A new species of Populus and the extensive hybrid speciation arising from it on the Qinghai-Tibet Plateau.

While the diversity of species formation is broadly acknowledged, significant debate exists regarding the universal nature of hybrid species formation. Through an 18-year comprehensive study of all Populus species on the Qinghai-Tibet Plateau, 23 previously recorded species and 8 new species were identified. Based on morphological characteristics, these can be classified into three groups: species in section Leucoides, species with large leaves, and species with small leaves in section Tacamahaca. By conducting whole-genome re-sequencing of 150 genotypes from these 31 species, 2.28 million single nucleotide polymorphisms (SNPs) were identified. Phylogenetic analysis utilizing these SNPs not only revealed a highly intricate evolutionary network within the large-leaf species of section Tacamahaca but also confirmed that a new species, P. curviserrata, naturally hybridized with P. cathayana, P. szechuanica, and P. ciliata, resulting in 11 hybrid species. These findings indicate the widespread occurrence of hybrid species formation within this genus, with hybridization serving as a key evolutionary mechanism for Populus on the plateau. A novel hypothesis, "Hybrid Species Exterminating Their Ancestral Species (HSEAS)," is introduced to explain the mechanisms of hybrid species formation at three different scales: the entire plateau, the southeastern mountain region, and individual river valleys.

Iridium-catalyzed selective arylation of B(6)-H of 3-aryl-o-carboranes with arylboronic acid via direct B-H activation.

This work discloses an iridium-catalyzed selective arylation of B(6)-H of 3-Ar-o-carboranes with arylboronic acid via direct B-H activation for the first time. A series of unsymmetric and symmetric 3,6-diaryl-o-carboranes decorated with diverse active groups have been synthesized with moderate to excellent yields under mild conditions. This work offers an efficient approach for selective arylation of B(6)-H with arylboronic acid and has important value for selective functionalization of o-carboranes.

A model of hybrid speciation process drawn from three new poplar species originating from distant hybridization between sections.

Although numerous studies have been conducted on hybrid speciation, our understanding of this process remains limited. Through an 18-year systematic investigation of all taxa of Populus on the Qinghai-Tibet Plateau, we discovered three new taxa with clear characteristics of sect. Leucoides. Further evidence was gathered from morphology, whole-genome bioinformatics, biogeography, and breeding to demonstrate synthetically that they all originated from distant hybridization between sect. Leucoides and sect. Tacamahaca. P. gonggaensis originated from the hybridization of P. lasiocarpa with P. cathayana, P. butuoensis from the hybridization of P. wilsonii with P. szechuanica, and P. dafengensis from the hybridization of P. lasiocarpa with P. szechuanica. Due to heterosis, the three hybrid taxa possess greater ecological adaptability than their ancestral species. We propose a hybrid speciation process model that incorporates orthogonal, reverse, and backcrossing events. This model can adequately explain some crucial evolutionary concerns, such as the nuclear-cytoplasmic conflict on phylogeny and the extinction of ancestral species within the distribution range of hybrid species.

Iridium-catalyzed selective amination of B(4)-H for the synthesis of o-carborane-fused indolines.

An iridium-catalyzed selective amination of B(4)-H via dehydrogenative cross-coupling of B-H/N-H bonds for the synthesis of o-carborane-fused indolines has been developed for the first time. Various types of unprecedented o-carborane-fused indolines have been synthesized, which would be potential candidates for applications in drug discovery, pharmaceutical chemistry and functional materials. This work offers a valuable reference for the designing and synthesis of o-carborane-fused heterocycles.

Morphology and phylogeny of ascomycetes associated with walnut trees (Juglans regia) in Sichuan province, China.

In Sichuan province, walnuts, consisting of Juglans regia, Juglans sigillata, and the hybrid J. regia × J. sigillata, are commercially important edible nuts, and J. regia is the most widespread plant. To date, the diversity and distribution of fungi inhabiting on Juglans have not received enough attention, although there have been studies focusing on pathogens from fruit and stem. In order to update the checklist of fungi associated with Sichuan walnuts, a survey on fungi associated with the three Juglans species from 15 representative regions in Sichuan was conducted. In this article, ten fungi distributed in two classes of Ascomycota (Dothideomycetes and Sordariomycetes) were described based on morpho-molecular analyses, and two novel species, Neofusicoccum sichuanense and Sphaerulina juglandina, a known species of Ophiognomonia leptostyla, and seven new hosts or geographical records of Cladosporium tenuissimum, Diatrypella vulgaris, Helminthosporium juglandinum, Helminthosporium velutinum, Loculosulcatispora hongheensis, Periconia byssoides, and Rhytidhysteron subrufulum were included. Morphological descriptions and illustrations of these fungi are provided.

Cu(OTf)2/NBS-Mediated Tandem Reaction of 1-Cinnamyl Alcohol-o-Carboranes via Ring Opening of Oxetane with Arenes: An Alternative Approach for the Synthesis of C-Alkenyl-o-Carboranes.

The Cu(OTf)2/NBS-mediated tandem reaction of 1-cinnamyl alcohol-o-carboranes for the synthesis of C-alkenyl-o-carboranes has been developed. Mechanism studies demonstrated that the Cu(OTf)2-promoted ring opening of oxetane with electron-rich arenes as soft nucleophiles was involved and was the key step for the transformation. This work provided an alternative strategy for the synthesis of C-alkenyl-o-carboranes, which has an important reference for the synthesis of o-carborane derivatives with diversity.

Genome-wide analysis and expression profiling of Cation/H+ exchanger (CAX) family genes reveal likely functions in cadmium stress responses in poplar.

Cadmium, a toxic heavy metal, seriously affects human health and ecological security. The cation/H+ exchanger (CAX) family is a unique metal transporter that plays a crucial role in Cd acquisition, transfer, and remission in plants. Although there are many studies related to the genome-wide analysis of Populus trichocarpa, little research has been done on the CAX family genes, especially concerning Cd stress. In this study, genome-wide analysis of the Populus CAX family identified seven stress-related CAX genes. The evolutionary tree indicated that the CaCA family genes were grouped into four clusters. Moreover, seven pairs of genes were derived by segmental duplication in poplars. Cis-acting element analysis identified numerous stress-related elements in the promoters of diverse PtrCAXs. Furthermore, some PtrCAXs were up-regulated by drought, beetle, and mechanical damage, indicating their possible function in regulating stress response. Under cadmium stress, all CAX genes in the roots were up-regulated. Our findings suggest that plants may regulate their response to Cd stress through the TF-CAXs module. Comprehensively investigating the CAX family provides a scientific basis for the phytoremediation of heavy metal pollution by Populus.

UVB-Pretreatment-Enhanced Cadmium Absorption and Enrichment in Poplar Plants.

The phenomenon of cross adaptation refers to the ability of plants to improve their resistance to other stress after experiencing one type of stress. However, there are limited reports on how ultraviolet radiation B (UVB) pretreatment affects the enrichment, transport, and tolerance of cadmium (Cd) in plants. Since an appropriate UVB pretreatment has been reported to change plant tolerance to stress, we hypothesized that this application could alter plant uptake and tolerance to heavy metals. In this study, a woody plant species, 84K poplar (Populus alba × Populus glandulosa), was pretreated with UVB and then subjected to Cd treatment. The RT-qPCR results indicated that the UVB-treated plants could affect the expression of Cd uptake, transport, and detoxification-related genes in plants, and that the UVB-Pretreatment induced the ability of Cd absorption in plants, which significantly enriched Cd accumulation in several plant organs, especially in the leaves and roots. The above results showed that the UVB-Pretreatment further increased the toxicity of Cd to plants in UVB-Cd group, which was shown as increased leaf malonaldehyde (MDA) and hydrogen peroxide (H2O2) content, as well as downregulated activities of antioxidant enzymes such as Superoxide Dismutase (SOD), Catalase (CAT), and Ascorbate peroxidase (APX). Therefore, poplar plants in the UVB-Cd group presented a decreased photosynthesis and leaf chlorosis. In summary, the UVB treatment improved the Cd accumulation ability of poplar plants, which could provide some guidance for the potential application of forest trees in the phytoremediation of heavy metals in the future.

Genome-wide investigation and expression profiling of polyphenol oxidase (PPO) family genes uncover likely functions in organ development and stress responses in Populus trichocarpa.

BACKGROUND: Trees such as Populus are planted extensively for reforestation and afforestation. However, their successful establishment greatly depends upon ambient environmental conditions and their relative resistance to abiotic and biotic stresses. Polyphenol oxidase (PPO) is a ubiquitous metalloproteinase in plants, which plays crucial roles in mediating plant resistance against biotic and abiotic stresses. Although the whole genome sequence of Populus trichocarpa has long been published, little is known about the PPO genes in Populus, especially those related to drought stress, mechanical damage, and insect feeding. Additionally, there is a paucity of information regarding hormonal responses at the whole genome level. RESULTS: A genome-wide analysis of the poplar PPO family was performed in the present study, and 18 PtrPPO genes were identified. Bioinformatics and qRT-PCR were then used to analyze the gene structure, phylogeny, chromosomal localization, gene replication, cis-elements, and expression patterns of PtrPPOs. Sequence analysis revealed that two-thirds of the PtrPPO genes lacked intronic sequences. Phylogenetic analysis showed that all PPO genes were categorized into 11 groups, and woody plants harbored many PPO genes. Eighteen PtrPPO genes were disproportionally localized on 19 chromosomes, and 3 pairs of segmented replication genes and 4 tandem repeat genomes were detected in poplars. Cis-acting element analysis identified numerous growth and developmental elements, secondary metabolism processes, and stress-related elements in the promoters of different PPO members. Furthermore, PtrPPO genes were expressed preferentially in the tissues and fruits of young plants. In addition, the expression of some PtrPPOs could be significantly induced by polyethylene glycol, abscisic acid, and methyl jasmonate, thereby revealing their potential role in regulating the stress response. Currently, we identified potential upstream TFs of PtrPPOs using bioinformatics. CONCLUSIONS: Comprehensive analysis is helpful for selecting candidate PPO genes for follow-up studies on biological function, and progress in understanding the molecular genetic basis of stress resistance in forest trees might lead to the development of genetic resources.

Genome-Wide Investigation of the NF-X1 Gene Family in Populus trichocarpa Expression Profiles during Development and Stress.

Poplar are planted extensively in reforestation and afforestation. However, their successful establishment largely depends on the environmental conditions of the newly established plantation and their resistance to abiotic as well as biotic stresses. NF-X1, a widespread transcription factor in plants, plays an irreplaceable role in plant growth, development, and stress tolerance. Although the whole genome sequence of Populus trichocarpa has been published for a long time, little is known about the NF-X1 genes in poplar, especially those related to drought stress, mechanical damage, insect feeding, and hormone response at the whole genome level. In this study, whole genome analysis of the poplar NF-X1 family was performed, and 4 PtrNF-X1 genes were identified. Then, bioinformatics analysis and qRT-PCR were applied to analyze the gene structure, phylogeny, chromosomal localization, gene replication, Cis-elements, and expression patterns of PtrNF-X1genes. Sequence analysis revealed that one-quarter of the PtrNF-X1 genes did not contain introns. Phylogenetic analysis revealed that all NF-X1 genes were split into three subfamilies. The number of two pairs of segmented replication genes were detected in poplars. Cis-acting element analysis identified a large number of elements of growth and development and stress-related elements on the promoters of different NF-X1 members. In addition, some PtrNF-X1 could be significantly induced by polyethylene glycol (PEG) and abscisic acid (ABA), thus revealing their potential role in regulating stress response. Comprehensive analysis is helpful in selecting candidate NF-X1 genes for the follow-up study of the biological function, and molecular genetic progress of stress resistance in forest trees provides genetic resources.

Identification of a novel autoantibody against heat shock factor 1 in idiopathic inflammatory myopathy.

OBJECTIVES: Myositis autoantibodies show great utility in the diagnosis and clinico-serological phenotyping of idiopathic inflammatory myopathy (IIM). We identified a novel autoantibody against heat shock factor 1 (HSF1) and further evaluated its disease specificity and clinical significance in IIM patients. METHODS: A human protein microarray was used to identify autoantibodies in myositis sera. ELISA, immunoblot and dot blot assays were applied to examine anti-HSF1 autoantibodies in IIM patients and controls. Immunofluorescence was used to detect HSF1 expression in muscle tissues. RESULTS: Anti-HSF1 was identified as a novel autoantibody by protein microarray and the seroreactivity was confirmed by immunoprecipitation, ELISA, immunoblot and dot blot assays. Anti-HSF1 autoantibodies were present in 64/581 (11.0%) IIM, 4/37 (10.8%) rheumatoid arthritis, 5/40 (12.5%) primary Sjögren's syndrome, 2/40 (5%) systemic lupus erythematosus, while largely negative in healthy controls. Anti-HSF1 autoantibodies were significantly associated with pruritus, hypergammaglobulinaemia, and elevated erythrocyte sedimentation rate in IIM patients. Anti-HSF1 autoantibodies were more prevalent in cancer-associated myositis (CAM) compared to non-CAM patients (17.2% vs. 7.5%, p=0.009), nevertheless were undetectable in cancer controls. Meanwhile, cross-sectional and longitudinal analyses revealed positive correlations between anti-HSF1 levels and disease activity in IIM patients without cancer. Additionally, increased expression of HSF1 was found in regenerating muscle cells of myositis muscle tissues. CONCLUSIONS: These data reveal anti-HSF1 as a new autoantibody associated with CAM in IIM. The autoimmunity against HSF1 may be involved in the immunopathogenesis of myositis.

The prevalence and clinical significance of anti-PUF60 antibodies in patients with idiopathic inflammatory myopathy.

Autoantibodies against poly-U-binding factor 60 kDa protein (PUF60) have been reported in Caucasian dermatomyositis (DM) patients. However, their clinical significance in idiopathic inflammatory myopathy (IIM) remains to be fully clarified. Our objective was to analyze the prevalence and clinical significance of anti-PUF60 antibodies in a large cohort of Chinese IIM patients. In our study, 388 IIM patients, 301 disease controls, and 167 healthy controls (HCs) were involved. An enzyme-linked immunosorbent assay (ELISA) was developed to detect serum anti-PUF60 levels and was validated using immunoblotting methods. Unpaired Mann-Whitney U test and Spearman correlation analysis were used when appropriate. Anti-PUF60 antibodies were observed in IIM patients at a frequency of 10.6% (41/388). Subgrouping analysis revealed that the prevalence of anti-PUF60 antibodies was 10% in DM, 5.5% in polymyositis (PM), 10% in immune-mediated necrotizing myositis (IMNM), and 26.5% in myositis-overlap syndrome. Anti-PUF60 antibodies were also observed in systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), and Sjögren's syndrome (SS) patients at a positive rate of 17.3, 14.5, and 10.1% respectively. Intriguingly, anti-PUF60 antibodies were frequently observed in clinically amyopathic dermatomyositis (CADM) patients and DM patients without currently known myositis autoantibodies. Furthermore, DM patients with anti-PUF60 antibodies had higher prevalence of skin ulcerations. Moreover, longitudinal investigation in eight DM patients with anti-PUF60 antibodies revealed that the antibodies levels decreased with disease remission. Anti-PUF60 antibodies were nonspecific for myositis, since they could be detected in other rheumatic diseases. Further investigation of anti-PUF60 antibodies may reveal shared pathogenic pathways in systemic autoimmune disorders.

A simple method for removing low-density granulocytes to purify T lymphocytes from peripheral blood mononuclear cells.

OBJECTIVE: Low-density granulocytes (LDGs) can form neutrophil extracellular traps (NETs) spontaneously and excessively. When peripheral blood mononuclear cells (PBMCs) are used for studying T lymphocytes, LDGs contained in the PBMCs may decrease the threshold of activating T lymphocytes by forming NETs. This study focused on the profiles of LDGs in common autoimmune diseases and methods for removing LDGs from PBMCs. METHODS: The percentages of LDGs in PBMCs from 55 patients with dermatomyositis (DM), 15 with polymyositis (PM), 42 with rheumatoid arthritis (RA), 25 with systemic lupus erythematosus (SLE), and 19 healthy controls were determined by flow cytometry. Three methods of removing LDGs were explored and compared. After removal, PBMCs from six patients with positive T-SPOT.TB were tested again to find out if LDGs contained in the PBMCs could influence T lymphocyte reactions. RESULTS: Significantly higher LDG percentages were found in PBMCs from patients with DM ((8.41±10.87)%, P<0.0001), PM ((8.41±10.39)%, P<0.0001), RA ((4.05±6.97)%, P=0.0249), and SLE ((7.53±11.52)%, P=0.0006), compared with the controls ((1.28±0.73)%). The T-SPOT.TB values significantly decreased after LDGs were removed. Increasing relative centrifugal force (RCF) within a limited range can decrease the LDG percentage from an initial high level, but not markedly increase the LDG clearance rate. Compared with the whole blood sediment method, the PBMC adherence method can significantly remove LDGs yet scarcely influence the T lymphocyte percentage in PBMCs. CONCLUSIONS: The LDG percentage in PBMCs is significantly increased in patients with SLE, DM, PM, and RA. The influence of LDGs on T lymphocytes cannot be ignored in PBMC cultures. The adherence method is a simple and easy-to-use method for removing LDGs and purifying T lymphocytes from PBMCs.

Transcriptomic profiling of long non-coding RNAs in dermatomyositis by microarray analysis.

Long non-coding RNAs (lncRNAs) are prevalently transcribed in the genome and have been found to be of functional importance. However, the potential roles of lncRNAs in dermatomyositis (DM) remain unknown. In this study, a lncRNA + mRNA microarray analysis was performed to profile lncRNAs and mRNAs from 15 treatment-naive DM patients and 5 healthy controls. We revealed a total of 1198 lncRNAs (322 up-regulated and 876 down-regulated) and 1213 mRNAs (665 up-regulated and 548 down-regulated) were significantly differentially expressed in DM patients compared with the healthy controls (fold change>2, P < 0.05). Subgrouping DM patients according to the presence of interstitial lung disease and anti-Jo-1 antibody revealed different expression patterns of the lncRNAs. Pathway and gene ontology analysis for the differentially expressed mRNAs confirmed that type 1 interferon signaling was the most significantly dysregulated pathway in all DM subgroups. In addition, distinct pathways that uniquely associated with DM subgroup were also identified. Bioinformatics prediction suggested that linc-DGCR6-1 may be a lncRNA that regulates type 1 interferon-inducible gene USP18, which was found highly expressed in the perifascicular areas of the muscle fibers of DM patients. Our findings provide an overview of aberrantly expressed lncRNAs in DM muscle and further broaden the understanding of DM pathogenesis.

[Characteristics of surface energy fluxes over a sparse shrubland ecosystem in the farming-pastoral zone of the Loess Plateau, Northwest China].

Based on the energy flux and meteorological data during 2011-2012 over a sparse shrubland ecosystem in the farming-pastoral zone of the Loess Plateau, this study investigated the diurnal and seasonal variations of the energy balance components, and discussed the responses of the latent and sensible heat fluxes to different intensities of rainfall events. In addition, we identified the major environmental controlling factors on latent and sensible heat fluxes via correlation analysis. The results showed that the diurnal and seasonal variations of net radiation (Rn), sensible heat flux (H), latent heat flux (LE) and soil heat flux (G) all showed single-peak curves. The annual mean values of Rn, H, LE and G were 78.19, 33.32, 24.91 and 2.65 W · m(-2), respectively. The ratios of energy budget components to net radiation were 43% (H/Rn), 32% (LE/Rn), and 3% (G/Rn), which indicated that sensible heat flux was the major form of energy loss at this site. In the growing season, the ratios of sensible heat flux and latent heat flux to net radiation were nearly the same (36%); while in the non-growing season, sensible heat flux accounted for 54% of net radiation. Latent heat flux increased sharply after heavy and weak rainfall events, while sensible heat flux decreased sharply at the same time. Continuous rainfall events would lead to fluctuations in latent and sensible heat fluxes. There were significant correlations between latent heat flux and net radiation, vapor pressure deficit and vegetation parameter, while remarkable correlations were found between sensible heat flux and net radiation, and air temperature gradient.

Elevated Serum Levels of Soluble CD163 in Polymyositis and Dermatomyositis: Associated with Macrophage Infiltration in Muscle Tissue.

OBJECTIVE: To investigate serum levels of soluble CD163 (sCD163) in patients with polymyositis (PM) and dermatomyositis (DM), and to correlate these to clinical manifestations and laboratory data. METHODS: Serum levels of sCD163 were detected in 24 patients with PM, 84 patients with DM, and 46 healthy controls by using the ELISA method. Immunohistochemistry staining of macrophage infiltration in muscle tissue using anti-CD163 monoclonal antibody was conducted on muscle biopsy specimens from 13 patients with PM and 17 with DM. RESULTS: Serum levels of sCD163 were significantly increased in patients compared with healthy controls (p < 0.001). Patients with interstitial lung disease (ILD) had statistically higher sCD163 levels than patients without ILD (p < 0.001). High serum sCD163 levels were associated with increased incidence of antinuclear antibody (p < 0.05), higher serum levels of immunoglobulin G (p < 0.01) and immunoglobulin A (p < 0.05), and increased erythrocyte sedimentation rates (p < 0.01). Serum sCD163 levels were inversely correlated with CD3+ T cell counts in peripheral blood of patients (r = -0.306, p < 0.01). Cross-sectional assessment and longitudinal study revealed a significant correlation between serum sCD163 levels and disease activity. Patients with high serum sCD163 levels showed a higher incidence of CD163+ macrophage infiltration in muscle tissue than patients with normal sCD163 levels (chi-square value = 10.804, p < 0.01). CONCLUSION: Serum levels of sCD163 were significantly elevated and correlated with disease severity in patients with PM/DM, suggesting serum sCD163 as a promising biomarker in the disease evaluation of PM/DM. Our finding of elevated serum sCD163 levels associated with muscle macrophage infiltration highlights the role activated macrophage plays in the pathogenesis of PM/DM.