Biology subjects

Li, A.

Publications and source records attributed to Li, A..

At least 181 records · Page 10Linked to original sources

bioRxiv2022

Divergent microbial structure still results in convergent microbial function during arrested anaerobic digestion of food waste at different hydraulic retention times

In this study, two arrested anaerobic digestion bioreactors fed with food waste operated under different hydraulic retention times (HRTs) exhibited long-term stable volatile fatty acid (VFA) production performance including similar total yields (p = .085) with propionic acid (PA) being the most abundant VFA. Meta-omics analysis revealed distinct microbial structures (p = .02) at the two HRTs while there were no differences in potential and extant functionality as indicated by the whole-genome and whole-transcriptome sequencing, respectively. The highest potential (relative abundance of DNA sequence reads) and extant (relative abundance of mRNA sequence reads) functionality corresponded with PA production compared to other acids. The most abundant genus Prevotella produced PA mainly through the acryloyl-CoA pathway. Based on our results, the mechanistic basis for the similar VFA production performance observed under the HRTs tested lies in the community-level redundancy in convergent acidification functions and pathways, rather than trends in community structure.

microbiology↗

bioRxiv2022

Architecture of chloroplast TOC-TIC translocon supercomplex

Chloroplasts rely on the translocon complexes in the outer and inner envelope membranes (termed TOC and TIC, respectively) to import thousands of different nuclear-encoded proteins from the cytosol1-4. While previous studies indicated that the TOC and TIC complexes may assemble into larger supercomplexes5-7, the overall architectures of the TOC-TIC supercomplexes and the mechanism of preprotein translocation are elusive. Here we report the cryo-electron microscopy (cryo-EM) structure of the TOC-TIC supercomplex from Chlamydomonas reinhardtii at an overall resolution of 2.8 [A]. The major subunits of the TOC complex (Toc75, Toc90 and Toc34) and TIC complex (Tic214, Tic20, Tic100 and Tic56), three chloroplast translocon-associated proteins (Ctap3, Ctap4 and Ctap5) and three newly-identified small inner-membrane proteins (Simp1-3) have been located in the supercomplex. As the largest protein, Tic214 traverses the inner membrane, the intermembrane space and the outer membrane, connecting the TOC complex with the TIC proteins. An inositol hexaphosphate (InsP6 or I6P) molecule is located at the Tic214-Toc90 interface and stabilizes their assembly. Moreover, four lipid molecules are located within or above an inner-membrane funnel formed by Tic214, Tic20, Simp1 and Ctap5. Furthermore, multiple potential pathways found in the TOC-TIC supercomplex may support translocation of different substrate preproteins into chloroplasts.

biophysics↗

bioRxiv2022

The Cul5 E3 Ligase Complex Is a Key Negative Feedback Regulator of TCR/IL2 Signaling and Anti-Tumor Activity in CD8+ T Cells

CD8+ T cells play an important role in tumor immune surveillance and control. Better understanding of the regulation of their anti-tumor actions and improving their cytotoxic function and persistence will help advancing cancer immunotherapies. Here, we report the development of a step-wise CRISPR knockout (KO) screening strategy under the selection of TGF-{beta}, a clinically relevant immunosuppressive pressure. The screen identifies Cul5 as a negative-feedback regulator of the core signaling pathways, differentiation, and persistence of CD8+ T cell. Cul5 KO in mouse CD8+ T cells significantly improves their tumor control ability in vitro and in vivo with significant proteomic alterations that generally enhance TCR and cytokine signaling, effector function, stemness, and survival of CD8+ T cell. Mechanistically, Cul5, whose protein content and active, neddylated form increase upon TCR-stimulation, interacts with SOCS-box-containing Pcmtd2 and negatively regulates TCR and IL2/STAT5 signaling by decreasing TCR and IL2 signaling molecules. Moreover, Cul5 KO in human CD8+ T cells phenocopies that in mouse CD8+ T cells. Furthermore, KO of CTLA4 that is markedly upregulated by Cul5 KO in mouse and human CD8+ cells further enhances anti-tumor effect of Cul5 KO, and a neddylation inhibitor enhances CD8 effector activities largely dependently of Cul5. These results together not only reveal a previously unknown negative-feedback regulatory mechanism for CD8+ T cells, but also have strong translational implications in cancer immunotherapy.

immunology↗

bioRxiv2022

Transforming inert cycloalkanes into alpha-omega-diamines through designed enzymatic cascade catalysis

Aliphatic ,{omega}-diamines (DAs) are important monomer precursors in polyamide plastic manufacturing. However, the dominant industrial process for DA synthesis involves energy-intensive, multistage chemical reactions that are harmful to the environment. For instance, 1,6-hexanediamine (HMD), one of most prominent monomers in nylon-66 synthesis, is mainly synthesized with currently high technological control by butadiene hydrocyanation, which suffers from the use of highly toxic hydrogen cyanide, unsatisfactory selectivity and a complex separation process. Thus, the development of sustainable green DA synthetic routes is highly desired. Herein, we report an efficient one-pot in vivo biocatalytic cascade for the transformation of cycloalkanes into DAs with the aid of advanced techniques, including the RetroBioCat tool for biocatalytic route design, enzyme mining for finding appropriate enzymes and microbial consortia construction for efficient pathway assembly. As a result, DAs are successfully produced by the developed microbial consortia-based biocatalytic system, especially HMD, and product concentrations as high as 16.5 mM and 7.6 mM are achieved when using cyclohexanol (CHOL) or cyclohexane (CH) as substrates, respectively. This also represents the highest HMD biosynthesis productivity to date. Other cycloalkanes also serve as substrates, indicating the generality of our approach.

synthetic biology↗

bioRxiv2022

CD46 targeted 212Pb alpha particle radioimmunotherapy for prostate cancer treatment

We recently identified CD46 as a novel prostate cancer cell surface antigen that shows lineage independent expression in both adenocarcinoma and small cell neuroendocrine subtypes of metastatic castration resistant prostate cancer (mCRPC), discovered an internalizing human monoclonal antibody YS5 that binds to a tumor selective CD46 epitope, and developed a microtubule inhibitor-based antibody drug conjugate that is in a multi-center phase I trial for mCRPC (NCT03575819). Here we report the development of a novel CD46-targeted alpha therapy based on YS5. We conjugated 212Pb, an in vivo generator of alpha-emitting 212Bi and 212Po, to YS5 through the chelator TCMC to create the radioimmunoconjugate, 212Pb-TCMC-YS5. We characterized 212Pb-TCMC-YS5 in vitro and established a safe dose in vivo. We next studied therapeutic efficacy of a single dose of 212Pb-TCMC-YS5 using three prostate cancer small animal models: a subcutaneous mCRPC cell line-derived xenograft (CDX) model (subcu-CDX), an orthotopically grafted mCRPC CDX model (ortho-CDX), and a prostate cancer patient-derived xenograft model (PDX). In all three models, a single dose of 20 Ci 212Pb-TCMC-YS5 was well tolerated and caused potent and sustained inhibition of established tumors, with significant increases of survival in treated animals. A lower dose (10 Ci 212Pb-TCMC-YS5) was also studied on the PDX model, which also showed a significant effect on tumor growth inhibition and prolongation of animal survival. These results demonstrate that 212Pb-TCMC-YS5 has an excellent therapeutic window in preclinical models including PDXs, opening a direct path for clinical translation of this novel CD46-targeted alpha radioimmunotherapy for mCRPC treatment. SignificanceThis study reports a novel CD46 targeted 212Pb alpha particle radioimmunotherapy, 212Pb-TCMC-YS5, that is well tolerated and shows potent anti-tumor activity (tumor growth inhibition and increase of animal survival) in vivo in three prostate cancer small animal models, i.e., a subcutaneous and an intraprostate orthotopic mCRPC cell line-derived xenograft models, and a prostate cancer patient-derived xenograft model. Given that YS5 is a clinical stage human antibody, this YS5-based 212Pb alpha particle therapy has potential of translation to the clinic for treatment of mCRPC patients.

bioengineering↗

bioRxiv2022

Multi-omic profiling of the developing human cerebral cortex at the single cell level

The cellular complexity of the human brain is established via dynamic changes in gene expression throughout development that is mediated, in part, by the spatiotemporal activity of cis-regulatory elements. We simultaneously profiled gene expression and chromatin accessibility in 45,549 cortical nuclei across 6 broad developmental time-points from fetus to adult. We identified cell-type specific domains in which chromatin accessibility is highly correlated with gene expression. Differentiation pseudotime trajectory analysis indicates that chromatin accessibility at cis-regulatory elements precedes transcription and that dynamic changes in chromatin structure play a critical role in neuronal lineage commitment. In addition, we mapped cell-type and temporally specific genetic loci implicated in neuropsychiatric traits, including schizophrenia and bipolar disorder. Together, our results describe the complex regulation of cell composition at critical stages in lineage determination, serve as a developmental blueprint of the human brain and shed light on the impact of spatiotemporal alterations in gene expression on neuropsychiatric disease. One-Sentence SummarySimultaneous profiling of gene expression and chromatin accessibility in single nuclei from 6 developmental time-points sheds light on cell fate determination in the human cerebral cortex and on the molecular basis of neuropsychiatric disease.

neuroscience↗

bioRxiv2022

Spatiotemporal orchestration of multicellular transcriptional programs and communications in spinal cord injury

While spinal cord injury (SCI) involves a complex cascade of cellular and pathological changes that last for months to years, the most dramatic and comprehensive molecular rewiring and multicellular re-organization occur in the first few days, which determine the overall progression and prognosis of SCI, yet remain poorly understood. Here, we resolved the spatiotemporal architecture of multicellular gene expression in a mouse model of acute SCI, and revealed the coordinated gene co-expression networks, the upstream regulatory programs, and in situ cell-cell interactions that underlay the anatomic disorganization as well as the immune and inflammatory responses conferring the secondary injury. The spatial transcriptomic analysis highlights that the genes and cell types in the white matter (WM) play a more active and predominant role in the early stage of SCI. In particular, we identified a distinct population of WM-originated, Igfbp2-expressing reactive astrocytes, which migrated to the grey matter and expressed multiple axon/synapse-supporting molecules that may foster neuron survival and spinal cord recovery in the acute phase. Together, our dataset and analyses not only showcase the spatially-defined molecular features endowing the cell (sub)types with new biological significance but also provide a molecular atlas for disentangling the spatiotemporal organization of the mammalian SCI and advancing the injury management.

neuroscience↗

bioRxiv2022

Engineered RecA constructs reveal the minimal SOS activation complex

The SOS response is a bacterial DNA damage response pathway that has been heavily implicated in bacterias ability to evolve resistance to antibiotics. Activation of the SOS response is dependent on the interaction between two bacterial proteins, RecA and LexA. RecA acts as a DNA damage sensor by forming lengthy oligomeric filaments (RecA*) along single-stranded DNA (ssDNA) in an ATP-dependent manner. RecA* can then bind to LexA, the repressor of SOS response genes, triggering LexA degradation and leading to induction of the SOS response. Formation of the RecA*-LexA complex therefore serves as the key SOS activation signal. Given the challenges associated with studying a complex involving multiple macromolecular interactions, the essential constituents of RecA* that permit LexA cleavage are not well defined. Here, we leverage head-to-tail linked and end-capped RecA constructs as tools to define the minimal RecA* filament that can engage LexA. In contrast to previously postulated models, we found that as few as three linked RecA units are capable of ssDNA binding, LexA binding, and LexA cleavage. We further demonstrate that RecA oligomerization alone is insufficient for LexA cleavage, with an obligate requirement for ATP and ssDNA binding to form a competent SOS activation signal with the linked constructs. Our minimal system for RecA* highlights the limitations of prior models for the SOS activation signal and offers a novel tool that can inform efforts to slow acquired antibiotic resistance by targeting the SOS response. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/510415v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@149d719org.highwire.dtl.DTLVardef@c8dd3corg.highwire.dtl.DTLVardef@1349098org.highwire.dtl.DTLVardef@fb29_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2022

DeDoc2 identifies and characterizes the hierarchy and dynamics of chromatin TAD-like domains in the single cells

Topologically associating domains (TAD) are functional chromatin units with hierarchical structure. However, the existence, prevalence and dynamics of such hierarchy in single cells remain unexplored. Here, we report a new generation TAD-like domain (TLD) detection algorithm, named deDoc2, to decode the hierarchy of TLDs in single cells. With dynamic programming, deDoc2 seeks genome partitions with global minimal structure entropy for both whole and local contact matrix. Compared to state-of-the-art tools, deDoc2 can uniquely identify the hierarchy of TLDs in single cells, in addition to outperforming its competitors. By applying deDoc2, we showed that the hierarchy of TLDs in single cells is highly dynamic during cell cycle, as well as among human brain cortex cells, and that it is associated with cellular identity and functions. Thus, our results demonstrated the abundance of information potentially encoded by TLD hierarchy for functional regulation. The deDoc2 can be freely accessed at https://github.com/zengguangjie/deDoc2.

bioinformatics↗

bioRxiv2022

High-throughput profiling of sequence recognition by tyrosine kinases and SH2 domains using bacterial peptide display

Tyrosine kinases and SH2 (phosphotyrosine recognition) domains have binding specificities that depend on the amino acid sequence surrounding the target (phospho)tyrosine residue. Although the preferred recognition motifs of many kinases and SH2 domains are known, we lack a quantitative description of sequence specificity that could guide predictions about signaling pathways or be used to design sequences for biomedical applications. Here, we present a platform that combines genetically-encoded peptide libraries and deep sequencing to profile sequence recognition by tyrosine kinases and SH2 domains. We screened several tyrosine kinases against a million-peptide random library and used the resulting profiles to design high-activity sequences. We also screened several kinases against a library containing thousands of human proteome-derived peptides and their naturally-occurring variants. These screens recapitulated independently measured phosphorylation rates and revealed hundreds of phosphosite-proximal mutations that impact phosphosite recognition by tyrosine kinases. We extended this platform to the analysis of SH2 domains and showed that screens could predict relative binding affinities. Finally, we expanded our method to assess the impact of non-canonical and post-translationally modified amino acids on sequence recognition. This specificity profiling platform will shed new light on phosphotyrosine signaling and could readily be adapted to other protein modification/recognition domains.

biochemistry↗

bioRxiv2022

mBAT-combo: a more powerful test to detect gene-trait associations from GWAS data

Gene-based association tests aggregate multiple SNP-trait associations into sets defined by gene boundaries. Since genes have a direct biological link to downstream function, gene-based test results are widely used in post-GWAS analysis. A common approach for gene-based tests is to combine SNPs associations by computing the sum of{chi} 2 statistics. However, this strategy ignores the directions of SNP effects, which could result in a loss of power for SNPs with masking effects (e.g., when the product of the effects of two SNPs and their linkage disequilibrium (LD) correlation is negative). Here, we introduce "mBAT-combo", a new set-based test that is better powered than other methods to detect multi-SNP associations in the context of masking effects. We validate the method through simulations and applications to real data. We find that of 35 blood and urine biomarker traits in the UK Biobank, 34 traits show evidence for masking effects in a total of 4,175 gene-trait pairs, indicating that masking effects in complex traits is common. We further validate the improved power of our method in height, body mass index and schizophrenia with different GWAS sample sizes and show that on average 95.7% of the genes detected only by mBAT-combo with smaller sample sizes can be identified by the single-SNP approach with larger sample sizes (average sample size increased by 1.7-fold). For instance, LRRC4B is significant only in our method for schizophrenia, which has been shown to play a role in presynaptic pathology using genetic fine-mapping and evidence-based synaptic annotations. As a more powerful gene-based method, mBAT-combo is expected to improve the downstream pathway analysis or tissue and cell-type enrichment analysis that takes genes identified from GWAS data as input to understand the biological mechanisms of the trait or disease. Despite our focus on genes in this study, the framework of mBAT-combo is general and can be applied to any set of SNPs to refine trait-association signals hidden in genomic regions with complex LD structures.

genetics↗

bioRxiv2022

Simultaneously cholinergic projection in Ascending and Descending Circuits from Midbrain

The midbrain participates in complex neural information processing in the ascending and descending circuits, but their organization remains unclear due to the lack of comprehensive dissection of the characterization of individual neurons. Combining fluorescent micro-optical sectional tomography with sparse labeling, we acquired the whole-brain dataset with high resolution and reconstructed the detailed morphology of the pontine-tegmental cholinergic neurons (PTCNs). As the main cholinergic system of the midbrain, the individual PTCNs own abundant axons with length up to 60 cm and 5000 terminal branches and innervate multiple brain regions from the spinal cord to cortex in both hemispheres. According to various targeting regions in the ascending and descending circuits, individual PTCNs could be grouped into four types and the axonal fibers of cholinergic neurons in the pedunculopontine nucleus present more divergent while neurons in the laterodorsal tegmental nucleus contain richer axonal fibers and dendrites. In the axonal targeting nuclei, such as in the thalamus or cortex, the individual neurons innervate multiple sub-regions with separate pathways. These results provide the detailed organization characterization of the cholinergic neurons to understand the connection logic of the midbrain.

neuroscience↗

bioRxiv2022

CPPVec: an accurate coding potential predictor based on adistributed representation of protein sequence

Long non-coding RNAs (lncRNAs) play a crucial role in numbers of biological processes and have received wide attention during the past years. Meanwhile, the rapid development of high-throughput transcriptome sequencing technologies (RNA-seq) lead to a large amount of RNA data, it is urgent to develop a fast and accurate coding potential predictor. Many computational methods have been proposed to alleviate this issue, they usually exploit information on open reading frame (ORF), k-mer, evolutionary signatures, or known protein databases. Despite the effectiveness, these methods still have much room to improve. Indeed, none of these methods exploit the context information of sequence, simple measures that are calculated with the continuous nucleotides are not enough to reflect global sequence order information. In view of this shortcoming, here, we present a novel alignment-free method, CPPVec, which exploits the global sequence order information of transcript for coding potential prediction for the first time, it can be easily implemented by distributed representation (e.g., doc2vec) of protein sequence translated from the longest ORF. Tests on human, mouse, zebrafish, fruit fly and Saccharomyces cerevisiae datasets demonstrate that CPPVec is an accurate coding potential predictor and significantly outperforms existing state-of-the-art methods.

bioinformatics↗

bioRxiv2022

The ATLAS™ screening assay reveals distinct CD4+ and CD8+ SARS-CoV-2 antigen response profiles which have implications to Omicron cellular immunity

The emergence of SARS-CoV-2 variants are a persistent threat to the efficacy of currently developed prophylactic vaccines and therapeutic antibodies. These variants accumulate mutations in the spike protein which encodes the epitopes necessary for neutralizing antibody binding. Moreover, emerging evidence suggest that robust antibody responses are insufficient to prevent severe disease and long-lasting viral immunity requires T cells. Thus, understanding how the T cell antigen landscape evolves in the context of these emerging variants remains crucial. T cells responses are durable and recognize a wider breadth of epitopes reducing the possibility of immune escape through mutation. Here, we deploy the ATLAS assay which identifies CD4+ and CD8+ T cell antigens by utilizing the endogenous HLA class-I and class-II peptide processing pathways. Profiling of T cells from exposed and unexposed donors revealed rich and complex patterns which highlighted the breadth of antigenic potential encoded in SARS-CoV-2. ATLAS revealed several common or frequent antigenic regions as well as an abundance of responses in the unexposed cohort potentially the result of pre-exposure to related coronaviruses. ORF10 was a common CD4+ response in the unexposed cohort while spike was identified as a common and frequent target in both cohorts. Moreover, the spike response profiles allowed us to accurately predict the impact of Omicron spike mutations. This analysis could thus be applied to study the impact of future emerging VOCs.

immunology↗

bioRxiv2022

A new paradigm for personal protection against ticks: efficacy of spatial repellents to reduce host seeking activities in three major tick species of medical importance

Addressing the prevalence of tick-borne disease requires robust chemical options as an integral component of Integrative Vector Management (IVM) program. Spatial repellency is a novel concept in tick bite prevention. To date, there is no standard for the evaluation of spatial repellency against ticks, despite the speculated value of volatilized chemicals in control systems. This study reports a novel vertical climb assay that was specifically created for the quantitative evaluation of spatial repellency in ticks. Controlled release devices (CRDs) were used to control the dispersion of multiple Active Ingredients (AIs) transfluthrin, metofluthrin, nootkatone, and DEET against adult females of three medically important tick species: Dermacentor variabilis, Amblyomma americanum, and Ixodes scapularis. Results of our study indicate significant associations between AI exposure and changing in tick climbing behavior when compared controls in the absence of the AI, from several perspectives, including changes in tick movement velocity, displacement, detachment, and rate of successful vertical climbing. Metofluthrin and transfluthrin caused strong reductions in host seeking activities against D. variabilis and A. americanum, while both demonstrated slightly weaker effects against I. scapularis. Further work is planned to evaluate spatial repellency in ticks in more natural environments and assess their potential in future tick control programs.

zoology↗

bioRxiv2022

MorphoGNN: Morphological Embedding for Single Neuron with Graph Neural Networks

With the development of optical imaging systems, neuroscientists can now obtain large datasets of morphological structure at a single neuron scale positioned across the whole mouse brain. However, the enormous amount of morphological data challenges the classic approach of neuron classification, indexing and other analysis tasks. In this paper, we propose MorphoGNN, a single neuron morphological embedding based on the graph neural networks (GNN). This method learns the spatial structure information between the nodes of reconstructed neuron fibers by its nearest neighbors on each layer and captures the lower-dimensional representation of a single neuron through an end-to-end model. This model is composed of densely connected edge convolution (EdgeConv) layers and a double pooling operator, regularized with joint cross-entropy loss and triplet loss. An increasing population of the neighbor nodes meets the need of learning more information with features expanding at the deep layer. We tested the proposed embeddings on the neuron classification and retrieval tasks. Our method achieves competitive performance both on the general point cloud dataset and the neuron morphology dataset.

neuroscience↗

bioRxiv2022

Scalable production of recombinant three-finger proteins: from inclusion bodies to high quality molecular probes

We introduce a working pipeline for expression, purification and validation of disulfide-bond rich three-finger proteins using E. coli as the expression host. With this pipeline, we have successfully obtained highly purified and bioactive recombinant -Bungarotoxin, k-Bungarotoxin, Hannalgesin, Mambalgin-1, -Cobratoxin, MT, Slurp1, Pate B etc. Milligrams to hundreds of milligrams of recombinant three finger proteins were obtained within weeks in the lab. The recombinant proteins showed specificity in binding assay and six of them were crystallized and structurally validated using X-ray diffraction protein crystallography. As many three finger proteins have attractive therapeutic or research interests and due to the extremely high quality of the recombinant three finger proteins we obtained, our method provides a competitive alternative to either their native counterparts or chemically synthetic ones, and should facilitate related research and applications.

biochemistry↗

bioRxiv2022

The Gene Knockout of Angiotensin II Type 1a Receptor Improves High-fat Diet-Induced Obesity in rat via Promoting Adipose Lipolysis

AimsThe renin-angiotensin system (RAS) is over-activated and the serum angiotensin II (Ang II) level increased in obese patients, while their correlations were incompletely understood. This study aims to explore the role of Ang II in diet-induced obesity by focusing on adipose lipolysis. MethodsRat model of AT1aR gene knockout were established to investigate the special role of Ang II. Wild-type (WT) and AT1aR gene knockout (AT1aR-/-) SD rats were fed with normal diet or high-fat diet for 12 weeks. Adipose morphology and adipose lipolysis were examined. ResultsAT1aR deficiency activated lipolysis-related enzymes and increased the levels of NEFAs and glycerol released from adipose tissue in high-fat diet rats, while did not affect triglycerides synthesis. Besides, AT1aR knockout promoted energy expenditure and fatty acids oxidation in adipose tissue. cAMP levels and PKA phosphorylation in the adipose tissue were significantly increased in AT1aR-/- rats fed with high-fat. Activated PKA could promote adipose lipolysis and thus improved adipose histomorphology and insulin sensitivity in high-fat diet rats. ConclusionsAT1aR deficiency alleviated adipocyte hypertrophy in high-fat diet rats by promoting adipose lipolysis via cAMP/PKA pathway, and thereby delayed the onset of obesity and related metabolic diseases.

physiology↗