Molecular phylogeny and species delimitation of Stachyuraceae: Advocating a herbarium specimen‐based phylogenomic approach in resolving species boundaries

Species concept and delimitation are fundamental to taxonomic and evolutionary studies. Both inadequate informative sites in the molecular data and limited taxon sampling have often led to poor phylogenetic resolution and incorrect species delineation. Recently, the whole chloroplast genome sequences from extensive herbarium specimen samples have been shown to be effective to amend the problem. Stachyuraceae are a small family consisting of only one genus Stachyurus of six to 16 species. However, species delimitation in Stachyurus has been highly controversial because of few and generally unstable morphological characters used for classification. In this study, we sampled 69 individuals of seven species (each with at least three individuals) covering the entire taxonomic diversity, geographic range, and morphological variation of Stachyurus from herbarium specimens for genome‐wide plastid gene sequencing to address species delineation in the genus. We obtained high‐quality DNAs from specimens using a recently developed DNA reconstruction technique. We first assembled four whole chloroplast genome sequences. Based on the chloroplast genome and one nuclear ribosomal DNA sequence of Stachyurus, we designed primers for multiplex polymerase chain reaction and high throughput sequencing of 44 plastid loci for species of Stachyurus. Data of these chloroplast DNA and nuclear ribosomal DNA internal transcribed spacer sequences were used for phylogenetic analyses. The phylogenetic results showed that the Japanese species Stachyurus praecox Siebold & Zucc. was sister to the rest in mainland China, which indicated a typical Sino‐Japanese distribution pattern. Based on diagnostic morphological characters, distinct distributional range, and monophyly of each clade, we redefined seven species for Stachyurus following an integrative species concept, and revised the taxonomy of the family based on previous reports and specimens, in particular the type specimens. Furthermore, our divergence time estimation results suggested that Stachyuraceae split from its sister group Crossosomataceae from the New World at ca. 54.29 Mya, but extant species of Stachyuraceae started their diversification only recently at ca. 6.85 Mya. Diversification time of Stachyurus in mainland China was estimated to be ca. 4.45 Mya. This research has provided an example of using the herbarium specimen‐based phylogenomic approach in resolving species boundaries in a taxonomically difficult genus.     

Osmotic stress induces gut microbiota community shift in fish

Alteration of the gut microbiota plays an important role in animal health and metabolic diseases. However, little is known with respect to the influence of environmental osmolality on the gut microbial community. The aim of the current study was to determine whether the reduction in salinity affects the gut microbiota and identify its potential role in salinity acclimation. Using Oryzias melastigma as a model organism to perform progressive hypotonic transfer experiments, we evaluated three conditions: seawater control (SW), SW to 50% sea water transfer (SFW) and SW to SFW to freshwater transfer (FW). Our results showed that the SFW and FW transfer groups contained higher operational taxonomic unit microbiota diversities. The dominant bacteria in all conditions constituted the phylum Proteobacteria, with the majority in the SW and SFW transfer gut comprising Vibrio at the genus level, whereas this population was replaced by Pseudomonas in the FW transfer gut. Furthermore, our data revealed that the FW transfer gut microbiota exhibited a reduced renin–angiotensin system, which is important in SW acclimation. In addition, induced detoxification and immune mechanisms were found in the FW transfer gut microbiota. The shift of the bacteria community in different osmolality environments indicated possible roles of bacteria in facilitating host acclimation.     

Aging shifts mitochondrial dynamics toward fission to promote germline stem cell loss

Changes in mitochondrial dynamics (fusion and fission) are known to occur during stem cell differentiation; however, the role of this phenomenon in tissue aging remains unclear. Here, we report that mitochondrial dynamics are shifted toward fission during aging of Drosophila ovarian germline stem cells (GSCs), and this shift contributes to aging‐related GSC loss. We found that as GSCs age, mitochondrial fragmentation and expression of the mitochondrial fission regulator, Dynamin‐related protein (Drp1), are both increased, while mitochondrial membrane potential is reduced. Moreover, preventing mitochondrial fusion in GSCs results in highly fragmented depolarized mitochondria, decreased BMP stemness signaling, impaired fatty acid metabolism, and GSC loss. Conversely, forcing mitochondrial elongation promotes GSC attachment to the niche. Importantly, maintenance of aging GSCs can be enhanced by suppressing Drp1 expression to prevent mitochondrial fission or treating with rapamycin, which is known to promote autophagy via TOR inhibition. Overall, our results show that mitochondrial dynamics are altered during physiological aging, affecting stem cell homeostasis via coordinated changes in stemness signaling, niche contact, and cellular metabolism. Such effects may also be highly relevant to other stem cell types and aging‐induced tissue degeneration.     

Global Profiling of Alternative Splicing in Callus Induction of Immature Maize Embryo

In Vitro Cellular & Developmental Biology - Plant - Callus induction in plants is similar to pluripotent stem cell induction in animals and can incite global changes in gene expression....     

Introduction to Special Issue on ‘Statistical Methods for Cancer Immunotherapy’

Statistics in Biosciences -     

Binding mechanism of maltol with catalase investigated by spectroscopy,molecular docking,and enzyme activity assay

Maltol is a flavor additive that is widely used in the daily diet of humans, and its biosafety attention is concomitantly increasing. Catalase (CAT) is an antioxidant enzyme to maintain homeostasis in the tissue's environment of human body and protect cells from oxidative damages. The adverse effects of maltol to CAT activity within mouse hepatocytes as well as the structural and functional changes of CAT on molecular level were investigated by multiple spectroscopy techniques, enzyme activity experiments, and molecular docking. Results suggested that when the maltol concentrations reached to 8 × 10^?5 mol L^?1, the viability of hepatocytes decreased to 93%, and CAT activity was stimulated by maltol to 111% than the control group after exposure for 24 hours. Changes in CAT activity on molecular level were consistent with those on cellular level. The fluorescence quenching of CAT by maltol was static with the forming of maltol‐CAT complex. Moreover, ultraviolet‐visible (UV‐visible) absorption, synchronous fluorescence, and circular dichroism (CD) spectra reflected that the presence of maltol caused conformational change of CAT and made the CAT molecule skeleton loose and increased α‐helix of CAT. Maltol mainly bound with CAT through hydrogen bond, and binding site that is near the heme ring in the enzyme activity center did not interact with its main amino acid residues. This study explores the combination between maltol and CAT, providing references for evaluating health damages caused by maltol.     

大渡河中游干暖河谷区生境对植物群落分布格局和多样性的影响

大渡河中游干暖河谷区滑坡和泥石流灾害频发, 对该区域坡面植物群落的研究有助于揭示植被演替的方向, 为坡面植被生态恢复提供基本依据。本研究沿大渡河中游河谷区每隔约5 km设置典型样地, 调查了植被的物种组成和分布以及样地的地形、土壤等10个生境因子, 探讨河谷区植被的连续性变化, 并通过多元回归树(multivariate regression trees, MRT)、多样性指数和典范对应分析(canonical correspondence analysis, CCA)等方法对植物群落进行分类、比较和排序。结果表明: 大渡河中游干暖河谷植被以土壤碳含量、pH值和C : N等3个因子为节点, 可划分为多花胡枝子(Lespedeza floribunda)-荩草(Arthraxon hispidus)-香薷(Elsholtzia ciliate)(群落A)、地果(Ficus tikoua)-车桑子(Dodonaea viscosa)-川滇薹草(Carex schneideri)(群落B)、云南松(Pinus yunnanensis)-栓皮栎(Quercus variabilis)(群落C)和荩草-扭黄茅(Heteropogon contortus)(群落D)等4种群落。该区域以灌木和草本为主要植被类型(群落A、B、C), 间或有裸地分布, 易成为泥石流灾害产生的物源区; 以多花胡枝子为主的灌草群落A的物种丰富度、优势度与多样性表现一致, 均高于以乔木和草本为主的群落C和D, 但物种多样性优势并不显著, 灌草群落分布广而结构单一, 外来物种占比为8.33%, 是生态系统脆弱和不稳定的表现。多元回归树和典范对应分析结果表明, pH值、C : N、坡向和土壤容重等4个因子对植物群落组成和分布影响最大, 且土壤因子的影响大于地形因子。