Biology subjects

Lin, Q.

Publications and source records attributed to Lin, Q..

At least 91 records · Page 5Linked to original sources

bioRxiv2022

Allogeneic gene-edited HIV-specific CAR-T cells secreting PD-1 blocking scFv enhance anti-HIV activity in vitro

HIV-specific chimeric antigen receptor (CAR) T cells have been developed to target latently infected CD4+ T cells that express virus either spontaneously or after intentional latency reversal. However, the T-cell exhaustion and the patient-specific autologous paradigm of CAR-T hurdled the clinical application. Here, we created HIV-specific CAR-T cells using human peripheral blood mononuclear cells and a 3BNC117-E27 CAR (3BE CAR) construct that enables the expression of PD-1 blocking scFv E27 and the single-chain variable fragment of the HIV-1-specific broadly neutralizing antibody 3BNC117 to target native HIV envelope glycoprotein (Env). In comparison with T cells expressing 3BNC117-CAR alone, 3BE CAR-T cells showed greater anti-HIV potency with stronger proliferation capability, higher killing efficiency (up to ~75%) and enhanced cytokine secretion in the presence of HIV envelope glycoprotein-expressing cells. Furthermore, our approach achieved high levels (over 97%) of the TCR-deficient 3BE CAR-T cells with the functional inactivation of endogenous TCR to avoid graft-versus-host disease without compromising their antiviral activity relative to standard anti-HIV CAR-T cells. These data suggest that we have provided a feasible approach to large-scale generation of "off-the-shelf" anti-HIV CAR-T cells in combination with antibody therapy of PD-1 blockade, which can be a powerful therapeutic candidate for the functional cure of HIV.

bioengineering↗

bioRxiv2021

Selective inhibition of PfATP6 by artemisinins and identification of new classes of inhibitors after expression in yeast

Treatment failures with artemisinin combination therapies (ACTs) threaten global efforts to eradicate malaria. They highlight the importance of identifying drug targets and new inhibitors and of studying how existing antimalarial classes work. Herein we report the successful development of an heterologous expression-based compound screening tool. Validated drug target P. falciparum calcium ATPase6 (PfATP6) and a mammalian ortholog (SERCA1a) were functionally expressed in yeast providing a robust, sensitive, and specific screening tool. Whole-cell and in vitro assays consistently demonstrated inhibition and labelling of PfATP6 by artemisinins. Mutations in PfATP6 resulted in fitness costs that were ameliorated in the presence of artemisinin derivatives when studied in the yeast model. As previously hypothesised, PfATP6 is a target of artemisinins. Mammalian SERCA1a can be mutated to become more susceptible to artemisinins. The inexpensive, low technology yeast screening platform has identified unrelated classes of druggable PfATP6 inhibitors. Resistance to artemisinins may depend on mechanisms that can concomitantly address multi-targeting by artemisinins and fitness costs of mutations that reduce artemisinin susceptibility.

pharmacology and toxicology↗

bioRxiv2021

Autophagy in DG engrams mediates Rac1-dependent forgetting during aging via microglia-mediated synapse elimination

BACKGROUNDEngrams are considered to be substrates for memory storage, and the adaptive plasticity remolding that switch engrams to an inaccessible state cause forgetting. The normal function of engrams is ensured by the crosstalk between neurons and microglia, the major immune cells in the brain implicated in synapse remodeling and memory processing. However, the cellular processes and molecular mediators between engrams and microglia underlying forgetting are poorly understood. METHODSWe utilized doxycycline (Dox)-dependent robust activity marking (RAM) system to label and manipulate DG engrams encoding contexture fear memory in mice. Combining optogenetics, microglia-specific transcriptomics, fluorescence in situ hybridization and spine morphology analysis, we investigated the potential mechanisms of information exchange between engrams and microglia mediating memory forgetting. RESULTSThe expression of Rac1 in dentate gyrus (DG) engrams upregulated memory encoding. Increased Rac1 activity in DG engrams accelerated forgetting, upregulated autophagy influx and the expression of autophagy protein 7 (Atg7). The elevated ATG7 expression in the engrams activated of DG microglia and promoted forgetting. In addition, the Toll-like receptor (TLR) signal in DG microglia was upregulated when overexpressing ATG7 or activating Rac1 in DG engrams, and mediated the ATG7-dependent synapse remodeling and Rac1-dependent forgetting. CONCLUSIONSIn this study, we found that Rac1 increases ATG7-dependent autophagy in DG engrams, which activated microglia via TLR2/4, to promote spine remodeling and forgetting. These results unravel a novel pathway mediating memory forgetting, and provide a potential therapeutic strategy in the treatment of cognitive disorders such as Alzheimers disease.

neuroscience↗

bioRxiv2021

Epitranscriptomic reprogramming is required to prevent stress and damage from acetaminophen

Epitranscriptomic marks, in the form of enzyme catalyzed RNA modifications, play important gene regulatory roles in response to environmental and physiological conditions. However, little is known with respect to how pharmaceuticals influence the epitranscriptome. Here we define how acetaminophen (APAP) induces epitranscriptomic reprogramming and how the writer Alkylation Repair Homolog 8 (Alkbh8) plays a key gene regulatory role in the response. Alkbh8 modifies tRNA selenocysteine (tRNASec) to translationally regulate the production of glutathione peroxidases (Gpxs) and other selenoproteins, with Gpx enzymes known to play protective roles during APAP toxicity. We demonstrate that APAP increases toxicity and markers of damage, and decreases selenoprotein levels in Alkbh8 deficient mouse livers, when compared to wildtype. APAP also promotes large scale reprogramming of 31 RNA marks comprising the liver tRNA epitranscriptome including: 5-methoxycarbonylmethyluridine (mcm5U), isopentenyladenosine (i6A), pseudouridine ({Psi}), and 1-methyladenosine (m1A) modifications linked to tRNASec and many others. Alkbh8 deficiency also leads to wide-spread epitranscriptomic dysregulation in response to APAP, demonstrating that a single writer defect can promote downstream changes to a large spectrum of RNA modifications. Our study highlights the importance of RNA modifications and translational responses to APAP, identifies writers as key modulators of stress responses in vivo and supports the idea that the epitranscriptome may play important roles in responses to pharmaceuticals.

molecular biology↗

bioRxiv2021

The complete mitogenome of Lysmata vittata (Crustacea: Decapoda: Hippolytidae) and its phylogenetic position in Decapoda

In this study, the complete mitogenome of Lysmata vittata (Crustacea: Decapoda: Hippolytidae) has been determined. The genome sequence was 22003 base pairs (bp) and it included thirteen protein-coding genes (PCGs), twenty-two transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and three putative control regions (CRs). The nucleotide composition of AT was 71.50%, with a slightly negative AT skewness (-0.04). Usually the standard start codon of the PCGs was ATN, while cox1, nad4L and cox3 began with TTG, TTG and GTG. The canonical termination codon was TAA, while nad5 and nad4 ended with incomplete stop codon T, and cox1 ended with TAG. We compared the order of genes of Decapoda ancestor and found that the positions of the two tRNAs genes (trnA and trnR) of the L. vittata were translocated. The phylogenetic tree showed that L. vittata was an independent clade, namely Hippolytidae.

molecular biology↗

bioRxiv2021

Adult neuromarkers of sustained attention and working memory predict inter- and intra-individual differences in these processes in youth

Sustained attention (SA) and working memory (WM) are critical processes, but the brain networks supporting these abilities in development are unknown. We characterized the functional brain architecture of SA and WM in 9-11-year-old children and adults. First, we found that adult network predictors of SA generalized to predict individual differences and fluctuations in SA in youth. A WM network model predicted WM performance both across and within children--and captured individual differences in later recognition memory--but underperformed in youth relative to adults. We next characterized functional connections differentially related to SA and WM in youth compared to adults. Results revealed two network configurations: a dominant architecture predicting performance in both age groups and a secondary architecture, more prominent for WM than SA, predicting performance in one. Thus, functional connectivity predicts SA and WM in youth, with networks predicting WM changing more from preadolescence to adulthood than those predicting SA.

neuroscience↗

bioRxiv2021

AMP-Kinase mediates regulation of glomerular volume and podocyte survival

We reported that Shroom3 knockdown, via Fyn inhibition, induced albuminuria with foot process effacement (FPE) without glomerulosclerosis (FSGS) or podocytopenia. Interestingly, knockdown mice had reduced podocyte volumes. Human minimal change disease, where podocyte Fyn inactivation was reported, also showed lower glomerular volumes than FSGS. We hypothesized that lower glomerular volume prevented the progression to podocytopenia. To test this hypothesis, we utilized unilateral- and 5/6th nephrectomy models in Shroom3 knockdown mice. Knockdown mice exhibited lower glomerular volume, and less glomerular and podocyte hypertrophy after nephrectomy. FYN-knockdown podocytes had similar reductions in podocyte volume, implying Fyn was downstream of Shroom3. Using SHROOM3- or FYN-knockdown, we confirmed reduced podocyte protein content, along with significantly increased phosphorylated AMP-kinase, a negative regulator of anabolism. AMP-Kinase activation resulted from increased cytoplasmic redistribution of LKB1 in podocytes. Inhibition of AMP-Kinase abolished the reduction in glomerular volume and induced podocytopenia in mice with FPE, suggesting a protective role for AMP-Kinase activation. In agreement with this, treatment of glomerular injury models with AMP-Kinase activators restricted glomerular volume, podocytopenia and progression to FSGS. In summary, we demonstrate the important role of AMP-Kinase in glomerular volume regulation and podocyte survival. Our data suggest that AMP-Kinase activation adaptively regulates glomerular volume to prevent podocytopenia in the context of podocyte injury.

systems biology↗

bioRxiv2021

Microbial phylogenetic relatedness links to distinct successional patterns of bacterial and fungal communities

Development of soil microbial communities along ecological succession is crucial for ecosystem recovery and maintenance. However, mechanisms mediating microbial community dynamics and co-occurrence patterns along ecological succession remain unclear. Here, we explored community dynamics and taxa co-occurrence patterns in bacterial and fungal communities across a well-established chronosequence of post-mining lands spanning 54 years of recovery. Meanwhile, by synthesizing previous studies and ecological theories, we devised two conceptual models that integrate microbial phylogeny with patterns in community dynamics and in taxa co-occurrence. We further tested these models by using empirical data. At early successional stages, bacterial community structures became increasingly phylogenetically clustered with soil age, which was co-determined by the environmental selection from soil vegetation cover and by heterogeneous responses of less phylogenetically similar bacteria to the increasing resource availability along succession. At later successional stages, bacterial community phylogenetic structures displayed progressively lower variability. The fungal community phylogenetic structures varied relatively less and were independent of soil age, soil properties and vegetation cover, which was attributed to the dominance of stochastic processes in community turnover along succession. Network analysis revealed a decrease in bacterial co-occurrence complexity along succession, which aligned with a decrease in average pairwise phylogenetic distances between co-occurring bacteria. These patterns together implied a decrease in potential bacterial cooperation that was probably mediated by increasing resource availability along succession. The increased complexity of fungal co-occurrence along succession was independent of phylogenetic distances between co-occurring fungi. This study provides new sights into ecological mechanisms underlying bacterial and fungal community succession.

microbiology↗

bioRxiv2021

Deep learning identifies pathological abnormalities predictive of graft loss in kidney transplant biopsies

BackgroundInterstitial fibrosis, tubular atrophy, and inflammation are major contributors to renal allograft failure. Here we seek an objective, quantitative pathological assessment of these lesions to improve predictive utility. MethodsWe constructed a deep-learning-based pipeline recognizing normal vs. abnormal kidney tissue compartments and mononuclear leukocyte (MNL) infiltrates from Periodic acid-Schiff (PAS) stained slides of transplant biopsies (training: n=60, testing: n=33) that quantified pathological lesions specific for interstitium, tubules and MNL infiltration. The pipeline was applied to 789 whole slide images (WSI) from baseline (n=478, pre-implantation) and 12-month post-transplant (n=311) protocol biopsies in two independent cohorts (GoCAR: 404 patients, AUSCAD: 212 patients) of transplant recipients to correlate composite lesion features with graft loss. ResultsOur model accurately recognized kidney tissue compartments and MNLs. The digital features significantly correlated with Banff scores, but were more sensitive to subtle pathological changes below the thresholds in Banff scores. The Interstitial and Tubular Abnormality Score (ITAS) in baseline samples was highly predictive of 1-year graft loss (p=2.8e-05), while a Composite Damage Score (CDS) in 12-month post-transplant protocol biopsies predicted later graft loss (p=7.3e-05). ITAS and CDS outperformed Banff scores or clinical predictors with superior graft loss prediction accuracy. High/intermediate risk groups stratified by ITAS or CDS also demonstrated significantly higher incidence of eGFR decline and subsequent graft damage. ConclusionsThis deep-learning approach accurately detected and quantified pathological lesions from baseline or post-transplant biopsies, and demonstrated superior ability for prediction of posttransplant graft loss with potential application as a prevention, risk stratification or monitoring tool.

pathology↗

bioRxiv2021

A Chromosome-level Assembly of a Wild Castor Genome Provides New Insights into the Adaptive Evolution in a Tropical Desert

Wild castor grows in the high-altitude tropical desert of the African Plateau, a region known for high ultraviolet radiations, strong lights and extremely dry conditions. To investigate the potential genetic basis of adaptation to both highland and tropical deserts, we generated a chromosome-level genome sequence of the wild castor accession WT05, with genome size of 316 Mb and scaffold and contig N50 sizes of 31.93 Mb and 8.96 Mb, respectively. Compared with cultivated castor and other Euphorbiaceae species, the wild castor exhibits positive selection and gene family expansion for genes involved in DNA repair, photosynthesis and abiotic stress responses. Genetic variations associated with positive selection were identified in several key genes, such as LIG1, DDB2, and RECG1, involved in nucleotide excision repair. Moreover, a study of genomic diversity among wild and cultivated accessions revealed genomic regions containing selection signatures associated with the adaptation to extreme environments. The identification of the genes and alleles with selection signatures provides insights into the genetic mechanisms underlying the adaptation of wild castor to the high-altitude tropical desert and would facilitate direct improvement of modern castor varieties.

genomics↗

bioRxiv2021

A brain-based universal measure of attention: predicting task-general and task-specific attention performance and their underlying neural mechanisms from task and resting state fMRI

Attention is central for many aspects of cognitive performance, but there is no singular measure of a persons overall attentional functioning across tasks. To develop a universal measure that integrates multiple components of attention, we collected data from more than 90 participants performing three different attention-demanding tasks during fMRI. We constructed a suite of whole-brain models that can predict a profile of multiple attentional components - sustained attention, divided attention and tracking, and working memory capacity - from a single fMRI scan type within novel individuals. Multiple brain regions across the frontoparietal, salience, and subcortical networks drive accurate predictions, supporting a universal (general) attention factor across tasks, which can be distinguished from task-specific attention factors and their neural mechanisms. Furthermore, connectome-to-connectome transformation modeling enhanced predictions of an individuals attention-task connectomes and behavioral performance from their rest connectomes. These models were integrated to produce a new universal attention measure that generalizes best across multiple, independent datasets, and which should have broad utility for both research and clinical applications.

neuroscience↗

bioRxiv2021

Manipulation of stimulus waveform and frequency permits targeted fiber activation during vagus nerve stimulation in 2 rodent species

Afferent and efferent vagal fibers mediate bidirectional communication between the brain and visceral organs. Small, unmyelinated C-afferents constitute the majority of vagal fibers, play critical roles in numerous interoceptive circuits and autonomic reflexes in health and disease and may contribute to the efficacy and safety of vagus nerve stimulation (VNS). Selective engagement of C-afferents with electrical stimuli has not been feasible, due to the default fiber recruitment order: larger fibers first, smaller fibers last. Here, we determine and optimize an electrical stimulus that selectively engages vagal C-afferents. Intermittent KHz-frequency electrical stimulation (KES) activates motor and, preferentially, sensory vagal neurons in the brainstem. During KES, asynchronous activity of C-afferents increases, while that of larger fibers remains largely unchanged. In parallel, KES effectively blocks excitability of larger fibers while moderately suppressing excitability of C-afferents. By compiling selectivity indices in individual animals, we find that optimal KES parameters for C-afferents are >5KHz frequency and 7-10 times engagement threshold (xT) intensity in rats, 15-25xT in mice. These effects can be explained in computational models by how sodium channel responses to KES are shaped by axonal size and myelin. Our results indicate that selective engagement of vagal C-afferents is attainable by intermittent KES.

bioengineering↗

bioRxiv2021

Complex phyllosphere microbiome aids in the establishment of the invasive macrophyte Hydrilla verticillata (L.) under conditions of nitrogen scarcity

Despite the low availability of nitrogen (N), the highly productive macrophyte Hydrilla verticillata (L.) is a successful invader of the littoral zones at lake Atitlan, Guatemala, with profound implications for lake ecology. To help answer the question of how Hydrilla, accompanied by the filamentous green alga Cladophora Kutzing (Ulvophyceae), sustains fast growth under conditions of N scarcity, we studied the composition and potential biogeochemical function of the associated microbiomes. We combined results from next generation sequencing of associated bacterial and fungal assemblages with traditional microscopy-based taxonomical evaluation of algae and cyanobacteria. We focused on the presence of specific N2-fixing genera and their relative importance. Data on community composition are complemented with measurements of diazotrophic activity. The results expand our knowledge of the ecophysiology of these algae-plant-microbe consortia and suggest that several levels of biological complexity should be considered to fully understand aquatic plant ecology and the process of macrophyte invasions.

ecology↗

bioRxiv2020

Cystic Fibrosis Acidic Microenvironment Determines Antibiotic Susceptibility and Biofilm Formation of Pseudomonas aeruginosa

Pseudomonas aeruginosa is the most prevalent bacterial species that contributes to cystic fibrosis (CF) respiratory failure. The impaired function of cystic fibrosis transmembrane conductance regulator leads to abnormal epithelial Cl- / HCO3- transport and acidification of airway surface liquid. However, it remains unclear why Pseudomonas aeruginosa preferentially colonizes in the CF lungs. In this study, we carried out studies to investigate if lower pH helps Pseudomonas aeruginosa adapt and thrive in the CF-like acidic lung environment. Our results reveal that Pseudomonas aeruginosa generally forms more biofilm and induces antibiotic resistance faster in acidic conditions and that this can be reversed by returning the acidic environment to physiologically neutral conditions. Pseudomonas aeruginosa appears to be highly adaptive to the CF-like acidic pH environment. By studying the effects of an acidic environment on bacterial response, we may provide a new therapeutic option in preventing chronic Pseudomonas aeruginosa infection and colonization.

microbiology↗

bioRxiv2020

Microfluidic Isolation of Aptamers with Affinity towards Multiple Myeloma Monoclonal Immunoglobulins (M-Ig)

Multiple myeloma (MM) is a bone marrow cancer of resident plasma cells that affects 125,000 patients in the U.S. with [~] 30,000 new cases per year. Its signature is the clonal over-proliferation of a single plasma cell that secretes a patient specific monoclonal immunoglobulin (M-Ig). Detecting this patient specific M-Ig could allow sensitive detection of minimal residual disease in multiple myeloma from patient serum. Aptamers, single-stranded oligonucleotides with affinity and specificity to a target molecule, have recently been introduced as affinity reagents able to detect MM M-Igs. Here we adapt these benchtop M-Ig systematic evolution of ligands through exponential enrichment (SELEX) techniques to our bead integrated microfluidic SELEX (BIMS) device to rapidly generate patient specific aptamers. Using MM patient serum, we isolate patient M-Ig specific aptamers rapidly (runtime < 12 hours) with high affinity (KD < 20 nM) while consuming limited quantities of patient M-Ig (< 100 g).

bioengineering↗

bioRxiv2020

A connectome-based prediction model of long-term memory

Although many studies have investigated the neural basis of intra-individual fluctuations in long-term memory (LTM), few have explored the differences across individuals. Here, we characterize a whole-brain functional connectivity (FC) network based on fMRI data in an n-back task that robustly predicts individual differences in LTM. Critically, although FC during the n-back task also predicted working memory (WM) performance and the two networks had some shared components, they are also largely distinct from each other: the LTM model performance remained robust when we controlled for WM and vice versa. Furthermore, regions important for LTM such as the medial temporal lobe did contribute, but only partially, to predicting LTM. These results demonstrate that individual differences in LTM are dependent on the configuration of a whole-brain functional network including but not limited to regions traditionally associated with LTM during encoding and that such a network is separable from what supports WM.

neuroscience↗

bioRxiv2020

A Computer-aided Method for Identifying the Presence of Softwood Growth Ring Boundaries

ABSTRACTThe objective of this study was to develop a computer-aided method to quantify the obvious degree of growth ring boundaries of softwood species, based on data analysis with some image processing technologies. For this purpose, a 5× magnified cross-section color micro-image of softwood was cropped into 20 sub-images, then every image is binarized as a gray image according to an automatic threshold value. After that, the number of black pixels in the gray image was counted row by row and the number of black pixels was binarized to 0 or 100. Finally, a transition band from earlywood to latewood on the sub-image was identified. If this was successful, the growth ring boundaries of the sub-image are distinct, otherwise they were indistinct or absent. If 10 of the 20 sub-images are distinct, with the majority voting method, the growth ring boundaries of softwood are distinct, otherwise they are indistinct or absent. The proposed method has been visualized as a growth-ring-boundary detecting system based on the .NET Framework. A sample of 100 micro-images (Supplementary Images) of softwood cross-sections were selected for evaluation purposes. In short, this detecting system computes the obvious degree of growth ring boundaries of softwood species by image processing involved image importing, image cropping, image reading, image grayscale, image binarization, data analysis. The results showed that the method used avoided mistakes made by the manual comparison method of identifying the presence of growth ring boundaries, and it has a high accuracy of 98%.View Full Text

plant biology↗

bioRxiv2020

Flagellar targeting of an arginine kinase requires the conserved Lipidated Intraflagellar Transport (LIFT) pathway in Trypanosoma brucei

Both intraflagellar transport (IFT) and lipidated intraflagellar transport (LIFT) pathways are essential for cilia/flagella biogenesis, motility and sensory functions. In the LIFT pathway, lipidated cargoes are transported into the cilia through the coordinated actions of cargo carrier proteins such as Unc119 or PDE6{delta}, as well as small GTPases Arl13b and Arl3 in the cilium. Our previous studies revealed a single Arl13b ortholog in the evolutionarily divergent Trypanosoma brucei. TbArl13 catalyses two TbArl3 homologs, TbArl3A and TbArl3C, suggesting the presence of a conserved LIFT pathway in these protozoan parasites. Only a single homolog to the cargo carrier protein Unc119 was identified in T. brucei genome, but its function in lipidated protein transport has not been characterized. In this study, we exploited the proximity-based biotinylation approach to identify binding partners of TbUnc119. We showed that TbUnc119 binds to a flagellar arginine kinase TbAK3 in a myristoylation-dependent manner and is responsible for its targeting and enrichment in the flagellum. Interestingly, only TbArl3A, but not TbArl3C interacts with TbUnc119 in a GTP-dependant manner, suggesting functional specialization of Arl3-GTPases in T. brucei. This study establishes the function of TbUnc119 as a myristoylated cargo carrier and supports the presence of a conserved LIFT pathway in T. brucei.

cell biology↗