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.

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.

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.