Molecular analysis of circulating tumor cells (CTCs) at single-cell resolution offers great promise for cancer diagnostics and therapeutics from simple liquid biopsy. Recent development of massively ...parallel single-cell RNA-sequencing (scRNA-seq) provides a powerful method to resolve the cellular heterogeneity from gene expression and pathway regulation analysis. However, the scarcity of CTCs and the massive contamination of blood cells limit the utility of currently available technologies. Here, we present Hydro-Seq, a scalable hydrodynamic scRNA-seq barcoding technique, for high-throughput CTC analysis. High cell-capture efficiency and contamination removal capability of Hydro-Seq enables successful scRNA-seq of 666 CTCs from 21 breast cancer patient samples at high throughput. We identify breast cancer drug targets for hormone and targeted therapies and tracked individual cells that express markers of cancer stem cells (CSCs) as well as of epithelial/mesenchymal cell state transitions. Transcriptome analysis of these cells provides insights into monitoring target therapeutics and processes underlying tumor metastasis.
DNA sample contamination is a serious problem in DNA sequencing studies and may result in systematic genotype misclassification and false positive associations. Although methods exist to detect and ...filter out cross-species contamination, few methods to detect within-species sample contamination are available. In this paper, we describe methods to identify within-species DNA sample contamination based on (1) a combination of sequencing reads and array-based genotype data, (2) sequence reads alone, and (3) array-based genotype data alone. Analysis of sequencing reads allows contamination detection after sequence data is generated but prior to variant calling; analysis of array-based genotype data allows contamination detection prior to generation of costly sequence data. Through a combination of analysis of in silico and experimentally contaminated samples, we show that our methods can reliably detect and estimate levels of contamination as low as 1%. We evaluate the impact of DNA contamination on genotype accuracy and propose effective strategies to screen for and prevent DNA contamination in sequencing studies.
Lightening gravity-mediated dark matter Kang, Yoo-Jin; Lee, Hyun Min
The European physical journal. C, Particles and fields,
07/2020, Volume:
80, Issue:
7
Journal Article
Peer reviewed
Open access
We revisit the scenario of a massive spin-2 particle as the mediator for communicating between dark matter of arbitrary spin and the Standard Model. Taking the general couplings of the spin-2 ...particle in the effective theory, we discuss the thermal production mechanisms for dark matter with various channels and the dark matter self-scattering. For WIMP and light dark matter cases, we impose the relic density condition and various experimental constraints from direct and indirect detections, precision measurements as well as collider experiments. We show that it is important to include the annihilation of dark matter into a pair of spin-2 particles in both allowed and forbidden regimes, thus opening up the consistent parameter space for dark matter. The benchmark models of the spin-2 mediator are presented in the context of the warped extra dimension and compared to the simplified models.
Human umbilical cord blood‐derived mesenchymal stem cells (hUCB‐MSCs) exhibit potency for the regeneration of infarcted hearts. Vascular endothelial growth factor (VEGF) is capable of inducing ...angiogenesis and can boost stem cell‐based therapeutic effects. However, high levels of VEGF can cause abnormal blood vessel growth and hemangiomas. Thus, a controllable system to induce therapeutic levels of VEGF is required for cell therapy. We generated an inducible VEGF‐secreting stem cell (VEGF/hUCB‐MSC) that controls the expression of VEGF and tested the therapeutic efficacy in rat myocardial infarction (MI) model to apply functional stem cells to MI. To introduce the inducible VEGF gene cassette into a safe harbor site of the hUCB‐MSC chromosome, the transcription activator‐like effector nucleases system was used. After confirming the integration of the cassette into the locus, VEGF secretion in physiological concentration from VEGF/hUCB‐MSCs after doxycycline (Dox) induction was proved in conditioned media. VEGF secretion was detected in mice implanted with VEGF/hUCB‐MSCs grown via a cell sheet system. Vessel formation was induced in mice transplanted with Matrigel containing VEGF/hUCB‐MSCs treated with Dox. Moreover, seeding of the VEGF/hUCB‐MSCs onto the cardiac patch significantly improved the left ventricle ejection fraction and fractional shortening in a rat MI model upon VEGF induction. Induced VEGF/hUCB‐MSC patches significantly decreased the MI size and fibrosis and increased muscle thickness, suggesting improved survival of cardiomyocytes and protection from MI damage. These results suggest that our inducible VEGF‐secreting stem cell system is an effective therapeutic approach for the treatment of MI. Stem Cells Translational Medicine 2017;6:1040–1051
Ambient air particulate matter (PM) induces senescence in human skin cells. However, the underlying mechanisms remain largely unknown. We investigated how epigenetic regulatory mechanisms participate ...in cellular senescence induced by PM with a diameter <2.5 (PM
) in human keratinocytes and mouse skin tissues. PM
-treated cells exhibited characteristics of cellular senescence. PM
induced a decrease in DNA methyltransferase (DNMT) expression and an increase in DNA demethylase (ten-eleven translocation; TET) expression, leading to hypomethylation of the p16
promoter region. In addition, PM
led to a decrease in polycomb EZH2 histone methyltransferase expression, whereas the expression of the epigenetic transcriptional activator MLL1 increased. Furthermore, binding of DNMT1, DNMT3B, and EZH2 to the promoter region of p16
decreased in PM
-treated keratinocytes, whereas TET1 and MLL1 binding increased, leading to decreased histone H3 lysine 27 trimethylation (H3K27Me3) and increased H3K4Me3 in the promoter of p16
. PM
-induced senescence involved aryl hydrocarbon receptor (AhR)-induced reactive oxygen species (ROS) production. ROS scavenging dampened PM
-induced cellular senescence through regulation of DNA and histone methylation. Altogether, our work shows that skin senescence induced by environmental PM
occurs through ROS-dependent the epigenetic modification of senescence-associated gene expression. Our findings provide information for the design of preventive and therapeutic strategies against skin senescence, particularly in light of the increasing problem of PM
exposure due to air pollution.
This paper describes a humanoid robotics platform (DRC-HUBO+) developed for the Defense Advanced Research Projects Agency Robotics Challenge (DRC) Finals. This paper also describes the design ...criteria, hardware, software framework, and experimental testing of the DRC-HUBO+ platform. The purpose of DRC-HUBO+ is to perform tasks by teleoperation in hazardous environments that are unsafe for humans, such as disaster zones. We identified specific design concepts for DRC-HUBO+ to achieve this goal. For a robot to be capable of performing human tasks, a human-like shape and size, autonomy, mobility, manipulability, and power are required, among other features. Furthermore, modularized joints and a user-friendly software framework were emphasized as design concepts to facilitate research on the robot tasks. The DRC-HUBO+ platform is based on DRC-HUBO-1 and HUBO-2. The torque of each joint is increased compared to that in DRC-HUBO-1 owing to its high reduction ratio and air-cooling system. DRC-HUBO+ is designed with an exoskeletal structure to provide it with sufficient stiffness relative to its mass. All wires are enclosed within the robot body using a hollow shaft and covers to protect the wires from external shock. Regarding the vision system, active cognition of the environment can be realized using a light-detection and ranging sensor and vision cameras on the head. To achieve stable mobility, the robot can transition from the bipedal walking mode to the wheel mode using wheels located on both knees. DRC-HUBO+ has 32 degrees of freedom (DOFs), including seven DOFs for each arm and six DOFs for each leg, and a solid and light body with a height of 170 cm and a mass of 80 kg. A software framework referred to as PODO, with a Linux kernel and the Xenomai patch, is used in DRC-HUBO+.
A genetic variant can be represented in the Variant Call Format (VCF) in multiple different ways. Inconsistent representation of variants between variant callers and analyses will magnify ...discrepancies between them and complicate variant filtering and duplicate removal. We present a software tool vt normalize that normalizes representation of genetic variants in the VCF. We formally define variant normalization as the consistent representation of genetic variants in an unambiguous and concise way and derive a simple general algorithm to enforce it. We demonstrate the inconsistent representation of variants across existing sequence analysis tools and show that our tool facilitates integration of diverse variant types and call sets.
The source code is available for download at http://github.com/atks/vt. More detailed documentation is available at http://genome.sph.umich.edu/wiki/Variant_Normalization.
hmkang@umich.edu
Supplementary data are available at Bioinformatics online.
Cross-regulation of Toll-like receptor (TLR) responses by cytokines is essential for effective host defense, avoidance of toxicity and homeostasis, but the underlying mechanisms are not well ...understood. Our comprehensive epigenomics approach to the analysis of human macrophages showed that the proinflammatory cytokines TNF and type I interferons induced transcriptional cascades that altered chromatin states to broadly reprogram responses induced by TLR4. TNF tolerized genes encoding inflammatory molecules to prevent toxicity while preserving the induction of genes encoding antiviral and metabolic molecules. Type I interferons potentiated the inflammatory function of TNF by priming chromatin to prevent the silencing of target genes of the transcription factor NF-κB that encode inflammatory molecules. The priming of chromatin enabled robust transcriptional responses to weak upstream signals. Similar chromatin regulation occurred in human diseases. Our findings reveal that signaling crosstalk between interferons and TNF is integrated at the level of chromatin to reprogram inflammatory responses, and identify previously unknown functions and mechanisms of action of these cytokines.
This paper proposes a device that can change the payload of an unpowered lower-limb exoskeleton supporting the weights of humans and loads. Our previous exoskeletons used a cam–follower structure ...with a spring applied to the hip joint. This exoskeleton showed satisfying performance within the payload; however, the performance decreased when the payload was exceeded. Therefore, a payload adjustment device that can adjust the wearer’s required torque by easily applying it to the cam–follower structure was developed. An exoskeleton dynamic equation that can calculate a person’s required joint torque given the required payload and the wearer’s posture was derived. This dynamic equation provides a guideline for designing a device that can adjust the allowable joint torque range of an unpowered exoskeleton. In the Adams simulation environment, the payload adjustment device is applied to the cam–follower structure to show that the payload of the exoskeleton can be changed. User convenience and mass production were taken into account in the design of this device. This payload adjustment device should flexibly change the payload of the level desired by the wearer because it can quickly change the payload of the exoskeleton.
Poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) is most commonly used as an anode buffer layer in bulk-heterojunction (BHJ) polymer solar cells (PSCs). However, its hygroscopic ...and acidic nature contributes to the insufficient electrical conductivity, air stability and restricted photovoltaic (PV) performance for the fabricated PSCs. In this study, a new multifunctional additive, 2,3-dihydroxypyridine (DOH), has been used in the PEDOT: PSS buffer layer to obtain modified properties for PEDOT: PSS@DOH and achieve high PV performances. The electrical conductivity of PEDOT:PSS@DOH films was markedly improved compared with that of PEDOT:PSS. The PEDOT:PSS@DOH film exhibited excellent optical characteristics, appropriate work function alignment, and good surface properties in BHJ-PSCs. When a poly(3-hexylthiohpene):6,6-phenyl C
-butyric acid methyl ester blend system was applied as the photoactive layer, the power conversion efficiency of the resulting PSCs with PEDOT:PSS@DOH(1.0%) reached 3.49%, outperforming pristine PEDOT:PSS, exhibiting a power conversion enhancement of 20%. The device fabricated using PEDOT:PSS@DOH (1.0 wt%) also exhibited improved thermal and air stability. Our results also confirm that DOH, a basic pyridine derivative, facilitates adequate hydrogen bonding interactions with the sulfonic acid groups of PSS, induces the conformational transformation of PEDOT chains and contributes to the phase separation between PEDOT and PSS chains.
PDF
