Biology subjects

Chen, S.

Publications and source records attributed to Chen, S..

1,025 records · Page 57Linked to original sources

bioRxiv2017

Resting-state connectivity predicts patient-specific effects of deep brain stimulation for Parkinson’s disease

Neural circuit-based guidance for optimizing patient screening, target selection and parameter tuning for deep brain stimulation (DBS) remains limited. To this end, we propose a functional brain connectome-based modeling approach that simulates network-spreading effects of stimulating different brain regions and quantifies rectification of abnormal network topology in silico. We validate these analyses by predicting nuclei in basal-ganglia circuits as top-ranked targets for 43 local patients with Parkinsons disease and 90 patients from public database. However, individual connectome-based predictions demonstrate that globus pallidus and subthalamic nucleus (STN) constituted as the best choice for 21.1% and 19.5% of patients, respectively. Notably, the priority rank of STN significantly correlated with motor symptom severity in the local cohort. By introducing whole-brain network diffusion dynamics, these findings unfold a new dimension of brain connectomics and underscore the importance of neural network modeling for personalized DBS therapy, which warrants experimental investigation to validate its clinical utility.

neuroscience↗

bioRxiv2017

Association Analysis and Meta-Analysis of Multi-allelic Variants for Large Scale Sequence Data

MotivationThere is great interest to understand the impact of rare variants in human diseases using large sequence datasets. In deep sequences datasets of >10,000 samples, [~]10% of the variant sites are observed to be multi-allelic. Many of the multi-allelic variants have been shown to be functional and disease relevant. Proper analysis of multi-allelic variants is critical to the success of a sequencing study, but existing methods do not properly handle multi-allelic variants and can produce highly misleading association results.\n\nResultsWe propose novel methods to encode multi-allelic sites, conduct single variant and gene-level association analyses, and perform meta-analysis for multi-allelic variants. We evaluated these methods through extensive simulations and the study of a large meta-analysis of [~]18,000 samples on the cigarettes-per-day phenotype. We showed that our joint modeling approach provided an unbiased estimate of genetic effects, greatly improved the power of single variant association tests, and enhanced gene-level tests over existing approaches.\n\nAvailabilitySoftware packages implementing these methods are available at (https://github.com/zhanxw/rvtests http://genome.sph.umich.edu/wiki/RareMETAL).\n\nContactxiaowei.zhan@utsouthwestem.edu; dajiang.liu@psu.edu

bioinformatics↗

bioRxiv2017

A screen for combination therapies in BRAF/NRAS wild type melanoma identifies nilotinib plus MEK inhibitor as a synergistic combination

Despite recent therapeutic advances in the management of BRAFV600-mutant melanoma, there is still a compelling need for more effective treatments for patients who developed BRAF/NRAS wild type disease. Since the activity of single targeted agents is limited by innate and acquired resistance, we performed a high-throughput drug screen using 180 drug combinations to generate over 18,000 viability curves, with the aim of identifying agents that synergise to kill BRAF/NRAS wild type melanoma cells. From this screen we observed strong synergy between the tyrosine kinase inhibitor nilotinib and MEK inhibitors and validated this combination in an independent cell line collection. We found that AXL expression was associated with synergy to the nilotinib/MEK inhibitor combination, and that both drugs work in concert to suppress pERK. This finding was supported by genome-wide CRISPR screening which revealed that resistance mechanisms converge on regulators of the MAPK pathway. Finally, we validated the synergy of nilotinib/trametinib combination in vivo using patient-derived xenografts. Our results indicate that a nilotinib/MEK inhibitor combination may represent an effective therapy in BRAF/NRAS wild type melanoma patients.

cancer biology↗

bioRxiv2017

Improved Score Statistics for Meta-analysis in Single-variant and Gene-level Association Studies

Meta-analysis is now an essential tool for genetic association studies, allowing these to combine large studies and greatly accelerating the pace of genetic discovery. Although the standard meta-analysis methods perform equivalently as the more cumbersome joint analysis under ideal settings, they result in substantial power loss under unbalanced settings with various case-control ratios. Here, we investigate why the standard meta-analysis methods lose power under unbalanced settings, and further propose a novel meta-analysis method that performs as efficiently as joint analysis under general settings. Our proposed method can accurately approximate the score statistics obtainable by joint analysis, for both linear and logistic regression models, with and without covariates. In addition, we propose a novel approach to adjust for population stratification by correcting for known population structures through minor allele frequencies (MAFs). In the simulated gene-level association studies under unbalanced settings, our method recovered up to 85% power loss caused by the standard method. We further showed the power gain of our method in gene-level association studies with 26 unbalanced real studies of Age-related Macular Degeneration (AMD). In addition, we took the meta-analysis of three studies of type 2 diabetes (T2D) as an example to discuss the challenges of meta-analyzing multi-ethnic samples. In summary, we propose improved single-variant score statistics in meta-analysis, requiring \"accurate\" population-specific MAFs for multi-ethnic studies. These improved score statistics can be used to construct both single-variant and gene-level association studies, providing a useful framework for ensuring well-powered, convenient, cross-study analyses.

genetics↗

bioRxiv2017

A neural decoder for learned vocal behavior

Brain Machine Interfaces (BMIs) hold promise to restore impaired motor function and, because they decode neural signals to infer behavior, can serve as powerful tools to understand the neural mechanisms of motor control. Yet complex behaviors, such as vocal communication, exceed state-of-the-art decoding technologies which are currently restricted to comparatively simple motor actions. Here we present a BMI for birdsong, that decodes a complex, learned vocal behavior directly from neural activity.

neuroscience↗

bioRxiv2017

A Tetratricopeptide Repeat Protein Regulates Carotenoid Biosynthesis and Chromoplast Development in Monkeyflowers (Mimulus)

The incredible diversity of floral color and pattern in nature is largely determined by the transcriptional regulation of anthocyanin and carotenoid biosynthetic genes. While the transcriptional control of anthocyanin biosynthesis is well understood, little is known about the factors regulating the carotenoid biosynthetic pathway in flowers. Here, we characterize the Reduced Carotenoid Pigmentation 2 (RCP2) locus from two monkeyflower (Mimulus) species, the bumblebee-pollinated M. lewisii and hummingbird-pollinated M. verbenaceus. We show that loss-of-function mutations of RCP2 cause drastic down-regulation of the entire carotenoid biosynthetic pathway in these species. Through bulk segregant analysis and transgenic experiments, we have identified the causal gene underlying RCP2, encoding a tetratricopeptide repeat (TPR) protein that is closely related to the Arabidopsis Reduced Chloroplast Coverage (REC) proteins. RCP2 appears to regulate carotenoid biosynthesis independently of RCP1, a previously identified R2R3-MYB master regulator of carotenoid biosynthesis. We show that RCP2 is required for chromoplast development and suggest that it most likely regulates the expression of carotenoid biosynthetic genes through chromoplast-to-nucleus retrograde signaling. Furthermore, we demonstrate that M. verbenaceus is just as amenable to chemical mutagenesis and in planta transformation as the more extensively studied M. lewisii, making these two species an excellent platform for comparative developmental genetics studies of two closely related species with dramatic phenotypic divergence.

genetics↗

bioRxiv2017

Activation and desensitization mechanism of AMPA receptor-TARP complex by cryo-EM

Summary Summary Structure determination Agonists expand LBD gating... Activation by full and... Architecture of the ion... Ion-permeation profile of the... Asymmetric water/ion accessible... TARP modulation of receptor... TARP restricts LBD rearrangement... TARP modulation of AMPA... Materials and methods AUTHOR CONTRIBUTIONS AUTHOR INFORMATION References AMPA receptors mediate the majority of fast excitatory neurotransmission in the mammalian brain and transduce the binding of presynaptically released glutamate to the opening of a transmembrane cation channel. Within the postsynaptic density, however, AMPA receptors coassemble with transmembran ...

biophysics↗

bioRxiv2017

Instantaneous Brain Dynamics Mapped to a Continuous State Space

Measures of whole-brain activity, from techniques such as functional Magnetic Resonance Imaging, provide a means to observe the brains dynamical operations. However, interpretation of whole-brain dynamics has been stymied by the inherently high-dimensional structure of brain activity. The present research addresses this challenge through a series of scale transformations in the spectral, spatial, and relational domains. Instantaneous multispectral dynamics are first developed from input data via a wavelet filter bank. Voxel-level signals are then projected onto a representative set of spatially independent components. The correlation distance over the instantaneous wavelet-ICA state vectors is a graph that may be embedded onto a lower-dimensional space to assist the interpretation of state-space dynamics. Applying this procedure to a large sample of resting and task data (acquired through the Human Connectome Project), we segment the empirical state space into a continuum of stimulus-dependent brain states. We also demonstrate that resting brain activity includes brain states that are very similar to those adopted during some tasks, as well as brain states that are distinct from experimentally-defined tasks. Back-projection of segmented brain states onto the brains surface reveals the patterns of brain activity that support each experimental state.

neuroscience↗

bioRxiv2017

Direct in vivo mapping of functional suppressors in glioblastoma genome

Glioblastoma (GBM) is one of the deadliest cancers, with limited effective treatments and single-digit five-year survival 1-7. A causative understanding of genetic factors that regulate GBM formation is of central importance 8-19. However, a global, quantitative and functional understanding of gliomagenesis in the native brain environment has been lacking due to multiple challenges. Here, we developed an adeno-associated virus (AAV) mediated autochthonous CRISPR screen and directly mapped functional suppressors in the GBM genome. Stereotaxic delivery of an AAV library targeting significantly mutated genes into fully immunocompetent conditional Cas9 mice robustly led to gliomagenesis, resulting in tumors that recapitulate features of human GBM. Targeted capture sequencing revealed deep mutational profiles with diverse patterns across mice, uncovering in vivo roles of previously uncharacterized factors in GBM such as immune regulator B2m, zinc finger protein Zc3h13, transcription repressor Cic, epigenetic regulators Mll2/3 and Arid1b, alongside canonical tumor suppressors Nf1 and Pten. Comparative cancer genomics showed that the mutation frequencies across all genes tested in mice significantly correlate with those in human from two independent patient cohorts. Co-mutation analysis identified frequently co-occurring driver combinations, which were validated using AAV minipools, such as Mll2, B2m-Nf1, Mll3-Nf1 and Zc3h13-Rb1. Distinct from Nf1-oncotype tumors, Rb1-oncotype tumors exhibit undifferentiated histopathology phenotype and aberrant activation of developmental reprogramming signatures such as Homeobox gene clusters. The secondary addition of Zc3h13 or Pten mutations drastically altered the gene expression profiles of Rb1 mutants and rendered them more resistant to the GBM chemotherapeutic temozolomide. Our study provides a systematic functional landscape of GBM suppressors directly in vivo, opening new paths for high-throughput molecular mapping and cancer phenotyping.

systems biology↗

bioRxiv2017

Pooled AAV-CRISPR Screen with Targeted Amplicon Sequencing

High-resolution, high-throughput direct in vivo screening of functional genetic factors in native tissues has long been challenging. Adeno-associated viruses (AAV) are powerful carriers of transgenes and have been shown to mediate efficient genome editing in various organs in mice. Here, we developed a new technological approach, Pooled AAV-CRISPR Screen with Targeted Amplicon Sequencing (PASTAS), and demonstrated its application for directly mapping functional cancer driver variants in the mouse liver in an autochthonous manner. Intravenous delivery of an AAV-CRISPR library targeting a set of the most frequently mutated tumor suppressor genes into fully immunocompetent conditional Cas9 knock-in mice consistently generated highly complex autochthonous liver tumors. The molecular landscapes of these genetically diverse tumors were mapped out by deep direct readout of Cas9-generated variants at predicted sgRNA cut sites using molecular inversion probe sequencing. Co-occurrence and correlation analyses as well as validation with lower complexity minipools further confirmed the potency of various co-mutated drivers. The PASTAS method can be applied to virtually any gene sets, any cancer types, or any type of in vivo genetic studies other than cancer.

systems biology↗

bioRxiv2017

Mapping in vivo genetic interactomics through Cpf1 crRNA array screening

Genetic interactions lay the foundation of biological networks in virtually all organisms. Due to the complexity of mammalian genomes and cellular architectures, unbiased mapping of genetic interactions in vivo is challenging. Cpf1 is a single effector RNA-guided nuclease that enables multiplexed genome editing using crRNA arrays. Here we designed a Cpf1 crRNA array library targeting all pairwise permutations of the most significantly mutated nononcogenes, and performed double knockout screens in mice using a model of malignant transformation as well as a model of metastasis. CrRNA array sequencing revealed a quantitative landscape of all single and double knockouts. Enrichment, synergy and clonal analyses identified many unpredicted drivers and co-drivers of transformation and metastasis, with epigenetic factors as hubs of these highly connected networks. Our study demonstrates a powerful yet simple approach for in vivo mapping of unbiased genetic interactomes in mammalian species at a phenotypic level.

genetics↗

bioRxiv2017

Inoculation Of Biocontrol Bacteria Alleviated Panax ginseng Replanting Problem

Replanting problem is a common and serious issue hindering the continuous cultivation of Panax plants. Changes in soil microbial community driven by plant species of different ages and developmental stages are speculated to cause this problem. Inoculation of microbial antagonists is proposed to alleviate replanting issues efficiently.\n\nHigh-throughput sequencing revealed that bacterial diversity evidently decreased, and fungal diversity markedly increased in soils of adult ginseng plants in the root growth stage. Relatively few beneficial microbe agents, such as Luteolibacter, Cytophagaceae, Luteibacter, Sphingomonas, Sphingomonadaceae, and Zygomycota, were observed. On the contrary, the relative abundance of harmful microorganism agents, namely, Brevundimonas, Enterobacteriaceae, Pandoraea, Cantharellales, Dendryphion, Fusarium, and Chytridiomycota, increased with pant age. Furthermore, Bacillus subtilis 50-1 was isolated and served as microbial antagonists against pathogenic Fusarium oxysporum of ginseng root-rot, and its biocontrol efficacy was 67.8% using a dual culture assay. The ginseng death rate and relative abundance of Fusarium decreased by 63.3% and 46.1%, respectively, after inoculation with 50-1 in replanting soils. Data revealed that changes in the diversity and composition of rhizospheric microbial communities driven by ginseng of different ages and developmental stages could cause microecological degradation. Biocontrol using microbial antagonists was an effective method for alleviating the replanting problem.\n\nHighlightChanges in rhizospheric microbial communities driven by ginseng plants 13 of different ages and developmental stages could cause microecological degradation. 14 Biocontrol using microbial antagonists effectively alleviated the replanting problem.

microbiology↗

bioRxiv2017

Parsing Of Compositions And Microstructure Characteristics For Rust-Spots Of Pear Pericarp

The commercial value of Kurles pears pericarp, a popular and favored fruit for its unique aroma and refreshingly crisp texture, had sharply decreased because of a rust breakout of the beloved pear in China during the atmosphere-controlled storage. High performance liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LC-MS) were used to analyze rust spots on the pericarp of Kurle pears. Therefore, the chemical compounds of four various eluates, originating from the rust-colored substance collected from the pears pericarp effected, were identified successfully for the first time, which were just rhein, aloe-emodin, chrysophanol and emodin, respectively. Taken together with microstructure characteristics for rust-spots of Kurle pear pericarp, it was no doubt that these eluates were the main factors affecting the rust spots on the pericarp of the Kurle pears during the atmosphere-controlled storage, which was a sign and consequence resisting the undesirable stress of the external environment.

plant biology↗

bioRxiv2017

Root Interactions And Plant Growth In A Tomato/Potato Onion Intercropping System Under Different Phosphorus Levels

Intercropping systems have been implemented in many parts of the world due to their beneficial effects on yield and biomass. In intercropping systems, changes in plant growth are usually related to variations in root distribution and phosphorus (P) levels, however, root distributions and root tendencies are difficult to study, as root systems grow beneath the soil surface. Therefore, we have a relatively poor understanding of the relationship between plant root interactions and plant growth in intercropping systems. In this study, a custom apparatus consisting of a transparent manual root box was used to observe intact root systems in situ. We investigated how root distribution and root tendency changed in a tomato/potato onion intercropping system under two P treatments, and how tomato plant growth was influenced. The results showed that the shoot and total biomass for the tomato plants were increased by intercropping with potato onion plants under both tested P levels, the root distribution of intercropped tomato plants was deeper than that of monocultured plants, and the tomato roots tended to grow away from the potato onion roots. Our research reveals that a deeper and more evasive root distribution is more conductive to the plant growth of the intercropped tomato.\n\nSUMMARY STATEMENTOur study can help more people clearly know the relationship between the root interactions and plant growth in mixed cultures.

ecology↗

bioRxiv2017

Uncharacterized bacterial structures revealed by electron cryotomography

SUMMARY STATEMENTHere we present a survey of previously uncharacterized structures we have observed in bacterial cells by electron cryotomography, in the hopes of spurring their identification and study.\n\nABSTRACTElectron cryotomography (ECT) can reveal the native structure and arrangement of macromolecular complexes inside intact cells. This technique has greatly advanced our understanding of the ultrastructure of bacterial cells. Rather than undifferentiated bags of enzymes, we now view bacteria as structurally complex assemblies of macromolecular machines. To date, our group has applied ECT to nearly 90 different bacterial species, collecting more than 15,000 cryotomograms. In addition to known structures, we have observed several, to our knowledge, uncharacterized features in these tomograms. Some are completely novel structures; others expand the features or species range of known structure types. Here we present a survey of these uncharacterized bacterial structures in the hopes of accelerating their identification and study, and furthering our understanding of the structural complexity of bacterial cells.

microbiology↗

bioRxiv2016

Conformational landscape of the p28-bound human proteasome regulatory particle

The proteasome holoenzyme is activated by its regulatory particle (RP) consisting of two subcomplexes, the lid and the base. A key event in base assembly is the formation of a heterohexameric ring of AAA-ATPases, which is guided by at least four RP assembly chaperones in mammals: PAAF1, p28/gankyrin, p27/PSMD9 and S5b. We determined a cryo-EM structure of the human RP in complex with its assembly chaperone p28 at 4.5-[A] resolution. The Rpn1-p28-AAA subcomplex in the p28-bound RP is highly dynamic and was resolved to subnanometer resolution in seven states, which recapitulate the conformational landscape of the complex. Surprisingly, the p28-bound AAA ring does not form a channel in the free RP. Instead, it spontaneously samples multiple open and closed topologies. Our analysis suggests that p28 guides the proteolytic core particle to select certain conformation of the ATPase ring for RP engagement in the last step of the chaperone-mediated proteasome assembly.

biochemistry↗

bioRxiv2016

Cobalt enrichment in anaerobic microbial cocultures revealed by synchrotron X-ray fluorescence imaging

Metal cofactors are required for many enzymes in anaerobic microbial respiration. This study examined iron, cobalt, nickel, copper, and zinc in cellular and abiotic phases at the single-cell scale for a sulfate-reducing bacterium (Desulfococcus multivorans) and a methanogenic archaeon (Methanosarcina acetivorans) using synchrotron x-ray fluorescence microscopy. Relative abundances of cellular metals were also measured by inductively coupled plasma mass spectrometry. For both species, zinc and iron were consistently the most abundant cellular metals. M. acetivorans contained higher nickel and cobalt content than D. multivorans, likely due to elevated metal requirements for methylotrophic methanogenesis. Cocultures contained spheroid zinc sulfides and cobalt/copper-sulfides.

microbiology↗