-9 in a pair of flow representations, from high- and low-temperature expansions, respectively. By finite-size scaling analysis of susceptibilitylike quantities, we determine the critical points with a precision improving over the existing results. Due to the dual flow representations, each point in the critical region is observed to simultaneously exhibit a pair of anomalous dimensions, which are η_{1}=1/4 and η_{2}=4/q^{2} at the two BKT transitions. Further, the approximate self-dual points ß_{sd}(L), defined by the stringent condition that the susceptibilitylike quantities in both flow representations are identical, are found to be nearly independent of system size L and behave as ß_{sd}≃q/2π asymptotically at the large-q limit. The exponent η at ß_{sd} is consistent with 1/q within statistical error as long as q≥5. Based on this, we further conjecture that η(ß_{sd})=1/q holds exactly and is universal for systems in the q-state clock universality class. Our work provides a vivid demonstration of rich phenomena associated with the duality and self-duality of the clock model in two dimensions.

Intraspecific comparison of mitochondrial genomes reveals the evolution in medicinal fungus Ganoderma lingzhi.

Several mitogenomes of the genus Ganoderma have been assembled, but intraspecific comparisons of mitogenomes in Ganoderma lingzhi have not been reported. In this study, 19 G. lingzhi mitogenomes were assembled and analyzed combined with three mitogenomes of G. lingzhi from GenBank in term of the characteristics, evolution, and phylogeny. The results showed that the mitogenomes of the G. lingzhi strains are closed circular ranging from 49.23 kb to 68.37 kb. The genetic distance, selective pressure, and base variation indicate that the 14 common protein coding genes were highly conserved. The differences in introns, open reading frames, and repetitive sequences in the mitogenome were the main factors leaded to the variations in mitogenome. The introns were horizontally transferred in mitogenomes, and the differences between introns in the same insertion, which were primarily caused by the repetitive sequence, showed that the introns may be under degeneration. Besides, the frequent insertion and deletion of introns showed an evolutionary rate faster than protein coding genes. Phylogenetic analysis showed that the G. lingzhi strains gathered with high support, and those with the same intron distribution law had closer clustering relationships.

Cystathionine Gamma-Lyase Regulate Psilocybin Biosynthesis in Gymnopilus dilepis Mushroom via Amino Acid Metabolism Pathways.

As a potential medicine for the treatment of depression, psilocybin has gradually attracted attention. To elucidate the molecular mechanism regulating psilocybin synthesis in Gymnopilus dilepis, ultra-performance liquid chromatography (UPLC) was used to detect the changes in psilocybin content after S-adenosyl-l-homocysteine (SAH) treatment and the changes of psilocybin content in different parts (stipe and pileus), and RNA-Seq was used to explore the mechanism of psilocybin content changes. In this study, the psilocybin content in G. dilepis mycelia treated with SAH was significantly lower than that in the control group, and the content of psilocybin in the stipe was significantly higher than that in the pileus. Transcriptome analysis revealed that differential expression genes (DEGs) were associated with cysteine and methionine metabolism. In particular, the transcription levels of genes encoding Cystathionine gamma-lyase (CTH) in different treatments and different parts were positively correlated with psilocybin content. In addition, we found that the exogenous addition of CTH activity inhibitor (DL-propargylglycine, PAG) could reduce the content of psilocybin and L-serine, and the content of psilocybin and L-serine returned to normal levels after L-cysteine supplementation, suggesting that psilocybin synthesis may be positively correlated with L-cysteine or CTH, and L-cysteine regulates the synthesis of psilocybin by affecting L-serine and 4-hydroxy-L-tryptophan. In conclusion, this study revealed a new molecular mechanism that affects psilocybin biosynthesis, which can provide a theoretical basis for improving psilocybin synthesis and the possibility for the development of biomedicine.

Backbone and shortest-path exponents of the two-dimensional Q-state Potts model.

We present a Monte Carlo study of the backbone and the shortest-path exponents of the two-dimensional Q-state Potts model in the Fortuin-Kasteleyn bond representation. We first use cluster algorithms to simulate the critical Potts model on the square lattice and obtain the backbone exponents d_{B}=1.7320(3) and 1.794(2) for Q=2,3, respectively. However, for large Q, the study suffers from serious critical slowing down and slowly converging finite-size corrections. To overcome these difficulties, we consider the O(n) loop model on the honeycomb lattice in the densely packed phase, which is regarded to correspond to the critical Potts model with Q=n^{2}. With a highly efficient cluster algorithm, we determine from domains enclosed by the loops d_{B}=1.64339(5),1.73227(8),1.7938(3),1.8384(5),1.8753(6) for Q=1,2,3,2+sqrt[3],4, respectively, and d_{min}=1.0945(2),1.0675(3),1.0475(3),1.0322(4) for Q=2,3,2+sqrt[3],4, respectively. Our estimates significantly improve over the existing results for both d_{B} and d_{min}. Finally, by studying finite-size corrections in backbone-related quantities, we conjecture an exact formula as a function of n for the leading correction exponent.

Machine learning for percolation utilizing auxiliary Ising variables.

Machine learning for phase transition has received intensive research interest in recent years. However, its application in percolation still remains challenging. We propose an auxiliary Ising mapping method for the machine learning study of the standard percolation as well as a variety of statistical mechanical systems in correlated percolation representation. We demonstrate that unsupervised machine learning is able to accurately locate the percolation threshold, independent of the spatial dimension of system or the type of phase transition, which can be first-order or continuous. Moreover, we show that, by neural network machine learning, auxiliary Ising configurations for different universalities can be classified with a high confidence level. Our results indicate that the auxiliary Ising mapping method, despite its simplicity, can advance the application of machine learning in statistical and condensed-matter physics.

Interaction-induced particle-hole symmetry breaking and fractional exclusion statistics.

Quantum statistics plays a fundamental role in the laws of nature. Haldane fractional exclusion statistics (FES) generalizes the Pauli exclusion statistics, and can emerge in the properties of elementary particles and hole excitations of a quantum system consisting of conventional bosons or fermions. FES has a long history of intensive studies, but its simple realization in interacting physical systems is rare. Here we report a simple non-mutual FES that depicts the particle-hole symmetry breaking in interacting Bose gases at a quantum critical point. We show that the FES distribution directly comes from particle-hole symmetry breaking. Based on exact solutions, quantum Monte Carlo simulations and experiments, we find that, over a wide range of interaction strengths, the macroscopic physical properties of these gases are determined by non-interacting quasi-particles that obey non-mutual FES of the same form in one and two dimensions. Whereas strongly interacting Bose gases reach full fermionization in one dimension, they exhibit incomplete fermionization in two dimensions. Our results provide a generic connection between interaction-induced particle-hole symmetry breaking (depicted by FES) and macroscopic properties of many-body systems in arbitrary dimensions. Our work lays the groundwork for using FES to explore quantum criticality and other novel many-body phenomena in strongly correlated quantum systems.

Universal Critical Behavior of Percolation in Orientationally Ordered Janus Particles and Other Anisotropic Systems.

We combine percolation theory and Monte Carlo simulation to study in two dimensions the connectivity of an equilibrium lattice model of interacting Janus disks which self-assemble into an orientationally ordered stripe phase at low temperature. As the patch size is increased or the temperature is lowered, clusters of patch-connected disks grow, and a percolating cluster emerges at a threshold. In the stripe phase, the critical clusters extend longer in the direction parallel to the stripes than in the perpendicular direction, and percolation is thus anisotropic. It is found that the critical behavior of percolation in the Janus system is consistent with that of standard isotropic percolation, when an appropriate spatial rescaling is made. The rescaling procedure can be applied to understand other anisotropic systems, such as the percolation of aligned rigid rods and of the q-state Potts model with anisotropic interactions.

Genetic structure and evolutionary diversity of mating-type (MAT) loci in Hypsizygus marmoreus.

The mating compatibility in fungi is generally governed by genes located within a single or two unlinked mating type (MAT) loci. Hypsizygus marmoreus is an edible mushroom in the order Agaricales with a tetrapolar system, which contains two unlinked MAT loci-homeodomain (HD) transcription factor genes and pheromone/pheromone receptor genes (P/R). In this study, we analyzed the genetic structure and diversity of MAT loci in tetrapolar system of H. marmoreus through sequencing of 54 heterokaryon and 8 homokaryon strains. Although within the HD loci, the gene order was conserved, the gene contents were variable, and the HD loci haplotypes were further classified into four types. By analyzing the structure, phylogeny, and the HD transmissibility based on the progeny of these four HD mating-type loci types, we found that they were heritable and tightly linked at the HD loci. The P/R loci genes were found to comprise three pheromone receptors, three pheromones, and two pheromone receptor-like genes. Intra- and inter-specific phylogenetic analyses of pheromone receptors revealed that the STE3 genes were divided into three groups, and we thus theorize that they diverged before speciation. Comparative analysis of the MAT regions among 73 Basidiomycete species indicated that the diversity of HD and P/R loci in Agaricales and Boletales may contribute to mating compatibility. The number of HD genes were not correlated with the tetrapolar or bipolar systems. In H. marmoreus, the expression levels of these genes at HD and P/R loci of compatible strains were found higher than in those of homonuclear/homokaryotic strains, indicating that these mating genes acted as switches for mating processes. Further collinear analysis of HD loci in interspecific species found that HD loci contains conserved recombination hotspots showing major rearrangements in Coprinopsis cinerea and Schizophyllum commune, suggesting different mechanisms for evolution of physically linked MAT loci in these groups. It seems likely that gene rearrangements are common in Agaricales fungi around HD loci. Together, our study provides insights into the genomic basis of mating compatibility in H. marmoreus.