Biology subjects

Bin, X.

Publications and source records attributed to Bin, X..

3 recordsLinked to original sources

bioRxiv2021

Multidimensional molecular differences between artificial and wild Artemisia rupestris L.

Different ecological environments affect the active ingredients and molecular content of medicinal plants. Artemisia rupestris L. is a kind of traditional medicinal plant, and the shortages of the wild resource have led to increased use of artificial varieties. However, there have few investigations referring to molecular differences between them in a systematic manner. In the present study, artificial and wild Artemisia rupestris L. plants were collected in the Altay-Fuyun region, Xinjian, China. Untargeted metabolomics method based on liquid chromatography-mass spectrometry (LC-MS) technology was applied to profile flower, stem, and leaf samples, respectively, and levels of a panel of representative known metabolites in this plant were simultaneously analyzed. The genetic basis of these samples was explored using a de novo transcriptomics approach to investigate differentially expressed genes (DEGs) and their pathway annotations. Results indicated metabolic differences between the two varieties mainly reflected in flavonoids and chlorogenic acid/caffeic acid derivatives. 34 chemical markers (CMs) belonging to these two structural categories were discovered after validation using another batch of samples, including 19 potentially new compounds. After correlation analysis, total of six DEGs in different organs relating to 24 CMs were confirmed using quantitative real-time PCR (qPCR). These findings provided novel insight into the molecular landscape of this medicinal plant through metabolomics-transcriptomics integration strategy, and reference information of its quality control and species identification. ONE SENTENCE SUMMARYA metabolomics-transcriptomics research on Artemisia rupestris L. to discover metabolite differences and the genetic basis between artificial and wild varieties in systematic and novel manner.

systems biology↗

bioRxiv2020

Genomic Insights into the Demographic History of Southern Chinese

Southern China is the birthplace of rice-cultivating agriculture, different language families, and human migrations that facilitated these cultural diffusions. The fine-scale demographic history in situ, however, remains unclear. To comprehensively cover the genetic diversity in East and Southeast Asia, we generated genome-wide SNP data from 211 present-day Southern Chinese and co-analyzed them with more than 1,200 ancient and modern genomes. We discover that the previously described Southern East Asian or Yangtze River Farmer lineage is monophyletic but not homogeneous, comprising four regionally differentiated sub-ancestries. These ancestries are respectively responsible for the transmission of Austronesian, Kra-Dai, Hmong-Mien, and Austroasiatic languages and their original homelands successively distributed from East to West in Southern China. Multiple phylogenetic analyses support that the earliest living branching among East Asian-related populations is First Americans ([~]27,700 BP), followed by the pre-LGM differentiation between Northern and Southern East Asians ([~]23,400 BP) and the pre-Neolithic split between Coastal and Inland Southern East Asians ([~]16,400 BP). In North China, distinct coastal and inland routes of south-to-north gene flow had established by the Holocene, and further migration and admixture formed the genetic profile of Sinitic speakers by [~]4,000 BP. Four subsequent massive migrations finalized the complete genetic structure of present-day Southern Chinese. First, a southward Sinitic migration and the admixture with Kra-Dai speakers formed the Sinitic Cline. Second, a bi-directional admixture between Hmong-Mien and Kra-Dai speakers gave rise to the Hmong-Mien Cline in the interior of South China between [~]2,000 and [~]1,000 BP. Third, a southwestward migration of Kra-Dai speakers in recent [~]2,000 years impacted the genetic profile for the majority of Mainland Southeast Asians. Finally, an admixture between Tibeto-Burman incomers and indigenous Austroasiatic speakers formed the Tibeto-Burman speakers in Southeast Asia by [~]2,000 BP.

genomics↗

bioRxiv2019

Coloring Single Nanoparticle Trajectory on Live Cell Membrane with its Own History: a Presuppositionless Approach

Analyzing single particle trajectories is a prominent issue in understanding complex dynamics such as nanoparticle-cell interactions. Existing methods treat data points as isolated \"atoms\" and use predefined mechanical models to \"frame\" their complicated relationship. Herein, we propose a \"historical evolution\" based model-free strategy. It allows spatiotemporal heterogeneity embedded in a trajectory to self-emerge as consecutive colored segments before any model assumption, provide both an overall picture and local state transitions on the particle movement with minimum information loss, and inspire further model-based investigation. We demonstrate with simulations and experiments that the underlying mechanisms of various time-series and motion states of single nanoparticles on live cell membranes could all be revealed successfully. Since complexity studies at different levels of molecules, particles, cells, human beings, vehicles, and even stars could all be reduced to analyzing spatiotemporal trajectories of \"single particles\", this presuppositionless approach will help fundamental researches on many important systems.\n\nImpact StatementA preprocessing strategy for single particle trajectory analysis is established by providing an intuitive global pattern from \"historical experiences\" of the particle without predefining any mechanical models.

biophysics↗