Nanopore sequencing of full rRNA operon improves resolution in mycobiome analysis and reveals high diversity in both human gut and environments.

High-throughput sequencing has substantially improved our understanding of fungal diversity. However, the short read (<500 bp) length of current second-generation sequencing approaches provides limited taxonomic and phylogenetic resolution for species discrimination. Longer sequences containing more information are highly desired to provide greater taxonomic resolution. Here, we amplified full-length rRNA operons (~5.5 kb) and established a corresponding fungal rRNA operon database for ONT sequences (FRODO), which contains ONT sequences representing eight phyla, 41 classes, 109 orders, 256 families, 524 genera and 1116 species. We also benchmarked the optimal method for sequence classification and determined that the RDP classifier based on our FRODO database was capable of improving the classification of ONT reads, with an average of 98%-99% reads correctly classified at the genus or species level. We investigated the applicability of our approach in three representative mycobiomes, namely, the soil, marine and human gut mycobiomes, and found that the gut contains the largest number of unknown species (over 90%), followed by the marine (42%) and soil (33.8%) mycobiomes. We also observed a distinct difference in the composition of the marine and soil mycobiomes, with the highest richness and diversity detected in soils. Overall, our study provides a systematic approach for mycobiome studies and revealed that the previous methods might have underestimated the diversity of mycobiome species. Future application of this method will lead to a better understanding of the taxonomic and functional diversity of fungi in environmental and health-related mycobiomes.

Ferrostatin-1 attenuates pathological angiogenesis in oxygen-induced retinopathy via inhibition of ferroptosis.

Retinopathy of prematurity (ROP) is a vision-threatening ocular disease that occurs in premature infants, but the underlying mechanism is still unclear. Since oxidative stress has been well documented in the ROP development, we aimed to investigate whether ferroptosis, a new type of cell death characterized by lipid peroxidation and iron overload, is also involved in ROP. We detected the lipid peroxidation, oxidative stress and the expression of ferroptosis markers in the retina of mouse model of oxygen-induced retinopathy. After ferroptosis inhibitor, ferrostatin-1, was administered by intravitreal injection, ferroptosis marker, lipid peroxidation, retinal vasculature and glial cell activation were examined. We found decreased expression of SLC7A11 and GPX4, increased expression of FTH1 and TFRC, as well as increase of lipid peroxidation in the retina of OIR mice. Ferrostatin-1 administration significantly reduced lipid peroxidation, and also reversed the change of ferroptosis marker. Neovascular area and avascular area were suppressed and the pathological vasculature changes including acellular vessels and ghost pericytes were decreased. Microglial cell and Müller cell activation was not evidently influenced by ferrostatin-1 treatment. Our findings suggest that ferroptosis is involved in the pathological angiogenesis and might be a promising target for ROP therapy.

Transcriptome Reveals Roles of Lignin-Modifying Enzymes and Abscisic Acid in the Symbiosis of Mycena and Gastrodia elata.

Gastrodia elata is a well-known medicinal and heterotrophic orchid. Its germination, limited by the impermeability of seed coat lignin and inhibition by abscisic acid (ABA), is triggered by symbiosis with fungi such as Mycena spp. However, the molecular mechanisms of lignin degradation by Mycena and ABA biosynthesis and signaling in G. elata remain unclear. In order to gain insights into these two processes, this study analyzed the transcriptomes of these organisms during their dynamic symbiosis. Among the 25 lignin-modifying enzyme genes in Mycena, two ligninolytic class II peroxidases and two laccases were significantly upregulated, most likely enabling Mycena hyphae to break through the lignin seed coats of G. elata. Genes related to reduced virulence and loss of pathogenicity in Mycena accounted for more than half of annotated genes, presumably contributing to symbiosis. After coculture, upregulated genes outnumbered downregulated genes in G. elata seeds, suggesting slightly increased biological activity, while Mycena hyphae had fewer upregulated than downregulated genes, indicating decreased biological activity. ABA biosynthesis in G. elata was reduced by the downregulated expression of 9-cis-epoxycarotenoid dioxygenase (NCED-2), and ABA signaling was blocked by the downregulated expression of a receptor protein (PYL12-like). This is the first report to describe the role of NCED-2 and PYL12-like in breaking G. elata seed dormancy by reducing the synthesis and blocking the signaling of the germination inhibitor ABA. This study provides a theoretical basis for screening germination fungi to identify effective symbionts and for reducing ABA inhibition of G. elata seed germination.

A similar effect of P16 hydroxymethylation and true-methylation on the prediction of malignant transformation of oral epithelial dysplasia: observation from a prospective study.

BACKGROUND: Total P16 methylation (P16M), including P16 hydroxymethylation (P16H) and true-P16M, correlates with malignant transformation of oral epithelial dysplasia (OED). Both true-P16M and P16H are early events in carcinogenesis. The aim of this study is to prospectively determine if discrimination of true-P16M from P16H is necessary for prediction of cancer development from OEDs. METHODS: Patients (n = 265) with mild or moderate OED were recruited into the double blind two-center cohort. Total-P16M and P16H were analyzed using the 115-bp MethyLight, TET-assisted bisulfite (TAB) methylation-specific PCR (MSP), and TAB-sequencing. Total-P16M-positive and P16H-negative samples were defined as true-P16M-positive. Progression of OEDs was monitored for a minimum 24 months follow-up period. RESULTS: P16H was detected in 23 of 73 (31.5%) total-P16M-positive OEDs. Follow-up information was obtained from 247 patients with an ultimate compliance rate of 93.2%. OED-derived squamous cell carcinomas were observed in 13.0% (32/247) patients during follow-up (median, 41.0 months). The cancer progression rate for total-P16M-positive patients was significantly increased when compared to total-P16M-negative patients [23.3% vs 8.6%; adjusted odds ratio = 2.67 (95% CI: 1.19-5.99)]. However, the cancer progression rates were similar between P16H- and true-P16M-positive OEDs [26.1% (6/23) vs 22.0% (11/50); odds ratio = 0.80 (95% CI: 0.22-2.92)]. The cancer-free survival was also similar for these patients. CONCLUSION: P16H and true-P16M are similar biomarkers for determining malignant potential of OEDs. Discrimination of P16H from true-P16M, at least in OED, may be not necessary in clinical applications. TRIAL REGISTRATION: This study is registered prospectively in the U.S. National Institutes of Health Clinical Trials Protocol Registration System (trial number NCT02967120, available at https://ClinicalTrials.gov/ct2/show/NCT02967120 ).

A study on the relationship between waist phenotype, hypertriglyceridemia, coronary artery lesions and serum free fatty acids in adult and elderly patients with coronary diseases.

BACKGROUND: Abdominal obesity is an independent risk factor for coronary heart disease (CHD) and high serum triglyceride (TG) and free fatty acid levels may precipitate or aggravate CHD. METHODS: We enrolled patients with coronary heart disease in our hospital from October 2008 to July 2009. Patients with high TG and increased WC, i.e. waist phenotype WP were included in group A. In group B, were included patients with high TG but not WP. Group C consisted of patients with WP but not high TG. Finally, Group D was composed of patients without high TG or WP. Serum FFA levels for all patients were measured by ELISA. The relationship between TG levels, WC, FFA levels, and coronary artery score was analysed by a single variable regression. RESULTS: Group A had a significantly higher FFA level than the other groups. Regression analysis showed that FFA, TG, WC, hip circumference, waist-to-height ratio, systolic blood pressure, pulse pressure index, and low-density lipoprotein cholesterol all positively correlated with CAS (r = 0.160 ~ 0.415, P = 0.000 ~ 0.032). After we controlled for traditional risk factors for cardiovascular disease, FFA levels remained positively correlated to the CAS (r = 0.365, P < 0.001). CONCLUSION: The serum FFA level for patients with complications of both increased WC and high TG levels was significantly higher than that of patients without either of these complications. The close correlation between the CAS and FFA levels showed by regression analysis suggested that inflammation in these patients was more serious. Increased WC and high TG levels as well as FFA level are valuable for the prediction of cardiovascular disease and can be applied as a clinical guidance for early intervention in the treatment of coronary heart diseases.

Increased interleukin 1α and interleukin 1ß expression is involved in the progression of periapical lesions in primary teeth.

BACKGROUND: Interleukin 1 (IL-1) is involved in bone resorption. However, the role of IL-1 in periapical lesions characterized by periapical bone destruction in primary teeth has not yet been fully elucidated. This study aimed to detect the distribution and expression of IL-1 in periapical lesions in primary teeth and assess the relationship between the cytokines and the degree of inflammatory cell infiltration. METHODS: A total of 106 chronic periapical lesions in primary teeth were harvested. Haematoxylin and eosin (H&E) staining was used to determine the histological type and the inflammatory cell infiltration grade (mild, moderate, and severe), and immunohistochemistry and enzyme-linked immunosorbent assay (ELISA) were used to detect the distribution and expression of IL-1α and IL-1ß. RESULTS: Of the 106 chronic periapical lesion samples, there were 85 cases of periapical granuloma, accounting for 80.19% of the total samples, and 21 cases of radicular cysts, accounting for 19.81%; no cases of abscess were detected. Immunohistochemistry results showed that both IL-1α and IL-1ß were expressed in periapical granulomas and cysts. ELISA results showed that IL-1α and IL-1ß levels were higher in the periapical granuloma group than in the radicular cyst and normal control groups (P < 0.05). In the periapical granuloma group, IL-1α and IL-1ß were detected at higher levels in the severe inflammatory cell infiltration subgroup than in the mild-inflammatory cell infiltration subgroup (P < 0.05), and IL-1ß expression was also higher in the moderate inflammatory cell infiltration subgroup than in the mild inflammatory cell infiltration subgroup (P < 0.01). A significant positive correlation was observed between the protein expression levels of IL-1α and IL-1ß and the inflammation grade in periapical granulomas from primary teeth (P < 0.05). CONCLUSION: Expression levels of the cytokines IL-1α and IL-1ß in periapical granulomas from primary teeth increased with increasing inflammatory severity and appeared to be a contributing factor to the progression of periapical lesions.

STM study of electrical transport properties of one dimensional contacts between MnSi(~1.7) nanowires and Si(111) and (110) substrates.

We demonstrate the formation of contact barriers at the interfaces between MnSi1.7 nanowires (NWs) and Si substrates by the current-voltage (I-V) curves measured by scanning tunneling microscope with the tip contacting the NWs. The NWs on Si(110) exhibit linear reverse bias I-V curves, which suggests a parallel Ohmic surface state conductance of the Si(110) surface. The NWs on Si(111) exhibit nonlinear reverse bias I-V behavior, which indicates a considerable amount of minority carrier recombination-generation current. The NW length-dependence study of the forward bias current clearly shows that the quantitative change in NW length leads to a qualitative change in electrical transport properties. We derive a characteristic length LC ≈ 200 nm and the corresponding aspect ratio of ∼12-18 for MnSi1.7 NWs according to the variation of current density with the NW length.

Umbelopsis longicollis comb. nov. and the synonymy of U. roseonana and U. versiformis with U. nana.

Based on maximum growth temperatures, morphological characteristics and multilocus phylogenies (partial 18S and 28S, internal transcribed spacer regions of nuc rDNA and a fragment of an actin gene), Umbelopsis roseonana and U. versiformis are treated as heterotypic synonyms of U. nana, while the phylogenetically closely related U. dimorpha is retained as a separate species. Mortierella longicollis is reclassified as a new combination, U. longicollis. In addition, lectotypes and epitypes for the basionyms of U. longicollis and U. nana are designated here.

Photodynamic therapy in combination with CO2 laser for the treatment of Bowen's disease.

Photodynamic therapy (PDT) involves the activation of a previously administered photosensitizing agent by visible light to induce tumor necrosis. Photosensitizers are topically applied in the treatment of skin tumors to avoid systemic side effects. In this study, we evaluated the feasibility and efficacy of aminolevulinic acid (ALA) as a photosensitizer (ALA-PDT) in combination with CO2 laser in the treatment of Bowen's disease (BD; intraepithelial squamous cell carcinoma). Twenty-two lesions from 18 patients were randomized into two groups: 11 lesions were treated with topical ALA-PDT (180 J/cm(2) at 100 mW/cm(2)) + CO2 laser for one to three sessions. The remaining 11 lesions were treated with CO2 laser alone, serving as control group. All patients were reviewed at ≤1-week intervals. Biopsies were taken from BD lesions prior to treatment. The initial evaluation was undertaken 1 month after treatment, and biopsies were harvested for histological evaluation. Patients who did not respond to the three sessions of treatment were referred to surgical treatment. In the ALA-PDT + CO2 laser group, 72.73 % (8/11) of BD lesions showed complete remission, with an overall clearance of 90.91 %, and only one recurred (9 %) during follow-up. Local side effects included mild erythema, edema, erosion, and burning and/or stinging sensation. No systemic side effects were observed. In the control group, 63.63 % (7/11) of lesions had complete remission and the overall clearance was 54.55 %. However, five lesions (45.45 %) had recurrence. Local side effects included mild to moderate edema, erosion, ulceration, delayed healing, prolonged pain, and scarring. There existed a significant difference in recurrence rate between the two groups (P < 0.05). Moreover, after ALA-PDT plus CO2 laser treatment, complete necrosis was observed in responsive lesions, and 3 months later, the atypical BD cells were replaced by normal keratinocytes. Topical ALA-PDT in combination with CO2 laser is safe, effective, and is associated with low recurrence and reduced side effects.

High-throughput screening carbon and nitrogen sources to promote growth and sporulation in Rhizopus arrhizus.

Rhizopus arrhizus is a saprotrophic, sometimes clinically- and industrially-relevant mold (Mucorales) and distributed worldwide, suggesting it can assimilate a broad spectrum of substrates. Here, 69 strains of R. arrhizus were investigated by using the Biolog FF MicroPlate for the profiles of utilizing 95 carbon and nitrogen substrates. The study showed that most R. arrhizus strains were similar in average well color development (AWCD) and substrate richness (SR). Nevertheless, 13 strains were unique in principal component analyses, heatmap, AWCD, and SR analyses, which may imply a niche differentiation within R. arrhizus. The species R. arrhizus was able to utilize all the 95 carbon and nitrogen substrates, consistent with the hypothesis of a great metabolic diversity. It possessed a substrate preference of alcohols, and seven substrates were most frequently utilized, with N-acetyl-D-galactosamine and L-phenylalanine ranking at the top of the list. Eight substrates, especially L-arabinose and xylitol, were capable of promoting sporulation and being applied for rejuvenating degenerated strains. By phenotyping R. arrhizus strains in carbon and nitrogen assimilation capacity, this study revealed the extent of intra-specific variability and laid a foundation for estimating optimum substrates that may be useful for industrial applications.

[Spatial-temporal Variations and Driving Factors of Surface Ozone over the Qinghai-Xizang Plateau from 2015 to 2021].

The spatial-temporal distribution pattern of surface O3 over the Qinghai-Xizang Plateau （QXP） was analyzed based on air quality monitoring data and meteorological data from 12 cities on the QXP from 2015 to 2021. Kolmogorov-Zurbenko （KZ） filtering was employed to separate the original O3-8h series into components at different time scales. Then, multiple linear regression of meteorological variables was used to quantitatively isolate the effects of meteorology and emissions. The results revealed that the annual mass concentrations of surface O3-8h from 2015 to 2021 in 12 cities over the QXP ranged from 78.7 to 156.7 µg·m-3, and the exceedance rates of O3 mass concentrations （National Air Quality Standard of grade II） ranged from 0.7%-1.5%. The monthly O3-8h mass concentration displayed a single-peak inverted "V"-shape and a multi-peak "M"-shape. The maximum monthly concentration of O3 occurred in April to July, and valleys occurred in July, September, and December. The short-term, seasonal, and long-term components of O3-8hdecomposed by KZ filtering contributed 29.6%, 51.4%, and 9.1% to the total variance in the original O3 sequence in 12 cities, respectively. From the whole region, the meteorological conditions were unfavorable for O3 reduction on the QXP from 2015 to 2017, which made the long-term component of O3 increase by 0.2-2.1 µg·m-3. The meteorological conditions were favorable for O3-8h reduction from 2018 to 2021, which led to the long-term component of O3-8h decrease by 0.4-1.1 µg·m-3. The meteorological conditions increased the long-term component of O3-8h in Ngari, Lhasa, Naqu, Nyingchi, Qamdo, Haixi, and Xining, with an average contribution of 30.1%. The meteorological conditions decreased the long-term component of O3-8h in Shigatse and Golog, with contributions of 359.0% and 56.5%, respectively. The increase in the long-term component of O3-8h in Ngari, Shigatse, Nagqu, Haixi, and Xining could be due to the rapid decrease in the long-term component of PM2.5 （4.04 µg·ï¼ˆm3·a）-1）.

Detecting and characterizing new endofungal bacteria in new hosts: Pandoraea sputorum and Mycetohabitans endofungorum in Rhizopus arrhizus.

The fungus Rhizopus arrhizus (=R. oryzae) is commonly saprotrophic, exhibiting a nature of decomposing organic matter. Additionally, it serves as a crucial starter in food fermentation and can act as a pathogen causing mucormycosis in humans and animals. In this study, two distinct endofungal bacteria (EFBs), associated with individual strains of R. arrhizus, were identified using live/dead staining, fluorescence in situ hybridization, transmission electron microscopy, and 16S rDNA sequencing. The roles of these bacteria were elucidated through antibiotic treatment, pure cultivation, and comparative genomics. The bacterial endosymbionts, Pandoraea sputorum EFB03792 and Mycetohabitans endofungorum EFB03829, were purified from the host fungal strains R. arrhizus XY03792 and XY03829, respectively. Notably, this study marks the first report of Pandoraea as an EFB genus. Compared to its free-living counterparts, P. sputorum EFB03792 exhibited 28 specific virulence factor-related genes, six specific CE10 family genes, and 74 genes associated with type III secretion system (T3SS), emphasizing its pivotal role in invasion and colonization. Furthermore, this study introduces R. arrhizus as a new host for EFB M. endofungorum, with EFB contributing to host sporulation. Despite a visibly reduced genome, M. endofungorum EFB03829 displayed a substantial number of virulence factor-related genes, CE10 family genes, T3SS genes, mobile elements, and significant gene rearrangement. While EFBs have been previously identified in R. arrhizus, their toxin-producing potential in food fermentation has not been explored until this study. The discovery of these two new EFBs highlights their potential for toxin production within R. arrhizus, laying the groundwork for identifying suitable R. arrhizus strains for fermentation processes.

Fucoxanthin Alleviates Dextran Sulfate Sodium-Induced Colitis and Gut Microbiota Dysbiosis in Mice.

The purpose of this study was to evaluate the preventive role and underlying mechanisms of fucoxanthin (Fx) on dextran sulfate sodium (DSS)-induced colitis in mice. The present data demonstrated that oral administration of Fx (50 and 200 mg/kg body weight/day) for 36 days significantly alleviated the severity of colitis in DSS-treated mice, as evidenced by attenuating body weight loss, bloody stool, diarrhea, shortened colon length, colonic epithelium distortion, a thin mucus layer, goblet cell depletion, damaged crypts, and extensive infiltration of inflammatory cells in the colonic mucosa. Additionally, Fx notably relieved DSS-induced intestinal epithelial barrier dysfunction via maintaining the tight junction function and preventing excessive apoptosis of colonic epithelial cells. Moreover, Fx effectively diminished colonic inflammation and oxidative stress in DSS-treated mice, and its mechanisms might be due to blunting the activation of NF-κB and NLRP3 inflammasome signaling pathways. Furthermore, Fx also modulates DSS-induced gut microbiota dysbiosis via recovering the richness and diversity of gut microbiota and reshaping the structure of gut microbiota, such as increasing the Firmicutes and Bacteroidota (F/B) ratio and elevating the relative abundance of some potential beneficial bacteria, including Lactobacillaceae and Lachnospiraceae. Overall, Fx might be developed as a promising functional ingredient to prevent colitis and maintain intestinal homeostasis.

The genome and transcriptome of Sarocladium terricola provide insight into ergosterol biosynthesis.

Sarocladium terricola is a species of ascomycete fungus that has been recognized as a biocontrol agent for managing animal and plant pathogens, and exhibits significant potential as a feed additive. In this study, we utilized a combination of short-read Illumina sequencing and long-read PacBio sequencing to sequence, assemble, and analyze the genome of S. terricola. The resulting genome consisted of 11 scaffolds encompassing 30.27 Mb, with a GC content of 54.07%, and 10,326 predicted protein coding gene models. We utilized 268 single-copy ortholog genes to reconstruct the phylogenomic relationships among 26 ascomycetes, and found that S. terricola was closely related to two Acremonium species. We also determined that the ergosterol content of S. terricola was synthesized to nearly double levels when cultured in potato dextrose media compared to bean media (4509 mg/kg vs. 2382 mg/kg). Furthermore, transcriptome analyses of differentially expressed genes suggested that the ergosterol synthesis genes ERG3, ERG5, and ERG25 were significantly up-regulated in potato dextrose media. These results will help us to recognize metabolic pathway of ergosterol biosynthesis of S. terricloa comprehensivelly.

Spatiotemporal variations of ecosystem security pattern in Horqin sandy dune meadow alternating area, China.

The natural and geographical environment of ecologically fragile areas in northern China is complex. Due to heavy human disturbance and impacts of climate change, the sustainable development of ecosystems is facing serious challenges. Constructing ecological security pattern can provide decision-making basis for ecological environment protection in desertification areas. Based on land use change data of Horqin dune-meadow interphase area from 1985 to 2021, we identified ecological sources with the importance of ecosystem services and ecological sensitivity, and constructed the ecological security pattern using the minimum cumulative resistance model. We further analyzed the ecological security pattern and its development trend in 1985, 1995, 2005, 2015 and 2021, and explored the ecological spatial layout adjustment strategy. The results showed that the proportion of source area in the ecological security pattern of the study area was always small and scattered from 1985 to 2021, the network of ecological corridors was low, and the connectivity between ecological patches was lacking. The ecological security pattern had experienced a trend of deterioration first and then gradually improving. Ecological policies such as returning farmland to forest and grassland and afforestation had significantly improved the environmental security. We optimized the study area by combining the cultivated land suitability evaluation method. The ecological security pattern showed a spatial trend of 'dual-core, scattered and semi-surrounded'. The results could provide references for the construction of county-scale ecological security pattern in ecologically fragile areas and the ecological management of Horqin sands.

Three New Species of Gongronella (Cunninghamellaceae, Mucorales) from Soil in Hainan, China Based on Morphology and Molecular Phylogeny.

The genus Gongronella is important in agriculture and industry by secreting various natural bioactive metabolites such as chitosanases and organic acids. During the most recent 8 years, a total of 14 new species have been described, remarkably enriching the diversity of this genus. In this study, we added three more new species to this valuable genus, based on a combination of morphological traits and phylogenetic information. Six strains of the genus Gongronella were isolated from soil collected in Hainan Province, China. Phylogenetic analyses of ITS and LSU rDNA sequences grouped these strains into three independent clades. According to their unique morphological characteristics, they were classified as G. multiramosa sp. nov., G. qichaensis sp. nov. and G. oleae sp. nov. The G. multiramosa was characterized by multiple branched sporangiophores and was closely related to G. pedratalhadensis. The G. qichaensis was characterized by obscure collars and closely related to G. butleri, G. hydei and G. banzhaoae. The G. oleae was characterized by the presence of oil droplets in the sporangiospores and was closely related to G. chlamydospora and G. multispora. Their descriptions and illustrations were provided, and their differences from morphological allies and phylogenetic-related species are discussed.

Insights into the Ecological Diversification of the Hymenochaetales based on Comparative Genomics and Phylogenomics With an Emphasis on Coltricia.

To elucidate the genomic traits of ecological diversification in the Hymenochaetales, we sequenced 15 new genomes, with attention to ectomycorrhizal (EcM) Coltricia species. Together with published data, 32 genomes, including 31 Hymenochaetales and one outgroup, were comparatively analyzed in total. Compared with those of parasitic and saprophytic members, EcM species have significantly reduced number of plant cell wall degrading enzyme genes, and expanded transposable elements, genome sizes, small secreted proteins, and secreted proteases. EcM species still retain some of secreted carbohydrate-active enzymes (CAZymes) and have lost the key secreted CAZymes to degrade lignin and cellulose, while possess a strong capacity to degrade a microbial cell wall containing chitin and peptidoglycan. There were no significant differences in secreted CAZymes between fungi growing on gymnosperms and angiosperms, suggesting that the secreted CAZymes in the Hymenochaetales evolved before differentiation of host trees into gymnosperms and angiosperms. Nevertheless, parasitic and saprophytic species of the Hymenochaetales are very similar in many genome features, which reflect their close phylogenetic relationships both being white rot fungi. Phylogenomic and molecular clock analyses showed that the EcM genus Coltricia formed a clade located at the base of the Hymenochaetaceae and divergence time later than saprophytic species. And Coltricia remains one to two genes of AA2 family. These indicate that the ancestors of Coltricia appear to have originated from saprophytic ancestor with the ability to cause a white rot. This study provides new genomic data for EcM species and insights into the ecological diversification within the Hymenochaetales based on comparative genomics and phylogenomics analyses.

An integrated high-flux cold atomic beam source for strontium.

We present the design, construction, and characterization of an integrated cold atomic beam source for strontium (Sr), which is based on a compact Zeeman slower for slowing the thermal atomic beam and an atomic deflector for selecting the cold flux. By adopting arrays of permanent magnets to produce the magnetic fields of the slower and the deflector, we effectively reduce the system size and power compared to traditional systems with magnetic coils. After the slower cooling, one can employ additional transverse cooling in the radial direction and improve the atom collimation. The atomic deflectors employ two stages of two-dimensional magnetic-optical trapping (MOT) to deflect the cold flux, whose atomic speed is lower than 50 m/s, by 20° from the thermal atomic beam. We characterize the cold atomic beam flux of the source by measuring the loading rate of a three-dimensional MOT. The loading rates reach up to 109 atoms/s. The setup is compact, highly tunable, lightweight, and requires low electrical power, which addresses the challenge of reducing the complexity of building optical atomic clocks and quantum simulation devices based on Sr.

Comparative proteome analysis of silkworm in its susceptibility and resistance responses to Bombyx mori densonucleosis virus.

Bombyx mori densonucleosis virus (BmDNV) is one of the most disastrous viruses in cocoon production. Silkworm resistance to BmDNV has been examined previously using a number of traditional biochemical and molecular techniques. In this study, a near isogenic line, BC(6), was constructed to eliminate the difference in inherited background, which has 99.9% identity with the susceptible strain but carries a resistant gene. We utilized a proteomic approach involving two-dimensional differential gel electrophoresis and mass spectrometry to examine changes in the midgut proteins from the susceptible and resistant silkworm larvae infected with BmDNV. The protein profiles were compared and 9 differentially expressed proteins were identified by mass spectrometry. In the resistant strains, the heat-shock 70-kDa protein cognate, cytochrome P450, vacuolar ATP synthase subunit B, arginine kinase, vacuolar ATP synthase subunit D and glutathione S-transferase sigma were strongly upregulated and α-tubulin was downregulated. Our results imply that these upregulated genes and the downregulated genes might be involved in B. mori immune responses against BmDNV-Z infection.

The complete mitochondrial genome of Porodaedalea mongolica (Hymenochaetaceae, Basidiomycota).

Most Porodaedalea species are important phytopathogenic and medicinal fungi. Recently, several Porodaedalea species including P. mongolica were newly described. In the present study, the complete sequence of mitochondrial genome of P. mongolica was determined, with a size of 114,176 bp and a GC content of 28.98%, containing two ribosomal RNA subunit, 26 transfer RNA, and 54 protein-coding genes (PCGs). The comparative analyses indicated that the amino acids of 14 core PCGs were highly conserved in Porodaedalea. Phylogenetic analysis of Porodaedalea was performed based on mitogenomic data and provided a new insight to the phylogeny of the Porodaedalea. The complete mitogenome sequence provides important data for further study of Porodaedalea.