The tea plant CsLHT1 and CsLHT6 transporters take up amino acids, as a nitrogen source, from the soil of organic tea plantations

Organic tea is more popular than conventional tea that originates from fertilized plants.Amino acids inorganic soils constitute a substantial pool nitrogen(N)available for plants.However,the amino-acid contents in soils of tea plantations and how tea plants take up these amino acids remain largely unknown.In this study,we show that the amino-acid content in the soil of an organic tea plantation is significantly higher than that of a conventional tea plantation.Glutamate,alanine,valine,and leucine were the most abundant amino acids in the soil of this tea plantation.When 15 N-glutamate was fed to tea plants,it was efficiently absorbed and significantly increased the contents of other amino acids in the roots.We cloned seven CsLHT genes encoding amino-acid transporters and found that the expression of CsLHT1,CsLHT2,and CsLHT6 in the roots significantly increased upon glutamate feeding.Moreover,the expression of CsLHT1 or CsLHT6 in a yeast amino-acid uptake-defective mutant,22Δ10α,enabled growth on media with amino acids constituting the sole N source.Amino-acid uptake assays indicated that CsLHT1 and CsLHT6 are H^(+)-dependent high-and low-affinity amino-acid transporters,respectively.We further demonstrated that CsLHT1 and CsLHT6 are highly expressed in the roots and are localized to the plasma membrane.Moreover,overexpression of CsLHT1 and CsLHT6 in Arabidopsis significantly improved the uptake of exogenously supplied 15 N-glutamate and 15 N-glutamine.Taken together,our findings are consistent with the involvement of CsLHT1 and CsLHT6 in amino-acid uptake from the soil,which is particularly important for tea plants grown inorganic tea plantations.

Reconstruction and Dynamics of the Human Intestinal Microbiome Observed In Situ

The human gut microbiome has primarily been studied through the use of fecal samples,a practice that has generated vital knowledge on the composition and functional capacities of gastrointestinal microbial communities.However,this reliance on fecal materials limits the investigation of microbial dynamics in other locations along the gastrointestinal tract(in situ),and the infrequent availability of fecal samples prevents analysis at finer temporal scales(e.g.,hours).In our study,we utilized colonic transendoscopic enteral tubing,a technology originally developed for fecal microbiota transplantation,to sample the ileocecal microbiome twice daily;metagenomic and metatranscriptomic analyses were then conducted on these samples.A total of 43 ileocecal and 28 urine and fecal samples were collected from five healthy volunteers.The ileocecal and fecal microbiomes,as profiled in the five volunteers,were found to be similar in metagenomic profiling,yet their active genes(metatranscriptome)were found to be highly distinct.Both microbiomes were perturbed after laxative exposure;over time,they exhibited reduced dissimilarity to their pre-treatment state,thereby demonstrating resilience as an innate property of the gut microbiome,although they did not fully recover within our observation time window.Sampling of the ileocecal microbiome during the day and at night revealed the existence of diurnal rhythms in a series of bacterial species and functional pathways,particularly those related to short-chain fatty acid production,such as Propionibacterium acnes and coenzyme A biosynthesis Ⅱ.Autocorrelation analysis and fluctuations decomposition further indicated the significant periodicity of the diurnal oscillations.Metabolomic profiling in the fecal and urine samples mirrored the perturbance and recovery in the gut microbiome,indicating the crucial contribution of the gut microbiome to many key metabolites involved in host health.This study provides novel insights into the human gut microbiome and its inner resilience and diurnal rhythms,as well as the potential consequences of these to the host.

Instability of Nucleic Acids in Airborne Microorganisms under Far Infrared Radiation

Emergence of zoonotic-human pathogens is proven to be a lethal threat to public health, and RNA virus including influenza viruses, severe acute respiratory syndrome coronavirus, middle east respiratory syndrome coronavirus, and COVID-19, plays a pivotal role. As those viruses as airborne microorganisms spread mainly by tiny airborne particles, it is important to de-active those airborne particles before their entry into human bodies. In this study, we investigated the effect of far infrared (FIR) radiation on inhibition of airborne microorganisms. The result confirmed that double stand DNA from airborne microorganisms containing RNA viruses was stable under mild FIR radiation. However, single strand RNA from them was found to be sensitive to FIR radiation, indicating that RNA virus in airborne particles is instable under FIR radiation. Based on this observation, two models on usage of FIR radiation to prevent RNA virus transmission by air and cure RNA virus infection were proposed. Then, this study suggests that FIR radiation has the potential to be a cheap, convenient, and efficient method in clinic to treat RNA virus.

Inaugural Editorial:Seed Biology

Seed is the most important reproductive organ in plant.Since its first emergence approximately 370 million years ago,seed plant had overwhelming advantage to non-seed plants in reproduction,spreading and colonization in terrestrial land.Beside its essential function in the sexual reproduction of plants,seed is the most economically important agricultural product,offering necessity food for human and wildlife,nutritious feed for livestock.Seeds and grains also provide massive amount of raw materials for manufactured goods,such as coffee,starch,and oil.Seeds also play a pivotal role in development of fruits which supplement significant portion of food and nutrition for human and wildlife.

Haem Oxygenase 1 is a potential target for creating etiolated/albino tea plants (Camellia sinensis) with high theanine accumulation

Theanine content is highly correlated with sensory quality and health benefits of tea infusion.The tender shoots of etiolated and albino tea plants contain higher theanine than the normal green tea plants and are valuable materials for high quality green tea processing.However,why these etiolated or albino tea plants can highly accumulate theanine is largely unknown.In this study,we observed an Arabidopsis etiolated mutant hy1–100(mutation in Haem Oxygenase 1,HO1)that accumulated higher levels of glutamine(an analog of theanine).We therefore identified CsHO1 in tea plants and found CsHO1 is conserved in amino acid sequences and subcellular localization with its homologs in other plants.Importantly,CsHO1 expression in the new shoots was much lower in an etiolated tea plants‘Huangkui’and an albino tea plant‘Huangshan Baicha’than that in normal green tea plants.The expression levels of CsHO1 were negatively correlated with theanine contents in these green,etiolated and albino shoots.Moreover,CsHO1 expression levels in various organs and different time points were also negatively correlated with theanine accumulation.The hy1–100 was hypersensitive to high levels of theanine and accumulated more theanine under theanine feeding,and these phenotypes were rescued by the expression of CsHO1 in this mutant.Transient knockdown CsHO1 expression in the new shoots of tea plant using antisense oligonucleotides(asODN)increased theanine accumulation.Collectively,these results demonstrated CsHO1 negatively regulates theanine accumulation in tea plants,and that low expression CsHO1 likely contributes to the theanine accumulation in etiolated/albino tea plants.

Emerging roles and therapeutic potentials of sphingolipids in pathophysiology:emphasis on fatty acyl heterogeneity

Sphingolipids not only exert structural roles in cellular membranes,but also act as signaling molecules in various physiological and pathological processes.A myriad of studies have shown that abnormal levels of sphingolipids and their metabolic enzymes are associated with a variety of human diseases.Moreover,blood sphingolipids can also be used as biomarkers for disease diagnosis.This review summarizes the biosynthesis,metabolism,and pathological roles of sphingolipids,with emphasis on the biosynthesis of ceramide,the precursor for the biosynthesis of complex sphingolipids with different fatty acyl chains.The possibility of using sphingolipids for disease prediction,diagnosis,and treatment is also discussed.Targeting endogenous ceramides and complex sphingolipids along with their specific fatty acyl chain to promote future drug development will also be discussed.

GreenPhos,a universal method for in-depth measurement of plant phosphoproteomes with high quantitative reproducibility

Protein phosphorylation regulates a variety of important cellular and physiological processes in plants.In-depth profiling of plant phosphoproteomes has been more technically challenging than that of animal phosphoproteomes.This is largely due to the need to improve protein extraction efficiency from plant cells,which have a dense cell wall,and to minimize sample loss resulting from the stringent sample clean-up steps required for the removal of a large amount of biomolecules interfering with phosphopeptide purification and mass spectrometry analysis.To this end,we developed a method with a streamlined workflow for highly efficient purification of phosphopeptides from tissues of various green organisms including Arabidopsis,rice,tomato,and Chlamydomonas reinhardtii,enabling in-depth identification with high quantitative reproducibility of about 11000 phosphosites,the greatest depth achieved so far with single liquid chromatography-mass spectrometry(LC-MS)runs operated in a data-dependent acquisition(DDA)mode.The mainstay features of the method are the minimal sample loss achieved through elimination of sample clean-up before protease digestion and of desalting before phosphopeptide enrichment and hence the dramatic increases of time-and cost-effectiveness.The method,named GreenPhos,combined with single-shot LC-MS,enabled in-depth quantitative identification of Arabidopsis phosphoproteins,including differentially phosphorylated spliceosomal proteins,at multiple time points during salt stress and a number of kinase substrate motifs.GreenPhos is expected to serve as a universal method for purification of plant phosphopeptides,which,if samples are further fractionated and analyzed by multiple LC-MS runs,could enable measurement of plant phosphoproteomes with an unprecedented depth using a given mass spectrometry technology.

Erratum to “Lipidome Atlas of the Developing Heart Uncovers Dynamic Membrane Lipid Attributes Underlying Cardiac Structural and Metabolic Maturation”

Main Text In the Research Article“Lipidome Atlas of the Developing Heart Uncovers Dynamic Membrane Lipid Attributes Underlying Cardiac Structural and Metabolic Maturation”[1],there was an error in Fig.2B.The authors mistakenly repeated the chord diagram designated for P7 with that from P1.The figure amendment did not affect the in-text discussion of the figure,which was focused on changes between P0 and P21,and did not alter the conclusion.Figure 2B has now been corrected in the PDF and HTML(full text).

Molecular insights into the transgenerational inheritance of stress memory

There is accumulating evidence to show that environmental stressors can regulate a variety of phenotypes in descendants through germline-mediated epigenetic inheritance. Studies of model organisms exposed to environmental cues(e.g., diet, heat stress, toxins) indicate that altered DNA methylations, histone modifications, or non-coding RNAs in the germ cells are responsible for the transgenerational effects. In addition,it has also become evident that maternal provision could provide a mechanism for the transgenerational inheritance of stress adaptations that result from ancestral environmental cues. However, how the signal of environmentally-induced stress response transmits from the soma to the germline, which may influence offspring fitness, remains largely elusive. Small RNAs could serve as signaling molecules that transmit between tissues and even across generations. Furthermore, a recent study revealed that neuronal mitochondrial perturbations induce a transgenerational induction of the mitochondrial unfolded protein response mediated by a Wnt-dependent increase in mitochondrial DNA levels. Here, we review recent work on the molecular mechanism by which parental experience can affect future generations and the importance of soma-to-germline signaling for transgenerational inheritance.

PRMT5 determines the pattern of polyploidization and prevents liver from cirrhosis and carcinogenesis

Human hepatocellular carcinoma(HCC)occurs almost exclusively in cirrhotic livers.Here,we report that hepatic loss of protein arginine methyltransferase 5(PRMT5)in mice is sufficient to cause cirrhosis and HCC in a clinically relevant way.Furthermore,pathological polyploidization induced by hepatic loss of PRMT5 promotes liver cirrhosis and hepatic tumorigenesis in aged liver.The loss of PRMT5 leads to hyperaccumulation of P21 and endoreplication-dependent formation of pathological mono-nuclear polyploid hepatocytes.PRMT5 and symmetric dimethylation at histone H4 arginine 3(H4R3me2s)directly associate with chromatin of P21 to suppress its transcription.More importantly,loss of P21 rescues the pathological mono-nuclear polyploidy and prevents PRMT5-deficiency-induced liver cirrhosis and HCC.Thus,our results indicate that PRMT5-mediated symmetric dimethylation at histone H4 arginine 3(H4R3me2s)is crucial for preventing pathological polyploidization,liver cirrhosis and tumorigenesis in mouse liver.

Temporospatial inhibition of Erk signaling is required for lymphatic valve formation

Intraluminal lymphatic valves(LVs)and lymphovenous valves(LVs)are critical to ensure the unidirectional flow of lymphatic fluid.Morphological abnormalities in these valves always cause lymph or blood reflux,and result in lymphedema.

Erratum to“Nucleolar histone deacetylases HDT1,HDT2,and HDT3 regulate plant reproductive development”[Journal of Genetics and Genomics(2022)49,30–39]

This erratum clarifies information in the article“Nucleolar histone deacetylases HDT1,HDT2,and HDT3 regulate plant reproductive development”by Luo et al.(2021).In the section on“Phenotype of hdt mutants”,the T-DNA insertional knockdown mutant for HDT2(hdt2,salk_1247_A02)should be“Sail_1247_A02”in the main text and Fig.3A.

AB013.Tear lipidome and its implications

The tear film covers the anterior eye and the precise balance of its various constituting components is critical for maintaining ocular health.The composition of the tear film amphiphilic lipid sublayer,in particular,has largely remained a matter of contention.The limiting concentrations of lipid amphiphiles in tears have also posed considerable challenges to their detection and accurate quantitation.Using systematic and sensitive lipidomic approaches,we reported the most comprehensive human tear lipidome to date;and conferred novel insights to the compositional details of the existent tear film model,in particular the disputable amphiphilic lipid sublayer constituents,by demonstrating the presence of cholesteryl sulfate,O-acyl-ω-hydroxy fatty acids,and various sphingolipids and phospholipids in tears.Lipidomic analysis of human tear fluid from patients with various subtypes of dry eye syndrome(DES)revealed structure-specific lipid alterations in DES,which could potentially serve as unifying indicators of disease symptoms and signs.The meibomian glands constitute the predominant source of lipid supply to the human tear fluid.Meibomian gland dysfunction(MGD)is a leading cause of evaporative dry eye and ocular discomfort,characterized by an unstable tear film principally attributed to afflicted delivery of lipids to the ocular surface.We investigated the longitudinal tear lipid alterations associated with disease alleviation and symptom improvement in a cohort of MGD patients undergoing eyelid-warming treatment for 12 weeks.Our preliminary data indicated that excess ocular surface phospholipase activity detrimental to tear film stability could be alleviated by eyelid warming alone without application of steroids and identify tear OAHFAs as suitable markers to monitor treatment response in MGD.

Visualization of in vivo cell-cell contact in the present and in the past

Cells are specialized to perform diverse functions to support the development and homeostasis of a multicellular organism.Cell-cell contact can mediate important communications between cells to coordinate cellular activities,which are essential in multiple biological processes to maintain tissue structure and function(Armingol et al.,2021).In vivo cell-cell contact remains largely unexplored.Recently,Zhang et al.(2022)report a comprehensive toolbox to label ongoing cell-cell contact or to trace the historical cell-cell contact in vivo.

A Spacetime Odyssey of Neural Progenitors to Generate Neuronal Diversity

To understand how the nervous system develops from a small pool of progenitors during early embryonic development,it is fundamentally important to identify the diversity of neuronal subtypes,decode the origin of neuronal diversity,and uncover the principles governing neuronal specification across different regions.Recent single-cell analyses have systematically identified neuronal diversity at unprecedented scale and speed,leaving the deconstruction of spatiotemporal mechanisms for generating neuronal diversity an imperative and paramount challenge.In this review,we highlight three distinct strategies deployed by neural progenitors to produce diverse neuronal subtypes,including predetermined,stochastic,and cascade diversifying models,and elaborate how these strategies are implemented in distinct regions such as the neocortex,spinal cord,retina,and hypothalamus.Importantly,the identity of neural progenitors is defined by their spatial position and temporal patterning factors,and each type of progenitor cell gives rise to distinguishable cohorts of neuronal subtypes.Microenvironmental cues,spontaneous activity,and connectional pattern further reshape and diversify the fate of unspecialized neurons in particular regions.The illumination of how neuronal diversity is generated will pave the way for producing specific brain organoids to model human disease and desired neuronal subtypes for cell therapy,as well as understanding the organization of functional neural circuits and the evolution of the nervous system.

Transplantation of neural stem progenitor cells from different sources for severe spinal cord injury repair in rat

Neural stem progenitor cell(NSPC)transplantation has been regarded as a promising therapeutic method for spinal cord injury(SCI)repair.However,different NSPCs may have different therapeutic effects,and it is therefore important to identify the optimal NSPC type.In our study,we compared the transcriptomes of human fetal brain-derived NSPCs(BNSPCs),spinal cord-derived NSPCs(SCNSPCs)and H9 embryonic stem-cell derived NSPCs(H9-NSPCs)in vitro and subsequently we transplanted each NSPC type on a collagen scaffold into a T8-9 complete SCI rat model in vivo.In vitro data showed that SCNSPCs had more highly expressed genes involved in nerve-related functions than the other two cell types.In vivo,compared with BNSPCs and H9-NSPCs,SCNSPCs exhibited the best therapeutic effects;in fact,SCNSPCs facilitated electrophysiological and hindlimb functional recovery.This study demonstrates that SCNSPCs may be an appropriate candidate cell type for SCI repair,which is of great clinical significance.

Corrigendum to“Actin polymerization induces mitochondrial distribution during collective cell migration”[Journal of Genetics and Genomics(2023)50 46-49]

This erratum clarifies information in the Letter to the Editor“Actin polymerization induces mitochondrial distribution during collective cell migration”by Qu et al.(2023).In the section for the list of author names,“Chen Qu,Yating Kan,Hui Zuo,Mengqi Wu,Zhixiang Dong,Xinyi Wang,Qing Zhang,Heng Wang,Dou Wang,Jiong Chen”should be“Chen Qu,Yating Kan,Xinyi Wang,Hui Zuo,Mengqi Wu,Zhixiang Dong,Qing Zhang,Heng Wang,Dou Wang,Jiong Chen”.

WDR62-deficiency Causes Autism-like Behaviors Independent of Microcephaly in Mice

Brain size abnormality is correlated with an increased frequency of autism spectrum disorder(ASD)in offspring.Genetic analysis indicates that heterozygous mutations of the WD repeat domain 62(WDR62)are associated with ASD.However,biological evidence is still lacking.Our study showed that Wdr62 knockout(KO)led to reduced brain size with impaired learning and memory,as well as ASD-like behaviors in mice.Interestingly,Wdr62 Nex-cKO mice(depletion of WDR62 in differentiated neurons)had a largely normal brain size but with aberrant social interactions and repetitive behaviors.WDR62 regulated dendritic spinogenesis and excitatory synaptic transmission in cortical pyramidal neurons.Finally,we revealed that retinoic acid gavages significantly alleviated ASD-like behaviors in mice with WDR62 haploinsufficiency,probably by complementing the expression of ASD and synapse-related genes.Our findings provide a new perspective on the relationship between the microcephaly gene WDR62 and ASD etiology that will benefit clinical diagnosis and intervention of ASD.

Comprehensive analysis of mRNA poly(A)tails by PAIso-seq2

Dear Editor,Poly(A)tails are added to the 3’-end of most mRNAs(Colgan and Manley,1997;Yu and Kim,2020).The regulatory roles of poly(A)tails have long been underestimated due to technical difficulties in analyzing homopolymers(Chang et al.,2014;Subtelny et al.,2014).Several methods were recently developed to accurately measure their length(Chang et al.,2014;Legnini et al.,2019;Liu et al.,2019;Liu et al.

Lipidome Atlas of the Developing Heart Uncovers Dynamic Membrane Lipid Attributes Underlying Cardiac Structural and Metabolic Maturation

Precise metabolic rewiring during heart organogenesis underlies normal cardiac development.Herein,we utilized high-coverage,quantitative lipidomic approaches to construct lipidomic atlases of whole hearts(861 lipids;31 classes)and mitochondria(587 lipids;27 classes)across prenatal and postnatal developmental stages in mice.We uncovered the progressive formation of docosahexaenoyl-phospholipids and enhanced remodeling of C18:2,C20:3,and C20:4 fatty acyl moieties into cardiolipins as cardiac development progresses.A preferential flow of ceramides toward sphingomyelin biosynthesis over complex glycosphingolipid formation was also noted.Using maSigPro and GPclust algorithms,we identified a repertoire of 448 developmentally dynamic lipids and mapped their expression patterns to a library of 550 biologically relevant developmentally dynamic genes.Our combinatorial transcriptomics and lipidomics approaches identified Hadha,Lclat1,and Lpcat3 as candidate molecular drivers governing the dynamic remodeling of cardiolipins and phospholipids,respectively,in heart development.Our analyses revealed that postnatal cardiolipin remodeling in the heart constitutes a biphasic process,which first accumulates polyunsaturated C78-cardiolipins prior to tetralinoleoyl cardiolipin forming the predominant species.Multiomics analyses supplemented with transmission electron microscopy imaging uncovered enhanced mitochondria–lipid droplet contacts mediated by perilipin-5.Our combinatorial analyses of multiomics data uncovered an association between mitochondrial-resident,docosahexaenoic acid-phospholipids and messenger RNA levels of proton-transporting adenosine triphosphate synthases on inner mitochondrial membranes,which adds credence to the membrane pacemaker theory of metabolism.The current findings offer lipid-centric biological insights potentially important to understanding the molecular basis of cardiac metabolic flexibility and disease pathology.