Biology subjects

Lee, S.

Publications and source records attributed to Lee, S..

At least 451 records · Page 25Linked to original sources

bioRxiv2022

Posteromedial thalamic nucleus activity significantly contributes to perceptual discrimination

Higher-order sensory thalamic nuclei are densely connected with multiple cortical and subcortical areas, yet the role of these nuclei remains elusive. The posteromedial (POm) thalamic nucleus, the higher-order thalamic nucleus in the rodent somatosensory system, is an anatomical hub broadly connected with multiple sensory and motor brain areas, yet weakly responds to passive sensory stimulation and whisker movements. To understand the role of POm in sensory perception, we developed a self-initiated, two-alternative forced-choice task in freely moving mice during active sensing. Using optogenetic and chemogenetic manipulation, we show that POm thalamic nucleus plays a significant role in sensory perception and the projection from the primary somatosensory cortex to POm is critical for the contribution of POm in sensory perception during active sensing.

neuroscience↗

bioRxiv2022

Telomere-to-Telomere and Haplotype-Phased Genome Assemblies of the Heterozygous Octoploid 'Florida Brilliance' Strawberry (Fragaria x ananassa)

The available haplotype-resolved allo-octoploid strawberry (Fragaria x ananassa Duch.) (2n = 8x = 56) genomes were assembled with the trio-binning pipeline, supplied with parental short-reads. We report here a high-quality, haplotype-phased genome assembly of a short-day cultivar, Florida Brilliance (FaFB2) without the use of parental sequences. Using Pacific Biosciences (PacBio) long reads and high-throughput chromatic capture (Hi-C) data, we completed telomere-to-telomere phased genome assemblies of both haplotypes. The N50 continuity of the two haploid assemblies were 23.7 Mb and 26.6 Mb before scaffolding and gap-filling. All 56 pseudochromosomes from the phased-1 and phased-2 assemblies contained putative telomere sequences at the 5 and/or 3 ends. A high level of collinearity between the haplotypes was confirmed by high-density genetic linkage mapping with 10,269 SNPs, and a high level of collinearity with the Royal Royce FaRR1 reference genome was observed. Genome completeness was further confirmed by consensus quality. The LTR assembly Index score for entire genome assembly was 19.72. Moreover, the BUSCO analysis detected over 99% of conserved genes in the combined phased-1 and phased-2 assembly. Both haploid assemblies were annotated using Iso-Seq data from six different Florida Brilliance tissues and RNA-Seq data representing various F. x ananassa tissues from the NCBI sequence read archive, resulting in a total of 104,099 genes. This telomere-to-telomere reference genome of Florida Brilliance will advance our knowledge of strawberry genome evolution and gene functions, and facilitate the development of new breeding tools and approaches.

genomics↗

bioRxiv2022

Neuronal E93 regulates metabolic homeostasis

Metamorphosis is a transition from growth to reproduction, through which an animal adopts adult behavior and metabolism. Yet the mechanisms underlying the switch is unclear. Here we report that neuronal E93, a transcription factor essential for metamorphosis, regulates the adult metabolism and circadian rhythm in Drosophila melanogaster. When E93 is specifically knocked down in neurons, the flies become hyperphagic and obese with increased energy stores and disrupted circadian rhythms. A screen of Gal4 lines targeting subsets of neurons and endocrine cells identified neurons producing GABA and myoinhibitory peptide (MIP) as the main sites of E93 action. Knockdown of the ecdysone receptor specifically in MIP neurons partly phenocopies the MIP neuron-specific knockdown of E93 suggesting the steroid signal coordinates adult metabolism via E93. The circadian disruption caused by neuronal knockdown of E93 is also observed when E93 is knockdown in GABA and MIP neurons. Based on these results we suggest that neuronal E93 is a key switch for metabolic transition representing an intersectional node between metabolism and circadian biology.

physiology↗

bioRxiv2022

Targeting tumour-intrinsic neural vulnerabilities of glioblastoma

Glioblastoma is the most common yet deadliest primary brain cancer1. The neural behavior of glioblastoma, including the formation of synaptic circuitry and tumour microtubes, is increasingly understood to be pivotal for disease manifestation2-9. Nonetheless, the few approved treatments for glioblastoma target its oncological nature, while its neural vulnerabilities remain incompletely mapped and clinically unexploited. Here, we systematically survey the neural molecular dependencies and cellular heterogeneity across glioblastoma patients and diverse model systems. In 27 surgical patient samples, we identify cancer cell morphologies indicative of poor prognosis, and discover repurposable neuroactive drugs with anti-glioblastoma efficacy by image-based drug screening. Glioblastoma cells exhibit functional dependencies on highly expressed neuroactive drug targets, while interpretable molecular machine learning (COSTAR) reveals their downstream convergence on AP-1-driven tumour suppression. This drug-target connectivity signature is confirmed by accurate in silico drug screening on >1 million compounds, as well as by multi-omic profiling of glioblastoma drug responses. Thus, Ca2+-driven AP-1 pathway induction represents a tumour-intrinsic vulnerability at the intersection of oncogenesis and neural activity-dependent signaling. Opportunities for clinical translation of this neural vulnerability are epitomized by the antidepressant Vortioxetine synergizing with current standard of care treatments in vivo. Together, the results presented here provide a mechanistic foundation and conceptual framework for the treatment of glioblastoma based on its neural origins.

cancer biology↗

bioRxiv2022

A Protocol for Single Nucleus RNAseq from Frozen Skeletal Muscle

Single cell technologies are a method of choice to obtain vast amounts of cell-specific transcriptional information under physiological and diseased states. Myogenic cells are resistant to single nucleus RNA sequencing (snRNAseq) due to their large, multinucleated nature. Here, we report a novel, reliable, and cost-effective method to analyze frozen human skeletal muscle by snRNAseq. This method yields all expected cell types for human skeletal muscle and works on tissue frozen for long periods of time and with significant pathological changes. Our method is ideal for studying banked samples with the intention of studying human muscle disease.

genomics↗

bioRxiv2022

Consistent, linear phenological shifts across a century of observations in South Korea

The Korea Meteorological Agency (KMA) has monitored flowering dates over the past 100 years for seven economically important woody plant species. This unique dataset is perfect for understanding whether historical patterns of phenological plasticity are breaking down in the face of recent and rapid climate change. Here we show that a scientist armed only 50 years into this study would have been able to predict the phenological shifts of the last 50 years with a high degree of accuracy. This is despite record-breaking warm temperatures and unprecedented early flowering, suggesting consistency in phenological shifts over time.

ecology↗

bioRxiv2022

Decoding Age-specific Changes in Brain Functional Connectivity Using a Sliding-window Based Clustering Method

Functional magnetic resonance imaging (fMRI) permits detailed study of human brain function. Understanding the age-specific development of neural circuits in the typically developing brain may help us generate new hypotheses for developmental psychopathologies. Functional connectivity (FC), defined as the statistical associations between two brain regions, has been widely used in estimating functional networks from fMRI data. Previous research has shown that the evolution of FC does not follow a linear trend, particularly from childhood to young adulthood. Thus, this work aims to detect the nuanced FC changes with age from the non-linear curves and identify age-period-specific FC development patterns. We proposed a sliding-window based clustering approach to identify refined age interval of FC development. We used resting-state fMRI (rs-fMRI) data from the human connectome project-development (HCP-D), which recruited children, adolescents, and young adults aged from 5 to 21 years. Our analyses revealed different developmental patterns of resting-state FC by sex. In general, females matured earlier than males, but males had a faster development rate during age 100 -120 months. We identified four developmental phases: network construction in late childhood, segregation and integration construction in adolescence, network pruning in young adulthood, and a unique phase in males -- U-shape development. In addition, we investigated the sex effect on the slopes of FC-age correlation. Males had higher slopes during late childhood and young adulthood. These results inform trajectories of normal FC development, information that can in the future be used to pinpoint when development might go awry in neurodevelopmental disorders. HighlightO_LIPropose a novel sliding-window-based framework to identify refined age intervals of functional connectivity (FC) development. C_LIO_LIIdentify four developmental phases: network construction in late childhood, segregation and integration in adolescence, network pruning in young adulthood, and a unique phase in males -- U-shape development. C_LIO_LICharacterize the representative FC pattern for each developmental phase based on global network statistics, modular connectivity, and hub ROIs. C_LIO_LIReveal sex differences in developmental timing, rate, and patterns of resting-state FC. C_LI

neuroscience↗

bioRxiv2022

A Visual, Inexpensive, and Wireless Capillary Rheometer

Complex fluid systems can exhibit highly non-linear and time-dependent flow behaviors that arise from microscale reorganization. Rheological measurements to understand these flow-induced properties in soft condensed matter and biology are critical to optimize manufacturing processes that rely upon the use of complex fluids, such as the creation of viscoelastic bioinks for 3D bioprinting. While typical rheological characterizations are performed on bulky and expensive rheometers, these options do not readily enable in situ microscopic visualization of flow behavior, which can provide microstructural insights into the mechanisms and patterns of yielding. To address these limitations, we present a visual, inexpensive (approximately $200), and wireless capillary rheometer (VIEWR) assembled from chiefly 3D printed components. We validate the accuracy and reliability of the portable rheometer by comparing measurements of multiple rheological parameters, including viscosity and yield stress, with measurements obtained from a commercial oscillatory rheometer. At its core, VIEWR employs an easily interchangeable glass capillary channel to enable real-time microscopic observation under flow conditions. To facilitate various experimental conditions, a communication protocol based on Internet of Things (IoT) is adapted to support wireless transmission of data. This unique rheometer design can be used for characterizing and visualizing numerous living and non-living complex fluids. Specifications table O_TBL View this table: org.highwire.dtl.DTLVardef@1be2128org.highwire.dtl.DTLVardef@172d43eorg.highwire.dtl.DTLVardef@1cc6eaforg.highwire.dtl.DTLVardef@76c6f5org.highwire.dtl.DTLVardef@3882_HPS_FORMAT_FIGEXP M_TBL C_TBL

bioengineering↗

bioRxiv2022

Cryo-EM analyses of wild-type and oncogenic KIT mutants reveal structural oncogenic plasticity and a novel Achilles heel for therapeutic intervention

The receptor tyrosine kinase KIT and its ligand SCF are required for the development of hematopoietic stem cells, germ cells, and other cells. A variety of human cancers, such as acute myeloid leukemia and mast cell leukemia, are driven by somatic gain-of-function KIT mutations. Here, we report cryo-EM structural analyses of full-length wild-type and two oncogenic KIT mutants, which show that the symmetric arrangement of ligand-occupied KIT dimers is converted into asymmetric D5 homotypic contacts juxtaposing the plasma membrane. Mutational analysis of KIT reveals in D5 region an "Achilles heel" for therapeutic intervention. A ligand-sensitized oncogenic KIT mutant exhibits a more comprehensive and stable D5 asymmetric conformation. A constitutively active ligand-independent oncogenic KIT mutant adopts a V-shaped conformation solely held by D5-mediated contacts. SCF binding to this mutant fully restores the conformation of wild-type KIT dimers, revealing an unexpected structural plasticity of oncogenic mutants that may offer new therapeutic modality.

biochemistry↗

bioRxiv2022

bootRanges: Flexible generation of null sets of genomic ranges for hypothesis testing

bootRanges provides fast functions for generation of bootstrapped genomic ranges representing the null sets in enrichment analysis. We show that shuffling or permutation schemes may result in overly narrow test statistics null distributions, while creating new ranges sets with a block bootstrap preserves local genomic correlation structure and generates more reliable null distributions. It can also be used in more complex analyses, such as accessing correlations between cis-regulatory elements (CREs) and genes across cell types or providing optimized thresholds, e.g. log fold change (logFC) from differential analysis. The bootRanges functions are available in the R/Bioconductor package nullranges at https://bioconductor.org/packages/nullranges.

bioinformatics↗

bioRxiv2022

Solid-State Single-Molecule Sensing with the Electronic Life-detection Instrument for Enceladus/Europa (ELIE)

Growing evidence of the potential habitability of Ocean Worlds across our Solar System is motivating the advancement of technologies capable of detecting life as we know it - sharing a common ancestry or common physicochemical origin to life on Earth - or dont know it, representing a distinct genesis event of life quite different than our one known example. Here, we propose the Electronic Life-detection Instrument for Enceladus/Europa (ELIE), a solid-state single-molecule instrument payload that aims to search for life based on the detection of amino acids and informational polymers (IPs) at the parts per billion to trillion level. As a first proof-of- principle in a laboratory environment, we demonstrate single-molecule detection of the amino acid L-proline at a 10 {micro}M concentration in a compact system. Based on ELIEs solid-state quantum electronic tunneling sensing mechanism, we further propose the quantum property of the HOMO-LUMO gap (energy difference between a molecules highest energy occupied molecular orbital and lowest energy unoccupied molecular orbital) as a novel approach to measure amino acid complexity. Finally, we assess the potential of ELIE to discriminate between abiotically and biotically derived (-amino acids in order to reduce false positive risk for life detection. Nanogap technology can also be applied to the detection of nucleobases and short sequences of IPs such as, but not limited to, RNA and DNA. Future missions may utilize ELIE to target preserved biosignatures on the surface of Mars, extant life in its deep subsurface, or life or its biosignatures in the plume, surface, or subsurface of ice moons such as Enceladus or Europa. One Sentence SummaryA solid-state nanogap can determine the abundance distribution of amino acids, detect nucleic acids, and shows potential for detecting life as we know it and life as we dont.

biophysics↗

bioRxiv2022

IndepthPathway: an integrated tool for in-depth pathway enrichment analysis based on bulk and single cell sequencing data

Single-cell sequencing (SCS) enables exploring the pathways and processes of cells, and cell populations. However, there is a paucity of pathway enrichment methods designed to tolerate the high noise and low gene coverage of this technology. When gene expression data are noisy and signals are sparse, testing pathway enrichment based on the genes expression may not yield statistically significant results which is particularly problematic when detecting the pathways enriched in less abundant cells that are vulnerable to disturbances. In this project, we developed a Weighted Concept Signature Enrichment Analysis (WCSEA) algorithm specialized for pathway enrichment analysis from single cell transcriptomics (scRNA-seq). WCSEA took a broader approach for assessing the functional relations of pathway gene sets to differentially expressed genes, and leverage the cumulative signature of molecular concepts characteristic of the highly differentially expressed genes, which we termed as the universal concept signature, to tolerate the high noise and low coverage of this technology. We then incorporated WCSEA into a R package called "IndepthPathway" for biologists to broadly leverage this method for pathway analysis based on bulk and single cell sequencing data. Through simulating technical variability and dropouts in gene expression characteristic of scRNA-seq as well as benchmarking on a real dataset of matched single cell and bulk RNAseq data, we demonstrate that IndepthPathway presents outstanding stability and depth in pathway enrichment results under stochasticity of the data, thus will substantially improve the scientific rigor of the pathway analysis for single cell sequencing data. The IndepthPathway package is available through: https://github.com/wangxlab/IndepthPathway.

bioinformatics↗

bioRxiv2022

Improved methodology for protein NMR structure calculation using hydrogen bond restraints and ANSURR validation: the SH2 domain of SH2B1

Protein structures calculated using NMR data are less accurate and less well defined than they could be. Here we use the program ANSURR to show that this deficiency is at least in part due to a lack of hydrogen bond restraints. We then describe a protocol to introduce hydrogen bond restraints into the structure calculation of the SH2 domain from SH2B1 in a systematic and transparent way, and show that the structures generated are more accurate and better defined as a result. We also show that ANSURR can be used as a guide to know when the structure calculation is good enough to stop.

biophysics↗

bioRxiv2022

Reduced oocyte quality and exacerbation of the maternal age effect are enduring consequences of low-level atrazine exposure in mouse

BACKGROUNDEgg development has unique features that render it vulnerable to environmental perturbation. The herbicide atrazine is an endocrine disruptor shown to have detrimental effects on reproduction across a number of vertebrate species. OBJECTIVESTo determine whether exposure to low levels of atrazine impairs meiosis in female mammals using a mouse model; in particular, whether and how the fidelity of oocyte chromosome segregation is affected, and whether the aging-related aneuploidy is exacerbated. METHODSFemale C57BL/6J mice were exposed to two levels of atrazine in drinking water, with the lower level corresponding to detected environmental contamination. To model exposure during development, atrazine was ingested by pregnant females at 0.5 days post coitum and continued until pups were weaned at 21 days post-partum. For adult exposure, 2-month-old females ingested atrazine for 3 months. For each exposure group, various indicators of oocyte quality were determined, including developmental capacity and chromosomal abnormalities during the two meiotic divisions. RESULTSDevelopmental exposure caused only minor effects on the fetal events of meiotic prophase-I and establishment of initial follicle pools. However, ovulation was enhanced while oocyte quality was significantly reduced. At the chromosome level, misalignment and numerical and structural abnormalities were increased at both meiotic divisions. Furthermore, fertilization efficiency was impaired in vitro, and apoptosis was elevated in blastocysts derived from the eggs of atrazine-exposed females. Similar levels of chromosomal defects were seen in oocytes following both developmental and adult exposure regimens suggesting that quiescent primordial follicles may be the consequential targets of atrazine. Importantly, defects were observed long after exposure was terminated. Moreover, dramatic increases in chromosomally abnormal oocytes were seen in older mice indicating that atrazine exposure during development exacerbates the effects of maternal aging on oocyte quality. Indeed, analogous to the effects of maternal age, atrazine exposure resulted in weakened cohesion between sister chromatids. CONCLUSIONLow-level atrazine exposure causes persistent changes to the female mammalian germline with potential consequences for reproductive lifespan and congenital disease.

pharmacology and toxicology↗

bioRxiv2022

Viruses of soil ammonia oxidising archaea identified using a novel DNA stable isotope probing approach for low GC mol% genomes

Ammonia-oxidising archaea (AOA) are a ubiquitous component of microbial communities and dominate the first stage of nitrification in some soils. While we are beginning to understand soil virus dynamics, we have no knowledge of the composition or activity of those infecting nitrifiers or their potential to influence processes. This study aimed to characterise viruses having infected autotrophic AOA in two nitrifying soils of contrasting pH by following transfer of assimilated CO2-derived 13C from host to virus via DNA stable-isotope probing and metagenomic analysis. Incorporation of 13C into low GC mol% AOA and virus genomes increased DNA buoyant density in CsCl gradients but resulted in co-migration with dominant non-enriched high GC mol% genomes, reducing sequencing depth and contig assembly. We therefore developed a hybrid approach where AOA and virus genomes were assembled from low buoyant density DNA with subsequent mapping of 13C isotopically enriched high buoyant density DNA reads to identify activity of AOA. Metagenome-assembled genomes were different between the two soils and represented a broad diversity of active populations. Sixty-four AOA-infecting viral operational taxonomic units (vOTUs) were identified with no clear relatedness to previously characterised prokaryote viruses. These vOTUs were also distinct between soils, with 42% enriched in 13C derived from hosts. The majority were predicted as capable of lysogeny and auxiliary metabolic genes included an AOA-specific multicopper oxidase suggesting infection may augment copper uptake essential for central metabolic functioning. These findings indicate virus infection of AOA may be a frequent process during nitrification with potential to influence host physiology and activity.

microbiology↗

bioRxiv2022

Npas4-mediated dopaminergic regulation of fear memory states

Amygdala circuitry encodes associations between conditioned stimuli and aversive unconditioned stimuli, and also controls fear expression (Pape and Pare, 2010). However, whether and how irrelevant information for unpaired conditioned stimuli (CS-) is discretely processed, and how it was influenced by stress remain unknown. CS- memory is retrievable immediately after fear conditioning, but then becomes silent after memory consolidation in mice. Synaptic pathway from the lateral to the anterior basal amygdala gates the expression of CS- memory, depending upon Npas4-mediated Drd4 synthesis. The upregulation of Npas4-Drd4 axis, which is precluded by corticosterone, shifts functional states of neural engrams for CS- memory toward silent states and limits its retrievability. In here, we demonstrate the cellular and molecular mechanisms regulating the functional states of neural engrams, which can be switched or maintained, supporting discriminative memory.

neuroscience↗

bioRxiv2022

Translation of dipeptide repeat proteins in C9ORF72-ALS/FTD through unique and redundant AUG initiation codons

A hexanucleotide repeat expansion in the first intron of C9ORF72 is the most common monogenic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). A hallmark of ALS/FTD pathology is the presence of dipeptide repeat (DPR) proteins, produced from both sense GGGGCC (poly-GA, poly-GP, poly-GR) and antisense CCCCGG (poly-PR, poly-PG, poly-PA) transcripts. Although initiation codons and regulatory factors have been identified for sense DPR translation, they remain mostly unknown for antisense DPRs. Here, we show that an AUG initiation codon is necessary for poly-PR synthesis, suggesting canonical AUG dependent translation. Remarkably, although an AUG located 194 base pairs (bp) upstream of the repeat is the main start codon for poly-PG synthesis, two other AUG codons (-212 bp, -113 bp) can also initiate translation, demonstrating a striking redundancy in start codon usage. eIF2D is required for CUG start codon-dependent poly-GA translation from the sense transcript in human motor neurons derived from induced pluripotent stem cells of C9ORF72 ALS/FTD patients, but AUG-dependent poly-PG or poly-PR synthesis does not require eIF2D, indicating that distinct translation initiation factors control DPR synthesis from sense and antisense transcripts. Our findings provide key molecular insights into DPR synthesis from the C9ORF72 locus, which may be broadly applicable to many other nucleotide-repeat expansion disorders.

molecular biology↗

bioRxiv2022

matchRanges: Generating null hypothesis genomic ranges via covariate-matched sampling

Deriving biological insights from genomic data commonly requires comparing attributes of selected genomic loci to a null set of loci. The selection of this null set is non trivial, as it requires careful consideration of potential covariates, a problem that is exacerbated by the non-uniform distribution of genomic features including genes, enhancers, and transcription factor binding sites. Propensity score-based covariate matching methods allow selection of null sets from a pool of possible items while controlling for multiple covariates; however, existing packages do not operate on genomic data classes and can be slow for large data sets making them difficult to integrate into genomic workflows. To address this, we developed matchRanges, a propensity score-based covariate matching method for the efficient and convenient generation of matched null ranges from a set of background ranges within the Bioconductor framework.

bioinformatics↗