A DNA barcode library for woody plants in tropical and subtropical China.

The application of DNA barcoding has been significantly limited by the scarcity of reliable specimens and inadequate coverage and replication across all species. The deficiency of DNA barcode reference coverage is particularly striking for highly biodiverse subtropical and tropical regions. In this study, we present a comprehensive barcode library for woody plants in tropical and subtropical China. Our dataset includes a standard barcode library comprising the four most widely used barcodes (rbcL, matK, ITS, and ITS2) for 2,520 species from 4,654 samples across 49 orders, 144 families, and 693 genera, along with 79 samples identified at the genus level. This dataset also provides a super-barcode library consisting of 1,239 samples from 1,139 species, 411 genera, 113 families, and 40 orders. This newly developed library will serve as a valuable resource for DNA barcoding research in tropical and subtropical China and bordering countries, enable more accurate species identification, and contribute to the conservation and management of tropical and subtropical forests.

Multidimensional beta-diversity across local and regional scales in a Chinese subtropical forest: The role of forest structure.

Beta-diversity, or the spatio-temporal variation in community composition, can be partitioned into turnover and nestedness components in a multidimensional framework. Forest structure, including comprehensive characteristics of vertical and horizontal complexity, strongly affects species composition and its spatial variation. However, the effects of forest structure on beta-diversity patterns in multidimensional and multiple-scale contexts are poorly understood. Here, we assessed beta-diversity at local (a 20-ha forest dynamics plot) and regional (a plot network composed of 19 1-ha plots) scales in a Chinese subtropical evergreen broad-leaved forest. We then evaluated the relative importance of forest structure, topography, and spatial structure on beta-diversity and its turnover and nestedness components in taxonomic, functional, and phylogenetic dimensions at local and regional scales. We derived forest structural parameters from both unmanned aerial vehicle light detection and ranging (UAV LiDAR) data and plot inventory data. Turnover component dominated total beta-diversity for all dimensions at the two scales. With the exception of some components (taxonomic and functional turnover at the local scale; functional nestedness at the regional scale), environmental factors (i.e., topography and forest structure) contributed more than pure spatial variation. Explanations of forest structure for beta-diversity and its component patterns at the local scale were higher than those at the regional scale. The joint effects of spatial structure and forest structure influenced component patterns in all dimensions (except for functional turnover) to some extent at the local scale, while pure forest structure influenced taxonomic and phylogenetic nestedness patterns to some extent at the regional scale. Our results highlight the importance and scale dependence of forest structure in shaping multidimensional beta-diversity and its component patterns. Clearly, further studies need to link forest structure directly to ecological processes (e.g., asymmetric light competition and disturbance dynamics) and explore its roles in biodiversity maintenance.

High expression of RASAL1, a hub gene in the progression of liver cancer, suggests a poor prognostis.

OBJECTIVE: Liver cancer (LC) is a frequently occurring lethal malignancy worldwide, yet the molecular mechanisms of carcinogenesis and their development remain uncharacterized. In this study, bioinformatics methods were used to find candidate hub genes for prognosis assessment and clinical treatment of LC. METHODS: Differential analysis was carried out based on the evidence of gene expression profiling in LC on The Cancer Genome Atlas (TCGA). The differentially expressed genes (DEGs) were constructed into co-expression networks and divided into modules by virtue of weighted gene co-expression network analysis (WGCNA). Based on the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG), the module genes were subjected to functional enrichment analysis. The LC microarray (GSE105130) in the Gene Expression Omnibus was selected to verify the hub genes' expression profiles. The validity of the hub genes was verified via survival analysis, as well as expression correlation with the clinicopathological features. Thereafter, gene set variation analysis (GSVA) and single-sample gene set enrichment analysis (GSEA) were applied to investigate the possible biological functions of the hub genes. RESULTS: In total, 3780 DEGs and 17 co-expression modules were obtained. The blue module had the strongest correlation with the tumour stage and the module genes were principally enriched in tumour-associated GO terms, as well as pathways such as Ras protein signal transduction, ERK1/2 cascade, Ras signal pathway, and ECM-receptor interaction. RASAL1, which is highly expressed in LC, was identified as a hub gene for LC progression. Its high expression suggested unfavorable patient prognosis and was correlated with T stage, gender and tumour stage. Further analysis identified that the overexpression of RASAL1 was substantially enriched in cancer-associated gene sets. CONCLUSION: RASAL1 is a hub gene that influences LC progression, constituting a novel biomarker and molecular target in the future diagnosis and therapy of LC.

Plastome-based phylogeny improves community phylogenetics of subtropical forests in China.

Phylogenetic trees have been extensively used in community ecology. However, how the phylogeny construction affects ecological inferences is poorly understood. In this study, we constructed three different types of phylogenetic trees (a synthetic-tree generated using V.PhyloMaker, a barcode-tree generated using rbcL+matK+trnH-psbA, and a plastome-tree generated from plastid genomes) that represented an increasing level of phylogenetic resolution among 580 woody plant species from six forest dynamic plots in subtropical evergreen broadleaved forests of China. We then evaluated the performance of each phylogeny in estimations of community phylogenetic structure, turnover and phylogenetic signal in functional traits. As expected, the plastome-tree was most resolved and most supported for relationships among species. For local phylogenetic structure, the three trees showed consistent results with Faith's PD and MPD; however, only the synthetic-tree produced significant clustering patterns using MNTD for some plots. For phylogenetic turnover, contrasting results between the molecular trees and the synthetic-tree occurred only with nearest neighbor distance. The barcode-tree agreed more with the plastome-tree than the synthetic-tree for both phylogenetic structure and turnover. For functional traits, both the barcode-tree and plastome-tree detected phylogenetic signal in maximum height, but only the plastome-tree detected signal in leaf width. This is the first study that uses plastid genomes in large-scale community phylogenetics. Our results highlight the improvement of plastome-trees over barcode-trees and synthetic-trees for the analyses studied here. Our results also point to the possibility of type I and II errors in estimation of phylogenetic structure and turnover and detection of phylogenetic signal when using synthetic-trees.

Serum Cholinesterases, a Novel Marker of Clinical Activity in Inflammatory Bowel Disease: A Retrospective Case-Control Study.

BACKGROUND: The aim of our study was to investigate whether serum cholinesterase (ChE) levels were associated with inflammatory bowel disease (IBD). MATERIALS AND METHODS: We conducted a retrospective case-control study to clarify the relationship between serum ChE levels and IBD that included 142 patients with ulcerative colitis (UC), 60 patients with Crohn's disease (CD), and 264 healthy controls (HCs). We used ROC curves to evaluate the diagnostic value of serum ChE levels for IBD. RESULTS: Substantially lower serum ChE levels were detected in patients with UC than in HCs (6376 U/L versus 8418 U/L, P < 0.001) and in patients with CD than in HCs (5181 U/L versus 8418 U/L, P < 0.001). Additionally, patients with CD displayed significantly lower serum ChE levels than patients with UC (5181 U/L versus 6376 U/L, P < 0.01). We also found that there was a negative association between serum ChE levels and the Crohn's Disease Activity Index (CDAI) score of patients with CD (P = 0.011) and the Simple Clinical Colitis Activity Index (SCCAI) score of patients with UC (P = 0.018). The area under the curve (AUC) for serum ChE for the diagnosis of IBD was 0.826, and the AUCs of serum ChE for the diagnosis of CD and UC were 0.890 and 0.800, respectively. CONCLUSIONS: Serum ChE levels have important clinical significance in the diagnosis and assessment of clinical activity in patients with IBD, and the cholinergic anti-inflammatory pathway may provide new ideas for targeted treatment of IBD.

Changes in the human gut microbiota composition caused by Helicobacter pylori eradication therapy: A systematic review and meta-analysis.

BACKGROUND: The short-term and long-term effect of Helicobacter pylori (H pylori) eradication on the gut microbiota is controversial; hence, this study aimed to clarify changes in the gut microbiome and microbial diversity after H pylori eradication. MATERIALS AND METHODS: Articles published in PubMed, MEDLINE, and EMBASE were searched up to March 20, 2020, with English-language restriction. The outcomes including gut microbiota and alpha diversity were extracted to analysis. And then, Review Manager 5.3 software was used to conduct the data analysis. RESULTS: At phylum level, next-generation sequencing was performed. Meta-analysis results showed that Actinobacteria decreased compared with baseline throughout the follow-up period. Proteobacteria increased during short-term follow-up and then returned to normal. In addition, Bacteroidetes decreased and Firmicutes increased only during long-term follow-up. At family or genus level, conventional microbiological culturing was performed. Enterobacteriaceae and Enterococcus both increased during the short-term and interim follow-up. In addition, Lactobacillus only showed a decreasing trend during short-term follow-up, but it appeared statistical decreasing during interim follow-up. Moreover, relatively sufficient evidence showed that alpha diversity decreased during short-term follow-up, and no reliable data were obtained to confirm the change of alpha diversity during interim and long-term follow-up. CONCLUSION: In different follow-up periods after H pylori eradication, changes in gut microbiota were inconsistent. Microbial diversity decreased in the short-term follow-up, while there was no data to confirm subsequent alterations. The results provided a basis for the rational selection of probiotics in the eradication process. However, further studies are needed to obtain more clues.

Expression analysis of microRNAs and their target genes during experimental diabetic renal lesions in rats administered with ginsenoside Rb1 and trigonelline.

Purpose: To appraise the curative effect of ginsenoside Rb1 and trigonelline in diabetic nephropathy and to analyze the expression analysis of microRNAs and their target genes during experimental diabetic renal lesions in rats. Methods: Wistar rats were made diabetic by intraperitoneal injection of 55 mg/kg streptozotocin. According to their fasting blood glucose values and initial body weight, diabetic rats were assigned to specific groups and treated as follows: DN group (tap water, n = 10), A group (ginsenoside Rb1, 40 mg/kg, n = 10), B group (trigonelline, 20 mg/kg, n = 10) and the C group (ginsenoside Rb1 and trigonelline, 60 mg/kg, m(ginsenoside Rb1) : m (trigonelline) = 2:1, n = 10). The control group was treated with tap water (n = 10). All rats were gavaged with drugs or tap water once daily for 12 weeks. Results: Renal dysfunction, oxidative stress, and pathological alteration were significantly alleviated by a combination of ginsenoside Rb1 and trigonellin (C group). Some miRNAs were expressed differentially in Con, DN, A and C groups. Results of immunohistochemistry and western blotting showed that Wnt and ß-catenin were expressed differentially in Con, DN, and C groups. Conclusion: Ginsenoside Rb1 and trigonelline could prevent the development of diabetic renal lesions by regulating the expression of miR-3550 and further associating with the Wnt/ß-catenin signaling.

Intra-specific relatedness, spatial clustering and reduced demographic performance in tropical rainforest trees.

Intra-specific negative density dependence promotes species coexistence by regulating population sizes. Patterns consistent with such density dependence are frequently reported in diverse tropical tree communities. Empirical evidence demonstrating whether intra-specific variation is related to these patterns, however, is lacking. The present study addresses this important knowledge gap by genotyping all individuals of a tropical tree in a long-term forest dynamics plot in tropical China. We show that related individuals are often spatially clustered, but having closely related neighbours reduces the growth performance of focal trees. We infer from the evidence that dispersal limitation and negative density dependence are operating simultaneously to impact the spatial distributions of genotypes in a natural population. Furthermore, dispersal limitation decreases local intra-specific genetic diversity and increases negative density dependence thereby promoting niche differences and species coexistence as predicted by theory.

Urinary kidney injury molecule­1 as an early diagnostic biomarker of obstructive acute kidney injury and development of a rapid detection method.

The aim of the present study was to investigate whether urinary kidney injury molecule­1 (KIM­1) presents a suitable early diagnostic biomarker of obstructive nephropathy­induced acute kidney injury (AKI), and to develop a rapid detection method for urinary KIM­1. Obstructive AKI was induced in an experimental rat model by a unilateral ureteral obstruction (UUO) operation. Macro­ and micromorphological kidney alterations were determined by visual observation and hematoxylin and eosin (HE) staining, respectively. Kidney functions were evaluated by detecting urea nitrogen and creatinine levels in rat urine and blood. Urinary KIM­1 levels were measured using an enzyme­linked immunosorbent assay, and the protein expression levels of KIM­1, α­smooth muscle actin (α­SMA) and vimentin in kidney tissues were detected using immunohistochemical assays. In order to measure KIM­1 levels, colloidal gold immunochromatographic strips were developed based on the colloidal gold immunochromatographic assay. The results indicated that KIM­1 levels were significantly higher in the UUO group when compared with the Sham group. KIM­1 levels in the urine and kidney tissues exhibited a time­dependent increase, together with increasing obstructive AKI in the UUO group. In addition, KIM­1 levels were demonstrated to be a more sensitive biomarker of early obstructive AKI, when compared with α­SMA and vimentin. A colloidal gold­based immunochromatographic strip was developed, whereby the detection of urinary KIM­1 could be completed within 5­10 min. In conclusion, results of the present study demonstrated that urinary KIM­1 may be a valuable biomarker for the early diagnosis of obstructive AKI, and the use of a colloidal gold immunochromatographic strip may be a promising method for the rapid detection of urinary KIM­1.

A new model for the discrimination between ulcerative colitis and Crohn's disease.

Distinguishing ulcerative colitis (UC) from Crohn's disease (CD) is sometimes difficult in a clinical setting. The purpose of this study was to identify a series of independent serum markers capable of distinguishing between UC and CD. 140 UC and 174 CD patients hospitalized at The First Affiliated Hospital, College of Medicine, Zhejiang University were recruited into this study. A panel of serum markers was quantified for each patient and the Bayesian information criterion (BIC) was used to determine a discrimination model. The receiver operating characteristic (ROC) was used to evaluate the performance of the model, and the area under the ROC curve (AUC) was used to evaluate the accuracy of the model. Serum albumin (Alb), total cholesterol (TC), total calcium (TCa), platelet (Plt), glycyl proline dipeptidyl aminopeptidase (GPDA) and their ratios (Alb: Plt, Alb: GPDA, TCa: TC, and Plt: GPDA) were selected into the diagnosis model using BIC. The resulting CD/UC Index (CUI) is CUI = 1.901 + 0.425 Alb - 3.324 TC - 7.444 TCa + 0.018 Plt + 0.087 GPDA - 0.0007 Alb: Plt - 0.004 Alb: GPDA + 1.839 TC: TCa + 0.003 Plt: GPDA, with CUI > 0 incrementally favored a diagnosis of UC, while CUI < 0 corresponded to a higher likelihood of a diagnosis of CD. An average value of the AUC for the CUI model is 0.73 (95% confidence interval: 0.67-0.80). The CUI, derived from commonly available serum biomarkers, could try to differentiate UC from CD in patients with unclear clinical features as a new approach to diagnosis.

Noncovalent binding of xanthene and phthalocyanine dyes with graphene sheets: the effect of the molecular structure revealed by a photophysical study.

The fluorescence and absorption properties of several xanthene and phthalocyanine dyes were measured in the presence and absence of chemically derived graphene (CDG) sheets. The interaction of pyronine Y (PYY) with graphene sheets was compared with that of rhodamine 6G (R6G) to reveal the effect of the molecular structure. Although the presence of the perpendicular benzene moiety in a R6G or phthalocyanine molecule does cause the difficulty for forming dye-CDG complex and make CDG less efficient in quenching the fluorescence intensity and shortening the fluorescence lifetime, it does not affect the band position of charge transfer absorption, suggesting that no molecular shape change occurred in a dye molecule caused by the interaction with CDG sheets. The spectroscopic and thermodynamic data indicated that the dye-CDG binding is of charge transfer nature, while the dynamic fluorescence quenching is due to photoinduced energy and electron transfer.

Dual fluorescence of graphene oxide: a time-resolved study.

The fluorescence properties of graphene oxide (GO) was studied by recording the fluorescence lifetime, fluorescence emission, and excitation spectra, as well as UV-visible and near-IR absorption spectra. For the first time, we showed that a blue band (ca. 440 nm) and a long wavelength (LW) band (ca. 700 nm) are coexistent, which can be recorded simultaneously by controlling concentration, excitation wavelength, and pH values. Two bands are closely related by the protonation or deprotonation of GO. The blue band is favored by low GO concentration, short excitation wavelength, and high pH value, while the LW band is favored by low pH and long excitation wavelength. To reveal the nature of the dual emission of GO, the fluorescence lifetimes under various conditions were also measured. The blue band contains three emitting components; one of them has a lifetime as long as 10 ns, and its emitting intensity is fairly sensitive to pH, showing the potential for applications in sensing H(+) and fluorescence lifetime imaging. Combining the results under various conditions, we conclude that the electronic transition for this component is very likely due to n-π* transition. The LW band contains two main emitting components (0.2 and 2.1 ns) that also appear in the blue band as minor contributors; the related emission is assigned to π-π* transition. In summary, GO emission is of broadband (300-1250 nm), long-lived, pH sensitive, and excitation wavelength dependent. This makes it easily tailored for versatile applications.