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Luo, Z.

Publications and source records attributed to Luo, Z..

At least 145 records · Page 8Linked to original sources

No solid evidence of soil carbon loss under warming in tropical forests along a 3000 m elevation gradient

Soil organic carbon (SOC) decomposition is inherently sensitive to temperature. As such, a big concerning is the potential SOC loss under climatic warming, but field empirical evidences are lacking, particularly in tropical forest soils in which [~]10% of global SOC is stored. Recently Nottingham et al. (2019) assessed the data collected from a novel experiment translocating soils across a 3000 m tropical forest elevation gradient to mimic temperature changes in situ, and concluded that warming caused considerable SOC loss. However, this conclusion was based on a metric with a strong assumption that soil cores translocated to other elevations on average had the same initial SOC content to control soil cores reinstalled at their original elevation. Because of limited replicates (n =3) in the data, an approach ignoring spatial heterogeneity of SOC content may undermine the credibility of the results. Here, we used a nonparametric bootstrap approach to re-analyze the data, explicitly taking data variability into account. Contrary to Nottingham et al. (2019), we found that SOC content did not show significant differences among translocated soils from the same elevation origin. Further looking into six chemical fractions determined by 13C NMR spectroscopy shown that they had similar, insignificant response to translocation-induced temperature changes, which also does not support the conclusion of Nottingham et al (2019) that labile SOC is more sensitive to warming. We concluded that temperature changes did not significantly alter either total SOC content or its six chemical fractions after five years of shift of temperature regimes in tropical forests. This may largely due to thermal adaptation of microbial decomposition and environmental constrains (e.g., low pH) which suppress the effect of temperature changes. Longer term experiment with more sampling replicates are required to maximize the value of soil translocation experiments to address the effect of warming on SOC dynamics.

ecology↗

An RNA degradation complex required for silencing of Polycomb target genes

Polycomb Repressive Complex (PRC) 1 and 2 are histone-modifying and chromatin-binding complexes that are required for silencing of developmental regulatory genes and genes that control cellular proliferation. Their gene silencing functions are thought to involve chromatin compaction and condensate formation but whether other mechanisms contribute to silencing is unknown. Here we show that the rixosome, a conserved RNA degradation complex with roles in ribosomal RNA processing and heterochromatic RNA degradation in fission yeast, associates with human PRC complexes, is recruited to promoters of Polycomb target genes in differentiated cell lines and embryonic stem cells, and is required for efficient silencing of Polycomb target genes. These findings reveal an unanticipated role for RNA degradation in Polycomb-mediated silencing.

molecular biology↗

A novel antiviral lncRNA EDAL shields a T309 O-GlcNAcylation site to promote EZH2 degradation

The central nervous system (CNS) is vulnerable for viral infection, yet few host factors in the CNS are known to defend invasion by neurotropic viruses. We report here that multiple neurotropic viruses, including rabies virus (RABV), vesicular stomatitis virus (VSV), Semliki Forest virus (SFV) and herpes simplex virus 1 (HSV-1), elicit the neuronal expression of a host-encoded lncRNA EDAL. EDAL inhibits the replication of these neurotropic viruses in neuronal cells and RABV infection in mouse brains. EDAL binds to the conserved histone methyltransferase enhancer of zest homolog 2 (EZH2) and specifically causes EZH2 degradation via lysosomes, reducing the cellular H3K27me3 level. The antiviral function of EDAL resides in a 56-nt antiviral substructure through which its 18-nt helix-loop intimately contacts multiple EZH2 sites surrounding T309, a known O-GlcNAcylation site. EDAL positively regulate the transcription of Pcp4l1 encoding a 10 kDa peptide, which inhibits the replication of mutiple neurotropic viruses. Our findings proposed a model in which a neuronal lncRNA can exert an effective antiviral function via blocking a specific O-GlcNAcylation that determines EZH2 lysosomal degradation.

microbiology↗

Reproducibility warning: The curious case of Polyethylene glycol 6000 and spheroid cell culture

In this study we report about the reproducibility of three-dimensional cell culture of floating cell spheroids on PEG6000 treated cell culture dishes. Three-dimensional tumour spheroids or organoids present an interesting test platform for nanoparticulated drug delivery or nanoparticle toxicity. We tested the reproducibility of spheroid formation induced by the PEG coated surface. Interestingly we found that the results were different in a reproducible manner depending on the distributors of PEG6000.\n\nDespite the nearly identical physicochemical properties of PEG6000 (MALDI-MS, NMR, FTIR, Triple SEC) with only minor differences, we observed only for one PEG6000 a highly reproducible formation of spheroids with different cell lines such as HT-29, HeLa, Caco2, and PANC-1. The surface coating with the different PEG6000 was studied by AFM. The surface coating as well as the physicochemical characterization showed only small differences in mass and hydrodynamic radius between the different PEGs. A direct coating of the cells with PEG from two distributors indicate that the spheroid formation in due to direct interaction of the polymer with the cell rather than by interaction of cells with the coated surface.\n\nThe experiments point out that for biological entities, such as cells or tissues, even very small differences such as impurities or batch-to-batch variations in the purchased product can have a very strong impact.

scientific communication and education↗

Enhance genome editing efficiency and specificity by a quick CRISPR/Cas9 system

CRISPR/Cas9 is a powerful genome editing tool that has been successfully applied to a variety of species, including zebrafish. However, targeting efficiencies vary greatly at different genomic loci, the underlying causes of which were still elusive. Here we report a quick CRISPR/Cas9 system, designated as qCas9, which exhibits accelerated turnover of Cas9 protein in zebrafish. Our data showed that qCas9 significantly improved targeting efficiency, including both knock-out and knock-in in F0 embryos, and yielded higher germline transmission rate in founder screen. Importantly, qCas9 showed little to no off-target editing in zebrafish and profoundly reduced off-target effect in HEK293T cell line. In summary, our findings demonstrate that qCas9 is a simple, economic and highly effective method to improve genome editing efficiency in zebrafish embryos and also holds great potential in reducing off-target effect in mammalian cell lines.

genetics↗

Microbial community dynamics of surface water in British Columbia, Canada

Traditional methods for monitoring the microbiological quality of water focus on the detection of fecal indicator bacteria such as Escherichia coli, often tested as a weekly grab sample. To understand the stability of E.coli concentrations over time, we evaluated three approaches to measuring E. coli levels in water: microbial culture using Colilert, quantitative PCR for uidA and next-generation sequencing of the 16S rRNA gene. Two watersheds, one impacted by agricultural and the other by urban activities, were repeatedly sampled over a simultaneous ten-hour period during each of the four seasons. Based on 16S rRNA gene deep sequencing, each watershed showed different microbial community profiles. The bacterial microbiomes varied with season, but less so within each 10-hour sampling period. Enterobacteriaceae comprised only a small fraction (<1%) of the total community. The qPCR assay detected significantly higher quantities of E. coli compared to the Colilert assay and there was also variability in the Colilert measurements compared to Health Canadas recommendations for recreational water quality. From the 16S data, other bacteria such as Prevotella and Bacteroides showed promise as alternative indicators of fecal contamination. A better understanding of temporal changes in watershed microbiomes will be important in assessing the utility of current biomarkers of fecal contamination, determining the best timing for sample collection, as well as searching for additional microbial indicators of the health of a watershed.

microbiology↗

Recombinase system-dependent copackaging strategy for highly efficient neurocircuit tracing

Mapping the detailed cell-type-specific input networks and neuronal projectomes are essential to understand brain function in normal and pathological states. However, several properties of current tracing systems, including labeling sensitivity, trans-synaptic efficiencies, reproducibility among different individuals and different Cre-driver animals, still remained unsatisfactory. Here, we developed MAP-ENVIVIDERS, a recombinase system-dependent vector mixing-based strategy for highly efficient neurocircuit tracing. MAP-ENVIVIDERS enhanced tracing efficiency of input networks across the whole brain, with over 10-fold improvement in diverse previously poor-labeled input brain regions and particularly, up to 70-fold enhancement in brainstem compared with the current standard rabies-virus-mediated systems. MAP-ENVIVIDERS was over 10-fold more sensitive for cell-type-specific labeling than previous strategies, enabling us to capture individual cell-type-specific neurons with extremely complex axonal branches and presynaptic axonal boutons, both about one order of magnitude than previously reported and considered. MAP-ENVIVIDERS provides powerful tools for deconstructing novel input/output circuitry towards functional studies and disorders-related mechanisms.

neuroscience↗

HIV-1 Nef interacts with LMP7 to attenuate immunoproteasome formation and MHC-I antigen presentation

AbstractProteasome is major protein degradation machinery and plays essential roles in diverse biological functions. Upon cytokine inductions, proteasome subunits {beta}1, {beta}2, and {beta}5 are replaced by {beta}1i/LMP2, {beta}2i/MECL-1, and {beta}5i/LMP7, leading to the formation of immunoproteasome. Immunoproteasome-degraded products are loaded onto the major histocompatibility complex class I (MHC-I) to regulate immune responses and induce cytotoxic-T-lymphocytes (CTLs). Human immunodeficiency virus type 1 (HIV-1) is the causal agent of acquired immunodeficiency syndrome (AIDS). HIV-1-specific CTLs represent critical immune responses to limit viral replication. HIV-1 negative regulatory factor (Nef) counteracts host immunity, especially the MHC-I/CTL. This study reveals a distinct mechanism by which Nef facilitates immune evasion through attenuating the functions of immunoproteasome and MHC-I. Nef interacts with LMP7 on the endoplasmic reticulum (ER) to down-regulate the incorporation of LMP7 into immunoproteasome, and thereby attenuating immunoproteasome formation. Moreover, Nef represses immunoproteasome protein degradation function, MHC-I trafficking, and antigen presentation activity.\n\nImportanceUbiquitin-proteasome system (UPS) is essential for degradation of damaged proteins, which takes place in proteasome. Upon cytokine inductions, proteasome catalytic activities are replaced by distinct isoforms resulting in formation of immunoproteasome. Immunoproteasome generates peptides for MHC-I antigen presentation and plays important roles in immune responses. HIV-1 is the agent of AIDS, and HIV-1-specific CTLs represent immune responses to limit viral replication. This study reveals a distinct mechanism by which HIV-1 promotes immune evasion. Viral protein Nef interacts with immunoproteasome component LMP7 to attenuate immunoproteasome formation and protein degradation function, and repress MHC-I antigen presentation activity. Therefore, HIV-1 targets LMP7 to inhibit immunoproteasome activation and LMP7 may be used as a target for the development of anti-HIV-1/AIDS therapy.

microbiology↗

Three-dimensional genome reorganization during mouse spermatogenesis

Three-dimensional genome organization plays an important role in many biological processes. Yet, how the genome is packaged at the molecular level during mammalian spermatogenesis remains unclear. Here, we performed Hi-C in seven sequential stages during mouse spermatogenesis. We found that topological associating domains (TADs) and chromatin loops underwent highly dynamic reorganization. They displayed clear existence in primitive type A spermatogonia, disappearance at pachytene stage, and reestablishment in spermatozoa. Surprisingly, even in the absence of TADs and chromatin loops at pachytene stage, CTCF remained bound at TAD boundary regions (identified in primitive type A spermatogonia). Additionally, many enhancers and promoters exhibited features of open chromatin and transcription remained active at pachytene stage. A/B compartmentalization and segmentation ratio were conserved in different stages of spermatogenesis in autosomes, although there were A/B compartment switching events correlated with gene activity changes. Intriguingly, A/B compartment structure on the X chromosome disappeared during pacSC, rST and eST stages. Together, our work uncovered a dynamic three-dimensional chromatin organization during mouse spermatogenesis and suggested that transcriptional regulation could be independent of TADs and chromatin loops at specific developmental stages.

genomics↗

Programming conventional electron microscopes for solving ultrahigh-resolution structures of small and macro-molecules

Microcrystal electron diffraction (MicroED) is becoming a powerful tool in determining the crystal structures of biological macromolecules and small organic compounds. However, wide applications of this technique are still limited by the special requirement for radiation-tolerated movie-mode camera and the lacking of automated data collection method. Herein, we develop a stage-camera synchronization scheme to minimize the hardware requirements and enable the use of the conventional electron cryo-microscope with single-frame CCD camera, which ensures not only the acquisition of ultrahigh-resolution diffraction data but also low cost in practice. This method renders the structure determination of both peptide and small organic compounds at ultrahigh resolution up to ~0.60 [A] with unambiguous assignment of nearly all hydrogen atoms. The present work provides a widely applicable solution for routine structure determination of MicroED, and demonstrates the capability of the low-end 120kV microscope with a CCD camera in solving ultra-high resolution structures of both organic compound and biological macromolecules.

biophysics↗

The role of SLC7A5 (LAT1) in endocrine therapy resistant breast cancer

Resistance to endocrine therapies remains a major challenge for the successful management of patients with estrogen receptor-positive (ER+) breast cancers. Central to the development of resistance is the adaptive reprogramming of cellular metabolism in response to treatment. Solute carriers (SLCs) play a key role in metabolic reprogramming by transporting sugars, amino acids, and other nutrients and regulating their abundance within the cell and its subcellular organelles. We found 109 SLC mRNAs to be differentially expressed between endocrine sensitive and resistant breast cancer cells. In univariate analyses, 55 of these SLCs were associated with poor outcome in ER+ breast cancer patients. Data from TMT and SILAC studies then led us to focus on SLC7A5 (LAT1). In complex with SLC3A2 (CD98), LAT1 is the primary transporter of large, neutral amino acids including leucine and tyrosine. LAT1 expression is estrogen-regulated in endocrine sensitive cells but this regulation is lost in resistant cells. Pharmacologic inhibition or genetic depletion of LAT1 each suppressed growth in two models of endocrine resistant breast cancer. Autophagy was activated with LAT1 inhibition, but cells failed to degrade p62 showing that flux was blocked. Overexpression of the LAT1 cDNA increased protein synthesis and high LAT1 expression correlated with poor disease-free survival in ER+ breast cancer patients. This study uncovers a novel LAT1 mediated adaptive response that contributes to the development of endocrine resistance. Blocking LAT1 function may offer a new avenue for effective therapeutic intervention against endocrine resistant ER+ breast cancers.

cancer biology↗

Distribution Pattern and Diversity Maintenance Mechanism of the Denitrifier Community in Alkaline Copper Mine Drainage

Denitrifiers have been shown to vary in abundance and diversity across the environmental gradients; however, the factors that determine the type and magnitude of the response of the denitrifier communities remain unclear. In order to reveal the effects of alkaline mine drainage (AlkMD) on the denitrifier community composition and diversity maintenance mechanism in a tailings reservoir, we examined the diversity patterns and adaptation mechanisms of different denitrifier communities in Shibahe copper tailings water in Zhongtiaoshan, China. The results showed that the -diversity of Proteobacteria and the nosZI-bearing denitrifier community in downstream seeping water (SDSW) were the highest, while those in the upstream tailings water (STW1) were the lowest. The highest nirS and nirK-bearing denitrifier community -diversity were measured in STW1, and the lowest in STW3. The community dissimilarity of the denitrifier communities was strongly correlated with environment parameters, but the factors varied in different groups. The Proteobacteria community was correlated strongly with nitrate (NO3-); the nirS and nirK-bearing denitrifier communities were correlated strongly with pH, total carbon (TC), NO3- and ammonia nitrogen (NH4+), and the nosZI-bearing denitrifier community was correlated strongly with total organic carbon (TOC), dissolved oxygen (DO), NO3-, electroconductibility (EC) and spatial distance (PCNM1). Our results indicated that environmental changes were valuable index reflecting variations in denitrifier community composition in AlkMD. Additionally, the findings in this study are helpful in understanding the relationship between the microbial community composition changes and functional adaptation in different ecosystems. IMPORTANCEMetal mine tailings pond is an important site polluted by heavy metals and nitrogen, and excess nitrogen is mainly removed by microorganisms through denitrification. Although many studies have reported that Proteobacteria is the main denitrifying bacteria, and nirS, nirK and nosZ-bearing denitrifiers are three key functional groups in denitrification process. However, less is known of their response to discharge of alkaline copper tailings wastewater (AlkMD). AlkMD exerts an adverse impact on composition and structure of denitrifying bacteria community. The change of nitrogen and carbon concentration along the flow direction of wastewater resulted in the change of denitrifying bacteria community diversity pattern, that is to say, environmental filtering force drove the denitrifier community structure in this highly polluted ecosystem.

microbiology↗

Dean flow assisted single cell and bead encapsulation for high performance single cell expression profiling

Single-cell RNA sequencing examines the transcriptome of individual cells and reveals the inter-cell transcription heterogeneity, playing a critical role in both scientific research and clinical applications. Recently, droplet microfluidics-based platform for expression profiling has been shown as a powerful tool to capture of the transcriptional information on single cell level. Despite the breakthrough this platform brought about, it required the simultaneous encapsulation of single cell and single barcoded bead, the incidence of which was very low. Suboptimal capturing efficiency limited the throughput of the Drop-seq platform. In this work, we leveraged the advance in inertial microfluidics-based cell sorting and designed a microfluidic chip for high efficiency cell-bead co-encapsulation, increasing the capturing rate by more than four folds. Specifically, we adopted spiral and serpentine channels and ordered cells/beads before the encapsulation region. We characterized the effect of cell concentration on the capturing rate and achieved a cell-bead co-capturing rate up to 3%. We tested this platform by co-encapsulating barcoded beads and human-mouse cell mixtures. The sequencing data distinguished the majority of human and mice expressions, with the doublet rate being as low as 5.8%, indicating that the simultaneous capturing of two or more cells in one droplet was minimal even when using high cell concentration. This chip design showed great potential in improving the efficiency for future single cell expression profiling.

bioengineering↗

Long Non-Coding RNA LncKdm2b Regulates Cortical Neuronal Differentiation by Cis-Activating Kdm2b

The mechanisms underlying spatial and temporal control of cortical neurogenesis of the brain are largely elusive. Long non-coding RNAs (lncRNAs) have emerged as essential cell fate regulators. Here we found LncKdm2b (also known as Kancr), a lncRNA divergently transcribed from a bidirectional promoter of Kdm2b, is transiently expressed during early differentiation of cortical projection neurons. Interestingly, Kdm2bs transcription is positively regulated in cis by LncKdm2b, which has intrinsic-activating function and facilitates a permissive chromatin environment at the Kdm2bs promoter by associating with hnRNPAB. Lineage tracing experiments and phenotypic analyses indicated LncKdm2b and Kdm2b are crucial in proper differentiation and migration of cortical projection neurons. Moreover, KDM2B exerts its role relying on its leucine-rich repeats (LRR) but independent of its PRC1-related function. These observations unveiled a lncRNA-dependent machinery in regulating cortical neuronal differentiation.

molecular biology↗

Vitamin A supplement after neonatal Streptococcus pneumoniae pneumonia alters CD4+T cell subset and inhibits allergic asthma in mice model

BackgroundPreviously, we showed that neonatal pneumonia caused by Streptococcus pneumoniae (S. pneumoniae) promoted adulthood ovalbumin (OVA) induced allergic asthma. Many studies have demonstrated that vitamin A deficiency induced the development of allergic asthma. Whether neonatal S. pneumoniae pneumonia promoted allergic asthma development was associated with vitamin A concentrations remains unclear.\n\nMethodsFemale BALB/c neonates were infected with S. pneumoniae strain D39 and subsequently treated with vitamin A. Vitamin A concentrations in lung, serum and liver were monitored on 2, 5, 7, 14, 21, 28 days post infection. Four weeks after infection, mice were sensitized and challenged with OVA to induce allergic airway disease (AAD) in early adulthood. Twenty-four hours after the final challenge, lung histo-pathology, cytokine concentrations in bronchoalveolar lavage fluid (BALF), airway hyperresponsiveness (AHR) and lung CD4+T cells were measured.\n\nResultsWe demonstrated that neonatal S. pneumoniae pneumonia induce lung vitamin A deficiency up to early adulthood. Moreover, neonatal S. pneumoniae pneumonia aggravated airway inflammatory cells accumulation and increased AHR during AAD, decreased Foxp3+Treg and Th1 productions remarkably, while Th2 cell expression was increased significantly. Further study indicated that vitamin A supplement after neonatal S. pneumoniae pneumonia can promote Foxp3+Treg and Th1 productions, decrease Th2 cell expressions, alleviate AHR and inflammatory cells infiltration during AAD.\n\nConclusionsUsing a mouse model, we demonstrate that Vitamin A supplement after neonatal Streptococcus pneumoniae pneumonia alters the CD4+T cell subset and inhibits the development of early adulthood allergic asthma.

immunology↗

Microbial Cells Harboring a Mitochondrial Gene Are Capable of CO2 Capture

Global warming is escalating with increased temperatures reported worldwide. Given the enormous land mass on the planet, biological capture of CO2 remains a viable approach to mitigate the crisis as it is economical and easy to implement. In this study, a gene capable of CO2 capture was identified via selection in minimal media. This mitochondrial gene named as OG1 encodes the OK/SW-CL.16 protein and shares homology with cytochrome oxidase subunit III of various species and PII uridylyl-transferase from Loktanella vestfoldensis SKA53. CO2 capture experiments indicate that {delta}13C was substantially higher in the cells harboring the gene OG1 than the control in the nutrition-poor media. This study suggests that CO2 capture using engineered microorganisms in barren land can be exploited to address the soaring CO2 level in the atmosphere, opening up vast land resources to cope with global warming.\n\nIMPORTANCEGlobal warming crisis is deteriorating with increased CO2 levels in the atmosphere each year. Action must be taken before catastrophic consequences occur in the not-so-distant future. Biological capture of CO2 is a feasible approach to alleviate the current crisis. We have identified a mitochondrial gene which demonstrated CO2 utilization capability. Data presented in this study suggest that CO2 capture using engineered microorganisms can be harnessed to address the ever-rising CO2 level in the atmosphere.

bioengineering↗

Genome-wide association study of multiple yield components in a diversity panel of polyploid sugarcane (Saccharum spp.)

Sugarcane (Saccharum spp.) is an important economic crop, contributes up to 80% of sugar and approximately 60% bio-fuel globally. To meet the increased demand for sugar and bio-fuel supplies, it is critical to breed sugarcane cultivars with robust performance in yield components. Therefore, dissection of causal DNA sequence variants is of great importance by providing genetic resources and fundamental information for crop improvement. In this study, we evaluated and analyzed nine yield components in a sugarcane diversity panel consisting of 308 accessions primarily selected from the \"world collection of sugarcane and related grasses\". By genotyping the diversity panel using target enrichment sequencing, we identified a large number of sequence variants. Genome-wide association study between the markers and traits were conducted with dosages and gene actions taken into consideration. In total, 217 non-redundant markers and 225 candidate genes were identified to be significantly associated with the yield components, which can serve as a comprehensive genetic resource database for future gene identification, characterization, and selection for sugarcane improvement. We further investigated runs of homozygosity (ROH) in the sugarcane diversity panel. We characterized 282 ROHs, and found that the occurrence of ROH in the genome were non-random and probably under selection. ROHs were associated with total weight and dry weight, and high ROHs resulted in decrease of the two traits. This study approved that genomic inbreeding has led to negative impacts on sugarcane yield.

genomics↗

Molecular Identification and Characterization of Two Rubber Dandelion Amalgaviruses

The Amalgaviridae family comprise persistent viruses that share the genome architecture of Totiviridae and gene evolutionary resemblance to Partitiviridae. Two genera have been assigned to this family, including genus Amalgavirus consisting in nine recognized species, corresponding to plant infecting viruses with dsRNA monosegmented genomes of ca. 3.4 kb. Here, we present the molecular characterization of two novel viruses detected in rubber dandelion (Taraxacum kok-saghyz). The sequenced viruses are 3,409 and 3,413 nt long, including two partially overlapping ORFs encoding a putative coat protein and an RNA-dependent RNA polymerase (RdRP). Phylogenetic insights based on the RdRP suggest them to be members of two new species within the Amalgavirus genus. Multiple independent RNAseq data suggest that the identified viruses have a dynamic distribution and low relative RNA levels in infected plants. Virus presence was not associated with any apparent symptoms on the plant hosts. We propose the names rubber dandelion latent virus 1 & 2 to the detected amalgaviruses; the first viruses to be associated to this emergent and sustainable natural rubber crop.

microbiology↗