Biology subjects

Wen, J.

Publications and source records attributed to Wen, J..

At least 91 records · Page 5Linked to original sources

bioRxiv2022

A wheat resistosome defines common principles of immune receptor channels

Plant intracellular nucleotide-binding leucine-rich repeat (NLRs) receptors detect pathogen effectors to trigger immune responses. Indirect recognition of a pathogen effector by the dicotyledonous Arabidopsis thaliana coiled-coil (CC) domain containing NLR (CNL) ZAR1 induces the formation of a large hetero-oligomeric protein complex, termed the ZAR1 resistosome, which functions as a calcium channel required for ZAR1-mediated immunity (1-3). Whether the resistosome and channel activities are conserved among plant CNLs remains unknown. We report here a cryogenic electron microscopy (cryo-EM) structure of the wheat CNL Sr35 in complex with the effector AvrSr35 of the wheat stem rust pathogen at 3.0 [A] resolution. Direct effector binding to the leucine-rich repeats (LRRs) of Sr35 results in the formation of a pentameric Sr35-AvrSr35 complex, which we designate the Sr35 resistosome. Wheat Sr35 and Arabidopsis ZAR1 resistosomes bear striking structural similarity, including a previously unnoticed arginine cluster in the LRR domain that co-occurs and forms intramolecular interactions with the EDVID motif in the CC domain. Electrophysiological measurements show that the Sr35 resistosome exhibits non-selective cation channel activity. These structural insights allowed us to generate novel variants of closely related wheat and barley orphan NLRs that recognize AvrSr35. Our data support the evolutionary conservation of CNL resistosomes in plants and demonstrate proof of principle for structure-based engineering of NLRs for crop improvement.

plant biology↗

bioRxiv2022

A comprehensive comparison on cell type composition inference for spatial transcriptomics data

Spatial transcriptomic (ST) technologies allow researchers to examine high-quality RNA-sequencing data along with maintained two-dimensional positional information as well as a co-registered histology image. A popular use of ST omics data is to provide insights about tissue structure and spatially unique features. However, due to the technical nature unique to most ST data, the resolution varies from a diameter of 2-10m to 50-100m instead of single-cell resolution, which brings uncertainty into cell number and cell mixture within each ST spot. Motivated by the important role for spatial arrangement of cell types within a tissue in physiology and disease pathogenesis, several ST deconvolution methods have been developed and are being used to explore gene expression variation and identification of spatial domains. The aim of this work is to review state-of-the-art methods for ST deconvolution, while comparing their strengths and weaknesses. Specifically, we use four real datasets to examine the performance of eight methods across different tissues and technological platforms. Key PointsO_LICell mixture inference is a critical step in the analysis of spatial transcriptomics (ST) data to prevent downstream analysis suffering from confounding factors at the spot level. C_LIO_LIExisting ST deconvolution methods can be classified into three groups: probabilistic-based, non-negative matrix factorization and non-negative least squares based, and other deep learning framework-based methods. C_LIO_LIWe compared eight ST deconvolution methods by using two single cell level resolution datasets and two spot level resolution ST datasets. We provided practical guidelines for the choice of method under different scenarios as well as the optimal subsets of genes to use for each method. C_LI

genetics↗

bioRxiv2022

Transcriptomics informs design of a planar human enterocyte culture system that reveals metformin enhances fatty acid export

Background & AimsAbsorption, metabolism, and export of dietary lipids occurs in the small intestinal epithelium. Caco-2 and organoids have been used to study these processes but are limited in physiological relevance or preclude simultaneous apical and basal access. Here, we develop a high-throughput planar human absorptive enterocyte (AE) monolayer system for investigating lipid-handling, then evaluate the role of fatty acid oxidation (FAO) in fatty acid (FA) export, using etomoxir, C75, and anti-diabetic drug, metformin. MethodsSingle-cell RNA-sequencing (scRNAseq), transcriptomics, and lineage trajectory was performed on primary human jejunum. In vivo AE maturational states informed conditions used to differentiate human intestinal stem cells (ISCs) that mimic in vivo AE maturation. The system was scaled for high-throughput drug screening. Fatty acid oxidation (FAO) was pharmacologically modulated and BODIPY (B)-labelled FAs were used to evaluate FA-handling via fluorescence and thin layer chromatography (TLC). ResultsscRNAseq shows increasing expression of lipid-handling genes as AEs mature. Culture conditions promote ISC differentiation into confluent AE monolayers. FA-handling gene expression mimics in vivo maturational states. FAO inhibitor, etomoxir, decreased apical-to-basolateral export of medium-chain B-C12 and long-chain B-C16 FAs whereas CPT1 agonist, C75, and antidiabetic drug, metformin, increased apical-to-basolateral export. Short-chain B-C5 was unaffected by FAO inhibition and diffused through AEs. ConclusionsPrimary human ISCs in culture undergo programmed maturation. AE monolayers demonstrate in vivo maturational states and lipid-handling gene expression profiles. AEs create strong epithelial barriers in 96-Transwell format. FA export is proportional to FAO. Metformin enhances FAO and increases basolateral FA export, supporting an intestine-specific role.

cell biology↗

bioRxiv2021

Leveraging TOPMed Imputation Server and Constructing a Cohort-Specific Imputation Reference Panel to Enhance Genotype Imputation among Cystic Fibrosis Patients

Cystic fibrosis (CF) is a severe genetic disorder that can cause multiple comorbidities affecting the lungs, the pancreas, the luminal digestive system and beyond. In our previous genome-wide association studies (GWAS), we genotyped [~]8,000 CF samples using a mixture of different genotyping platforms. More recently, the Cystic Fibrosis Genome Project (CFGP) performed deep ([~]30x) whole genome sequencing (WGS) of 5,095 samples to better understand the genetic mechanisms underlying clinical heterogeneity among CF patients. For mixtures of GWAS array and WGS data, genotype imputation has proven effective in increasing effective sample size. Therefore, we first performed imputation for the [~]8,000 CF samples with GWAS array genotype using the TOPMed freeze 8 reference panel. Our results demonstrate that TOPMed can provide high-quality imputation for CF patients, boosting genomic coverage from [~]0.3 - 4.2 million genotyped markers to [~]11 - 43 million well-imputed markers, and significantly improving Polygenic Risk Score (PRS) prediction accuracy. Furthermore, we built a CF-specific CFGP reference panel based on WGS data of CF patients. We demonstrate that despite having [~]3% the sample size of TOPMed, our CFGP reference panel can still outperform TOPMed when imputing some CF disease-causing variants, likely due to allele and haplotype differences between CF patients and general populations. We anticipate our imputed data for 4,656 samples without WGS data will benefit our subsequent genetic association studies, and the CFGP reference panel built from CF WGS samples will benefit other investigators studying CF.

genetics↗

bioRxiv2021

Heat activation and inactivation of bacterial spores. Is there an overlap?

Heat activation at a sublethal temperature is widely applied to promote Bacillus species spore germination. This treatment also has potential to be employed in food processing to eliminate undesired bacterial spores by enhancing their germination, and then inactivating the less heat resistant germinated spores at a milder temperature. However, incorrect heat treatment could also generate heat damage in spores, and lead to more heterogeneous spore germination. Here, the heat activation and heat damage profile of Bacillus subtilis spores was determined by testing spore germination and outgrowth at both population and single spore levels. The heat treatments used were 40-80{degrees}C, and for 0-300 min. The results were as follows. 1) Heat activation at 40-70{degrees}C promoted L-valine and L-asparagine-glucose-fructose-potassium (AGFK) induced germination in a time dependent manner. 2) The optimal heat activation temperatures for AGFK and L-valine germination via the GerB plus GerK or GerA germinant receptors were 65 and 50-65{degrees}C, respectively. 3) Heat inactivation of dormant spores appeared at 70{degrees}C, and the heat damage of molecules essential for germination and growth began at 70 and 65{degrees}C, respectively. 4) Heat treatment at 75{degrees}C resulted in both activation of germination and damage to the germination apparatus, and 80{degrees}C treatment caused more pronounced heat damage. 5) For the spores that should withstand adverse environmental temperatures in nature, heat activation seems functional for a subsequent optimal germination process, while heat damage affected both germination and outgrowth.

microbiology↗

bioRxiv2021

Organization and dynamics of the SpoVAEa protein, and its surrounding inner membrane lipids upon germination of Bacillus subtilis spores

The SpoVA proteins make up a channel in the inner membrane (IM) of B. subtilis spore. This channel responds to signals from activated germinant receptors (GRs), and allows release of Ca2+-DPA from the spore core during germination. In the current work, we studied the location and dynamics of SpoVAEa in dormant spores. Notably, the SpoVAEa-SGFP2 proteins were present in a single spot in spores, similar to the complex formed by all GRs. However, while the GRs spot remains in one location, the SpoVAEa-SGFP2 spot in the IM moved randomly with high frequency. The dynamics of the SpoVAEa-SGFP2 and its surrounding IM region as stained by fluorescent dyes were also tracked during spore germination, as the dormant spore IM appeared to have an immobile germination related functional microdomain. This microdomain disappeared around the time of appearance of a germinated spore, the loss of fluorescence of the IM by fluorescent dyes, as well as the appearance of SpoVAEa-SGFP2 peak fluorescent intensity occurred in parallel. These observed events were highly related to the rapid phase darkening, which is considered as the Ca2+DPA rapid release. We also tested the response of SpoVAEa and the IM to thermal treatments at 40-80{degrees}C. Heat treatment triggered an increase of green autofluorescence, which is speculated to be due to coat protein denaturation, and 80{degrees}C treatments induce the appearance of phase-grey-like spores. These spores presumably have a similar intracellular physical state as the phase grey spores detected in the germination but lack the functional proteins for further germination events.

microbiology↗

bioRxiv2021

Persistent CAD activity in memory CD8+ T cells supports rRNA synthesis and ribosomal biogenesis required at rechallenge

Memory CD8+ T cells are characterized by their ability to persist long after the initial antigen encounter and their ability to generate a rapid recall response. Recent studies have identified a role for metabolic reprogramming and mitochondrial function in promoting the longevity of memory T cells. However, detailed mechanisms involved in promoting the rapid recall response are incompletely understood. Here we identify a novel role for the initial and continued activation of the trifunctional rate-limiting enzyme of the de novo pyrimidine synthesis pathway CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase) as critical in promoting the rapid recall response of previously-activated CD8+ T cells. CAD is rapidly phosphorylated upon T cell activation in an mTORC1-dependent manner yet remains phosphorylated long after initial activation. Previously-activated CD8+ T cells display continued de novo pyrimidine synthesis in the absence of mitogenic signals and interfering with this pathway diminishes the speed and magnitude of cytokine production upon rechallenge. Inhibition of CAD does not affect cytokine transcript levels, but diminishes available pre-rRNA, the polycistronic rRNA precursor whose synthesis is the rate-limiting step in ribosomal biogenesis. CAD inhibition additionally decreases levels of detectable ribosomal proteins in previously-activated CD8+ T cells. Overexpression of CAD improves both the cytokine response and proliferation of memory T cells. Overall, our studies reveal a novel and critical role for CAD-induced pyrimidine synthesis and ribosomal biogenesis in promoting the rapid recall response characteristic of memory T cells. One Sentence SummaryPyrimidine synthesis fuels ribosomal biogenesis to facilitate rapid recall responses in CD8+ T cells

immunology↗

bioRxiv2021

Transcriptional integration of distinct microbial and nutritional signals by the small intestinal epithelium

To preserve its physiologic functions, the intestine must interpret and adapt to complex combinations of stimuli from dietary and microbial sources. However, the transcriptional strategies by which the intestinal epithelium integrates and adapts to dietary and microbial information remains unresolved. We compared adult mice reared germ free (GF) or conventionalized with a microbiota (CV) either fed normally or after a single high-fat meal (HFM). Jejunal epithelium preparations were queried using genomewide assays for RNA-seq, the activating histone mark H3K27ac ChIP-seq, and ChIP-seq of the microbially-responsive transcription factor HNF4A. We identified distinct nutritional and microbial responses at certain genes, but also apparent simultaneous influence of both stimuli at many other loci and regulatory regions. Increased expression levels and H3K27ac enrichment following HFM at a subset of these sites was dependent on microbial status. H3K27ac sites that were preferentially increased by HFM in the presence of microbes neighbor lipid anabolism and proliferation genes as well as intestinal stem cell (ISC) markers, were usually active only in ISCs, and were not HNF4A targets. In contrast, H3K27ac sites that were preferentially increased by HFM in the absence of microbes neighbored targets of the nuclear receptor and energy homeostasis regulator PPARA, were frequently accessible only in enterocytes, and were HNF4A bound. These results reveal that HNF4A supports a differentiated enterocyte and FAO program in GF, and that suppression of HNF4A by the combination of microbes and HFM may result in preferential activation of IEC proliferation programs. Microbial and nutritional responses are therefore integrated with some of the same transcriptional programs that regulate intestinal proliferation and differentiation.

genomics↗

bioRxiv2021

Tropical-temperate dichotomy falls apart in the Asian Palmate Group of Araliaceae

PREMISEThe use of climatic data on phylogenetic studies has greatly increased in the last decades. High-quality spatial data and accurate climatic information are essential to minimize errors in the climatic reconstructions to the past. However, despite the huge amount of already available biodiversity digital information, the process of compiling, cleaning, and comparing spatial data from different open data sources is a time-consuming task that sometimes ends up with low-quality geographical information. For this reason, researchers often resort qualitative approximations among which World bioclimatic classification systems or the experts criteria are the most used. Our aim is to evaluate the climatic characterization of the genera of the Asian Palmate Group (AsPG) of the ginseng family (Araliaceae), one of the classical examples of tropical-temperate plant families. METHODSWe compiled a curated worldwide spatial database of the AsPG genera. We then created five raster layers representing bioclimatic regionalizations of the World. Finally, we crossed the database with the layers to characterize the AsPG genera. RESULTSWe found large disagreement in the climatic characterization of genera among regionalizations and little support for the tropical-temperate dichotomy. Both results are attributed to the complexity of delimiting tropical, subtropical and temperate climates in the World and to the distribution of the study group in regions with transitional climatic conditions. CONCLUSIONSThe complexity in the climatic classification of this classical example tropical-temperate dichotomy, calls for a general revision in other families. In fact, we claim that to properly evaluate tropical-temperate transitions we cannot ignore the complexity of distribution ranges.

plant biology↗

bioRxiv2021

Phylogenomic analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving the diversifications, with insights into the complex biogeographic history in the Northern Hemisphere

Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, hundreds of single-copy nuclear (SCN) genes (785) and complete plastomes (75) were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, it was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event best explains the cytonuclear discordance that occurred in the Eocene in western North America. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. We detected one deep hybridization event (Malus doumeri) involving the ancestor of pome-bearing species and Docynia delavayi, and one recent hybridization event (Malus coronaria) between M. sieversii and a combined clade of M. ioensis and M. angustifolia. Furthermore, our historical biogeographic analysis combining living and fossil species supported a widespread East Asian-western North American origin of Malus s.l., followed by a series of extinction events in the Eocene in northern East Aisa and western North America. This study provides a valuable evolutionary framework for the breeding and crop improvement of apples and their close relatives.

evolutionary biology↗

bioRxiv2021

{micro}-Theraphotoxin-Pn3a inhibition of Cav3.3 channels reveals a novel isoform-selective drug binding site

Low voltage-activated calcium currents are mediated by T-type calcium channels CaV3.1, CaV3.2, and CaV3.3, which modulate a variety of physiological processes including sleep, cardiac pace-making, pain, and epilepsy. CaV3 isoforms biophysical properties, overlapping expression and lack of subtype-selective pharmacology hinder the determination of their specific physiological roles in health and disease. Notably, CaV3.3s contribution to normal and pathophysiological function has remained largely unexplored. We have identified Pn3a as the first subtype-selective spider venom peptide inhibitor of CaV3.3, with >100-fold lower potency against the other T-type isoforms. Pn3a modifies CaV3.3 gating through a depolarizing shift in the voltage dependence of activation thus decreasing CaV3.3-mediated currents in the normal range of activation potentials. Paddle chimeras of KV1.7 channels bearing voltage sensor sequences from all four CaV3.3 domains revealed preferential binding of Pn3a to the S3-S4 region of domain II (CaV3.3DII). This novel T-type channel pharmacological site was explored through computational docking simulations of Pn3a into all T-type channel isoforms highlighting it as subtype-specific pharmacophore with therapeutic potential. This research expands our understanding of T-type calcium channel pharmacology and supports the suitability of Pn3a as a molecular tool in the study of the physiological roles of CaV3.3 channels.

pharmacology and toxicology↗

bioRxiv2021

Ancient genomes redate the extinction of Sussemionus, a subgenus of Equus, to late Holocene

The exceptionally-rich fossil record available for the equid family has provided textbook examples of macroevolutionary changes. Horses, asses and zebras represent three extant subgenus of Equus lineage, while the Sussemionus subgenus is another remarkable Equus lineage ranging from North America to Ethiopia in Pleistocene. We sequenced 26 archaeological specimens from northern China in Holocene showing morphological features reminiscent of Equus ovodovi, a species representative of Sussemionus, and further confirmed them as this species by genetic analyses. Thus, we present the first high-quality complete genome of the Sussemionus that we sequenced to 12.0x depth-of-coverage and demonstrate that it survived until [~]3,500 years ago, despite the continued demographic collapse during the Last Glacial Maximum and the great human expansion in East Asia. We also confirmed the Equus phylogenetic tree, and found Sussemionus diverged from the ancestor of non-caballine equids [~]2.3-2.7 Million years ago and admixture events could have taken place between them. Our works suggest the small genetic diversity but not the enhanced inbreeding mainly limited the chances of survival of the species, and illustrates how ancient DNA can inform on extinction dynamics and the long-term resilience of species surviving in cryptic population pockets.

genomics↗

bioRxiv2021

TET1 controls Cxcl1 induction by DNA demethylation and promotes neutrophil recruitment during acute lung injury

Neutrophils are rapidly recruited from the peripheral blood to the inflammatory site to initiate inflammatory response against pathogenic infections. The process to recruit neutrophils must be properly regulated since the abnormal accumulation of neutrophils can cause organ damage and dysfunction. The acute respiratory distress syndrome (ARDS)/acute lung injury (ALI) is a common cause of respiratory failure that is characterized by the infiltration of neutrophils and epithelial integrity disruption. Indeed, recent studies suggest a pathogenic role of neutrophils in the clinic severity of the coronavirus disease 2019 (COVID-19) ARDS. The chemokine CXCL1, which is rapidly induced by inflammatory stimuli, plays a key role in neutrophil influx during lung inflammation. The molecular basis of Cxcl1 induction is not fully understood. Here we report that TET1, a member of the ten eleven translocation (TET) methylcytosine dioxygenase protein family, displays a striking specificity in the regulation of gene expression in macrophages. RNA sequencing (RNA-seq) analysis showed that Tet1 disruption significantly altered the expression of only 48 genes that include Cxcl1 and several other genes known to be important for cell migration and trafficking in bone marrow derived macrophages (BMDMs) in response to LPS stimulation. TET1 regulates the induction of Cxcl1 by facilitating the DNA demethylation of the Cxcl1 promoter. In Tet1-/- mice, the induction of Cxcl1 was suppressed, resulting in defective neutrophil recruitment to the lung during LPS-induced acute lung injury. Our results identify a novel epigenetic mechanism that selectively controls Cxcl1 induction and neutrophil recruitment during acute lung injury. Key PointsO_LITET1 has a striking specificity in macrophage gene regulation and controls Cxcl1 induction by inflammatory stimuli via DNA demethylation C_LIO_LINeutrophil recruitment is defective in Tet1 deficient mice during acute lung injury C_LI

immunology↗

bioRxiv2021

Transcriptome-wide association study in UK Biobank Europeans identifies associations with blood cell traits.

Previous genome-wide association studies (GWAS) of hematological traits have identified over 10,000 distinct trait-specific risk loci, but the underlying causal mechanisms at these loci remain incompletely characterized. We performed a transcriptome-wide association study (TWAS) of 29 hematological traits in 399,835 UK Biobank (UKB) participants of European ancestry using gene expression prediction models trained from whole blood RNA-seq data in 922 individuals. We discovered 557 TWAS signals associated with hematological traits distinct from previously discovered GWAS variants, including 10 completely novel gene-trait pairs corresponding to 9 unique genes. Among the 557 associations, 301 were available for replication in a cohort of 141,286 participants of European ancestry from the Million Veteran Program (MVP). Of these 301 associations, 199 replicated at a nominal threshold ( = 0.05) and 108 replicated at a strict Bonferroni adjusted threshold ( = 0.05/301). Using our TWAS results, we systematically assigned 4,261 out of 16,900 previously identified hematological trait GWAS variants to putative target genes. Compared to coloc, our TWAS results show reduced specificity and increased sensitivity to assign variants to target genes.

genetics↗

bioRxiv2021

A phylotranscriptome study using silica gel-dried leaf tissues produces an updated robust phylogeny of Ranunculaceae

The utility of transcriptome data in plant phylogenetics has gained popularity in recent years. However, because RNA degrades much more easily than DNA, the logistics of obtaining fresh tissues has become a major limiting factor for widely applying this method. Here, we used Ranunculaceae to test whether silica-dried plant tissues could be used for RNA extraction and subsequent phylogenomic studies. We sequenced 27 transcriptomes, 21 from silica gel-dried (SD-samples) and six from liquid nitrogen-preserved (LN-samples) leaf tissues, and downloaded 27 additional transcriptomes from GenBank. Our results showed that although the LN-samples produced slightly better reads than the SD-samples, there were no significant differences in RNA quality and quantity, assembled contig lengths and numbers, and BUSCO comparisons between two treatments. Using this data, we conducted phylogenomic analyses, including concatenated- and coalescent-based phylogenetic reconstruction, molecular dating, coalescent simulation, phylogenetic network estimation, and whole genome duplication (WGD) inference. The resulting phylogeny was consistent with previous studies with higher resolution and statistical support. The 11 core Ranunculaceae tribes grouped into two chromosome type clades (T- and R-types), with high support. Discordance among gene trees is likely due to hybridization and introgression, ancient genetic polymorphism and incomplete lineage sorting. Our results strongly support one ancient hybridization event within the R-type clade and three WGD events in Ranunculales. Evolution of the three Ranunculaceae chromosome types is likely not directly related to WGD events. By clearly resolving the Ranunculaceae phylogeny, we demonstrated that SD-samples can be used for RNA-seq and phylotranscriptomic studies of angiosperms.

evolutionary biology↗

bioRxiv2021

Evolution of a chordate-specific mechanism for myoblast fusion

The size of an animal is determined by the size of its musculoskeletal system. Myoblast fusion is an innovative mechanism that allows for multinucleated muscle fibers to compound the size and strength of individual mononucleated cells. However, the evolutionary history of the control mechanism underlying this important process is currently unknown. The phylum Chordata hosts closely related groups that span distinct myoblast fusion states: no fusion in cephalochordates, restricted fusion and multinucleation in tunicates, and extensive, obligatory fusion in vertebrates. To elucidate how these differences may have evolved, we studied the evolutionary origins and function of membrane-coalescing agents Myomaker and Myomixer in various groups of chordates. Here we report that Myomaker likely arose through gene duplication in the last common ancestor of tunicates and vertebrates, while Myomixer appears to have evolved de novo in early vertebrates. Functional tests revealed an unexpectedly complex evolutionary history of myoblast fusion in chordates. A pre-vertebrate phase of muscle multinucleation driven by Myomaker was followed by the later emergence of Myomixer that enables the highly efficient fusion system of vertebrates. Thus, our findings reveal the evolutionary origins of chordate-specific fusogens and illustrate how new genes can shape the emergence of novel morphogenetic traits and mechanisms.

developmental biology↗

bioRxiv2021

Amino acid-derived quorum sensing molecule alanine on the GIT tolerance of the lactobacillus strains in the co-cultured fermentation model

As the importance of gut microbiota in health is increasingly recognized, the interest in interventions that can modulate the microbiota and its interactions with its host has soared. The survival status of the probiotics in the gastrointestinal environment and the microbial interactions between the LAB have also received considerable attention. In the present research, the gastrointestinal environment tolerance, adhesion ability, and biofilm formation of the lactobacillus strains in the co-culture system were explored, through the real-time fluorescence-based quantitative PCR, UPLC-MS/MS metabolic profiling analysis and Live/Dead(R) BacLight cell staining methods. The results show that the co-culture system can promote the release of signal molecules and can effectively protect the liability of the Lactobacillus acidophilus in the gastrointestinal environment. Meanwhile, amino acid-derived quorum sensing molecule L-alanine (1 %) can effectively enhance the communication of the cells in the complex fermentation model, which leads to the increase of the liability of the L. acidophilus in the gastrointestinal environment. ImportanceThe findings of this study provide a clue to the amino acid-derived metabolites in the communication among cells in the GIT environment, which can enhance the communication of the lactobacillus strains in the complex fermentation model. Meanwhile, the liability of Lactobacillus acidophilus could be enhanced in the co-culture system during the gastrointestinal environment stress with the amino acid-derived quorum sensing (QS) components, and it will shed some light to the application of the amino acid-derived QS molecules in the fermentation stater industry.

microbiology↗

bioRxiv2021

Phylogenomic insights into biogeographic diversification and character evolution of the Sino-Japanese disjunctive Diabelia (Caprifoliaceae)

Understanding biological diversity and the mechanisms of the Sino-Japanese disjunctions are major challenges in eastern Asia biogeography. The Sino-Japanese flora has been broadly studied as an ideal model for plant phylogeography. Diabelia (Caprifoliaceae) is an East Asian genus, with a disjunctive distribution across the Sino-Japanese region. However, relationships within Diabelia remain elusive. In this study, we reconstructed the phylogeny of Diabelia and inferred historical biogeography and evolutionary patterns based on nuclear and plastid sequences from target enrichment and genome skimming approaches, respectively. We found that the main clades within Diabelia were discordant between nuclear and plastid trees. Both nuclear and plastid phylogenetic analyses supported five main clades: D. serrata, D. tetrasepala, D. sanguinea, D. spathulata var. stenophylla and D. spathulata var. spathulata. Species network analyses revealed that Diabelia tetrasepala is likely the result of a hybridization event. Divergence time estimation and ancestral area reconstructions showed that Diabelia originated in Japan during the early Miocene, with subsequent vicariance and dispersal events between Japan and Korea, and between Japan and China. Overall, our results support the division of Diabelia into five main clades and the recognition of five species in the genus. This research provides new insights in the species delimitation and speciation processes of taxonomically complex lineages such as Diabelia.

evolutionary biology↗