Biology subjects

Lee, H.

Publications and source records attributed to Lee, H..

At least 415 records · Page 23Linked to original sources

bioRxiv2020

Autophagy is required for self-incompatible pollen rejection in two transgenic Arabidopsis thaliana accessions

Successful reproduction in the Brassicaceae is mediated by a complex series of interactions between the pollen and the pistil, and some species have an additional layer of regulation with the self-incompatibility trait. While the initial activation of the self-incompatibility pathway by the pollen S-locus protein11/S-locus cysteine-rich peptide and the stigma S Receptor Kinase is well characterized, the downstream mechanisms causing self-pollen rejection are still not fully understood. In previous studies, we had detected the presence of autophagic bodies with self-incompatible pollinations in Arabidopsis lyrata and transgenic A. thaliana lines, but it was not known if autophagy was essential for self-pollen rejection. Here, we investigated the requirement of autophagy in this response by crossing mutations in the essential AUTOPHAGY7 (ATG7) or AUTOPHAGY5 (ATG5) genes into two different transgenic self-incompatible A. thaliana lines in the Col-0 and C24 accessions. By using these previously characterized transgenic lines that express A. lyrata and A. halleri self-incompatibility genes, we demonstrated that disrupting autophagy can weaken their self-incompatible responses in the stigma. When the atg7 or atg5 mutations were present, an increased number of self-incompatible pollen were found to hydrate and form pollen tubes that successfully fertilized the self-incompatible pistils. Additionally, we confirmed the presence of GFP-ATG8a labelled autophagosomes in the stigmatic papillae following self-incompatible pollinations. Together, these findings support the requirement of autophagy in the self-incompatibility response and add to the growing understanding of the cellular events that take place in the stigma to reject self-pollen. One Sentence SummaryIn self-incompatible transgenic Arabidopsis thaliana lines, autophagy is an integral part of the cellular responses in the stigma to efficiently block fertilization by self-incompatible pollen.

plant biology↗

bioRxiv2020

CRISPR/Cas9-mediated gene editing induces neurological recovery in an A53T-SNCA overexpression rat model of Parkinson's disease

To date, no publicly available disease-modifying therapy for Parkinsons disease has been developed. This can be partly attributed to the absence of techniques for in vivo deletion of the SNCA gene (encoding -synuclein), which is one of the key players in Parkinsons disease pathology. In particular, A53T-mutated SNCA (A53T-SNCA) is one of the most studied familial pathologic mutations in Parkinsons disease. Here we utilized a recently discovered genome editing technique, CRISPR/Cas9, to delete A53T-SNCA in vitro and in vivo. Among various CRISPR/Cas9 systems, SaCas9-KKH with a single guide RNA (sgRNA) targeting A53T-SNCA was packaged into adeno-associated virus. Adeno-associated virus carrying SaCas9-KKH significantly reduced A53T-SNCA levels in A53T-SNCA-overexpressed HEK293T cells, without off-target effects on wild-type SNCA. Furthermore, we tested the techniques in vivo therapeutic potential in a viral A53T-SNCA overexpression rat model of Parkinsons disease. Gene deletion of A53T-SNCA significantly prevented the overexpression of -synuclein, dopaminergic neurodegeneration, and parkinsonian motor symptoms, whereas a negative control without sgRNA did not. Our findings propose CRISPR/Cas9 system as a potential therapeutic tool for A53T-SNCA familial Parkinsons disease.

genetics↗

bioRxiv2020

Thyroid hormone regulates proximodistal identity in the fin skeleton

Across the [~]30,000 species of ray-finned fish, fins show incredible diversity in overall shape and in the patterning of the supportive bony rays. Fin length mutant zebrafish have provided critical insights into the developmental pathways that regulate relative fin size. However, the processes that govern skeletal patterning along the proximodistal axis of the fin have remained less well understood. Here, we show that thyroid hormone regulates proximodistal identity of fin rays, distalizing gene expression profiles, morphogenetic processes during outgrowth, and ultimate morphology of the fin. This role for thyroid hormone in specifying proximodistal identity appears conserved between development and regeneration, in all the fins, and between species. We demonstrate that proximodistal identity is regulated independently from pathways that determine size, and we show that modulating proximodistal patterning relative to growth can recapitulate the spectrum of fin ray diversity found in nature.

developmental biology↗

bioRxiv2020

Body mass variations relate to fractionated functional brain hierarchies

AO_SCPLOWBSTRACTC_SCPLOWVariations in body mass index (BMI) have been suggested to relate to atypical brain organization, yet connectome-level substrates of BMI and their neurobiological underpinnings remain unclear. Studying 325 healthy young adults, we examined association between functional connectome organization and BMI variations. We capitalized on connectome manifold learning techniques, which represent macroscale functional connectivity patterns along continuous hierarchical axes that dissociate low level and higher order brain systems. We observed an increased differentiation between unimodal and heteromodal association networks in individuals with higher BMI, indicative of an increasingly segregated modular architecture and a disruption in the hierarchical integration of different brain system. Transcriptomic decoding and subsequent gene enrichment analyses identified genes previously implicated in genome-wide associations to BMI and specific cortical, striatal, and cerebellar cell types. These findings provide novel insights for functional connectome substrates of BMI variations in healthy young adults and point to potential molecular associations.

neuroscience↗

bioRxiv2020

Environmental fluctuations reshape an unexpected diversity-disturbance relationship in a microbial community

Environmental disturbances have long been theorized to play a significant role in shaping the diversity and composition of ecosystems1,2. However, fundamental limitations in our ability to specify the characteristics of a disturbance in the field and laboratory have produced an inconsistent picture of diversity-disturbance relationships (DDRs) that shape the structure of ecosystems3. Here, using a recently developed continuous culture system with tunable environmental control4, we decomposed a dilution disturbance into intensity and fluctuation components5,6, and tested their effects on the diversity of a soil-derived bacterial community across hundreds of replicate cultures. We observed an unexpected U-shaped relationship between community diversity and disturbance intensity in the absence of fluctuations, an observation counter to classical intuition. Adding fluctuations erased the U-shape and increased community diversity across all disturbance intensities. All of these results are well-captured by a Monod consumer resource model, which further reveals how U-shaped DDRs emerge based on a novel "niche flip" mechanism in which competitive outcomes flip and coexistence regimes subsequently collapse at intermediate disturbance levels. Broadly, our results demonstrate how distinct features of an environmental disturbance can interact in complex ways to govern ecosystem assembly and produce all the major classes of DDRs, without invoking other organizational principles. With these findings, we construct a unifying framework that reconciles the disparate DDRs observed in nature, and propose strategies for predictively reshaping the compositional complexity of microbiomes and other ecosystems.

bioengineering↗

bioRxiv2020

INTS13 Mutations Causing a Developmental Ciliopathy Disrupt Integrator Complex Assembly

Oral-facial-digital syndromes (OFD) are a heterogeneous group of congenital disorders characterized by malformations of the face and oral cavity, and digit anomalies. To date, mutations in 12 ciliary-related genes have been identified that cause several types of OFD, suggesting that OFDs constitute a subgroup of developmental ciliopathies. Through homozygosity mapping and exome sequencing of two families with variable OFD type 2, we identified distinct germline mutations in INTS13, a subunit of the Integrator complex. This 14-component complex associates with RNAPII and can cleave nascent RNA to modulate gene expression. We determined that INTS13 utilizes a discrete domain within its C-terminus to bind the Integrator cleavage module, which is disrupted by the identified germline INTS13 mutations. Depletion of INTS13 disrupts ciliogenesis in human cultured cells and causes dysregulation of a broad collection of ciliary genes. Accordingly, its knockdown in Xenopus embryos lead to motile cilia anomalies. Altogether, we show that mutations in INTS13 cause an autosomal recessive ciliopathy, which reveals key interactions within Integrator components.

biochemistry↗

bioRxiv2020

Discovery of potential imaging and therapeutic targets for severe inflammation in COVID-19 patients

The COVID-19 pandemic has caused more than 540,000 deaths globally. Hyperinflammation mediated by dysregulated monocyte/macrophage function is considered to be the key factor that triggers severe illness in COVID-19. However, no specific targeting molecule has been identified for detecting or treating hyperinflammation related to dysregulated macrophages in severe COVID-19. Herein, we suggest candidate targets for imaging and therapy in severe COVID-19 by analyzing single-cell RNA-sequencing data based on bronchoalveolar lavage fluid of COVID-19 patients. We found that expression of SLC2A3, which can be imaged by [18F]fluorodeoxyglucose, was higher in macrophages from severe COVID-19 patients. Furthermore, by integrating the surface target database and drug-target binding database with RNA-sequencing data of severe COVID-19, we identified CCR1 and FPR1 as surface and druggable targets for drug delivery as well as molecular imaging. Our results provide a resource for candidate targets in the development of specific imaging and therapy for COVID-19-related hyperinflammation.

bioinformatics↗

bioRxiv2020

De novo design of modular and tunable allosteric biosensors

Naturally occurring allosteric protein switches have been repurposed for developing novel biosensors and reporters for cellular and clinical applications 1, but the number of such switches is limited, and engineering them is often challenging as each is different. Here, we show that a very general class of allosteric protein-based biosensors can be created by inverting the flow of information through de novo designed protein switches in which binding of a peptide key triggers biological outputs of interest 2. Using broadly applicable design principles, we allosterically couple binding of protein analytes of interest to the reconstitution of luciferase activity and a bioluminescent readout through the association of designed lock and key proteins. Because the sensor is based purely on thermodynamic coupling of analyte binding to switch activation, only one target binding domain is required, which simplifies sensor design and allows direct readout in solution. We demonstrate the modularity of this platform by creating biosensors that, with little optimization, sensitively detect the anti-apoptosis protein Bcl-2, the hIgG1 Fc domain, the Her2 receptor, and Botulinum neurotoxin B, as well as biosensors for cardiac Troponin I and an anti-Hepatitis B virus (HBV) antibody that achieve the sub-nanomolar sensitivity necessary to detect clinically relevant concentrations of these molecules. Given the current need for diagnostic tools for tracking COVID-19 3, we use the approach to design sensors of antibodies against SARS-CoV-2 protein epitopes and of the receptor-binding domain (RBD) of the SARS-CoV-2 Spike protein. The latter, which incorporates a de novo designed RBD binder, has a limit of detection of 15pM with an up to seventeen fold increase in luminescence upon addition of RBD. The modularity and sensitivity of the platform should enable the rapid construction of sensors for a wide range of analytes and highlights the power of de novo protein design to create multi-state protein systems with new and useful functions.

synthetic biology↗

bioRxiv2020

Does visitation dictate animal welfare in captivity? A case study of tigers and leopards from National Zoological Park, New Delhi

Zoological Parks serve a salient purpose of entertaining many visitors by housing various exclusive animal species. Big cats like tigers and leopard are among the most visited species in zoos globally. We investigated the behavioral response of the zoo-housed big cats to visitor densities and noise. We also aimed to understand the relationship between stereotypy, animal history, feeding schedules, and enclose design. The behavior of eight big cats housed in the National Zoological Park, New Delhi, was monitored using the focal sampling technique during the May and June 2019 to construct the ethograms. We also recorded the visitor density, ambient noise, for the same duration. Both species were found devoting a significant amount (>50%) of time in displaying inactive behaviors. Tigers and leopards performed stereotypic behaviors for 22% and 28% of their time, respectively. Pearson chi-square analysis revealed a significant variation of stereotypy in association with biological (age, sex, and rearing history) and captive (enclosure design) variables. Big cats stereotypic behaviors were found significantly influenced by the high visitor density. However, ambient noise did not impact the stereotypy of both the felid species. Visitors form an integral part of zoos, and their detrimental impact diminishes the well-being of captive animals. This study revealed that tigers and leopards in NZP display a high proportion of inactive and stereotypic behaviors. Thus, we suggest zoo authorities adopt more enclosure enrichment initiatives.

animal behavior and cognition↗

bioRxiv2020

Stereotypic Neutralizing VH Clonotypes Against SARS-CoV-2 RBD in COVID-19 Patients and the Healthy Population

In six of seven severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) patients, VH clonotypes, encoded by either immunoglobin heavy variable (IGHV)3-53 or IGHV3-66 and immunoglobin heavy joining (IGHJ)6, were identified in IgG1, IgA1, and IgA2 subtypes, with minimal mutations, and could be paired with diverse light chains, resulting in binding to the SARS-CoV-2 receptor-binding domain (RBD). Because most human antibodies against the RBD neutralized the virus by inhibiting host cell entry, we selected one of these clonotypes and demonstrated that it could potently inhibit viral replication. Interestingly, these VH clonotypes pre-existed in six of 10 healthy individuals, predominantly as IgM isotypes, which could explain the expeditious and stereotypic development of these clonotypes among SARS-CoV-2 patients.One Sentence Summary Stereotypic-naïve SARS-CoV-2 neutralizing antibody clonotypes, encoded by IGHV3-53/IGHV3-66 and IGHJ6, were identified in most patients and pre-exist in the majority of the healthy population, predominantly as an IgM isotype.Competing Interest StatementThe authors have declared no competing interest.View Full Text

immunology↗

bioRxiv2020

Unique K-mer sequences for validating cancer-related substitution, insertion and deletion mutations

The cancer genome sequencing has led to important discoveries such as identifying cancer gene. However, challenges remain in the analysis of cancer genome sequencing. One significant issue is that mutations identified by multiple variant callers are frequently discordant even when using the same genome sequencing data. For insertion and deletion mutations, oftentimes there is no agreement among different callers. Identifying somatic mutations involves read mapping and variant calling, a complicated process that uses many parameters and model tuning. To validate the identification of true mutations, we developed a method using k-mer sequences. First, we characterized the landscape of unique versus non-unique k-mers in the human genome. Second, we developed a software package, KmerVC, to validate the given somatic mutations from sequencing data. Our program validates the occurrence of a mutation based on statistically significant difference in frequency of k-mers with and without a mutation from matched normal and tumor sequences. Third, we tested our method on both simulated and cancer genome sequencing data. Counting k-mer involving mutations effectively validated true positive mutations including insertions and deletions across different individual samples in a reproducible manner. Thus, we demonstrated a straightforward approach for rapidly validating mutations from cancer genome sequencing data.

bioinformatics↗

bioRxiv2020

Model of intracellular ATP production reproduces common electrophysiological signatures of anesthesia

Accumulating evidence suggest that general anesthetics with diverse chemical structure reduce cerebral metabolism with consequent reduction of intracellular adenosine triphosphate (ATP) levels. How cerebral hypometabolism is associated with the typical electroencephalographic (EEG) changes under general anesthesia remains largely unknown.. We hypothesized that the deficit in ATP production would reduce high-frequency activity, increase low-frequency activity, and cause burst suppression, which are common dose-dependent anesthetic effects on the EEG. To test the hypothesis, we developed a novel neural network model consisting of leaky integrate-and-fire neurons with additional dependency on ATP dynamics. The effect of varying rate of ATP production on neuronal and population activity patterns was simulated under various excitatory/inhibitory balance conditions. A decrease of ATP production suppressed neuronal spiking and enhanced synchronization of neurons over a range of excitatory/inhibitory synaptic strength ratios. As anticipated, the initially asynchronous fast activity was replaced by globally desynchronized slow oscillation and, on further decrease of ATP production, changed into burst suppression with enhanced global synchronization. This study substantiates a novel biophysical mechanism for anesthetic-induced EEG changes through a relationship between energy production and synchronization of neural network.

neuroscience↗

bioRxiv2020

State-dependent cortical unit activity reflects dynamic brain state transitions in anesthesia

How anesthesia affects cortical neuronal spiking and information transfer could help understand the neuronal basis of conscious state. Recent investigations suggest that global state of the anesthetized brain is not stationary but changes spontaneously at a fixed level of anesthetic concentration. How cortical unit activity changes with dynamically transitioning brain states under anesthesia is unclear. We hypothesized that distinct cortical states are characterized by distinct neuronal spike patterns. Extracellular unit activity was measured with sixty-four-channel silicon microelectrode arrays in cortical layers 5/6 of primary visual cortex of chronically instrumented, freely moving male rats (N = 7) during stepwise reduction of the anesthetic desflurane (6, 4, 2, and 0%). Unsupervised machine learning applied to multi-unit spike patterns revealed five distinct brain states of which four occurred at various anesthetic concentrations and shifted spontaneously. In deeper anesthesia states, the number of active units and overall spike rate decreased while the remaining active units showed increased bursting (excitatory neurons), spike timing variability, unit-to-population correlation and unit-to-unit transfer entropy, especially among putative excitatory units, despite the overall decrease in transfer entropy. A novel desynchronized brain state with increased spike timing variability, entropy and electromyographic activity that occurred mostly in deep anesthesia was discovered. These results provide evidence for distinct unit activity patterns associated with spontaneous changes in local cortical brain states at stationary anesthetic conditions. The appearance of a paradoxical, desynchronized brain state in deep anesthesia contends the prevailing view of monotonic dose-dependent anesthetic effects on the brain. SIGNIFICANCE STATEMENTRecent studies suggest that spontaneous changes in brain state occur under anesthesia. However, the spiking behavior of cortical neurons associated with such state changes has not been investigated. We found that local brain states defined by multi-unit activity had non-unitary relationship with the current anesthetic level. A paradoxical brain state displaying asynchronous firing pattern and high electromyographic activity was found unexpectedly at high-dose anesthesia. In contrast, the synchronous fragmentation of neuronal spiking appeared to be a robust signature of the state of anesthesia. The findings challenge the assumption of monotonic, anesthetic dose-dependent behavior of cortical neuron populations. They enhance the interpretation of neuroscientific data obtained under anesthesia and understanding of the neuronal basis of anesthetic-induced state of unconsciousness.

neuroscience↗

bioRxiv2020

Differential effect of anesthesia on visual cortex neurons with diverse population coupling

IntroductionFiring rate (FR) and population coupling (PC) are intrinsic properties of cortical neurons. Neurons with different FR and PC have diverse excitability to stimulation, tuning curve, and synaptic plasticity. Therefore, investigation of the effect of anesthesia on neurons with different FR and PC would be important to understand state-dependent information processing in neuronal circuits. MethodsTo test how anesthesia affects neurons with diverse PC and FR, we measured single-unit activities in deep layers of primary visual cortex at three levels of anesthesia with desflurane and in wakefulness. Based on PC and FR in wakefulness, neurons were classified into three distinct groups: high PC-high FR (HPHF), low PC-high FR (LPHF), and low PC-low FR (LPLF) neurons. ResultsApplying repeated light flashes as visual stimuli, HPHF neurons showed the strongest early response (FR at 20-150ms post-stimulus) among the three groups, whereas the response of LPHF neurons persisted longest (up to 440ms). Anesthesia profoundly altered PC and FR, and differently affected the three neuron groups: (i) PC and FR became strongly correlated suppressing population-independent spike activity; (ii) Pairwise correlation of spikes between neurons could be predicted by a PC-based raster model suggesting uniform neuron-to-neuron coupling; (iii) Contrary to evoked-potential studies under anesthesia, the flash-induced early response of HPHF neurons was attenuated, and their spike timing was split and delayed; (iv) Late response (FR at 200-400ms post-stimulus) was suppressed both in HPHF and LPHF neurons. ConclusionsAnesthetic-induced association between PC and FR suggests reduced information content in the neural circuit. Altered response of HPHF neurons to visual stimuli suggests that anesthesia interferes with conscious sensory processing in primary sensory cortex.

neuroscience↗

bioRxiv2020

Single cell fitness landscapes induced by genetic and pharmacologic perturbations in cancer

Tumour fitness landscapes underpin selection in cancer, impacting etiology, evolution and response to treatment. Progress in defining fitness landscapes has been impeded by a lack of timeseries perturbation experiments over realistic intervals at single cell resolution. We studied the nature of clonal dynamics induced by genetic and pharmacologic perturbation with a quantitative fitness model developed to ascribe quantitative selective coefficients to individual cancer clones, enable prediction of clone-specific growth potential, and forecast competitive clonal dynamics over time. We applied the model to serial single cell genome (>60,000 cells) and transcriptome (>58,000 cells) experiments ranging from 10 months to 2.5 years in duration. We found that genetic perturbation of TP53 in epithelial cell lines induces multiple forms of copy number alteration that confer increased fitness to clonal populations with measurable consequences on gene expression. In patient derived xenografts, predicted selective coefficients accurately forecasted clonal competition dynamics, that were validated with timeseries sampling of experimentally engineered mixtures of low and high fitness clones. In cisplatin-treated patient derived xenografts, the fitness landscape was inverted in a time-dependent manner, whereby a drug resistant clone emerged from a phylogenetic lineage of low fitness clones, and high fitness clones were eradicated. Moreover, clonal selection mediated reversible drug response early in the selection process, whereas late dynamics in genomically fixed clones were associated with transcriptional plasticity on a fixed clonal genotype. Together, our findings outline causal mechanisms with implication for interpreting how mutations and multi-faceted drug resistance mechanisms shape the etiology and cellular fitness of human cancers.

cancer biology↗

bioRxiv2020

Decreased investigatory head scanning during exploration in learning-impaired, aged rats

"Head scanning" is an investigatory behavior that has been linked to spatial exploration and the one-trial formation or strengthening of place cells in the hippocampus. Previous studies have demonstrated that a subset of aged rats with normal spatial learning performance show head scanning rates during a novel, local-global cue-mismatch manipulation that are similar to those of young rats. However, these aged rats demonstrated different patterns of expression of neural activity markers in brain regions associated with spatial learning, perhaps suggesting neural mechanisms that compensate for age-related brain changes. These prior studies did not investigate the head scanning properties of aged rats that had spatial learning impairments. The present study analyzed head scanning behavior in young, aged-unimpaired, and aged-impaired Long Evans rats. Aged-impaired rats performed the head scan behavior at a lower rate than the young rats. These results suggest that decreased attention to spatial landmarks may be a contributing factor to the spatial learning deficits shown by the aged-impaired rats.

animal behavior and cognition↗

bioRxiv2020

Impaired hand dexterity function in a non-human primate model with chronic Parkinson's disease

Symptoms of Parkinsons disease (PD) caused by loss of dopaminergic neurons are accompanied by movement disorders, including tremors, rigidity, bradykinesia, and akinesia. Non-human primate (NHP) models with PD play an essential role in the analysis of PD pathophysiology and behavior symptoms. As impairments of hand dexterity function can affect activities of daily living in patients with PD, research on hand dexterity function in NHP models with chronic PD is essential. Traditional rating scales previously used in the evaluation of animal spontaneous behavior were insufficient due to factors related to subjectivity and passivity. Thus, experimentally designed applications for an appropriate apparatus are necessary. In this study, we aimed to longitudinally assess hand dexterity function using hand dexterity task (HDT) in NHP-PD models. To validate this assessment, we analyzed an alteration in Parkinsonian tremor symptoms, loss of dopaminergic neuron, and positron emission tomography (PET) imaging of dopamine transporters (DAT) in these models. HDT latency significantly increased in NHP-PD models. In addition, a significant inverse correlation between HDT and DAT was identified, but no local bias was found. The correlation with intention tremor symptoms was lower than the resting tremor. In conclusion, the evaluation of HDT may reflect behavioral symptoms of NHP-PD models. Furthermore, HDT was effectively used to experimentally distinguish intention tremors from other tremors.

neuroscience↗

bioRxiv2020

RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes

Recent advances in long-read sequencing have the potential to produce more complete genome assemblies using sequence reads which can span repetitive regions. However, overlap based assembly methods routinely used for this data require significant computing time and resources. Here, we have developed RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel followed by a final bin-stitching step. During benchmarking, we assembled the wheat Chinese Spring (CS) genome using publicly available PacBio reads in parallel in 168 wall hours on a 250 CPU system. The maximum RAM used was 300 Gb and the computing time was 42,000 CPU hours. The approach opens applications for the assembly of other large and complex genomes with much-reduced computing requirements. The RefKA pipeline is available at https://github.com/AppliedBioinformatics/RefKA

bioinformatics↗