ROS-mediated MAPK activation aggravates hyperoxia-induced acute lung injury by promoting apoptosis of type II alveolar epithelial cells via the STAT3/miR-21-5p axis.

Inhibition of type II alveolar epithelial (AE-II) cell apoptosis is a critical way to cure hyperoxia-induced acute lung injury (HALI). It has been reported that miR-21-5p could reduce H2O2-induced apoptosis in AE-II cells. However, the upstream molecular mechanism remains unclear. Herein, we established a cellular model of HALI by exposing AE-II cells to H2O2 treatment. It was shown that miR-21-5p alleviated H2O2-induced apoptosis in AE-II cells. ROS inhibition decreased apoptosis of H2O2-evoked AE-II cells via increasing miR-21-5p expression. In addition, ROS induced MAPK and STAT3 phosphorylation in H2O2-treated AE-II cells. MAPK inactivation reduces H2O2-triggered AE-II cell apoptosis. MAPK activation inhibits miR-21-5p expression by promoting STAT3 phosphorylation in H2O2-challenged AE-II cells. Furthermore, STAT3 activation eliminated MAPK deactivation-mediated inhibition on the apoptosis of AE-II cells under H2O2 condition. In conclusion, ROS-mediated MAPK activation promoted H2O2-triggered AE-II cell apoptosis by inhibiting miR-21-5p expression via STAT3 phosphorylation, providing novel targets for HALI treatment.

Life Cycle and Phylogeography of True Truffles.

True truffle (Tuber spp.) is one group of ascomycetes with great economic importance. During the last 30 years, numerous fine-scale population genetics studies were conducted on different truffle species, aiming to answer several key questions regarding their life cycles; these questions are important for their cultivation. It is now evident that truffles are heterothallic, but with a prevalent haploid lifestyle. Strains forming ectomycorrhizas and germinating ascospores act as maternal and paternal partners respectively. At the same time, a number of large-scale studies were carried out, highlighting the influences of the last glaciation and river isolations on the genetic structure of truffles. A retreat to southern refugia during glaciation, and a northward expansion post glaciation, were revealed in all studied European truffles. The Mediterranean Sea, acting as a barrier, has led to the existence of several refugia in different peninsulas for a single species. Similarly, large rivers in southwestern China act as physical barriers to gene flow for truffles in this region. Further studies can pay special attention to population genetics of species with a wide distribution range, such as T. himalayense, and the correlation between truffle genetic structure and the community composition of truffle-associated bacteria.

Elevation Matters More than Season in Shaping the Heterogeneity of Soil and Root Associated Ectomycorrhizal Fungal Community.

Ectomycorrhizal (EcM) fungi play important roles in forest ecosystems, and their richness and composition can change along with elevation and season changes. However, no study has estimated the relative importance of altitudinal and seasonal heterogeneity in predicting the distribution of EcM fungal communities by simultaneously considering different sample types (root versus soil). In this study, we collected root and soil samples along a > 1,500-m elevation gradient during wet and dry seasons from Baima Snow Mountain, located in "the Mountains of Southwest China," one of the 34 biodiversity hot spots, and we analyzed them using next-generation sequencing. Regardless of the sample type, similar EcM fungal richness pattern with increasing elevation (decline in the forest zone, and an increase at the alpine meadow zone) and strong community turnovers among different elevational zones and between two seasons were detected, and changes of EcM fungal community similarity on 400-m altitude gradient were equivalent to the community turnover between dry and wet seasons. Elevation and edaphic factors were shown to have the largest effects on EcM fungal community. The heterogeneity of richness and community composition was stronger among different elevational zones than across different seasons, mainly because the elevation variations in the EcM fungal community were shaped by the combined effects of different environmental factors, while seasonal changes were mainly controlled by temperature and fast-changing soil nutrients. IMPORTANCE Altitude and season represent two important environmental gradients that shape the structure of biome, including the heterogeneity of EcM fungi. Previous studies have separately considered the influences of altitude and season on EcM fungal communities, but the relative importance of altitude and season is still unknown. The present study revealed that elevation influences the heterogeneity of EcM fungal community more than season; this may be because the variability of environmental factors is higher across different elevations than that across seasons.

Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales.

We aimed to identify genomic traits of transitions to ectomycorrhizal ecology within the Boletales by comparing the genomes of 21 symbiotrophic species with their saprotrophic brown-rot relatives. Gene duplication rate is constant along the backbone of Boletales phylogeny with large loss events in several lineages, while gene family expansion sharply increased in the late Miocene, mostly in the Boletaceae. Ectomycorrhizal Boletales have a reduced set of plant cell-wall-degrading enzymes (PCWDEs) compared with their brown-rot relatives. However, the various lineages retain distinct sets of PCWDEs, suggesting that, over their evolutionary history, symbiotic Boletales have become functionally diverse. A smaller PCWDE repertoire was found in Sclerodermatineae. The gene repertoire of several lignocellulose oxidoreductases (e.g. laccases) is similar in brown-rot and ectomycorrhizal species, suggesting that symbiotic Boletales are capable of mild lignocellulose decomposition. Transposable element (TE) proliferation contributed to the higher evolutionary rate of genes encoding effector-like small secreted proteins, proteases, and lipases. On the other hand, we showed that the loss of secreted CAZymes was not related to TE activity but to DNA decay. This study provides novel insights on our understanding of the mechanisms influencing the evolutionary diversification of symbiotic boletes.

Reversible Patterning Cross-Linked, Humidity-Responsive Polymer Films with Programmatically and Accurately Controlled Deformation.

A series of novel humidity-responsive and photosensitive polymer films (PCA-PAA-PEG) are prepared. These films can be patterning cross-linked by the photodimerization of coumarin pendant groups. The humidity-induced deformation can be well controlled by the pattern because of the different modulus and hydrophilicity between cross-linked and un-cross-linked segments. In addition, the pattern can be erased and the deformation direction can be changed programmatically by the de-cross-linking-re-cross-linking approach due to the reversible photodimerization of coumarin groups. The cross-linking degree also affects the humidity responsiveness of the film. The deformation of the gradient patterning cross-linked film can be more accurately controlled. Moreover, the length and width ratio (L/Ws/Wh) of the un-cross-linked segment to the cross-linked segment affects the deformation of the films as well. When L/Ws/Wh is 5/2/1 or 5/3/1, the deformation is controllable, and when L/Ws/Wh is 5/1/1 or 5/4/1, the deformation is random at the initial stage, but the whole film will bend along the short axis in the end.

UPLC-ESI-MS/MS based identification and antioxidant, antibacterial, cytotoxic activities of aqueous extracts from storey onion (Allium cepa L. var. proliferum Regel).

Storey onion (Allium cepa L. var. proliferum Regel) is a variety of onion commonly grown in northern China that has not been researched in detail. This study aimed to identify the chemical compositions of storey onion aqueous extracts by UPLC-ESI-MS/MS, as well as characterize the antioxidant, antibacterial and cytotoxic activities, compared with welsh onion and onion. A total of 42 compounds were identified, among which the contents of organosulfur compounds (962.20 ± 34.55 µg/g), polyphenols (100.40 ± 12.55 µg/g) and organic acids (54.04 ± 2.69 µg/g) in storey onion were higher than those in welsh onion and onion. Additionally, the contents of cycloalliin (551.74 ± 8.12 µg/g), ajoene (159.31 ± 5.30 µg/g) and (E)-1-propene-1-sulfenic acid (72.12 ± 2.98 µg/g) in storey onion were the highest. Storey onion had pronounced DPPH• (IC50 = 1.24 ± 0.52 mg/mL) and OH• scavenging activities (IC50 = 14.45 ± 1.29 mg/mL) as well as ferric ion reducing power (absorbance from 0.32 to 2.21). Onion had the highest ABTS•+ scavenging activity (IC50 = 1.64 ± 0.64 mg/mL), while welsh onion had the lowest antioxidant activity. Storey onion had the strongest inhibitory effect on all the tested strains (MIC 31.3-125 mg/mL), and cell viability assays against human liver (HepG2) cancer cell lines also illustrated that aqueous extracts from storey onion significantly inhibited cell proliferation (when incubated for 24 h, IC50 = 33.21 ± 1.12 mg/mL) and induced cell apoptosis. Welsh onion and onion also had weaker antibacterial and anticancer activites, with those of onion being the weakest. The results showed that storey onion with excellent biological activity may benefit to human health and can be developed into functional foods.

Compound heterozygous mutations in the ALDH3A2 gene cause Sjögren-Larsson syndrome: a case report.

Purpose: Sjögren-Larsson syndrome is a rare, autosomal, recessive neurocutaneous disorder caused by mutations in the ALDH3A2 gene, which encodes the fatty aldehyde dehydrogenase enzyme. Deficiency in fatty aldehyde dehydrogenase results in an abnormal accumulation of toxic fatty aldehydes in the brain and skin, which cause spasticity, intellectual disability, ichthyosis, and other clinical manifestations. We present the clinical features and mutation analyses of a case of SLS.Materials and Methods: The family history and clinical data of the patient were collected. Genomic DNA was extracted from peripheral blood samples of the patient and her parents, and next-generation sequencing was performed. The candidate mutation sites that required further validation were then sequenced by Sanger sequencing. Bioinformatics software PSIPRED and RaptorX were used to predict the secondary and tertiary structures of proteins.Results: The patient, a five-year-old girl with complaints of cough for three days and intermittent convulsions for seven hours, was admitted to the hospital. Other clinical manifestations included spastic paraplegia, mental retardation, tooth defects, and ichthyosis. Brain magnetic resonance imaging showed periventricular leukomalacia. Genetic screening revealed compound heterozygous mutations in the ALDH3A2 gene: a frameshift mutation c.779delA (p.K260Rfs*6) and a missense mutation c.1157A > G (p.N386S). Neither of the ALDH3A2 alleles in the compound heterozygote patient were able to generate normal fatty aldehyde dehydrogenase, which were likely responsible for her phenotype of Sjögren-Larsson syndrome.Conclusion: The compound heterozygous mutations found in the ALDH3A2 gene support the diagnosis of Sjögren-Larsson syndrome in the patient and expand the genotype spectrum of the gene.

Using mating-type loci to improve taxonomy of the Tuber indicum complex, and discovery of a new species, T. longispinosum.

Black truffles that morphologically resemble Tuber indicum have been known to occur in Japan since 1979. Our previous studies showed that there are two phylotypes of these truffles, both of which fell into the T. indicum complex (hereinafter "Tuber sp. 6" and "Tuber sp. 7"). However, their taxonomic treatment is still unclear. In this study, we conducted morphological and phylogenetic analyses for a total of 52 specimens from Japan (16 Tuber sp. 6 and 13 Tuber sp. 7), China (10 T. himalayense and 8 T. indicum), and Taiwan (5 T. formosanum). We compared ascospore ornamentation, size, distribution of asci with average number of spores per ascus, spine size and shape of the Japanese specimens with their allied taxa. For phylogenetic analysis, we sequenced two mating loci (MAT1-1-1 and MAT1-2-1) and three commonly used loci (ITS, ß-tubulin, and TEF1-α). Three distinct lineages were recognized by phylogenetic analyses based on the sequences of the two mating-related loci and three independent loci. The Tuber sp. 6 sequences clustered with those of T. himalayense and T. formosanum, and there was no clear difference in morphology among them. Tuber sp. 7 formed a distinct lineage in each phylogram. The specimens tended to have five-spored asci more frequently than other allied species and could be characterized as having ascospore ornamentation with longer spines and narrower spine bases. We therefore described Tuber sp. 7 as a new species (T. longispinosum), and treat Tuber sp. 6 and T. formosanum as synonyms of T. himalayense.

Studies on diversity of higher fungi in Yunnan, southwestern China: A review.

Yunnan is exceedingly rich in higher fungi (Ascomycota and Basidiomycota). Given that the number of fungi (including lichens) occurring in a given area is, as Hawksworth suggested, roughly six times that of local vascular plants, a total of approximately 104,000 fungal species would be expected in Yunnan. However, to date only about 6000 fungal species, including roughly 3000 species of higher fungi, have been reported from the province. Although studies on Yunnan's fungi started in the late nineteenth century, significant progress has been made only in the last forty-five years. Over the first twenty-five years of this period, studies on fungal diversity in this area have largely been about taxonomy based on morphological characters and partially on geographical distribution. Over the past twenty years, the combination of both morphological and molecular phylogenetic approaches has become the preferred method to help understand the diversity and evolution of higher fungi. This review focuses on our current knowledge of how geological, geographical, and ecological factors may have contributed to the diversity patterns of higher fungi in Yunnan. Based on this knowledge, three aspects for future studies are suggested.

Ecological and physical barriers shape genetic structure of the Alpine porcini (Boletus reticuloceps).

The Alpine porcini, Boletus reticuloceps, is an ectomycorrhizal mushroom distributed in subalpine areas of Southwest China, central China, and Taiwan Island. This distribution pattern makes it an ideal organism to infer how ectomycorrhizal fungi have reacted to historical tectonic and climatic changes, and to illustrate the mechanism for the disjunction of organisms between Southwest China and Taiwan. In this study, we explored the phylogeographic pattern of B. reticuloceps by microsatellite genotyping, DNA sequencing, ecological factor analysis, and species distribution modeling. Three genetic groups from the East Himalayas (EH), northern Hengduan Mountains (NHM), and southern Hengduan Mountains (SHM), were identified. The earlier divergent SHM group is found under Abies in moister environments, whereas the EH and NHM groups, which are physically separated by the Mekong-Salween Divide, are found mainly under Picea in drier environments. Samples from Taiwan showed a close relationship with the SHM group. High mountains did not form dispersal barriers among populations in each of the EH, NHM, and SHM groups, probably due to the relatively weak host specificity of B. reticuloceps. Our study indicated that ecological heterogeneity could have contributed to the divergence between the SHM and the NHM-EH groups, while physical barriers could have led to the divergence of the NHM and the EH groups. Dispersal into Taiwan via Central China during the Quaternary glaciations is likely to have shaped its disjunct distribution.

Genetic diversity and breeding history of Winter Mushroom (Flammulina velutipes) in China uncovered by genomic SSR markers.

Flammulina velutipes is one of the most widely cultivated mushroom species in China. However, its genetic background remains poorly understood due to the limited sampling and poor molecular markers used. In this study, 124 F. velutipes strains were employed, including 110 cultivars and 14 wild strains, and 25 new SSR markers were developed based on the genome of F. velutipes. A total of 153 alleles were detected in 124 strains to investigate the improper cultivar naming, genetic diversity and breeding history of F. velutipes in China. Our fingerprinting analyses indicated that 65 strains can be differentiated from the total of 124 strains, and over 53% of the strains are labeled with improper commercial names. The genetic diversities of wild strains are higher than those of the cultivars, suggesting that wild strains may harbor a large "arsenal" gene pool in nature available for strain breeding. The white cultivars in China were originally introduced from Japan, while the yellow cultivars were directly domesticated from wild strains isolated from southeastern China or hybridized between the white cultivars and yellow strains.

Multilocus phylogenetic analyses reveal unexpected abundant diversity and significant disjunct distribution pattern of the Hedgehog Mushrooms (Hydnum L.).

Hydnum is a fungal genus proposed by Linnaeus in the early time of modern taxonomy. It contains several ectomycorrhizal species which are commonly consumed worldwide. However, Hydnum is one of the most understudied fungal genera, especially from a molecular phylogenetic view. In this study, we extensively gathered specimens of Hydnum from Asia, Europe, America and Australasia, and analyzed them by using sequences of four gene fragments (ITS, nrLSU, tef1α and rpb1). Our phylogenetic analyses recognized at least 31 phylogenetic species within Hydnum, 15 of which were reported for the first time. Most Australasian species were recognized as strongly divergent old relics, but recent migration between Australasia and the Northern Hemisphere was also detected. Within the Northern Hemisphere, frequent historical biota exchanges between the Old World and the New World via both the North Atlantic Land Bridge and the Bering Land Bridge could be elucidated. Our study also revealed that most Hydnum species found in subalpine areas of the Hengduan Mountains in southwestern China occur in northeastern/northern China and Europe, indicating that the composition of the mycobiota in the Hengduan Mountains reigion is more complicated than what we have known before.

Drainage isolation and climate change-driven population expansion shape the genetic structures of Tuber indicum complex in the Hengduan Mountains region.

The orogenesis of the Qinghai-Tibetan Plateau and the Quaternary climate changes have played key roles in driving the evolution of flora and fauna in Southwest China, but their effects on higher fungi are poorly addressed. In this study, we investigated the phylogeographic pattern of the Tuber indicum species complex, an economically important fungal group distributed in the Hengduan Mountains region. Our data confirmed the existence of two distinct lineages, T. indicum and T. himalayense, within this species complex. Three geographic groups (Groups W, N and C) were revealed within T. indicum, with Group W found in the paleo-Lancang River region, while Groups N and C corresponded to the two banks along the contemporary Jinsha River, suggesting that rivers have acted as barriers for gene flow among populations from different drainages. Historical range expansion resulted from climate changes was inferred in Group C, contributing to the observed gene flow among geographic populations within this group. Although no significant geographic structure was identified in T. himalayense, evidence of drainage isolation for this species was also detected. Our findings demonstrate that both topographic changes and Quaternary climate oscillations have played important roles in driving the genetic structures of the T. indicum species complex.

The taxonomic foundation, species circumscription and continental endemisms of Singerocybe: evidence from morphological and molecular data.

The genus Singerocybe (Tricholomataceae, Agaricales, Basidiomycota) has been the subject of controversy since its proposal in 1988. Its taxonomic foundation, species circumscription and geographical distribution have not yet been examined with molecular sequence data. In this study phylogenetic analyses on this group of fungi were conducted based on collections from Europe, eastern Asia, southern Asia, North America and Australia, with four nuclear markers, ITS, nrLSU, tef1-α and rpb2. Molecular phylogenetic analyses, together with morphological observations, strongly support Singerocybe as a monophyletic group and identify the vesicles in the pileal and stipe cuticle as a synapomorphy of this genus. Seven species are recognized in the genus, including one new species and four new combinations. Clitocybe trogioides and Clitocybe trogioides var. odorifera are synonyms of Singerocybe humilis and Singerocybe alboinfundibuliformis respectively. Most of these species are geographically restricted in their distributions. Furthermore our study expands the distribution range of Singerocybe from the North Temperate Zone to Australia (Tasmania) and tropical southern Asia.

Molecular phylogeny and taxonomy of the genus Veloporphyrellus.

Veloporphyrellus is a genus known from North and Central America, southeastern Asia, and Africa. Because species of this genus are phenotypically similar to some taxa in several genera, such as Boletellus, Leccinum, Strobilomyces, Suillus and Tylopilus s.l. belonging to Boletales, its phylogenetic disposition has never been addressed. We analyzed four DNA regions, the nuclear ribosomal LSU and tef-1α, and the mitochondrial mtSSU and atp6 genes, to investigate the phylogenetic disposition of Veloporphyrellus. Although the monophyly of the genus and its systematic placement within the Boletaceae was well supported, its relationship to other genera was not resolved. Morphologically Veloporphyrellus is distinguished from other boletoid genera by the combination of the pinkish or grayish pink hymenophore, the membranous veil hanging on the pilea margin, the trichoderm-like pileus covering and the smooth basidiospores. Five species, including two new species and two new combinations, are described and illustrated. A key to the species of Veloporphyrellus also is provided.

Evidence against barium in the mushroom Trogia venenata as a cause of sudden unexpected deaths in Yunnan, China.

This study examined barium concentrations in the mushroom Trogia venenata, the leading culprit for sudden unexpected deaths in Yunnan, southwest China. We found that barium concentrations in T. venenata from Yunnan were low and comparable to other foods, inconsistent with barium concentrations in this mushroom as a significant contributor to these deaths.

Lateral gene transfer occurring in haloarchaea: an interpretative imitation study.

Lateral gene transfer (LGT) plays an important role in the molecular evolution of haloarchaea. Polyethylene glycol-mediated LGT in haloarchaea has been demonstrated in the laboratory, yet few explanations have been put forward for the apparently common, natural occurrence of plentiful plasmids within haloarchaeal cells. In this study, LGT was induced in two genera of haloarchaea, Haloferax and Halorubrum, by modification of salt concentration of media-a factor that may vary naturally in native haloarchaeal habitat. Minimal growth salt concentrations (MGSCs) of four strains of haloarchaea from these two genera were established, and transformations using two circular double-stranded DNAs (dsDNAs), pSY1 and pWL102, were then produced in media at strain-appropriate MGSCs. The four strains of haloarchaea were transformed successfully by both kinds of dsDNAs with an efficiency of 10(2)-10(3) transformants per microgram dsDNA. The transformation under reduced salt concentration may be an imitation of natural LGT of dsDNA into haloarchaea when salinity in normally hypersaline environments is altered by sudden introduction of fresh water--for example, by rainfall, snow-melt, or flooding--providing a reasonable interpretation for haloarchaea being naturally richer in plasmids than any other known organisms.

DNA sequence analyses reveal abundant diversity, endemism and evidence for Asian origin of the porcini mushrooms.

The wild gourmet mushroom Boletus edulis and its close allies are of significant ecological and economic importance. They are found throughout the Northern Hemisphere, but despite their ubiquity there are still many unresolved issues with regard to the taxonomy, systematics and biogeography of this group of mushrooms. Most phylogenetic studies of Boletus so far have characterized samples from North America and Europe and little information is available on samples from other areas, including the ecologically and geographically diverse regions of China. Here we analyzed DNA sequence variation in three gene markers from samples of these mushrooms from across China and compared our findings with those from other representative regions. Our results revealed fifteen novel phylogenetic species (about one-third of the known species) and a newly identified lineage represented by Boletus sp. HKAS71346 from tropical Asia. The phylogenetic analyses support eastern Asia as the center of diversity for the porcini sensu stricto clade. Within this clade, B. edulis is the only known holarctic species. The majority of the other phylogenetic species are geographically restricted in their distributions. Furthermore, molecular dating and geological evidence suggest that this group of mushrooms originated during the Eocene in eastern Asia, followed by dispersal to and subsequent speciation in other parts of Asia, Europe, and the Americas from the middle Miocene through the early Pliocene. In contrast to the ancient dispersal of porcini in the strict sense in the Northern Hemisphere, the occurrence of B. reticulatus and B. edulis sensu lato in the Southern Hemisphere was probably due to recent human-mediated introductions.

Genetic diversity of Dahongjun, the commercially important "Big Red Mushroom" from southern China.

BACKGROUND: In southern China, a wild ectomycorrhizal mushroom commonly called "Dahongjun" or "Big Red Mushroom" by the local residents, has been harvested, consumed, and/or exported as an exotic food for many years. Although ecologically and economically important, very little is known about this mushroom, including its diversity and population structure. METHODOLOGY AND PRINCIPAL FINDINGS: In this study, we analyzed 122 samples from five local populations representing the known distribution ranges of this mushroom in southern China. We investigated the genetic diversity and geographic structure of this mushroom using sequences from four DNA fragments. Our analyses identified that this mushroom contained at least three divergent lineages: one corresponds to a recently described species Russula griseocarnosa from southern China and the remaining two likely represent two novel species. While these lineages were prominently structured geographically based on ITS sequences, evidence for ancient and/or recent gene flow was also identified within individual lineages. In addition, a local population from Ailaoshan in central Yunnan Province where 85 of our 122 specimens came from showed clear evidence of recombination. CONCLUSION AND SIGNIFICANCE: The ectomycorrhizal mushroom "Dahongjun" from southern China is a species complex with at least three divergent lineages. These lineages are largely geographically structured and there is evidence for recombination in nature. Our results indicate mature Dahongjun mushrooms with abundant basidiospores are important for the reproduction of this mushroom in nature and that individual populations of this species should be managed separately.