Biology subjects

Liu, L.

Publications and source records attributed to Liu, L..

At least 721 records · Page 40Linked to original sources

bioRxiv2021

Predicting the current and future distribution of four original plants of Gentianae Macrophyllae Radix in China under climate change scenarios

The wild resources of the four original plants (Gentiana crasicaulis Duthie ex Burk, Gentiana daurica Fisch, Gentiana straminea Maxim, and Gentiana macrophylla Pall) of Gentianae Macrophyllae Radix are becoming exhausted. Predicting the distribution under current and future climate scenarios is of significance for the sustainable utilization of resources and ecological protection. In this study, we constructed four species distribution models (SDMs) combining species distribution informations, 19 bioclimatic variables, and the maximum entropy (MaxEnt) model. The results showed that these 4 plants prefer a cool and humid climate. Under the future climate scenarios, the areas of the highly suitable habitats for Gentiana crasicaulis Duthie ex Burk and Gentiana daurica Fisch were likely to decrease, while Gentiana straminea Maxim was likely to expand, and Gentiana macrophylla Pall was less affected. In addition, the centroids of the highly suitable habitats for the four species shifted north or west. Most notably, most of the highly suitable habitats for the four species remained unchanged, which would be the preferred area for semi-artificial cultivation. The above information in this study would contribute to the development of reasonable strategies to reduce the impact of climate change on the four original plants.

ecology↗

bioRxiv2021

Large field of view-spatially resolved transcriptomics at nanoscale resolution

Spatially resolved transcriptomic technologies are promising tools to study cell fate decisions in a physical microenvironment, which is fundamental for enhancing our knowledge of mammalian development. However, the imbalance between resolution, transcript capture and field of view of current methodologies precludes their systematic application to analyze relatively large and three-dimensional mid- and late-gestation mammalian embryos. Here, we combined DNA nanoball (DNB) patterned arrays and tissue RNA capture to create SpaTial Enhanced REsolution Omics-sequencing (Stereo-seq). This approach allows transcriptomic profiling of large histological sections with high resolution and sensitivity. We have applied Stereo-seq to study the kinetics and directionality of transcriptional variation in a time course of mouse organogenesis. We used this information to gain insight into the molecular basis of regional specification, neuronal migration and differentiation in the developing brain. Furthermore, we mapped the expression of a panel of developmental disease-related loci on our global transcriptomic maps to define the spatiotemporal windows of tissue vulnerability. Our panoramic atlas constitutes an essential resource to investigate longstanding questions concerning normal and abnormal mammalian development.

cell biology↗

bioRxiv2021

Brassinosteroid signaling component SlBES1 promotes tomato fruit softening through transcriptional repression of PMEU1

Firmness is one of the most important factors that affect postharvest properties of tomato fruit. However, the regulatory mechanism underlying firmness formation in tomato fruit is poorly understood. Here, we report a novel role of SlBES1, a transcriptional factor (TF) mediating brassinosteroid (BR) signaling, in tomato fruit softening. We first found that SlBES1 promotes fruit softening during tomato fruit ripening and postharvest storage. RNA-seq analysis suggested that PMEU1, which encodes a pectin de-methylesterification protein, might participate in SlBES1-mediated fruit softening. Biochemical and immunofluorescence assays in SlBES1 transgenic fruits indicated that SlBES1 inhibited PMEU1-related pectin de-methylesterification. Further molecular and genetic evidence verified that SlBES1 directly binds to the E-box in the promoter of PMEU1 to repress its expression, leading to the softening of the tomato fruits. Loss-of-function SlBES1 mutant generated by CRISPR/cas9 showed firmer fruits and longer shelf life during postharvest storage without the color, size and nutritional quality alteration. Collectively, our results indicated the potential of manipulating SlBES1 to regulate fruit firmness via transcriptional inhibition of PMEU1 without negative consequence on visual and nutrition quality.

plant biology↗

bioRxiv2021

Individual differences in representational similarity of first and second languages in the bilingual brain

Current theories of bilingualism disagree on the extent to which separate brain regions are used to maintain or process ones first and second language. The present study took a novel multivariate approach to address this question. We examined whether bilinguals maintain distinct neural representations of two languages; specifically, we tested whether brain areas that are involved in processing word meaning in either language are reliably representing each language differently, and whether language representation is influenced by individual differences in proficiency level and age of acquisition of L2. Thirty-one English-Mandarin bilingual adults performed a picture-word matching task in both languages. We then used representational similarity analysis to examine which brain regions reliably showed different patterns of activity for each language. As a group, there were no regions that reliably represented languages distinctly. However, both proficiency and age of acquisition predicted dissimilarity between language representations in several brain areas within the language network as well as several regions of the ventral visual pathway, demonstrating that top-down language knowledge and individual language experience shapes concept representation in the processing stream. The results support the model of an integrated language system in bilinguals, along with a novel description of how representations for each language change with proficiency level and L2 age of acquisition.

neuroscience↗

bioRxiv2021

Accurate bulk quantitation of droplet digital PCR

Droplet digital PCR provides superior accuracy in nucleic acid quantitation. The requirement of microfluidics to generate and analyze the emulsions, however, is a barrier to its adoption, particularly in low resource or clinical settings. Here, we report a novel method to prepare ddPCR droplets by vortexing and readout the results by bulk analysis of recovered amplicons. We demonstrate the approach by accurately quantitating SARS-CoV-2 sequences using entirely bulk processing and no microfluidics. Our approach for quantitating reactions should extend to all digital assays that generate amplicons, including digital PCR and LAMP conducted in droplets, microchambers, or nanoliter wells. More broadly, our approach combines important attributes of ddPCR, including enhanced accuracy and robustness to inhibition, with the high-volume sample processing ability of quantitative PCR.

molecular biology↗

bioRxiv2021

Mitotic R-loops direct Aurora b kinase to maintain centromeric cohesion

Recent work has shown that R-loops exist at mitotic centromeres, but the function of these R-loops is not well understood. Here, we report that mitotic R-loops arise in distinct locations from those formed during interphase. They accumulate on chromosome arms in prophase, where they are quickly resolved and continue to be produced at repetitive sequences including centromeres during a mitotic stall. Aurora B kinase activity is required to resolve R-loops during prophase and R-loops promote the localization of the Chromosome Passenger Complex (CPC) to the inner centromere. CPC purified from mitotic chromosomes interacts with thirty-two proteins involved with R-loop biology. One of these, the RNA regulator RBMX, controls Aurora B localization and activity in vivo. Perturbations in R-loop homeostasis or RBMX cause defects in the maintenance of centromeric cohesion due to the mislocalization of the CPC. We conclude that R-loops are generated by mitotic processes in repetitive DNA sequences, they play important roles in mitotic fidelity, and we have identified a set of mitotic R-loop regulators including the CPC and RBMX that will enable future studies of mitotic R-loops.

cell biology↗

bioRxiv2021

Modular basis for potent SARS-CoV-2 neutralization by a prevalent VH1-2-derived antibody class

Antibodies with heavy chains that derive from the VH1-2 gene constitute some of the most potent SARS-CoV-2-neutralizing antibodies yet identified. To provide insight into whether these genetic similarities inform common modes of recognition, we determined structures of the SARS-CoV-2 spike in complex with three VH1-2-derived antibodies: 2-15, 2-43, and H4. All three utilized VH1-2-encoded motifs to recognize the receptor-binding domain (RBD), with heavy chain N53I enhancing binding and light chain tyrosines recognizing F486RBD. Despite these similarities, class members bound both RBD-up and -down conformations of the spike, with a subset of antibodies utilizing elongated CDRH3s to recognize glycan N343 on a neighboring RBD - a quaternary interaction accommodated by an increase in RBD separation of up to 12 [A]. The VH1-2-antibody class thus utilizes modular recognition encoded by modular genetic elements to effect potent neutralization, with VH-gene component specifying recognition of RBD and CDRH3 component specifying quaternary interactions. HighlightsO_LIDetermine structures of VH1-2-derived antibodies 2-43, 2-15, and H4 in complex with SARS-CoV-2 spike C_LIO_LIDefine a multi-donor VH1-2-antibody class with modular components for RBD and quaternary recognition C_LIO_LIReveal structural basis of RBD-up and RBD-down recognition within the class C_LIO_LIShow somatic hypermutations and avidity to be critical for potency C_LIO_LIDelineate changes in spike conformation induced by CDRH3-mediated quaternary recognition C_LI

immunology↗

bioRxiv2021

Petabyte-Scale Multi-Morphometry of Single Neurons for Whole Brains

Recent advances in neuroscience make the extraction of full neuronal morphology at whole brain dataset available. To produce quality morphometry at large scale, it is highly desirable but extremely challenging to efficiently handle petabyte-scale high-resolution whole brain imaging database. Here, we developed a multi-level method to produce high quality somatic, dendritic, axonal, and potential synaptic morphometry, which was made possible by utilizing necessary petabyte hardware and software platform to optimize both the data and workflow management. Our method also boosts data sharing and remote collaborative validation. We highlight a petabyte application dataset involving 62 whole mouse brains, from which we identified 50,233 somata of individual neurons, profiled the dendrites of 11,322 neurons, reconstructed the full 3-D morphology of more than one thousand neurons including their dendrites and full axons, and detected million scale putative synaptic sites derived from axonal boutons. Analysis and simulation of these data indicate the promise of this approach for modern large-scale morphology applications.

neuroscience↗

bioRxiv2021

All-Flesh Tomato Regulated by Reduced Dosage of AFF Provides New Insights into Berry Fruit Evolution

The formation of locule gel is not only an important developmental process in tomato but also a typical characteristic of berry fruit. In this study, we collected a tomato material that produces all-flesh fruits (AFF), whose locule tissue remains in a solid state during fruit development. We built genetic populations to fine map the causal gene of AFF trait, investigate the function of AFF gene, and identified it as the causal locus conferring the locule gel formation. We determined the causal mutation as a 416-bp deletion that occurred in the promoter region of AFF, which reduces the expression dosage of AFF. The 416-bp deleted sequence has a high level of conservation among closely related Solanaceae species, as well as in the tomato population. The activity of the 416-bp deletion in down-regulating gene expression was further verified by the relative activity in a luciferase experiment. Furthermore, with the BC6 NIL materials, we reveal that the reduced expression dosage of AFF does not impact the normal development of seeds, while produces non-liquefied locule tissue, which is distinct from that of the normal tomatoes in terms of metabolic components. Based on these findings, we propose that the AFF gene is the core node in locule tissue liquefaction, whose function cannot be compensated by its paralogs TAG1, TAGL1, or TAGL11. Our findings provide clues to investigate fruit type differentiation among Solanaceae crops, and also contributes to the breeding application of all flesh fruit tomatoes for the tomato processing industry. One Sentence SummaryThe sequence deletion that occurred in the cis-regulatory region of AFF--the core node of locule tissue liquefaction determined here--reduced its expression dosage, and produced all flesh fruit tomato.

plant biology↗

bioRxiv2021

Paired heavy and light chain signatures contribute to potent SARS-CoV-2 neutralization in public antibody responses

Understanding protective mechanisms of antibody recognition can inform vaccine and therapeutic strategies against SARS-CoV-2. We discovered a new antibody, 910-30, that targets the SARS-CoV-2 ACE2 receptor binding site as a member of a public antibody response encoded by IGHV3-53/IGHV3-66 genes. We performed sequence and structural analyses to explore how antibody features correlate with SARS-CoV-2 neutralization. Cryo-EM structures of 910-30 bound to the SARS-CoV-2 spike trimer revealed its binding interactions and ability to disassemble spike. Despite heavy chain sequence similarity, biophysical analyses of IGHV3-53/3-66 antibodies highlighted the importance of native heavy:light pairings for ACE2 binding competition and for SARS-CoV-2 neutralization. We defined paired heavy:light sequence signatures and determined antibody precursor prevalence to be ~1 in 44,000 human B cells, consistent with public antibody identification in several convalescent COVID-19 patients. These data reveal key structural and functional neutralization features in the IGHV3-53/3-66 public antibody class to accelerate antibody-based medical interventions against SARS-CoV-2. HighlightsO_LIA molecular study of IGHV3-53/3-66 public antibody responses reveals critical heavy and light chain features for potent neutralization C_LIO_LICryo-EM analyses detail the structure of a novel public antibody class member, antibody 910-30, in complex with SARS-CoV-2 spike trimer C_LIO_LICryo-EM data reveal that 910-30 can both bind assembled trimer and can disassemble the SARS-CoV-2 spike C_LIO_LISequence-structure-function signatures defined for IGHV3-53/3-66 class antibodies including both heavy and light chains C_LIO_LIIGHV3-53/3-66 class precursors have a prevalence of 1:44,000 B cells in healthy human antibody repertoires C_LI

immunology↗

bioRxiv2020

Humans use minimum cost movements in a whole-body task

Humans have elegant bodies that allow gymnastics, piano playing, and tool use, but understanding how they do this in detail is difficult because their musculoskeletal systems are extraordinarily complicated. Nonetheless, common movements like walking and reaching can be stereotypical, and a very large number of studies have shown their movement cost a major factor. In contrast, one might think that general movements are very individuated and intractable, but a recent study has shown that in an arbitrary set of whole-body movements used to trace large-scale closed curves, near-identical posture sequences were chosen across different subjects, both in the average trajectories of the bodys limbs and in the variance within trajectories. The commonalities in that result motivate explanations for its generality. One possibility could be that humans also choose trajectories that are economical in energetic cost. To test this hypothesis, we situate the tracing data within a fifty degree of freedom dynamic model of the human skeleton that allows the computation of movement cost. Comparing the model movement cost data from nominal tracings against various perturbed tracings shows that the latter are more energetically expensive, inferring that the original traces were chosen on the basis of minimum cost.

systems biology↗

bioRxiv2020

An Ultrasensitive Biosensor for Quantifying the Interaction of SARS-CoV-2 and Its Receptor ACE2 in Cells and in vitro

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is currently spreading and mutating with increasing speed worldwide. Therefore, there is an urgent need for a simple, sensitive, and high-throughput (HTP) assay to quantify virus-host interaction in order to quickly evaluate infectious ability of mutant virus and develop or validate virus-inhibiting drugs. Here we have developed an ultrasensitive bioluminescent biosensor to evaluate virus-cell interaction by quantifying the interaction between SARS-CoV-2 receptor binding domain (RBD) and its cellular receptor angiotensin-converting enzyme 2 (ACE2) both in living cells and in vitro. We have successfully used this novel biosensor to analyze SARS-CoV-2 RBD mutants, and evaluated candidate small molecules (SMs), antibodies, and peptides that may block RBD:ACE2 interaction. This simple, rapid and HTP biosensor tool will significantly expedite detection of viral mutants and anti-COVID-19 drug discovery processes.

biochemistry↗

bioRxiv2020

ADH5-mediated NO Bioactivity Maintains Metabolic Homeostasis in Brown Adipose Tissue

Brown adipose tissue (BAT) thermogenic activity is tightly regulated by cellular redox status but the molecular mechanisms underlying this regulation are incompletely understood. Protein S-nitrosylation, the nitric oxide-mediated cysteine thiol modification of proteins, plays important roles in cellular redox regulation. Here we show that both diet-induced obesity (DIO) and acute cold exposure elevates protein S-nitrosylation of BAT proteins, including UCP1, to regulate thermogenesis. This effect in BAT is regulated largely by S-nitrosoglutathione reductase (GSNOR, ADH5), a denitrosylase that balances the intracellular nitroso-redox status. Loss of ADH5 specifically in BAT impairs UCP1-dependent thermogenesis during acute cold challenge and worsens metabolic dysfunction during diet-induced obesity. Mechanistically, we demonstrate that Adh5 expression in BAT is controlled by the transcription factor heat shock factor 1 (HSF1) and administration of an HSF1 activator to the BAT of mice with DIO increased Adh5 expression and significantly improved UCP1-mediated mitochondrial respiration. Together, these data demonstrate that ADH5 controls BAT nitroso-redox homeostasis to regulate adipose thermogenesis which may be therapeutically targeted to improve metabolic health. HighlightsO_LIThermogenesis induces protein S-nitrosylation modification in the BAT; C_LIO_LIADH5, a major cellular denitrosylase, is required for maintaining BAT metabolic homeostasis under both overnutrition and cold stress conditions; C_LIO_LIDiet-induced obesity suppresses HSF1-mediated activation of Adh5 in the BAT; C_LIO_LIADH5 overexpression in BAT improves whole-body glucose homeostasis in obesity. C_LI

molecular biology↗

bioRxiv2020

Light-activated tetrazines enable live-cell spatiotemporal control of bioorthogonal reactions

Bioorthogonal ligations encompass coupling chemistries that have considerable utility in living systems.1-3 Among the numerous bioorthogonal chemistries described to date, cycloaddition reactions between tetrazines and strained dienophiles are widely used in proteome, lipid, and glycan labeling due to their extremely rapid kinetics.4,5 In addition, a variety of functional groups can be released after the cycloaddition reaction,6,7 and drug delivery triggered by in vivo tetrazine ligation8 is in human phase I clinical trials.9 While applications of tetrazine ligations are growing in academia and industry, it has so far not been possible to control this chemistry to achieve the high degrees of spatial and temporal precision necessary for modifying mammalian cells with single-cell resolution. Here we demonstrate visible light-activated formation of tetrazines from photocaged dihydrotetrazines, which enables live-cell spatiotemporal control of rapid biorthogonal cycloaddition reactions between tetrazines and dienophiles such as trans-cyclooctenes (TCOs). Photocaged dihydrotetrazines are stable in conditions that normally degrade tetrazines, enabling efficient early-stage incorporation of bioorthogonal handles into biomolecules such as peptides. Photocaged dihydrotetrazines allow the use of non-toxic visible light to trigger tetrazine ligations on live mammalian cells. By tagging reactive phospholipids with fluorophores, we demonstrate modification of HeLa cell membranes with single-cell spatial resolution. Finally, we show that photo-triggered therapy is possible by coupling tetrazine photoactivation with strategies that uncage prodrugs in response to tetrazine ligation, opening up new methods for photopharmacology and precision drug delivery using bioorthogonal chemistry.

biochemistry↗

bioRxiv2020

Reduced listener-speaker neural coupling underlies speech understanding difficulty in older adults

An increasing body of studies have highlighted the importance of listener-speaker neural coupling in successful speech communication. How this mechanism may change with normal aging and the association of this change with age-related decline in speech understanding remain unexplored. In this study, we scanned with fMRI a young and an older speaker telling real-life stories, and then played the audio recordings to groups of young (N = 28, aged 19-27y) and older adults (N = 27, aged 58-75y) during scanning, respectively. The older listeners understood the story worse than the young, and the advancing age of the older listeners was associated with poorer speech understanding. Compared to the young listener-speaker dyads, the older dyads exhibited weaker neural couplings in both linguistic and extra-linguistic areas. Moreover, within the older group, the listeners age was negatively correlated with the overall strength of interbrain coupling, which in turn was associated with poorer speech understanding. These results reveal the deficits of older adults in achieving neural alignment with other brains, which may underlie the age-related decline in speech understanding.

neuroscience↗

bioRxiv2020

A body map of somatic mutagenesis in morphologically normal human tissues

Somatic mutations accumulated in normal tissues are associated with aging and disease. Here, we performed a comprehensive genomic analysis of 1,737 morphologically normal tissue biopsies (~ 600 cells each), mostly from the epithelia, of nine organs from five donors. We found that somatic mutation accumulations and clonal expansions are widespread, although with variable extent, in morphologically normal human tissues. Somatic copy number alterations were rarely detected, except for tissues from esophagus and cardia. Endogenous mutational processes like SBS1 and SBS5 are ubiquitous among normal tissues though exhibiting different relative activities. Exogenous mutational processes like SBS22 were found in different tissues from the same donor. We reconstructed the spatial somatic clonal architecture with sub-millimeter resolution. In epithelial tissues from esophagus and cardia, macroscopic somatic clones expanded to several millimeters were frequently seen, whereas in tissues from colon, rectum, and duodenum somatic clones were microscopic in size and evolved independently. Our study depicted a body map of somatic mutations and clonal expansions from the same individuals, and it revealed that the degree of somatic clonal expansion and enrichment of driver mutations are highly organ specific.

genomics↗

bioRxiv2020

Mechanism and consequences of herpes simplex virus 1-mediated regulation of host mRNA alternative polyadenylation

Eukaryotic gene expression is extensively regulated by cellular stress and pathogen infections. We have previously shown that herpes simplex virus 1 (HSV-1) and several cellular stresses cause widespread disruption of transcription termination (DoTT) of RNA polymerase II (RNAPII) in host genes and that the viral immediate early factor ICP27 plays an important role in HSV-1-induced DoTT. Here, we show that HSV-1 infection also leads to widespread changes in alternative polyadenylation (APA) of host mRNAs. In the majority of cases, polyadenylation shifts to upstream poly(A) sites (PAS), including many intronic PAS. Mechanistically, ICP27 contributes to HSV-1-mediated APA regulation. HSV-1- and ICP27-induced activation of intronic PAS is sequence-dependent and does not involve general inhibition of U1 snRNP. HSV1-induced intronic polyadenylation is accompanied by early termination of RNAPII. Finally, HSV-1-induced mRNAs polyadenylated at intronic PAS are exported into the cytoplasm while APA isoforms with extended 3 UTRs are sequestered in the nuclei, both preventing the expression of the full-length gene products. Together with other recent studies, our results suggest that viral infection and cellular stresses induce a multi-faceted host shutoff response that includes DoTT and changes in APA profiles.

molecular biology↗

bioRxiv2020

Template-independent genome editing and repairing correct frameshift disease in vivo

Frameshift mutation caused by small insertions/deletions (indels) often generate truncated and non-functional proteins, which underlies 22% inherited Mendelian disorders in humans. However, there is no efficient in vivo gene therapy strategies available to date, especially in postmitotic systems. Here, we leveraged the non-homologous end joining (NHEJ) mediated non-random editing profiles to compensate the frameshift mutation in a USH1F mouse model - av3j. After treatment by the selected gRNA, about 50% editing products showed reading-frame restoration, and more than 70% targeted hair cells recovered mechanotransduction. In vivo treatment ameliorated the hearing and balance symptoms in homozygous mutant mice. Furthermore, a scale-up analysis of 114 gRNAs targeting 40 frameshift deafness mutations reveals that 65% loci have at least one gRNA with predicted therapeutic potential. Together, our study demonstrates that the NHEJ-mediated frame restoration is a simple and highly efficient therapeutic strategy for small-indel induced frameshift mutations.

neuroscience↗