Biology subjects

Kim, S.

Publications and source records attributed to Kim, S..

At least 685 records · Page 38Linked to original sources

bioRxiv2018

Dendritic spikes in hippocampal granule cells are necessary for long-term potentiation at the perforant path synapse

Long-term potentiation (LTP) of synaptic responses is essential for hippocampal memory function. Perforant-path (PP) synapses on hippocampal granule cells (GCs) contribute to the formation of associative memories, which are considered the cellular correlates of memory engrams. However, the mechanisms of LTP at these synapses are not well understood. Due to sparse firing activity and the voltage attenuation in their dendrites, it remains unclear how associative LTP at distal synapses occurs. Here we show that NMDA receptor-dependent LTP can be induced at PP-GC synapses without backpropagating action potentials (bAPs) in acute rat brain slices. Dendritic recordings reveal substantial attenuation of bAPs as well as local dendritic Na+ -spike generation during PP-GC input. Inhibition of Na+ -spikes impairs LTP suggesting that LTP at PP-GC synapse requires local Na+ -spikes. Thus, dendritic spikes are essential for LTP induction at PP-GC synapse and may constitute a key cellular mechanism for memory formation in the dentate gyrus.

neuroscience↗

bioRxiv2017

Computational docking reveals evolutionary conservation of a specific interaction between 15d-Prostaglandin-J2 and eIF4A.

15-deoxy-delta 12,14-prostaglandin J2 (15d-PGJ2) is anti-inflammatory/antineoplastic prostaglandin which functions through covalent binding to cysteine residues of various target proteins. We previously showed that 15d-PGJ2 mediated anti-inflammatory responses are dependent on the translational inhibition through its interaction with eIF4A. Binding of 15d-PGJ2 to eIF4A specifically blocks the interaction between eIF4G and eIF4A leads to the formation of stress granules (SGs), which cluster mRNAs with inhibited translation. Here we show that the binding between 15d-PGJ2 and eIF4A specifically blocks the interaction between the MIF4G domain of eIF4G and eIF4A. To reveal the mechanism of this interaction, we used computational simulation-based docking studies and identified that the carboxyl tail of 15d-PGJ2 could stabilize the binding of 15d-PGJ2 to eIF4A through arginine 295 of eIF4A, which is the first suggestion that the 15d-PGJ2 tail play a physiological role. Interestingly, the putative 15d-PGJ2 binding site on eiF4A is conserved across many species, suggesting a biological role. Our data propose that studying 15d-PGJ2 and its targets will may uncover new therapeutic approaches in anti-inflammatory drug discovery.

molecular biology↗

bioRxiv2017

Directed evolution of CRISPR-Cas9 to increase its specificity

The use of CRISPR-Cas9 as a therapeutic reagent is hampered by its off-target effects. Although rationally designed S. pyogenes Cas9 (SpCas9) variants that display higher specificities than the wild-type SpCas9 protein are available, these attenuated Cas9 variants are often poorly efficient in human cells. Here, we have used a directed evolution approach in E. coli to obtain Sniper-Cas9, which shows high specificities without sacrificing on-target activities in human cells.

biochemistry↗

bioRxiv2017

The effect of macromolecular crowding on single-round transcription by E. coli RNA polymerase

Biological reactions in the cellular environment differ physicochemically from those performed in dilute buffer solutions due to, in part, slower diffusion of various components in the cellular milieu, increase in their chemical activities, and modulation of their binding affinities and conformational stabilities. In vivo transcription is therefore expected to be strongly influenced by the crowdedness of the cell. Previous studies of transcription under macromolecular crowding conditions have focused mainly on multiple cycles of RNAP-Promoter associations, assuming that the association is the rate-determining step of the entire transcription process. However, recent reports demonstrated that late initiation and promoter escape could be the rate-determining steps for some promoter DNA sequences. The investigation of crowding effects on these steps under single-round conditions is therefore crucial for better understanding of transcription initiation in vivo. Here, we have implemented an in vitro transcription quenched-kinetics single-molecule assay to investigate the dependence of transcription reaction rates on the sizes and concentrations of crowders. Our results demonstrate an expected slowdown of transcription kinetics due to increased viscosity, and an unexpected enhancement in transcription kinetics by large crowding agents (at a given viscosity). More importantly, the enhancements dependence on crowder size significantly deviates from hard-sphere model (scaled-particle theory) predictions, commonly used for description of crowding effects. Our findings shed new light on how enzymatic reactions are affected by crowding conditions in the cellular milieu.

biochemistry↗

bioRxiv2017

Combinatorial effect of promoter activity, mRNA degradation and site-specific transcriptional pausing in modulating protein expression noise

Genetically identical cells exhibit diverse phenotypes, even when experiencing the same environment. This phenomenon, in part, originates from cell-to-cell variability (noise) in protein expression. While various kinetic schemes of stochastic transcription initiation are known to affect gene expression noise, how post-transcription initiation events contribute to noise at the protein level remains incompletely understood. To address this question, we developed a stochastic simulation-based model of bacterial gene expression that integrates well-known dependencies between transcription initiation, transcription elongation dynamics, mRNA degradation and translation. We identified realistic conditions under which mRNA lifetime and transcriptional pauses modulate the protein expression noise initially introduced by the promoter architecture. For instance, we found that the short lifetime of bacterial mRNAs facilitates the production of protein bursts. Conversely, RNA polymerase (RNAP) pausing at specific sites during transcription elongation can attenuate protein bursts by fluidizing the RNAP traffic to the point of erasing the effect of a bursty promoter. Pause-prone sites, if located close to the promoter, can also affect noise indirectly by reducing both transcription and translation initiation due to RNAP and ribosome congestion. Our findings highlight how the interplay between transcription initiation, transcription elongation, translation and mRNA degradation shapes the distribution in protein numbers. They also have implications for our understanding of gene evolution and suggest combinatorial strategies for modulating phenotypic variability by genetic engineering.

systems biology↗

bioRxiv2017

Strelka2: Fast and accurate variant calling for clinical sequencing applications

We describe Strelka2 (https://github.com/Illumina/strelka), an open-source small variant calling method for clinical germline and somatic sequencing applications. Strelka2 introduces a novel mixture-model based estimation of indel error parameters from each sample, an efficient tiered haplotype modeling strategy and a normal sample contamination model to improve liquid tumor analysis. For both germline and somatic calling, Strelka2 substantially outperforms current leading tools on both variant calling accuracy and compute cost.

bioinformatics↗

bioRxiv2017

Replication Timing Networks: a novel class of gene regulatory networks

DNA replication occurs in a defined temporal order known as the replication-timing (RT) program and is regulated during development, coordinated with 3D genome organization and transcriptional activity. However, transcription and RT are not sufficiently coordinated to predict each other, suggesting an indirect relationship. Here, we exploit genome-wide RT profiles from 15 human cell types and intermediate differentiation stages derived from human embryonic stem cells to construct different types of RT regulatory networks. First, we constructed networks based on the coordinated RT changes during cell fate commitment to create highly complex RT networks composed of thousands of interactions that form specific functional sub-network communities. We also constructed directional regulatory networks based on the order of RT changes within cell lineages and identified master regulators of differentiation pathways. Finally, we explored relationships between RT networks and transcriptional regulatory networks (TRNs), by combining them into more complex circuitries of composite and bipartite networks, revealing novel trans interactions between transcription factors and downstream RT changes that were validated with ChIP-seq data. Our findings suggest a regulatory link between the establishment of cell type specific TRNs and RT control during lineage specification.

systems biology↗

bioRxiv2017

Correlative three-dimensional fluorescence and refractive index tomography: bridging the gap between molecular specificity and quantitative bioimaging

Optical diffraction tomography (ODT) provides label-free three-dimensional (3D) refractive index (RI) measurement of biological samples. However, due to the nature of the RI values of biological specimens, ODT has limited access to molecular specific information. Here, we present an optical setup combining ODT with three-channel 3D fluorescence microscopy, to enhance the molecular specificity of the 3D RI measurement. The 3D RI distribution and 3D deconvoluted fluorescence images of HeLa cells and NIH-3T3 cells are measured, and the cross-correlative analysis between RI and fluorescence of live cells are presented.

cell biology↗

bioRxiv2017

Genetic Architecture of Subcortical Brain Structures in Over 40,000 Individuals Worldwide

Subcortical brain structures are integral to motion, consciousness, emotions, and learning. We identified common genetic variation related to the volumes of nucleus accumbens, amygdala, brainstem, caudate nucleus, globus pallidus, putamen, and thalamus, using genome-wide association analyses in over 40,000 individuals from CHARGE, ENIGMA and the UK-Biobank. We show that variability in subcortical volumes is heritable, and identify 25 significantly associated loci (20 novel). Annotation of these loci utilizing gene expression, methylation, and neuropathological data identified 62 candidate genes implicated in neurodevelopment, synaptic signaling, axonal transport, apoptosis, and susceptibility to neurological disorders. This set of genes is significantly enriched for Drosophila orthologs associated with neurodevelopmental phenotypes, suggesting evolutionarily conserved mechanisms. Our findings uncover novel biology and potential drug targets underlying brain development and disease.

genetics↗

bioRxiv2017

The lawful imprecision of human surface tilt estimation in natural scenes

Estimating local surface orientation (slant and tilt) is fundamental to recovering the three-dimensional structure of the environment, but it is unknown how well humans perform this task in natural scenes. Here, with a high-fidelity database of natural stereo-images with groundtruth surface orientation at each pixel, we find dramatic differences in human tilt estimation with natural and artificial stimuli. With artificial stimuli, estimates are precise and unbiased. With natural stimuli, estimates are imprecise and strongly biased. An image-computable normative model grounded in natural scene statistics predicts human bias, precision, and trial-by-trial errors without fitting parameters to the human data. These similarities suggest that the complex human performance patterns with natural stimuli are lawful, and that human visual systems have internalized local image and scene statistics to optimally infer the three-dimensional structure of the environment. The current results help generalize our understanding of human vision from the lab to the real world.

neuroscience↗

bioRxiv2017

Accurate detection of low-level somatic mutations with technical replication for next-generation sequencing

Accurate genome-wide detection of somatic mutations with low variant allele frequency (VAF, <1%) has proven difficult, for which generalized, scalable methods are lacking. Herein, we describe a new computational method, called RePlow that we developed to detect low-VAF somatic mutations based on simple, library-level replicates for next-generation sequencing on any platform. Through joint analysis of replicates, RePlow is able to remove prevailing background errors in next-generation sequencing analysis, facilitating remarkable improvement in the detection accuracy for low-VAF somatic mutations (up to [~]99% reduction in false positives). The method was validated in independent cancer panel and brain tissue sequencing data. Our study suggests a new paradigm with which to exploit an overwhelming abundance of sequencing data for accurate variant detection.

genomics↗

bioRxiv2017

Xbra and Smad-1 response elements cooperate in PV.1 promoter to inhibit the early neurogenesis in Xenopus embryos

Crosstalk of signaling pathways plays crucial roles in cell fate determination, cell differentiation and proliferation. Both BMP-4/Smad-1 and FGF/Xbra signaling induce the expression of PV.1, leading to neural inhibition. However, BMP-4/Smad-1 and FGF/Xbra signaling crosstalk in the regulation of PV.1 transcription is still largely unknown. In this study, Smad-1 and Xbra physically interacted and regulated the PV.1 transcriptional activation in a synergistic manner. Xbra and Smad-1 directly bound within the proximal region of the PV.1 promoter and cooperatively enhanced the binding of an interacting partner within the promoter. Maximum cooperation was achieved in the presence of intact DNA binding sites of both Smad-1 and Xbra. Collectively, BMP-4/Smad-1 and FGF/Xbra signal crosstalk was required to activate the PV.1 transcription, synergistically. Suggesting that crosstalk of BMP-4 and FGF signaling facilitates the fine-tuning regulation of PV.1 transcription to inhibit neurogenesis during embryonic development of Xenopus.\n\nSummary statementFGF/Xbra positively regulates the PV.1 expression in the Xenopus via an unknown mechanism. Our study shows that both BMP-4/Smad-1 and FGF/Xbra exhibits a signaling crosstalk to regulate PV.1 transcription activation, promoting to ectoderm and mesoderm formation and inhibiting the early neurogenesis in Xenopus.

developmental biology↗

bioRxiv2017

Evidence for a role of calcium in STING signaling

STING, an ER resident cyclic dinucleotide (CDN) receptor, plays an important role in innate immune response signaling. Upon binding to CDNs, it activates the TBK1-IRF3 signaling axis, which stimulates gene expression including interferon beta. We hypothesized that the ER localization of STING reflects a role for calcium mobilization in its signaling. To test this hypothesis, we treated mouse cells with two STING agonists, the synthetic drug DMXAA and a natural ligand, cyclic GMP-AMP (cGAMP), and measured intracellular calcium. Both triggered a rapid rise in intracellular calcium that was partially inhibited by STING depletion. Intracellular calcium chelation blocked DMXAA induced signaling downstream of STING activation, but had no effect on cGAMP induced signaling. We propose that intracellular calcium plays an important role in the response of the STING pathway. In response to DMXAA, calcium is mobilized form the ER and required for signaling. In the case of cGAMP calcium is mobilized but not required. This difference could be explained by alternative modes of STING activation for the two ligands, or a combination of STING-dependent and -independent actions of extracellular cGAMP.

cell biology↗

bioRxiv2017

Genomic and chromatin features shaping meiotic double-strand break formation and repair in mice

The SPO11-generated DNA double-strand breaks (DSBs) that initiate meiotic recombination occur non-randomly across genomes, but mechanisms shaping their distribution and repair remain incompletely understood. Here, we expand on recent studies of nucleotide-resolution DSB maps in mouse spermatocytes. We find that trimethylation of histone H3 lysine 36 around DSB hotspots is highly correlated, both spatially and quantitatively, with trimethylation of H3 lysine 4, consistent with coordinated formation and action of both PRDM9-dependent histone modifications. In contrast, the DSB-responsive kinase ATM contributes independently of PRDM9 to controlling hotspot activity, and combined action of ATM and PRDM9 can explain nearly two-thirds of the variation in DSB frequency between hotspots. DSBs were modestly underrepresented in most repetitive sequences such as segmental duplications and transposons. Nonetheless, numerous DSBs form within repetitive sequences in each meiosis and some classes of repeats are preferentially targeted. Implications of these findings are discussed for evolution of PRDM9 and its role in hybrid strain sterility in mice. Finally, we document the relationship between mouse strain-specific DNA sequence variants within PRDM9 recognition motifs and attendant differences in recombination outcomes. Our results provide further insights into the complex web of factors that influence meiotic recombination patterns.

genetics↗

bioRxiv2017

Increasing Antibiotic Susceptibility In Staphylococcus aureus In Boston, Massachusetts, 2000-2014: An Observational Study

BackgroundMethicillin resistant S. aureus (MRSA) has been declining over the past decade, but changes in S. aureus overall and the implications for trends in antibiotic resistance remain unclear.\n\nObjectiveTo determine whether the decline in rates of infection by MRSA has been accompanied by changes in rates of infection by methicillin susceptible, penicillin resistant S. aureus (MSSA) and penicillin susceptible S. aureus (PSSA). We test if these dynamics are associated with specific genetic lineages and evaluate gains and losses of resistance at the strain level.\n\nMethodsWe conducted a 15 year retrospective observational study at two tertiary care institutions in Boston, MA of 31,589 adult inpatients with S. aureus infections. Surveillance swabs and duplicate specimens were excluded. We also sequenced a sample of contemporary isolates (n = 180) obtained between January 2016 and July 2016. We determined changes in the annual rates of infection per 1,000 inpatient admissions by S. aureus subtype and in the annual mean antibiotic resistance by subtype. We performed phylogenetic analysis to generate a population structure and infer gain and loss of the genetic determinants of resistance.\n\nResultsOf the 43,954 S. aureus infections over the study period, 21,779 were MRSA, 17,565 MSSA and 4,610 PSSA. After multivariate adjustment, annual rates of infection by S. aureus declined from 2003 to 2014 by 2.9% (95% CI, 1.6%-4.3%), attributable to an annual decline in MRSA of 9.1% (95% CI, 6.3%-11.9%) and in MSSA by 2.2% (95% CI, 0.4%-4.0%). PSSA increased over this time period by 4.6% (95% CI, 3.0%-6.3%) annually. Resistance in S. aureus decreased from 2000 to 2014 by 0.86 antibiotics (95% CI, 0.81-0.91). By phylogenetic inference, 5/35 MSSA and 2/20 PSSA isolates in the common MRSA lineages ST5/USA100 and ST8/USA300 arose from the loss of genes conferring resistance.\n\nConclusions and relevanceAt two large tertiary care centers in Boston, MA, S. aureus infections have decreased in rate and have become more susceptible to antibiotics, with a rise in PSSA making penicillin an increasingly viable and important treatment option.

epidemiology↗

bioRxiv2017

Multiple reference genome sequences of hot pepper reveal the massive evolution of plant disease resistance genes by retroduplication

Transposable elements (TEs) provide major evolutionary forces leading to new genome structure and species diversification. However, the role of TEs in the expansion of disease resistance gene families has been unexplored in plants. Here, we report high-quality de novo genomes for two peppers (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum). Dynamic genome rearrangements involving translocations among chromosome 3, 5 and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs exhibited great abundance across the angiosperms, with most cases lineage-specific and thus recent events. Our study revealed that retroduplication has played key roles in the emergence of new disease-resistance genes in plants.

plant biology↗

bioRxiv2016

Parkin knockout inhibits neuronal development via regulation of proteasomal degradation of p21

PARK2 encodes for the E3 ubiquitin ligase parkin and iimplicates in the development of Parkinsons disease (PD). Although the neuroprotective role of parkin is well known, the mechanism of parkins function in neural stem differentiation is not clear. Co-expressions network analysis showed that SNAP25 and BDNF were positively correlated with parkin, but negatively correlated with p21 in human patient brain. Therefore, we investigated a link between the ubiquitin E3 ligase parkin and proteasomal degradation of p21 for the control of neural stem cell differentiation. We discovered that p21 directly binds with parkin and is ubiquitinated by parkin resulting in the loss of cell differentiation ability. Tranfection of p21 shRNA in PARK2 KO mice significantly rescued the differentiation efficacy as well as SNAP25 and BDNF expression. We also defined the decreased p21 ubiquitination and differentiation ability were reversed after treatment with JNK inhibitor, SP600125 in PARK2 KO mice derived neural stem cells. Thus, the present study indicated that parkin knockout inhibits neural stem cell differentiation by JNK-dependent proteasomal degradation of p21.\n\nSummary statementThe present study indicated that parkin knockout inhibits neural stem cell differentiation by JNK-dependent proteasomal degradation of p21.

cell biology↗

bioRxiv2016

The dynamic three-dimensional organization of the diploid yeast genome

The budding yeast Saccharomyces cerevisiae is a long-standing model for the three-dimensional organization of eukaryotic genomes. Even in this well-studied model, it is unclear how homolog pairing in diploids and environment-induced gene relocalization influence overall genome organization. Here, we performed high-throughput chromosome conformation capture on diverged Saccharomyces hybrid diploids to obtain the first global view of chromosome conformation in diploid yeasts. After controlling for the Rabl-like orientation, we observe significant homolog proximity that increased in saturated culture conditions. Surprisingly, we observe a localized increase in homologous interactions between the HAS1 alleles specifically under galactose induction and saturated growth, mediated by association with nuclear pore complexes at the nuclear periphery. Together, these results reveal that the diploid yeast genome has a dynamic and complex 3D organization.

genomics↗