Biology subjects

Chang, L.

Publications and source records attributed to Chang, L..

At least 91 records · Page 5Linked to original sources

bioRxiv2021

Modeling Western Pacific Amyotrophic Lateral Sclerosis and Parkinsonism dementia Complex with Microglia Containing Cerebral Organoids Derived from Induced Pluripotent Stem Cells

Western Pacific Amyotrophic Lateral Sclerosis and Parkinsonism-dementia Complex (ALS-PDC) is a neurodegenerative disease linked to the traditional consumption of cycad seeds by the Chamorro people of Guam. Little is known about the etiological role of cycad toxin in ALS-PDC. Patient-derived induced pluripotent stem cells were derived from age- and sex-matched affected and unaffected patient lymphoid cells then differentiated into cerebral organoids. After three months, the ALS-PDC affected organoids were smaller, their neurons had less extensive neurite outgrowth, and the organoids had more reactive astrocytes and M1 microglia, fewer resting and M2 microglia, and more open extracellular space. Most of these phenomena could be recapitulated by exposing unaffected organoids to {beta}-methylamino L-alanine (BMAA), a toxic amino acid produced by cyanobacteria living with cycad plants. Furthermore, ALS-PDC affected organoids exhibited an exacerbated neuroinflammatory response to BMAA exposure via activation of caspase1/NLRP3 inflammasome. A genome-wide transcriptome analysis of the organoids showed that the most down-regulated pathways were taurine, alanine, aspartate, and glutamate metabolism; protein digestion; and absorption. The most down-regulated biological processes were type I interferon signaling, regulation of neuron differentiation and extracellular matrix organization. Our results suggested that the etiology of ALS-PDC is due to metabolic disorders that shifted microglia to a more pro-inflammatory M1 state instead of a non-inflammatory, repairing M2 state, which exacerbated inflammation and reduced extracellular matrix strength. Supplementation of transforming growth factor beta (TGF-{beta}) to ALS-PDC affected organoids increased the expression of interferon-induced transmembrane proteins (IFITMs) and restored M2 microglia populations and extracellular matrix organization. Organoids containing networks of neurons, astrocytes, microglia derived from iPSC with our protocol provides an excellent cellular model for neurodegenerative disease modeling. Significance StatementO_LIWestern Pacific Amyotrophic Lateral Sclerosis and Parkinsonism-dementia Complex (ALS-PDC) cerebral organoids containing networks of neurons, astrocytes, and microglia were generated from patient specific lymphoid derived induced pluripotent stem cells. C_LIO_LIALS-PDC affected organoids were smaller, with neurons had less extensive neurite outgrowth, more reactive astrocytes and M1 microglia, fewer resting and M2 microglia, and more open extracellular matrix spaces when compared to ALS-PDC unaffected organoids. C_LIO_LIGenome-wide transcriptome analysis indicated that ALS/PDC affected organoids had significantly lower expression of genes related to vitamin B6, amino acid and protein glycation metabolisms, down-regulated type I interferon signaling, the regulation of neuron differentiation and extracellular matrix production. C_LIO_LIOur results implicated that the etiology of ALS-PDC is due to metabolic disorders that led the shift of microglia to more pro-inflammatory M1 state and less non-inflammatory resting, repairing M2 state of microglia subpopulation, which primed the exacerbated inflammation and reduced extracellular matrix strength. TGF-{beta} promoted interferon-induced transmembrane protein (IFITMs) expression and restored the repairing M2 state of microglia population and extracellular matrix organization. C_LI

neuroscience↗

bioRxiv2021

Improving the analysis of biological ensembles through extended similarity measures

We present new algorithms to classify structural ensembles of macromolecules, based on the recently proposed extended similarity measures. Molecular Dynamics provides a wealth of structural information on systems of biologically interest. As computer power increases we capture larger ensembles and larger conformational transitions between states. Typically, structural clustering provides the statistical mechanics treatment of the system to identify relevant biological states. The key advantage of our approach is that the newly introduced extended similiarity indices reduce the computational complexity of assessing the similarity of a set of structures from O(N2) to O(N). Here we take advantage of this favorable cost to develop several highly efficient techniques, including a linear-scaling algorithm to determine the medoid of a set (which we effectively use to select the most representative structure of a cluster). Moreover, we use our extended similarity indices as a linkage criterion in a novel hierarchical agglomerative clustering algorithm. We apply these new metrics to analyze the ensembles of several systems of biological interest such as folding and binding of macromolecules (peptide,protein,DNA -protein). In particular, we design a new workflow that is capable of identifying the most important conformations contributing to the protein folding process. We show excellent performance in the resulting clusters (surpassing traditional linkage criteria), along with faster performance and an efficient cost-function to identify when to merge clusters.

biophysics↗

bioRxiv2021

Soil fauna may buffer the negative effects of drought on alien plant invasion

Although many studies have tested the direct effects of drought on alien plant invasion, less is known about how drought affects alien plant invasion indirectly via other groups of organisms such as soil fauna. To test for such indirect effects, we grew single plant of nine naturalized alien target species in pot-mesocosms with a native community of five native grassland species under four combinations of two drought (well-watered vs drought) and two soil-fauna-inoculation (with vs without) treatments. We found that drought decreased the absolute and the relative biomass production of the alien plants, and thus reduced their competitive advantage in the native community. Drought decreased the abundance of soil fauna, particularly the soil mites, but did not affect abundance and richness of soil herbivores. Soil-fauna inoculation increased the biomass of the native plant community and thereby decreased the relative biomass production of the alien species. The increased invasion resistance due to soil fauna, however, tended (p = 0.09) to be stronger for plants growing under well-watered conditions than under drought. Our multispecies experiment thus shows that soil fauna might help native resident communities to resist alien plant invasions, but that this effect might be diminished by drought.

ecology↗

bioRxiv2021

Structural basis of target DNA recognition by CRISPR-Cas12k for RNA-guided DNA transposition

The type V-K CRISPR-Cas system, featured by Cas12k effector with a naturally inactivated RuvC domain and associated with Tn7-like transposon for RNA-guided DNA transposition, is a promising tool for precise DNA insertion. To reveal the mechanism underlying target DNA recognition, we determined a cryo-EM structure of Cas12k from cyanobacteria Scytonema hofmanni in complex with a single guide RNA (sgRNA) and a double-stranded target DNA. Coupled with mutagenesis and in vitro DNA transposition assay, our results revealed mechanisms for the recognition of the GGTT PAM sequence and the structural elements of Cas12k critical for RNA-guided DNA transposition. These structural and mechanistic insights should aid in the development of type V-K CRISPR-transposon systems as tools for genome editing.

molecular biology↗

bioRxiv2021

A Comprehensive Overview of the Physical Health of the Adolescent Brain Cognitive Development Study (ABCD) Cohort at Baseline

Physical health in childhood is crucial for neurobiological as well as overall development, and can shape long-term outcomes into adulthood. The landmark, longitudinal Adolescent Brain Cognitive Development StudySM (ABCD study(R)), was designed to investigate brain development and health in almost 12,000 youth who were recruited when they were 9-10 years old and will be followed through adolescence and early adulthood. The overall goal of this paper is to provide descriptive analyses of physical health measures in the ABCD study at baseline, including but not limited to sleep, physical activity and sports involvement, and body mass index, and how these measures vary across demographic groups. This paper outlines how the physical health of the ABCD sample corresponds with that of the US population and highlights important avenues for health disparity research. This manuscript will provide important information for ABCD users and help guide analyses investigating physical health as it pertains to adolescent and young adult development.

developmental biology↗

bioRxiv2021

Cryo-EM reveals new species-specific proteins and symmetry elements in the Legionella pneumophila Dot/Icm T4SS

Legionella pneumophila is an opportunistic pathogen that causes the potentially fatal pneumonia known as Legionnaires Disease. The pathology associated with infection depends on bacterial delivery of effector proteins into the host via the membrane spanning Dot/Icm type IV secretion system (T4SS). We have determined sub-3.0 [A] resolution maps of the Dot/Icm T4SS core complex by single particle cryo-EM. The high-resolution structural analysis has allowed us to identify proteins encoded outside the Dot/Icm genetic locus that contribute to the core T4SS structure. We can also now define two distinct areas of symmetry mismatch, one that connects the C18 periplasmic ring (PR) and the C13 outer membrane cap (OMC) and one that connects the C13 OMC with a 16-fold symmetric dome. Unexpectedly the connection between the PR and OMC is DotH, with five copies sandwiched between the OMC and PR to accommodate the symmetry mismatch. Finally, we observe multiple conformations in the reconstructions that indicate flexibility within the structure. We hypothesize this conformational flexibility is likely to facilitate the Dot/Icm T4SSs ability to translocate a remarkably large set of [~]300 putative substrates across the inner and outer membranes of the bacterial cell.

microbiology↗

bioRxiv2021

Insights into early stages of the establishment of host:algal endosymbioses: Genetic responses to live versus heat-killed algae and bacterial prey in a sponge host

The freshwater sponge Ephydatia muelleri and its Chlorella-like green algal partner is an emerging model for studying animal:algal endosymbiosis. The sponge host is a highly tractable laboratory organism, and the symbiotic algae are easily cultured. We took advantage of these traits to experimentally interrogate fundamental questions about cellular mechanisms that govern the establishment of durable intracellular partnerships between hosts and symbionts in facultative symbioses. We modified a classical experimental approach to discern the phagocytotic mechanisms that might be co-opted to permit persistent infections, and identified genes differentially expressed in E. muelleri sponges early in the establishment of endosymbiosis. We exposed algal-free E. muelleri to live native algal symbionts, native heat-killed algae, and bacteria, and then performed RNASeq so we could compare patterns of gene expression in each treatment. We contrasted differential gene expression patterns between potential food items (bacteria and heat-killed algae) and the live native Chlorella-like symbiont. We found a relatively small but interesting suite of genes that are uniquely and differentially expressed in the host exposed to live algal symbionts, and a larger number of genes uniquely triggered by host exposure to heat-killed algae. One of the host genes, an ABC transporter that is downregulated in response to live algal symbionts, was further evaluated for its possible role in establishment of the algal symbiosis. We discuss the gene expression profiles associated with host responses to living algal cells in the context of conditions necessary for long-term residency within host cells by phototrophic symbionts as well as the genetic responses to sponge phagocytosis and immune driven pathways.

evolutionary biology↗

bioRxiv2021

Liana optical traits increase tropical forest albedo and reduce ecosystem productivity

Lianas are a key growth form in tropical forests. Their lack of self-supporting tissues and their vertical position on top of the canopy make them strong competitors of resources. A few pioneer studies have shown that liana optical traits differ on average from those of colocated tree. Those trait discrepancies were hypothesized to be responsible for the competitive advantage of lianas over trees. Yet, in the absence of reliable modelling tools, it is impossible to unravel their impact on the forest energy balance, light competition and on the liana success in Neotropical forests. To bridge this gap, we performed a meta-analysis of the literature to gather all published liana leaf optical spectra, as well as all canopy spectra measured over different levels of liana infestation. We then used a Bayesian data assimilation framework applied to two radiative transfer models (RTMs) covering the leaf and canopy scales to derive tropical tree and liana trait distributions, which finally informed a full dynamic vegetation model. According to the RTMs inversion, lianas grew thinner, more horizontal leaves with lower pigment concentrations. Those traits made the lianas particularly efficient at light interception and completely modified the forest energy balance and its carbon cycle. While forest albedo increased by 14% in the shortwave, light availability was dramatically reduced in the understory (-30% of the PAR radiation) and soil temperature decreased by 0.5{degrees}C. Those liana-specific traits were also responsible for a significant reduction of tree (-19%) and ecosystem (-7%) gross primary productivity (GPP) while lianas benefited from them (their GPP increased by +27%). This study provides a novel mechanistic explanation to the increase in liana abundance, new evidence of the impact of structural parasitism on forest functioning, and paves the way for the evaluation of the large-scale impacts of woody vines on forest biogeochemical cycles.

plant biology↗

bioRxiv2021

Involvement of denervated midbrain-derived factors in the formation of ectopic cortico-mesencephalicprojection after hemispherectomy

Neuronal remodeling after brain injury is essential for functional recovery. After unilateral cortical lesion, axons from the intact cortex ectopically project to the denervated midbrain to compensate for the lost function, but the underlying molecular mechanisms remain largely unknown. To address this issue, we examined gene expression profiles in denervated and intact mouse midbrains after hemispherectomy at P6, when ectopic contralateral projection occurs robustly. The analysis showed that various axon growth-related genes were upregulated in the denervated midbrain, and most of these genes are reportedly expressed by astrocytes or microglia. To identify the underlying molecules, the receptors for candidate upregulated molecules were knocked out in layer 5 projection neurons in the intact cortex, using the CRISPR/Cas9-mediated method, and axonal projection from the knocked-out cortical neurons was examined after hemispherectomy. We found that the ectopic projection was significantly reduced when integrin subunit beta 3 (Itgb3) or neurotrophic receptor tyrosine kinase 2 (Ntrk2, also known as TrkB) was knocked out. Overall, the present study suggests that midbrain-derived glial factors whose expression is upregulated after hemispherectomy are involved in lesion-induced remodeling of the cortico-mesencephalic projection.

neuroscience↗

bioRxiv2021

Complementary Maps for Location and Environmental Structure in CA1 and Subiculum

The dorsal subiculum lies among a network of interconnected brain regions that collectively map multiple spatial and orientational relationships between an organism and the boundaries and pathways composing its environment. A unique role of the subiculum in spatial information processing has yet to be defined despite reports of small neuron subpopulations that encode relationships to specific boundaries, axes of travel, or locations. We examined the activity patterns among populations of subiculum neurons during performance of a spatial working memory task performed within a complex network of interconnected pathways. Compared to neurons in hippocampal sub-region CA1, a major source of its afferents, subiculum neurons were far more likely to exhibit multiple firing fields at locations that were analogous with respect to path structure and function. Subiculum neuron populations were also found to exhibit a greater dynamic range in scale of spatial representation and for persistent patterns of spiking activity to be aligned to transitions between maze segments. Together, the findings indicate that the subiculum plays a unique role in spatial mapping, one that complements the location-specific firing of CA1 neurons with the encoding of emergent and recurring structural features of a complex path network.

neuroscience↗

bioRxiv2020

Structural basis for the dimerization-dependent CRISPR-Cas12f nuclease

Cas12f, also known as Cas14, is an exceptionally small type V-F CRISPR-Cas nuclease that is roughly half the size of comparable nucleases of this type. To reveal the mechanisms underlying substrate recognition and cleavage, we determined the cryo-EM structures of the Cas12f-sgRNA-target DNA and Cas12f-sgRNA complexes at 3.1 [A] and 3.9 [A], respectively. An asymmetric Cas12f dimer is bound to one sgRNA for recognition and cleavage of dsDNA substrate with a T-rich PAM sequence. Despite its dimerization, Cas12f adopts a conserved activation mechanism among the type V nucleases which requires coordinated conformational changes induced by the formation of the crRNA-target DNA heteroduplex, including the close-to-open transition in the lid motif of the RuvC domain. Only one RuvC domain in the Cas12f dimer is activated by substrate recognition, and the substrate bound to the activated RuvC domain is captured in the structure. Structure-assisted truncated sgRNA, which is less than half the length of the original sgRNA, is still active for target DNA cleavage. Our results expand our understanding of the diverse type V CRISPR-Cas nucleases and facilitate potential genome editing applications using the miniature Cas12f.

biophysics↗

bioRxiv2020

TIPS: Trajectory Inference of Pathway Significance through Pseudotime Comparison for Functional Assessment of single-cell RNAseq Data

Recent advances in bioinformatics analyses have led to the development of novel tools enabling the capture and trajectory mapping of single-cell RNA sequencing (scRNAseq) data. However, there is a lack of methods to assess the contributions of biological pathways and transcription factors to an overall developmental trajectory mapped from scRNAseq data. In this manuscript, we present a simplified approach for trajectory inference of pathway significance (TIPS) that leverages existing knowledgebases of functional pathways and transcription factor targets to enable further mechanistic insights into a biological process. TIPS returns both the key pathways whose changes are associated with the process of interest, as well as the individual genes that best reflect these changes. TIPS also provides insight into the relative timing of pathway changes, as well as a suite of visualizations to enable simplified data interpretation of scRNAseq libraries generated using a wide range of techniques. The TIPS package can be run through either a web server, or downloaded as a user-friendly GUI run in R, and may serve as a useful tool to help biologists perform deeper functional analyses and visualization of their single-cell and/or large cohort RNAseq data.

bioinformatics↗

bioRxiv2020

Oleic acid triggers hippocampal neurogenesis by binding to TLX/NR2E1

Adult hippocampal neurogenesis underpins learning, memory, and mood, but diminishes with age and illness. The orphan nuclear receptor TLX/NR2E1 is known to regulate neural stem and progenitor cell self-renewal and proliferation, but the precise mechanism by which it accomplishes this is unknown. We found that neural stem and progenitor cells require monounsaturated fatty acids to survive and proliferate. Specifically, oleic acid (18:1{omega}9) binds to TLX to convert it from a transcriptional repressor to a transcriptional activator of cell cycle and neurogenesis genes. We propose a model in which sufficient quantities of this endogenous ligand must bind to TLX to trigger the switch to proliferation. These findings pave the way for future therapeutic manipulations to counteract pathogenic impairments of neurogenesis.

neuroscience↗

bioRxiv2020

Steady-state visually evoked potentials and feature-based attention: Pre-registered null results and a focused review of methodological considerations.

Feature-based attention is the ability to selectively attend to a particular feature (e.g., attend to red but not green items while looking for the ketchup bottle in your refrigerator), and steady-state visually evoked potentials (SSVEPs) measured from the human electroencephalogram (EEG) signal have been used to track the neural deployment of feature-based attention. Although many published studies suggest that we can use trial-by-trial cues to enhance relevant feature information (i.e., greater SSVEP response to the cued color), there is ongoing debate about whether participants may likewise use trial-by-trial cues to voluntarily ignore a particular feature. Here, we report the results of a pre-registered study in which participants either were cued to attend or to ignore a color. Counter to prior work, we found no attention-related modulation of the SSVEP response in either cue condition. However, positive control analyses revealed that participants paid some degree of attention to the cued color (i.e., we observed a greater P300 component to targets in the attended versus the unattended color). In light of these unexpected null results, we conducted a focused review of methodological considerations for studies of feature-based attention using SSVEPs. In the review, we quantify potentially important stimulus parameters that have been used in the past (e.g., stimulation frequency; trial counts) and we discuss the potential importance of these and other task factors (e.g., feature-based priming) for SSVEP studies.

neuroscience↗

bioRxiv2020

A negative feedback model to explain regulation of SARS-CoV-2 replication and transcription

BackgroundCoronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although a preliminary understanding of the replication and transcription mechanisms of SARS-CoV-2 has recently emerged, their regulation remains unclear. ResultsBased on reanalysis of public data, we propose a negative feedback model to explain the regulation of replication and transcription in--but not limited to--SARS-CoV-2. The key step leading to new discoveries was the identification of the cleavage sites of nsp15--an RNA uridylate-specific endoribonuclease, encoded by CoVs. According to this model, nsp15 regulates the synthesis of subgenomic RNAs (sgRNAs) and genomic RNAs (gRNAs) by cleaving transcription regulatory sequences in the body. The expression level of nsp15 determines the relative proportions of sgRNAs and gRNAs, which in turn change the expression level of nps15 to reach equilibrium between the replication and transcription of CoVs. ConclusionsThe replication and transcription of CoVs are regulated by a negative feedback mechanism that influences the persistence of CoVs in hosts. Our findings enrich fundamental knowledge in the field of gene expression and its regulation, and provide new clues for future studies. One important clue is that nsp15 may be an important and ideal target for the development of drugs (e.g. uridine derivatives) against CoVs.

bioinformatics↗

bioRxiv2020

Gluconeogenic Enzyme PCK1 Deficiency Is Critical for CHK2 O-GlcNAcylation and Hepatocellular Carcinoma Growth upon Glucose Deprivation

Elevated hexosamine-biosynthesis pathway (HBP) activity and O-GlcNAcylation are emerging hallmarks of hepatocellular carcinoma (HCC). Inhibiting O-GlcNAcylation could be a promising anti-cancer strategy. Here, we investigate this possibility and demonstrate that deficiency of phosphoenolpyruvate carboxykinase 1 (PCK1), a rate-limiting enzyme in gluconeogenesis, promotes O-GlcNAcylation and hepatoma cell proliferation under low-glucose conditions. PCK1 loss results in oxaloacetate accumulation and AMPK inactivation, promoting uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc) synthesis and CHK2 threonine 378 O-GlcNAcylation and counteracting its ubiquitination and degradation. O-GlcNAcylation also promotes CHK2-dependent Rb phosphorylation and HCC cell proliferation. Therefore, blocking HBP-mediated O-GlcNAcylation suppresses tumor progression in liver-specific Pck1-knockout mice. We reveal a link between PCK1 depletion and hyper-O-GlcNAcylation that underlies HCC oncogenesis and suggest therapeutic targets for HCC that act by inhibiting O-GlcNAcylation.

cancer biology↗

bioRxiv2020

Mass-spectrometry-based near complete draft of the Saccharomyces cerevisiae proteome

Proteomics approaches designed to catalogue all open reading frames (ORFs) under a defined set of growth conditions of an organism have flourished in recent years. However, no proteome has been sequenced completely so far. Here we generate the largest yeast proteome dataset, including 5610 identified proteins using a strategy based on optimized sample preparation and high-resolution mass spectrometry. Among the 5610 identified proteins, 94.1% are core proteins, which achieves near complete coverage of the yeast ORFs. Comprehensive analysis of missing proteins in our dataset indicate that the MS-based proteome coverage has reached the ceiling. A review of protein abundance shows that our proteome encompasses a uniquely broad dynamic range. Additionally, these values highly correlate with mRNA abundance, implying a high level of accuracy, sensitivity and precision. We present examples of how the data could be used, including re-annotating gene localization, providing expression evidence of pseudogenes. Our near complete yeast proteome dataset will be a useful and important resource for further systematic studies.

biochemistry↗

bioRxiv2020

Structure-Based Design with Tag-Based Purification and In-Process Biotinylation Enable Streamlined Development of SARS-CoV-2 Spike Molecular Probes

Biotin-labeled molecular probes, comprising specific regions of the SARS-CoV-2 spike, would be helpful in the isolation and characterization of antibodies targeting this recently emerged pathogen. To develop such probes, we designed constructs incorporating an N-terminal purification tag, a site-specific protease-cleavage site, the probe region of interest, and a C-terminal sequence targeted by biotin ligase. Probe regions included full-length spike ectodomain as well as various subregions, and we also designed mutants to eliminate recognition of the ACE2 receptor. Yields of biotin-labeled probes from transient transfection ranged from [~]0.5 mg/L for the complete ectodomain to >5 mg/L for several subregions. Probes were characterized for antigenicity and ACE2 recognition, and the structure of the spike ectodomain probe was determined by cryo-electron microscopy. We also characterized antibody-binding specificities and cell-sorting capabilities of the biotinylated probes. Altogether, structure-based design coupled to efficient purification and biotinylation processes can thus enable streamlined development of SARS-CoV-2 spike-ectodomain probes.

immunology↗