Species delimitation of tea plants (Camellia sect. Thea) based on super-barcodes.

BACKGROUND: The era of high throughput sequencing offers new paths to identifying species boundaries that are complementary to traditional morphology-based delimitations. De novo species delimitation using traditional or DNA super-barcodes serve as efficient approaches to recognizing putative species (molecular operational taxonomic units, MOTUs). Tea plants (Camellia sect. Thea) form a group of morphologically similar species with significant economic value, providing the raw material for tea, which is the most popular nonalcoholic caffeine-containing beverage in the world. Taxonomic challenges have arisen from vague species boundaries in this group. RESULTS: Based on the most comprehensive sampling of C. sect. Thea by far (165 individuals of 39 morphospecies), we applied three de novo species delimitation methods (ASAP, PTP, and mPTP) using plastome data to provide an independent evaluation of morphology-based species boundaries in tea plants. Comparing MOTU partitions with morphospecies, we particularly tested the congruence of MOTUs resulting from different methods. We recognized 28 consensus MOTUs within C. sect. Thea, while tentatively suggesting that 11 morphospecies be discarded. Ten of the 28 consensus MOTUs were uncovered as morphospecies complexes in need of further study integrating other evidence. Our results also showed a strong imbalance among the analyzed MOTUs in terms of the number of molecular diagnostic characters. CONCLUSION: This study serves as a solid step forward for recognizing the underlying species boundaries of tea plants, providing a needed evidence-based framework for the utilization and conservation of this economically important plant group.

Phylotranscriptomic analyses reveal deep gene tree discordance in Camellia (Theaceae).

Gene tree discordance is a significant legacy of biological evolution. Multiple factors can result in incongruence among genes, such as introgression, incomplete lineage sorting (ILS), gene duplication or loss. Resolving the background of gene tree discordance is a critical way to uncover the process of species diversification. Camellia, the largest genus in Theaceae, has controversial taxonomy and systematics due in part to a complex evolutionary history. We used 60 transcriptomes of 55 species, which represented 15 sections of Camellia to investigate its phylogeny and the possible causes of gene tree discordance. We conducted gene tree discordance analysis based on 1,617 orthologous low-copy nuclear genes, primarily using coalescent species trees and polytomy tests to distinguish hard and soft conflict. A selective pressure analysis was also performed to assess the impact of selection on phylogenetic topology reconstruction. Our results detected different levels of gene tree discordance in the backbone of Camellia, and recovered rapid diversification as one of the possible causes of gene tree discordance. Furthermore, we confirmed that none of the currently proposed sections of Camellia was monophyletic. Comparisons among datasets partitioned under different selective pressure regimes showed that integrating all orthologous genes provided the best phylogenetic resolution of the species tree of Camellia. The findings of this study reveal rapid diversification as a major source of gene tree discordance in Camellia and will facilitate future investigation of reticulate relationships at the species level in this important plant genus.

To assess the cell lines on esophagogastroduod enoscopies of children with feeding difficulty, esophageal fistula and asthma with histologic abnormality.

The purpose of this study is to evaluate the cell lines seen on esophagogastoduodenoscopy (EGD) of children who have difficulties feeding, esophageal fistula, and asthma that has some histologic abnormalities.  This is a study that looked back at the medical records of 100 children whose cells had been surgically restored after being impacted by EA or TEF. A review of the instrumental tests that were carried out at our facility has been conducted in order to identify any lingering anatomic or functional abnormalities of the airways and gastrointestinal system that would explain the pulmonary clinical images. Due to neurodevelopmental sequelae and the existence of tracheostomies, only 26 sets of pre and post-bronchodilator spirometry data were available for children. 100 children cells with esophageal atresia and tracheoesophageal fistula were included in the study. The average number of weeks spent in gestation was 37.01± 2.33, and the average weight of a newborn was 2614±77.69 grammes. Twenty percent of the children's cells exhibited a syndromic appearance, and the VACTERL connection was identified in seventeen percent of the patients. In all, 80% of the children cells in the sample reported having respiratory symptoms, with 85% of patients experiencing symptoms of the lower respiratory tract and 15% experiencing symptoms of the upper respiratory tract. It is common practice to attribute children's symptoms to reflux and esophageal anomalies, despite the presence of respiratory symptoms and aberrant findings discovered by flexible bronchoscopy and CT assessment.

[Genetic Subtypes and Pretreatment Drug Resistance in the Newly Reported Human Immunodeficiency Virus-Infected Men Aged≥50 Years Old in Guangxi].

Objective To analyze the genetic subtypes of human immunodeficiency virus (HIV) and the prevalence of pretreatment drug resistance in the newly reported HIV-infected men in Guangxi. Methods The stratified random sampling method was employed to select the newly reported HIV-infected men aged≥50 years old in 14 cities of Guangxi from January to June in 2020.The pol gene of HIV-1 was amplified by nested reverse transcription polymerase chain reaction and then sequenced.The mutation sites associated with drug resistance and the degree of drug resistance were then analyzed. Results A total of 615 HIV-infected men were included in the study.The genetic subtypes of CRF01_AE,CRF07_BC,and CRF08_BC accounted for 57.4% (353/615),17.1% (105/615),and 22.4% (138/615),respectively.The mutations associated with the resistance to nucleoside reverse transcriptase inhibitors (NRTI),non-nucleoside reverse transcriptase inhibitors (NNRTI),and protease inhibitors occurred in 8 (1.3%),18 (2.9%),and 0 patients,respectively.M184V (0.7%) and K103N (1.8%) were the mutations with the highest occurrence rates for the resistance to NRTIs and NNRTIs,respectively.Twenty-two (3.6%) patients were resistant to at least one type of inhibitors.Specifically,4 (0.7%),14 (2.3%),4 (0.7%),and 0 patients were resistant to NRTIs,NNRTIs,both NRTIs and NNRTIs,and protease inhibitors,respectively.The pretreatment resistance to NNRTIs had much higher frequency than that to NRTIs (2.9% vs.1.3%;χ2=3.929,P=0.047).The prevalence of pretreatment resistance to lamivudine,zidovudine,tenofovir,abacavir,rilpivirine,efavirenz,nevirapine,and lopinavir/ritonavir was 0.8%, 0.3%, 0.7%, 1.0%, 1.3%, 2.8%, 2.9%, and 0, respectively. Conclusions CRF01_AE,CRF07_BC,and CRF08_BC are the three major strains of HIV-infected men≥50 years old newly reported in Guangxi,2020,and the pretreatment drug resistance demonstrates low prevalence.

Phylotranscriptomics of Theaceae: generic-level relationships, reticulation and whole-genome duplication.

BACKGROUND AND AIMS: Theaceae, with three tribes, nine genera and more than 200 species, are of great economic and ecological importance. Recent phylogenetic analyses based on plastomic data resolved the relationships among the three tribes and the intergeneric relationships within two of those tribes. However, generic-level relationships within the largest tribe, Theeae, were not fully resolved. The role of putative whole-genome duplication (WGD) events in the family and possible hybridization events among genera within Theeae also remain to be tested further. METHODS: Transcriptomes or low-depth whole-genome sequencing of 57 species of Theaceae, as well as additional plastome sequence data, were generated. Using a dataset of low-copy nuclear genes, we reconstructed phylogenetic relationships using concatenated, species tree and phylogenetic network approaches. We further conducted molecular dating analyses and inferred possible WGD events by examining the distribution of the number of synonymous substitutions per synonymous site (Ks) for paralogues in each species. For plastid protein-coding sequences , phylogenies were reconstructed for comparison with the results obtained from analysis of the nuclear dataset. RESULTS: Based on the 610 low-copy nuclear genes (858 606 bp in length) investigated, Stewartieae was resolved as sister to the other two tribes. Within Theeae, the Apterosperma-Laplacea clade grouped with Pyrenaria, leaving Camellia and Polyspora as sister. The estimated ages within Theaceae were largely consistent with previous studies based mainly on plastome data. Two reticulation events within Camellia and one between the common ancestor of Gordonia and Schima were found. All members of the tea family shared two WGD events, an older At-γ and a recent Ad-ß; both events were also shared with the outgroups (Diapensiaceae, Pentaphylacaceae, Styracaceae and Symplocaceae). CONCLUSIONS: Our analyses using low-copy nuclear genes improved understanding of phylogenetic relationships at the tribal and generic levels previously proposed based on plastome data, but the phylogenetic position of the Apterosperma-Laplacea clade needs more attention. There is no evidence for extensive intergeneric hybridization within Theeae or for a Theaceae-specific WGD event. Land bridges (e.g. the Bering land bridge) during the Late Oligocene may have permitted the intercontinental plant movements that facilitated the putative ancient introgression between the common ancestor of Gordonia and Schima.

Epidemiological and clinical characteristics of imported cases of COVID-19: a multicenter study.

BACKGROUND: The coronavirus disease 2019 (COVID-19) pandemic continues to expand. Herein, we report the epidemiological and clinical features of 478 patients with confirmed COVID-19 from a multicenter study conducted in four cities in China excluding Wuhan. METHODS: A total of 478 patients transferred by emergency medical services to designated hospitals in four major cities in China (Beijing, Chongqing, Jinan, and Nanning) were enrolled. We compared the characteristics of imported and indigenous cases and calculated the frequencies of fatal, severe, mild, and asymptomatic disease. The results were used to generate a pyramid of COVID-19 severity. RESULTS: The mean age of patients with COVID-19 was 46.9 years and 49.8% were male. The most common symptoms at onset were fever (69.7%), cough (47.5%), fatigue (24.5%), dyspnea (8.4%), and headache (7.9%). Most cases (313, 65.5%) were indigenous, while 165 (34.5%) were imported. Imported cases dominated during the early stages of the pandemic, but decreased from 1 February 2020 as indigenous cases rose sharply. Compared with indigenous cases, imported cases differed significantly in terms of sex (P = 0.002), severity of disease (P = 0.006), occurrence of fever (P < 0.001), family clustering (P < 0.001), history of contact (P < 0.001), and primary outcome (P < 0.001). CONCLUSIONS: Within the population studied, imported cases had distinct characteristics from those of indigenous cases, with lower fatality rates and higher discharge rates. New infections shifted from imported cases to local infection gradually, and overall infections have declined to a low level. We suggest that preventing import of cases and controlling spread within local areas can help prevent SARS-CoV-2 infection spread.

Evaluation of serum zinc level and IL-18 mRNA expression in children with pneumonia.

Pneumonia is currently one of the leading causes of death in children. Increased susceptibility to pneumonia may be due to their decreased immunity. One of the reasons for the decrease in immunity is zinc deficiency. In children with pneumonia, on the other hand, some cytokines are secreted, resulting in inflammation that spreads, persists, and makes treatment difficult for specialists. In this study, we investigated the serum zinc level in children with pneumonia and healthy children. Also, we tried to find its relationship with IL-18 mRNA expression as an inflammatory cytokine. For this purpose, serum zinc levels and IL-18 mRNA expression were evaluated in 120 children aged 3-60 months with pneumonia and 120 healthy children. After taking 2ml of blood from children and measuring serum zinc level, the level of the IL-18 mRNA was measured by real-time PCR. Total RNA was extracted by bioZOL™-G RNA Isolation Reagent kit. The primary cDNA was amplified by the extracted RNA, and in the next step, 2µl of cDNA were amplified by specific primers to measure IL-18 mRNA. The Beta-actin gene was also used as internal control and housekeeping gene. Results showed that the level of zinc in the patient group was 412.625±28.87?M and in the control group was 514.40±49.67?M. This difference was statistically significant (P=0.0053). Also, the expression of the IL-18 gene was increased in children with pneumonia, significantly (P=0.0015). Therefore, from the results, it can be deduced that children with zinc deficiency were at higher risk for a lung infection. Inflammatory cytokines such as IL-18 also were increased in these children. Hence, it can be concluded that zinc levels can reduce the expression of IL-18 mRNA and play an important role in the prevention and treatment of children with pneumonia.

Insights into the historical assembly of East Asian subtropical evergreen broadleaved forests revealed by the temporal history of the tea family.

Subtropical evergreen broadleaved forests (EBLFs) inhabit large areas of East Asia. Although paleovegetation reconstructions have revealed that the subtropical EBLFs existed in Southwest China during the Miocene, the historical construction of these forests remains poorly known. Here, we used the tea family (Theaceae), a characteristic component of the subtropical EBLFs, to gain new insights into the assembly of this important biome. Using a robust phylogenetic framework of Theaceae based on plastome and nuclear ribosomal DNA sequence data, the temporal history of the family was reconstructed. Data from other characteristic components of subtropical EBLFs, including Fagaceae, Lauraceae and Magnoliaceae, were also integrated. Most of the essential elements of the subtropical EBLFs appear to have originated around the Oligocene-Miocene (O-M) boundary. However, small woody lineages (e.g. Camellia, Hartia) from Theaceae were dated to the late Miocene. Accelerated net diversification rates within Theaceae were also detected near the O-M transition period and the late Miocene. Our results suggest that two independent intensifications of the East Asian summer monsoon (EASM) around the O-M boundary and the late Miocene may have facilitated the historical assembly of the subtropical EBLFs in East Asia.

Genetic diversity and domestication origin of tea plant Camellia taliensis (Theaceae) as revealed by microsatellite markers.

BACKGROUND: Tea is one of the most popular beverages in the world. Many species in the Thea section of the Camellia genus can be processed for drinking and have been domesticated. However, few investigations have focused on the genetic consequence of domestication and geographic origin of landraces on tea plants using credible wild and planted populations of a single species. Here, C. taliensis provides us with a unique opportunity to explore these issues. RESULTS: Fourteen nuclear microsatellite loci were employed to determine the genetic diversity and domestication origin of C. taliensis, which were represented by 587 individuals from 25 wild, planted and recently domesticated populations. C. taliensis showed a moderate high level of overall genetic diversity. The greater reduction of genetic diversity and stronger genetic drift were detected in the wild group than in the recently domesticated group, indicating the loss of genetic diversity of wild populations due to overexploitation and habitat fragmentation. Instead of the endangered wild trees, recently domesticated individuals were used to compare with the planted trees for detecting the genetic consequence of domestication. A little and non-significant reduction in genetic diversity was found during domestication. The long life cycle, selection for leaf traits and gene flow between populations will delay the emergence of bottleneck in planted trees. Both phylogenetic and assignment analyses suggested that planted trees may have been domesticated from the adjacent central forest of western Yunnan and dispersed artificially to distant places. CONCLUSIONS: This study contributes to the knowledge about levels and distribution of genetic diversity of C. taliensis and provides new insights into genetic consequence of domestication and geographic origin of planted trees of this species. As an endemic tea source plant, wild, planted and recently domesticated C. taliensis trees should all be protected for their unique genetic characteristics, which are valuable for tea breeding.

Ecological risk assessment of heavy metal(loid)s in riverine sediments along the East China Sea: A large-scale integrated analysis.

This study comprehensively assesses spatial distribution, pollution levels, and potential sources of heavy metal(loid)s in surface sediments across multiple river systems along the coastal area of the East China Sea. Copper in Qiantang River and Xiangshan Bay showed higher concentations and exceeded the threshold effect value, while the higher content of Lead was mainly found in the Saijiang River, Oujiang River, and Minjiang River. Heavy metal(loid)s in the alluvium of Qiantang River, Jiaojiang River, and Yangtze River showed low to moderate pollution levels, with Cd posing the highest ecological risk, followed by Hg. Meanwhile, Qiantang River, Jiaojiang River, Yangtze River, and Oujiang River exhibited considerable to moderate ecological risks and low toxic risk. PMF model analysis results reveal that concentrations of Cr, Ni, and As were closely related with natural geogenic input (36.56 %), while industrial and traffic activities (48.77 %) were primary source of Cu, Pb, Zn, and Hg, and main source of Cd was agricultural emissions (14.67 %).

Differential effects of warming on the complexity and stability of the microbial network in Phragmites australis and Spartina alterniflora wetlands in Yancheng, Jiangsu Province, China.

The impact of climate warming on soil microbial communities can significantly influence the global carbon cycle. Coastal wetlands, in particular, are susceptible to changes in soil microbial community structure due to climate warming and the presence of invasive plant species. However, there is limited knowledge about how native and invasive plant wetland soil microbes differ in their response to warming. In this study, we investigated the temporal dynamics of soil microbes (prokaryotes and fungi) under experimental warming in two coastal wetlands dominated by native Phragmites australis (P. australis) and invasive Spartina alterniflora (S. alterniflora). Our research indicated that short-term warming had minimal effects on microbial abundance, diversity, and composition. However, it did accelerate the succession of soil microbial communities, with potentially greater impacts on fungi than prokaryotes. Furthermore, in the S. alterniflora wetland, experimental warming notably increased the complexity and connectivity of the microbial networks. While in the P. australis wetland, it decreased these factors. Analysis of robustness showed that experimental warming stabilized the co-occurrence network of the microbial community in the P. australis wetland, but destabilized it in the S. alterniflora wetland. Additionally, the functional prediction analysis using the Faprotax and FunGuild databases revealed that the S. alterniflora wetland had a higher proportion of saprotrophic fungi and prokaryotic OTUs involved in carbon degradation (p < 0.05). With warming treatments, there was an increasing trend in the proportion of prokaryotic OTUs involved in carbon degradation, particularly in the S. alterniflora wetland. Therefore, it is crucial to protect native P. australis wetlands from S. alterniflora invasion to mitigate carbon emissions and preserve the health of coastal wetland ecosystems under future climate warming in China.

HLA-mismatched allogeneic adoptive immune therapy in patients with severely immunosuppressed AIDS: a multicenter, open-label, controlled, phase 2a study.

Recurrent opportunistic infections (OIs) in patients with severely immunosuppressed AIDS remain an unresolved medical challenge despite advancements in antiretroviral therapy (ART). To address this gap, we developed an HLA-mismatched allogeneic adoptive immune therapy (AAIT) specifically targeting this patient population. The safety and efficacy of this novel therapeutic approach were preliminarily confirmed in our phase 1 trial. Subsequently, a multicenter, open-label, controlled, phase 2a trial was conducted to evaluate the efficacy of AAIT in combination with ART compared with the conventional ART-only regimen. No difference in the incidence of adverse events (AEs) was observed between the two groups at the 96-week follow-up. AAIT treatment improved CD4+ T cell recovery at weeks 72 (P = 0.048) and 96 (P = 0.024) compared to the Control Group. Additionally, stratified analysis of patients in the AAIT Group showed that donor/recipient sex mismatch was significantly associated with the likelihood of patients achieving an immunological response (OR = 8.667; 95% CI, 2.010-37.377; P = 0.004). These findings suggest that AAIT serves as a promising adjunct therapy for improving the outcomes of patients with severely immunosuppressed AIDS. Further studies are needed to elucidate the immunological mechanisms underlying AAIT and identify the subpopulations that respond optimally to this therapeutic approach. This trial is registered at www.clinicaltrials.gov (NCT04098770).Trial registration: ClinicalTrials.gov identifier: NCT04098770.Trial registration: ClinicalTrials.gov identifier: NCT02651376.

Distribution and sources of fluvial pollen in the middle reaches of the Yellow River in China and their relationship with vegetation and land use.

Understanding the processes determining the composition of alluvial pollen assemblages and its relationship with watershed vegetation is a prerequisite for alluvial palynological study. Palynological analysis of a total of 45 river water samples collected from the middle reaches of the Yellow River and its major tributaries, identifies the distribution patterns, possible sources of pollen and relationship with the catchment vegetation. The results reveal that the pollen assemblages in the middle reaches of the Yellow River is dominated by herbaceous taxa, and the pollen is mainly derived from fluvial sources. Higher concentrations of the pollen tend to occur in the southern part of the study area. The Luo River is the main source of tree pollen in the Wei River Basin, while the Sanchuan River and Xinshui River are the main sources of tree pollen in the mainstream of the Yellow River. Herbaceous pollen mainly originates from the flood plain, and from channel bars and point bars, and there is no obvious relationship between herbaceous pollen and tributary inputs. The relative proportions of the various land use classes in the middle reaches of the Yellow River can be ordered as follows: grassland (GL) > cultivated land (CL) > forest (FO) > shrubland (SH) > water (WA). The herbaceous pollen of the Huangfuchuan River and Kuye River are closely related to the coverage of GL; cereal pollen is not fully representative of the CL coverage in the watershed; and the pollen of woody plants is extremely over-represented compared to the coverage of FO and SH in the watershed. Our results provide basic information about the sources of fluvial pollen and its indicative significance in the lower Yellow River and they are also potentially applicable to other major river basins.

Single-cell RNA sequencing revealed potential targets for immunotherapy studies in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is a solid tumor prone to chemotherapy resistance, and combined immunotherapy is expected to bring a breakthrough in HCC treatment. However, the tumor and tumor microenvironment (TME) of HCC is highly complex and heterogeneous, and there are still many unknowns regarding tumor cell stemness and metabolic reprogramming in HCC. In this study, we combined single-cell RNA sequencing data from 27 HCC tumor tissues and 4 adjacent non-tumor tissues, and bulk RNA sequencing data from 374 of the Cancer Genome Atlas (TCGA)-liver hepatocellular carcinoma (LIHC) samples to construct a global single-cell landscape atlas of HCC. We analyzed the enrichment of signaling pathways of different cells in HCC, and identified the developmental trajectories of cell subpopulations in the TME using pseudotime analysis. Subsequently, we performed transcription factors regulating different subpopulations and gene regulatory network analysis, respectively. In addition, we estimated the stemness index of tumor cells and analyzed the intercellular communication between tumors and key TME cell clusters. We identified novel HCC cell clusters that specifically express HP (HCC_HP), which may lead to higher tumor differentiation and tumor heterogeneity. In addition, we found that the HP gene expression-positive neutrophil cluster (Neu_AIF1) had extensive and strong intercellular communication with HCC cells, tumor endothelial cells (TEC) and cancer-associated fibroblasts (CAF), suggesting that clearance of this new cluster may inhibit HCC progression. Furthermore, ErbB signaling pathway and GnRH signaling pathway were found to be upregulated in almost all HCC tumor-associated stromal cells and immune cells, except NKT cells. Moreover, the high intercellular communication between HCC and HSPA1-positive TME cells suggests that the immune microenvironment may be reprogrammed. In summary, our present study depicted the single-cell landscape heterogeneity of human HCC, identified new cell clusters in tumor cells and neutrophils with potential implications for immunotherapy research, discovered complex intercellular communication between tumor cells and TME cells.

Phylogeography of Camellia taliensis (Theaceae) inferred from chloroplast and nuclear DNA: insights into evolutionary history and conservation.

BACKGROUND: As one of the most important but seriously endangered wild relatives of the cultivated tea, Camellia taliensis harbors valuable gene resources for tea tree improvement in the future. The knowledge of genetic variation and population structure may provide insights into evolutionary history and germplasm conservation of the species. RESULTS: Here, we sampled 21 natural populations from the species' range in China and performed the phylogeography of C. taliensis by using the nuclear PAL gene fragment and chloroplast rpl32-trnL intergenic spacer. Levels of haplotype diversity and nucleotide diversity detected at rpl32-trnL (h = 0.841; π = 0.00314) were almost as high as at PAL (h = 0.836; π = 0.00417). Significant chloroplast DNA population subdivision was detected (GST = 0.988; NST = 0.989), suggesting fairly high genetic differentiation and low levels of recurrent gene flow through seeds among populations. Nested clade phylogeographic analysis of chlorotypes suggests that population genetic structure in C. taliensis has been affected by habitat fragmentation in the past. However, the detection of a moderate nrDNA population subdivision (GST = 0.222; NST = 0.301) provided the evidence of efficient pollen-mediated gene flow among populations and significant phylogeographical structure (NST > GST; P < 0.01). The analysis of PAL haplotypes indicates that phylogeographical pattern of nrDNA haplotypes might be caused by restricted gene flow with isolation by distance, which was also supported by Mantel's test of nrDNA haplotypes (r = 0.234, P < 0.001). We found that chlorotype C1 was fixed in seven populations of Lancang River Region, implying that the Lancang River might have provided a corridor for the long-distance dispersal of the species. CONCLUSIONS: We found that C. taliensis showed fairly high genetic differentiation resulting from restricted gene flow and habitat fragmentation. This phylogeographical study gives us deep insights into population structure of the species and conservation strategies for germplasm sampling and developing in situ conservation of natural populations.

Species discrimination in Schima (Theaceae): Next-generation super-barcodes meet evolutionary complexity.

Plastid genome and nuclear ribosomal DNA (nrDNA) arrays, proposed recently as "super-barcodes," might provide additional discriminatory power and overcome the limitations of traditional barcoding loci, yet super-barcodes need to be tested for their effectiveness in more plant groups. Morphological homoplasy among Schima species makes the genus a model for testing the efficacy of super-barcodes. In this study, we generated multiple data sets comprising standard DNA barcodes (matK, rbcL, trnH-psbA, nrITS) and super-barcodes (plastid genome, nrDNA arrays) across 58 individuals from 12 out of 13 species of Schima from China. No samples were correctly assigned to species using standard DNA barcodes and nrDNA arrays, while only 27.27% of species with multiple accessions were distinguished using the plastid genome and its partitioned data sets-the lowest estimated rate of super-barcode success in the literature so far. For Schima and other taxa with similarly recently divergence and low levels of genetic variation, incomplete lineage sorting, hybridization or taxonomic oversplitting are all possible causes of the failure. Taken together, our study suggests that by no means are super-barcodes immune to the challenges imposed by evolutionary complexity. We therefore call for developing multilocus nuclear markers for species discrimination in plant groups.

Effect of nanoprocessing on the physicochemical properties of bovine, porcine, chicken, and rabbit bone powders.

The chemical composition and hardness of bovine bone, porcine bone, chicken bone, and rabbit bone were compared, as well as the influence of nanoprocessing on the physicochemical characteristics of these bone powders. A series of nanofabrication processes led to an increase in bone minerals and the loss of protein and fat. The hardness of softened bovine bone was still the largest, whereas chicken and rabbit bones were relatively soft. There were no significant differences in the functional groups between nanoscale bone powders. Overall, nanomachining significantly reduced and homogenized the bone particle size and improved the color and release rate of calcium ions of bone powders at the same time; these effects were different for several bones. Nanoscale rabbit bone had higher comminution efficiency, as well as satisfactory nutritional value, color, and product yield, which supports its strong development potential.

Prediction of Lymph-Node Metastasis in Cancers Using Differentially Expressed mRNA and Non-coding RNA Signatures.

Accurate prediction of lymph-node metastasis in cancers is pivotal for the next targeted clinical interventions that allow favorable prognosis for patients. Different molecular profiles (mRNA and non-coding RNAs) have been widely used to establish classifiers for cancer prediction (e.g., tumor origin, cancerous or non-cancerous state, cancer subtype). However, few studies focus on lymphatic metastasis evaluation using these profiles, and the performance of classifiers based on different profiles has also not been compared. Here, differentially expressed mRNAs, miRNAs, and lncRNAs between lymph-node metastatic and non-metastatic groups were identified as molecular signatures to construct classifiers for lymphatic metastasis prediction in different cancers. With this similar feature selection strategy, support vector machine (SVM) classifiers based on different profiles were systematically compared in their prediction performance. For representative cancers (a total of nine types), these classifiers achieved comparative overall accuracies of 81.00% (67.96-92.19%), 81.97% (70.83-95.24%), and 80.78% (69.61-90.00%) on independent mRNA, miRNA, and lncRNA datasets, with a small set of biomarkers (6, 12, and 4 on average). Therefore, our proposed feature selection strategies are economical and efficient to identify biomarkers that aid in developing competitive classifiers for predicting lymph-node metastasis in cancers. A user-friendly webserver was also deployed to help researchers in metastasis risk determination by submitting their expression profiles of different origins.

Pollen distribution and transportation patterns in surface sediments of Liaodong Bay, China.

Understanding pollen transport pathways and dispersal mechanism from the land to sea is a prerequisite for marine palynological study. Palynological analysis of 164 surface sediment samples in Liaodong Bay, and 39 analogous surface alluvium samples from its five inflowing rivers, identifies the distribution patterns, pathways and possible sources of pollen and spores. The results show that pollen and spore assemblages in surface sediments are well correlated to regional vegetation distribution, and the variations of pollen assemblage in different parts of Liaodong Bay reflected local vegetation changes along the coast. High pollen concentrations are mainly distributed in the estuaries of inflowing rivers, coastal waters and sea muddy areas. The pollen assemblage characteristics of alluvial samples are similar to those from coastal waters with water depths <8.5 m. Samples from the alluvium and surface sediments of coastal waters were dominated by herbaceous pollen taxa including Artemisia, Amaranthaceae, Poaceae, Cyperaceae and Typha. Herbaceous pollen percentages and concentrations decreased as the water depth increased, indicating that pollen and spores in the coastal waters of Liaodong Bay are mainly carried by the inflowing rivers. However, pollen assemblages for samples with water depth >8.5 m are significantly different from those of the alluvium. In samples taken below a depth of 8.5 m, the arboreal pollen is dominated by airborne Pinus, and there is a high number of the waterborne Selaginella fern spores, both of which are sourced from a wider region. In the Liaodong Bay, both wind and ocean current transportation determines the pollen distribution patterns in deeper waters, while fluvial and longshore current transportation determines the pollen assemblages found in shallow waters. The dispersal characteristics of pollen assemblages between the land and the sea in Liaodong Bay provide a theoretical basis for the interpretation of fossil pollen assemblages and past sea level changes.