Search

Analogous to molecular surfactants, amphiphilic Janus particles can function as surface active agents to stabilize emulsions. For molecular surfactants, the shape and amphiphilicity, described by packing parameters and hydrophilic–lipophilic balance (HLB), respectively, determine the type of emulsions that are produced. However, it remains unclear which features of Janus particles determine the type of emulsion that can be stabilized by these particles. In this study, a homologous series of amphiphilic Janus particles with shifting Janus boundaries and tunable chemical properties are synthesized via seeded emulsion polymerization. We systematically study the effect of the relative size of the hydrophilic domain to the total particle (configuration) and chemical nature of Janus particles on their emulsification properties. The concept of the Janus structure parameter (JSP) is introduced to describe the configuration of Janus particles. The emulsification results show that the configuration of Janus particl...

We present a combined numerical and experimental study of a novel design for a vortex-based mixer by virtue of easy insertion of inlet tubes into a capillary-based square channel. We show that, as the Reynolds number (Re) increases above 72, different patterns of vortices develop by changing the inlet configuration. At relatively higher Re, we observe that the disturbance posed by a vortex on the contact surface is not only dependent on its vorticity, but also correlates with the direction of vortex/vortex pair. As a consequence, recognition and application of suitable vortex pattern is of great importance for mixing enhancement. The designed mixer under four inflow confluence conditions, producing single vortex or vortex pair with different directions, shows different mixing performance in the Re range from 20 to 280, from which the optimum design approach capable of generating counter-rotating vortex pair along the outflow direction with higher mixing quality is found. This explains the mass transport and mixing observed in fluid flows with a vortex, which to date has not been studied before.

Background: β-thalassemia and sickle cell disease (SCD) are chronic hemolytic anemias caused by mutation or deletion of the β-globin gene. Reactivation of fetal γ-globin gene (HBG) expression can ameliorate the clinical course of β-hemoglobinopathies. Our current understanding of the globin switching mechanism is not comprehensive, and research into the roles of long non-coding RNAs (lncRNAs) in this process remains limited. Results: We collected umbilical cord blood samples from preterm and full-term infants, from which we enriched and isolated nucleated red blood cells (NRBCs) for transcriptome sequencing. We identified mRNAs, lncRNAs, and microRNAs that were differentially expressed in the preterm and full-term samples, and constructed hub gene network of differentially expressed transcription factors. Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes analysis revealed the biological significance of differentially expressed mRNAs and the targets of differentially expressed lncRNAs and microRNAs. Our analyses revealed that the Fanconi anemia pathway may be involved in the regulation of globin switching at birth. Using quantitative polymerase chain reaction, we confirm that BCL11A is more highly expressed in full-term samples than in preterm samples and is statistically differentially expressed based on biological sex. Results of RNA sequencing and quantitative polymerase chain reaction demonstrated that the lncRNA H19 was expressed at a statistically lower level in full-term samples than in preterm samples. Furthermore, we established the H19‑related lncRNA/miRNA/mRNA network to reveal the potential regulatory mechanisms of H19.Conclusions: Our results suggest that the Fanconi anemia pathway and the H19/let-7/LIN28B axis may be involved in globin switching in umbilical cord blood. The differentially expressed transcripts and related pathways may constitute novel therapeutic targets for β-thalassemia.

Microfluidic technologies have enabled generation of exquisite multiple emulsion droplets, which have been used in many fields, including single-cell assays, micro-sized chemical reactions, and material syntheses. Electrical controlling is an important technique for droplet manipulation in microfluidic systems, but the dielectrophoretic behaviors of multiple emulsion droplets in electrical fields are rarely studied. Here, we report on the dielectrophoresis response of double emulsion droplets in AC electric fields in microfluidic channel. A core-shell model is utilized for analyzing the polarization of droplet interfaces and the overall dielectrophoresis (DEP) force. The water-in-oil-in-water droplets, generated by glass capillary devices, experience negative DEP at low field frequency. At high frequency, however, the polarity of DEP is tunable by adjusting droplet shell thickness or core conductivity. Then, the behavior of droplets with two inner cores is investigated, where the droplets undergo rotation before being repelled or attracted by the strong field area. This work should benefit a wide range of applications that require manipulation of double emulsion droplets by electric fields.

Background: β-thalassemia and sickle cell disease (SCD) are chronic hemolytic anemias caused by mutation or deletion of the β-globin gene. Reactivation of fetal γ-globin gene (HBG) expression can ameliorate the clinical course of β-hemoglobinopathies. Our current understanding of the globin switching mechanism is not comprehensive, and research into the roles of long non-coding RNAs (lncRNAs) in this process remains limited. Results: We collected umbilical cord blood samples from preterm and full-term infants, from which we enriched and isolated nucleated red blood cells (NRBCs) for transcriptome sequencing. We identified mRNAs, lncRNAs, and microRNAs that were differentially expressed in the preterm and full-term samples. Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes analysis revealed the biological significance of differentially expressed mRNAs and the targets of differentially expressed lncRNAs and microRNAs. Our analyses revealed that the Fanconi anemia pathway may be involved in the regulation of globin switching at birth. Using quantitative polymerase chain reaction, we confirm that BCL11A is more highly expressed in full-term samples than in preterm samples and is statistically differentially expressed based on biological sex. Results of RNA sequencing and quantitative polymerase chain reaction demonstrated that the lncRNA H19 was expressed at a statistically lower level in full-term samples than in preterm samples.Conclusions: Our results suggest that the Fanconi anemia pathway and the H19/let-7/LIN28B axis may be involved in globin switching in umbilical cord blood. The differentially expressed transcripts and their related pathways may constitute novel therapeutic targets for β-thalassemia.

Genome-wide association studies (GWAS) have identified many genomic loci associated with risk for schizophrenia, but unambiguous identification of the relationship between disease-associated variants and specific genes, and in particular their effect on risk conferring transcripts, has proven difficult. To better understand the specific molecular mechanism(s) at the schizophrenia locus in 11q25, we undertook cis expression quantitative trait loci (cis-eQTL) mapping for this 2 megabase genomic region using postmortem human brain samples. To comprehensively assess the effects of genetic risk upon local expression, we evaluated multiple transcript features: genes, exons, and exon-exon junctions in multiple brain regions-dorsolateral prefrontal cortex (DLPFC), hippocampus, and caudate. Genetic risk variants strongly associated with expression of SNX19 transcript features that tag multiple rare classes of SNX19 transcripts, whereas they only weakly affected expression of an exon-exon junction that tags the majority of abundant transcripts. The most prominent class of SNX19 risk-associated transcripts is predicted to be overexpressed, defined by an exon-exon splice junction between exons 8 and 10 (junc8.10) and that is predicted to encode proteins that lack the characteristic nexin C terminal domain. Risk alleles were also associated with either increased or decreased expression of multiple additional classes of transcripts. With RACE, molecular cloning, and long read sequencing, we found a number of novel SNX19 transcripts that further define the set of potential etiological transcripts. We explored epigenetic regulation of SNX19 expression and found that DNA methylation at CpG sites near the primary transcription start site and within exon 2 partially mediate the effects of risk variants on risk-associated expression. ATAC sequencing revealed that some of the most strongly risk-associated SNPs are located within a region of open chromatin, suggesting a nearby regulatory element is involved. These findings indicate a potentially complex molecular etiology, in which risk alleles for schizophrenia generate epigenetic alterations and dysregulation of multiple classes of SNX19 transcripts.

Both epidemiological investigations and animal studies have linked arsenic-contaminated water to cancers, including skin, liver and lung cancers. Besides genotoxicity, arsenic exposure-related pathogenesis of disease is widely considered through epigenetic mechanisms; however, the underlying mechanism remains to be determined. Herein we explore the initial epigenetic changes via acute sodium arsenite (As) exposures of mouse embryonic fibroblast (MEF) cells and histone H3K79 methyltransferase Dot1L knockout (Dot1L(−/−)) MEF cells. Our RNA-seq and Western blot data demonstrated that, in both cell lines, acute As exposure abolished histone acetyltransferase p300 at the RNA level and subsequent protein level. Consequently, p300-specific main target histone H3K27ac, a marker separating active from poised enhancers, decreased dramatically as validated by both Western blot and ChIP-qPCR/seq analyses. Concomitantly, H3K4me1 as another well-known marker for enhancers also showed significant decreases, suggesting an underappreciated crosstalk between H3K4me1 and H3K27ac involved in As exposure. Significantly, As exposure-reduced H3K27ac and H3K4me1 inhibited the expression of genes including EP300 itself and Kruppel Like Factor 4(Klf4) that both are tumor suppressor genes. Collectively, our investigations identified p300 as an internal bridging factor within cells to sense external environmental As exposure to alter chromatin, thereby changing gene transcription for disease pathogenesis.

Continuous dielectrophoretic separation is recognized as a powerful technique for a large number of applications including early stage cancer diagnosis, water quality analysis, and stem-cell-based therapy. Generally, the prefocusing of a particle mixture into a stream is an essential process to ensure all particles are subjected to the same electric field geometry in the separation region. However, accomplishing this focusing process either requires hydrodynamic squeezing, which requires an encumbering peripheral system and a complicated operation to drive and control the fluid motion, or depends on dielectrophoretic forces, which are highly sensitive to the dielectric characterization of particles. An alternative focusing technique, induced charge electro-osmosis (ICEO), has been demonstrated to be effective in focusing an incoming mixture into a particle stream as well as nonselective regarding the particles of interest. Encouraged by these aspects, we propose a hybrid method for microparticle separation based on a delicate combination of ICEO focusing and dielectrophoretic deflection. This method involves two steps: focusing the mixture into a thin particle stream via ICEO vortex flow and separating the particles of differing dielectic properties through dielectrophoresis. To demonstrate the feasibility of the method proposed, we designed and fabricated a microfluidic chip and separated a mixture consisting of yeast cells and silica particles with an efficiency exceeding 96%. This method has good potential for flexible integration into other microfluidic chips in the future.

RNA sequencing (RNA-seq) is a powerful approach for measuring gene expression levels in cells and tissues, but it relies on high-quality RNA. We demonstrate here that statistical adjustment using existing quality measures largely fails to remove the effects of RNA degradation when RNA quality associates with the outcome of interest. Using RNA-seq data from molecular degradation experiments of human primary tissues, we introduce a method—quality surrogate variable analysis (qSVA)—as a framework for estimating and removing the confounding effect of RNA quality in differential expression analysis. We show that this approach results in greatly improved replication rates (>3×) across two large independent postmortem human brain studies of schizophrenia and also removes potential RNA quality biases in earlier published work that compared expression levels of different brain regions and other diagnostic groups. Our approach can therefore improve the interpretation of differential expression analysis of transcriptomic data from human tissue.

This paper takes the Iconic Tower as the background and combines the characteristics of overseas engineering projects. It mainly studies the influence of the leading layers of the super high-rise building’s corewall on the vertical displacement, and conducts construction simulation of the Iconic Tower based on the actual construction schedule. It analyzes in detail the vertical displacement and internal force variation laws of the corewall and frame column of the Iconic Tower, and studies the influence of concrete shrinkage and creep on the structure, which provides a reference for the project construction.

This work reports a simple microfluidic method for one-step encapsulation of two reagents with varying concentrations in water-in-oil-in-water (W/O/W) double-emulsion drops. This method not only enables nanoliter-scale reactions and analyses under a series of controlled concentrations of two reagents without stopping the experiments or changing solutions, but also protects the reactions from external disturbance for an extended amount of time by the core–shell structure. To achieve this, a capillary device embedded with a theta-shaped tube is fabricated to produce monodisperse emulsion drops, in which the concentrations of the reagents encapsulated are varied by tuning the flow rates in the two individual channels of the theta tube. The relative volume ratio of the encapsulated reagents can reach up to 1 : 20. In addition, microcapsules converted from emulsion drops have excellent long-term robustness. As a proof of concept, we conduct two frequently used reactions at the nanoliter scale with varying concentrations: acid–base reaction and enzyme-catalyzed redox reaction for glucose detection.

Histone modification including H3 lysine 79 methylation (H3K79me) plays a key role during gene transcription and DNA damage repair. DOT1L, the sole methyltransferase for three states of H3K79me, is implicated in leukemia, co-lorectal cancer, and dilated cardiomyopathy. However, understanding of DOT1L and H3K79me in these pathways and disease pathogenesis has been limited due to the difficulty of working with DOT1L protein. For instance, locus-specific or genome-wide binding sites of DOT1L revealed by chromatin immunoprecipitation (ChIP)-based methods are necessary for inferring its functions, but high-quality ChIP-grade antibodies are currently not available. Herein we have developed a knock-in approach to tag endogenous DOT1L with 3 × Flag at its C-terminal domain to follow functional analyses. The knock-in was facilitated by using TALENs to induce a targeted double-strand break at the endogenous DOTIL to stimulate local homologous recombination at that site. The single cell colonies with successful knock-in were isolated and verified by different methods. We also demonstrated that tagged DOT1L maintains its normal function in terms of methylation and that the engineered cells would be very useful for further studies.

Genetic disorders have been a major concern for public health in China, especially in the rural regions. However, there is little information available about prevalence of many common single-gene disorders in Guizhou Province in the south western part of China. In the present study, we performed a molecular newborn screening for four genetic disorders, including beta-thalassemia (β-thal), glucose-6-phosphate dehydrogenase (G6PD) deficiency, phenylketonuria (PKU), and non-syndromic hearing loss and deafness (NSHL) in this region. A total of 515 newborns were genotyped using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) developed for screening the mutations causing these four disorders, and then confirmed by Sanger sequencing. The results showed that 48 out of 515 newborns were carriers of mutations related to these four diseases, with a frequency of 1 in 11 (9.32%). The carrier frequencies for each disease are: β-thal 2.72%; G6PD deficiency 1.94%; PKU 0.78% and NSHL 4.47%. The genotyping results by MALDI-TOF MS were concordant with Sanger sequencing results within 30 randomly selected samples. This is the first study that reveals carrier frequencies of these four diseases in Guizhou Province. These data provide valuable information for the genetic counseling and disease prevention in Guizhou and southwest China.

By increasing the number of floating electrodes or enlarging the width of single floating electrode, this work provides effective ways to strongly improve the particle trapping performance of induced charge electroosmosis (ICEO). Particle trapping with double or triple separate narrow floating electrodes increases the effective actuating range of ICEO flow and therefore enhance the optimum trapping ability to be 1.63 or 2.34 times of that with single narrow electrode (width of L=200μm), and the ideal trapping frequency is independent of the electrode number due to the mutual independence of electrochemical ion relaxation over each electrode. Furthermore, using a single wide floating electrode with the effective width equal to three separate narrow floating electrodes (L=600μm) instead of a single narrow one slightly lowers the ideal trapping frequency due to an increase in the characteristic polarization length, but the trapping performance is only up to 1.59 times of that with original single narrow electrode, implying that vertical channel confinement effect may severely suppresses the effective actuating range of ICEO flow and renders the trapping performance not as expected. Trapping experiments over wide floating electrode with different channel height were carried out, showing that the trapping performance increases by correctly increasing the channel height.

Pickering emulsions are multiphasic liquid mixtures that are stabilized by solid particles. The strong attachment of particles to the interface makes these emulsions very stable. Additional functionality can be imparted to the emulsion by using particles with useful catalytic, electrical, photonic and magnetic properties. We highlight the most recent developments in polymer colloid-stabilized Pickering emulsions. Pickering emulsions are compared to conventional emulsions that are stabilized by molecular surfactants, focusing on the difference in thermodynamics of the formation of these two different emulsions. Pickering emulsions stabilized with anisotropic polymer particles with homogenous compositions, such as ellipsoids, microrods and thin sheets, are discussed in the second section. In the third section, we highlight recent advances in using Janus particles as solid surfactants for Pickering emulsions. The behavior of Janus particles at liquid–liquid interfaces, the thermodynamics of the formation of Pickering emulsions with Janus particles and the effect of Janus balance on emulsion stabilization are discussed. The fourth section discusses Pickering emulsions based on microgels, a unique class of polymer colloids. These microgels enable the preparation of stimuli-responsive Pickering emulsions as well as high internal phase emulsions for applications in cargo delivery and energy storage devices. The section highlights Pickering emulsions stabilized with polymer-grafted particles and recent developments in preparing Pickering emulsions stabilized by biopolymer colloids such as cellulose nanocrystals, proteins and fat crystals. The chapter concludes by presenting some of the outstanding questions that must be addressed to enable utilization of polymer colloids as effective and functional materials for emulsion stabilization.

Figure S1. Confirmation of neuronal- and glial-enriched identity of NeuN+ and NeuN- samples. Figure S2. Detecting developmental changes in homogenate vs. cell type-specific DNAm data. Figure S3. Unmethylated Regions (UMRs) and Low-methylated regions (LMRs). Figure S4. Partially methylated domains (PMDs). Figure S5. DNA methylation valleys (DMVs). Figure S6. Differentially methylated regions (DMRs). Figure S7. Cell type-specific developmental DMRs and neuronal subtype methylation and hydroxymethylation. Figure S8. cdDMR overlap of human brain developmental enhancers and Human Accelerated Regions (HARs). Figure S9. Cell type-specific, developmentally dynamic DMRs (cdDMRs) and epigenetic states. Figure S10. CpH methylation distribution, levels and context-specific biological process ontology. Figure S11. Trajectories of CpH methylation accumulation in cdDMR groups. Figure S12. Relationship between methylation and expression. Figure S13. Cellular compartment ontology. Figure S14. Web meQTL browser display. Figure S15. Raw sort data. Figure S16. Data processing/alignment pipeline. Figure S17. Genome coverage across processing stages. Figure S18. DMR sensitivity analyses. Figure S19. genome distance versus autocorrelation lag. (PDF 18992 kb)

The hazard analysis and control is one of the most significant issues of the safety management process. The paper proposes a new approach to systemically identify and analyze multi-hazards. The energy function was first studied, summing up the energies involved in production and lives of the national economy with a unified function. Relationships between common production accidents and corresponding energies was presented. In order to take measures in emergency rescue based on energy change, four properties of energy, storability, additivity, transitivity and transformability, were analyzed. The method provide guidance for hazard identification and prevention, and it is proved by guiding the hazard identification of coal mine and carry out effective measures to prevent occurrence of disaster. It indicates that the proposed approach propose a systemic method to analyze multiple hazards and reduce risk of abnormal energy transfer.

Increased expression of the 3.1 isoform of the KCNH2 potassium channel has been associated with cognitive dysfunction and with schizophrenia, yet little is known about the underlying pathophysiological mechanisms. Here, by using in vivo wireless local field potential recordings during working memory processing, in vitro brain slice whole-cell patching recordings and in vivo stereotaxic hippocampal injection of AAV-encoded expression, we identified specific and delayed disruption of hippocampal-mPFC synaptic transmission and functional connectivity associated with reductions of SERPING1, CFH, and CD74 in the KCNH2-3.1 overexpression transgenic mice. The differentially expressed genes in mice are enriched in neurons and microglia, and reduced expression of these genes dysregulates the complement cascade, which has been previously linked to synaptic plasticity. We find that knockdown of these genes in primary neuronal–microglial cocultures from KCNH2-3.1 mice impairs synapse formation, and replenishing reduced CFH gene expression rescues KCNH2-3.1-induced impaired synaptogenesis. Translating to humans, we find analogous dysfunctional interactions between hippocampus and prefrontal cortex in coupling of the fMRI blood oxygen level-dependent (BOLD) signal during working memory in healthy subjects carrying alleles associated with increased KCNH2-3.1 expression in brain. Our data uncover a previously unrecognized role of the truncated KCNH2-3.1 potassium channel in mediating complement activation, which may explain its association with altered hippocampal–prefrontal connectivity and synaptic function. These results provide a potential molecular link between increased KCNH2-3.1 expression, synapse alterations, and hippocampal–prefrontal circuit abnormalities implicated in schizophrenia.

Microfiber modules with controllable lengths emerged as novel biomimetic platforms and are significant for many tissue engineering applications. However, accurately controlling the length of microfibers on the scale of millimeter or even micrometer still remains challenging. Here, a novel and scalable strategy to generate microfiber modules with precisely tunable lengths ranging from 100 to 3500 μm via an alternating current (AC) electric field is presented. To control the microfiber length, double-emulsion droplets containing a chelating agent (sodium citrate) as a spacing node are first uniformly embedded in the microfibers in a controllable spatial arrangement. This process is precisely tuned by adjusting the flow rates, thus, tailoring the resulting multicompartmental microfiber structure. Next, an AC voltage signal is used to trigger the electric field-induced cutting process, where the time-averaged electrical force acting on the induced bipolar charge from the Maxwell-Wagner structural polarization mechanism breaks the stress balance at the interfaces, rupturing the double-emulsion droplets, and resulting in the burst release of the encapsulated chelating agents into the hydrogel cavity. The outer hydrogel shell is quickly dissolved by a chemical reaction, cutting the long fiber into a series of microfiber units of given length. Furthermore, adding magnetic nanoparticles endows magnetic functionality with these microfiber modules, which are allowed to serve as micromotors and building blocks. This electro-induced cutting method provides a facile strategy for the fabrication of microfibers with desired lengths, showing considerable promise for various chemical and biological applications.

We have characterized the landscape of DNA methylation (DNAm) across the first two decades of human neocortical development in NeuN+ neurons using whole-genome bisulfite sequencing and compared them to non-neurons (primarily glia) and prenatal homogenate cortex. We show that DNAm changes more dramatically during the first five years of postnatal life than during the entire remaining period. We further refined global patterns of increasingly divergent neuronal CpG and CpH methylation (mCpG and mCpH) into six developmental trajectories and found that in contrast to genome-wide patterns, neighboring mCpG and mCpH levels within these regions were highly correlated. We then integrated paired RNA-seq data and identified direct regulation of hundreds of transcripts and their splicing events exclusively by mCpH levels, independently from mCpG levels, across this period. We finally explored the relationship between DNAm patterns and development of brain-related phenotypes and found enriched heritability for many phenotypes within DNAm features we identify.

Genome-wide association studies (GWAS) have identified many genomic loci associated with risk for schizophrenia, but unambiguous identification of the relationship between disease-associated variants and specific genes, and in particular their effect on risk conferring transcripts, has proven difficult. To better understand the specific molecular mechanism(s) at the schizophrenia locus in 11q25, we undertook cis expression quantitative trait loci (cis-eQTL) mapping for this 2 megabase genomic region using postmortem human brain samples. To comprehensively assess the effects of genetic risk upon local expression, we evaluated multiple transcript features: genes, exons, and exon-exon junctions in multiple brain regions-dorsolateral prefrontal cortex (DLPFC), hippocampus, and caudate. Genetic risk variants strongly associated with expression of SNX19 transcript features that tag multiple rare classes of SNX19 transcripts, whereas they only weakly affected expression of an exon-exon junction that tags the majority of abundant transcripts. The most prominent class of SNX19 risk-associated transcripts is predicted to be overexpressed, defined by an exon-exon splice junction between exons 8 and 10 (junc8.10) and that is predicted to encode proteins that lack the characteristic nexin C terminal domain. Risk alleles were also associated with either increased or decreased expression of multiple additional classes of transcripts. With RACE, molecular cloning, and long read sequencing, we found a number of novel SNX19 transcripts that further define the set of potential etiological transcripts. We explored epigenetic regulation of SNX19 expression and found that DNA methylation at CpG sites near the primary transcription start site and within exon 2 partially mediate the effects of risk variants on risk-associated expression. ATAC sequencing revealed that some of the most strongly risk-associated SNPs are located within a region of open chromatin, suggesting a nearby regulatory element is involved. These findings indicate a potentially complex molecular etiology, in which risk alleles for schizophrenia generate epigenetic alterations and dysregulation of multiple classes of SNX19 transcripts.

Epidemiological investigations have validated the positive relationships between arsenic in drinking water and several cancers, including skin, liver and lung cancers. Besides genotoxicity, arsenic exposure-related pathogenesis of disease is widely considered through epigenetic mechanisms; however, the underlying mechanistic insight remains elusive. Herein we explore the initial epigenetic changes via acute low-dose arsenite exposures of mouse embryonic fibroblast (MEF) cells and Dot1L knockout MEF (Dot1L-/- for abbreviation) cells. Our RNA-seq and Western blot data demonstrated that, in both cell lines, acute low-dose arsenite exposure abolished histone acetyltransferase p300 at the RNA level and subsequent protein level. Consequently, p300-specific main target histone H3K27ac, a marker separating active from poised enhancers, decreased dramatically as validated by both Western blot and ChIP-seq analyses. Concomitantly, H3K4me1 as another well-known marker for enhancers also showed significant decreases, suggesting an underappreciated crosstalk between H3K4me1 and H3K27ac involved in arsenite exposure. Significantly, arsenite exposure-reduced H3K27ac and H3K4me1 inhibit the expression of genes includingEP300itself andKruppel Like Factor 4(Klf4), a tumor suppressor gene. Collectively, our investigations identify p300 as an internal bridging factor within cells to sense external environmental arsenite exposure to alter chromatin, thereby changing gene transcription for disease pathogenesis.

We outline an ambitious project to characterize the genetic and epigenetic regulation of multiple facets of transcription in distinct brain regions across the human lifespan in samples of major neuropsychiatric disorders and controls. Initially focused on schizophrenia and mood disorders, the goal of this consortium is to elucidate the underlying molecular mechanisms of genetic associations with the goal of identifying novel therapeutic targets. The consortium currently consists of seven pharmaceutical companies and a not-for-profit medical research institution working as a precompetitive team to generate and analyze publicly available archival brain genomic data related to neuropsychiatric illness.

This paper reports a microfluidic separation device combining 3D electrodes and vaulted obstacles to continuously separate particles experiencing strong positive dielectrophoresis (DEP) from particles experiencing weak positive DEP, or from particles experiencing negative DEP. The separation is achieved by first focusing the particle mixture into a narrow stream by a hydrodynamic focusing flow, and then deviating them into different outlets by AC DEP. The vaulted obstacles facilitate the separation by both increasing the non-uniformity of the electric field, and influencing the particles to move in regions strongly affected by DEP. The 3D electrodes give rise to a spatially non-uniform electric field and extend DEP effect to the channel height. Numerical simulations are performed to investigate the effects of the obstacles on electric field distribution and particle trajectories so as to optimize the obstacle height and compare with the experimental results. The performance of the device is assessed by separating 25 μm gold-coated particles from 10 μm particles in different flow rates by positive DEP and negative DEP, and also separating 25 μm gold-coated particles from yeast cells using only positive DEP. The experimental observation shows a reasonable agreement with numerical simulation results.

We propose a novel low-frequency strategy to trap 10 μm colloidal polystyrene (PS) particles of small buoyancy velocity on the surface of a floating electrode, on the basis of combined induced-charge electroosmotic (ICEO) flow and dipole-dipole chaining phenomenon. For field frequencies of 5-50 Hz, much lower than the reciprocal RC time scale, double-layer polarization makes electric field lines pass around the 'insulating' surface of the ideally polarizable floating electrode. Once the long-range ICEO convective micro-vortexes transport particles quickly from the bulk fluid to the electrode surface, neighbouring particles aligned along the local horizontal electric field attract one another by attractive dipolar interactions, and form arrays of particle chains that are almost parallel with the applied electric field. Most importantly, this low-frequency trapping method takes advantage of the dielectrophoretic (DEP) particle-particle interaction to enhance the downward buoyancy force of this dipolar chaining assembly structure, in order to overcome the upward ICEO fluidic drag and realize stable particle trapping around the flow stagnation region. For the sake of comparison, the field frequency is further raised far above the DC limit. At the intermediate frequencies of 200 Hz-2 kHz, this trapping method fails to work, since the normal electric field component emanates from the conducting electrode surface. Besides, at high field frequencies (>3 kHz), particles can be once again effectively trapped at the electrode center, though with a compact (3 kHz) or disordered (10 kHz) 2D packing state on the electrode surface and mainly governed by the short-range negative DEP force field, resulting in requiring a much longer trapping time. To gain a better interpretation of the various particle behaviours observed in experiments, we develop a theoretical framework that takes into account both Maxwell-Wagner interfacial charge relaxation at the particle/electrolyte interface and the field-induced double-layer polarization at the electrode/electrolyte interface, and apply it to quantify the particle-particle electrokinetic interactions. With this simple geometrical configuration of a floating electrode, our results provide a new way to realize trapping of colloidal particles with a small buoyancy velocity under the combined action of ICEO flow and an attractive dipole-dipole interaction.

We herein present for the first time a microfluidic device that utilizes AC induced-charge electro-osmosis (ICEO) to continuously focus microparticles from suspending medium. An advanced conducting silver-polydimethylsiloxane (AgPDMS) composite is chosen to fabricate three dimensional (3D) driving electrodes thereby to generate a uniform AC electric field, resulting in a vortex ICEO flow on a planar floating electrode positioned at the bottom of the main channel. The 3D electrodes are employed due to their advantage of avoiding negative effects of alternating current electro-osmosis (ACEO) and dielectrophoresis (DEP). The combination of the ICEO flow and forward flow in the device channel focuses the microparticles in a thin stream and collects them in a specific outlet. We design the device based on the non-linear electrokinetic theory and flow field simulation, and validated the device performance under different experimental conditions including signal frequency, potential amplitude, and inlet flow rate. The highest focusing efficiency for yeast cells can reach 96.6% at the frequency of 600 Hz and a potential amplitude of 15 Vp. The results provide a promising method to flow-focus microparticles in modern microfluidic systems by using ICEO.

We report herein a novel microfluidic particle concentrator that utilizes constriction microchannels to enhance the flow-focusing performance of induced-charge electroosmosis (ICEO), where viscous hemi-spherical oil droplets are embedded within the mainchannel to form deformable converging-diverging constriction structures. The constriction region between symmetric oil droplets partially coated on the electrode strips can improve the focusing performance by inducing a granular wake flow area at the diverging channel, which makes almost all of the scattered sample particles trapped within a narrow stream on the floating electrode. Another asymmetric droplet pair arranged near the outlets can further direct the trajectory of focused particle stream to one specified outlet port depending on the symmetry breaking in the shape of opposing phase interfaces. By fully exploiting rectification properties of induced-charge electrokinetic phenomena at immiscible water/oil interfaces of tunable geometry, the expected function of continuous and switchable flow-focusing is demonstrated by preconcentrating both inorganic silica particles and biological yeast cells. Physical mechanisms responsible for particle focusing and locus deflection in the droplet-assisted concentrentor are analyzed in detail, and simulation results are in good accordance with experimental observations. Our work provides new routes to construct flexible electrokinetic framework for preprocessing on-chip biological samples before performing subsequent analysis.

Advances in microfluidic emulsification have enabled the generation of exquisite multiple-core droplets, which are promising structures to accommodate microreactions. An essential requirement for conducting reactions is the sequential coalescence of the multiple cores encapsulated within these droplets, therefore, mixing the reagents together in a controlled sequence. Here, a microfluidic approach is reported for the conduction of two-step microreactions by electrically fusing three cores inside double-emulsion droplets. Using a microcapillary glass device, monodisperse water-in-oil-in-water droplets are fabricated with three compartmented reagents encapsulated inside. An AC electric field is then applied through a polydimethylsiloxane chip to trigger the sequential mixing of the reagents, where the precise sequence is guaranteed by the discrepancy of the volume or conductivity of the inner cores. A two-step reaction in each droplet is ensured by two times of core coalescence, which totally takes 20-40 s depending on varying conditions. The optimal parameters of the AC signal for the sequential fusion of the inner droplets are identified. Moreover, the capability of this technique is demonstrated by conducting an enzyme-catalyzed reaction used for glucose detection with the double-emulsion droplets. This technique should benefit a wide range of applications that require multistep reactions in micrometer scale.

Microfluidically generated double emulsions are promising templates for microreactions, which protect the reaction from external disturbance and enable in vitro analyses with large-scale samples. Controlled combination of their inner droplets in a continuous manner is an essential requirement toward truly applications. Here, we first generate dual-cored double-emulsion drops with different inner encapsulants using a capillary microfluidic device; next, we transfer the emulsion drops into another electrode-integrated polydimethylsiloxane microfluidic device and utilize external AC electric field to continuously trigger the coalescence of inner cores inside these emulsion drops in continuous flow. Hundreds of thousands of monodisperse microreactions with nanoliter-scale reagents can be conducted using this approach. The performance of core coalescence is investigated as a function of flow rate, applied electrical signal, and core conductivity. The coalescence efficiency can reach up to 95%. We demonstrate the utility of this technology for accommodating microreactions by analyzing an enzyme catalyzed reaction and by fabricating cell-laden hydrogel particles. The presented method can be readily used for the controlled triggering of microreactions with high flexibility for a wide range of applications, especially for continuous chemical or cell assays.

We report osmolarity-controlled swelling behaviors of dual-cored water-in-oil-in-water (W/O/W) double-emulsion drops, which are caused by the discrepancy of salt concentration of the inner cores and suspending medium. The expanding speed and resultant size can be manipulated independently according to salt concentration. The swelling behaviors result in two kinds of transformation in the emulsion drops. One is coalescence of the two inner aqueous cores, taking place when the cores are of the same salt concentrations and the double-emulsion drops swell to dumbbell-shaped morphology. Another is rupture of one inner core, which happens when the cores are of different salt concentrations and the double-emulsion drops swell to snowman-shaped structures. The conditions for core-coalescence and core-rupture are investigated, respectively. The swelling leading transformation of emulsion drops are of promising application as microreactors and tiny vesicles: The core-coalescence can lead to controlled reaction of two solvents while protecting the reaction form external contamination; the core-rupture may be utilized for targeted release of reagents at specific position.

Herein, we first describe a perfusion chip integrated with an AC electrothermal (ACET) micromixer to supply a uniform drug concentration to tumor cells. The in-plane fluid microvortices for mixing were generated by six pairs of reconstructed novel ACET asymmetric electrodes. To enhance the mixing efficiency, the novel ACET electrodes with rotating angles of 0°, 30°, and 60° were investigated. The asymmetric electrodes with a rotating angle of 60° exhibited the highest mixing efficiency by both simulated and experimental results. The length of the mixing area is 7 mm, and the mixing efficiency is 89.12% (approximate complete mixing) at a voltage of 3 V and a frequency of 500 kHz. The applicability of our micromixer with electrodes rotating at 60° was demonstrated by the drug (tamoxifen) test of human breast cancer cells (MCF-7) for five days, which implies that our ACET in-plane microvortices micromixer has great potential for the application of drug induced rapid death of tumor cells and mixing of biomaterials in organs-on-a-chip systems.

RNA sequencing (RNA-seq) is a powerful approach for measuring gene expression levels in cells and tissues, but it relies on high-quality RNA. We demonstrate here that statistical adjustment employing existing quality measures largely fails to remove the effects of RNA degradation when RNA quality associates with the outcome of interest. Using RNA-seq data from a molecular degradation experiment of human brain tissue, we introduce the quality surrogate variable (qSVA) analysis framework for estimating and removing the confounding effect of RNA quality in differential expression analysis. We show this approach results in greatly improved replication rates (>3x) across two large independent postmortem human brain studies of schizophrenia. Finally, we explored public datasets to demonstrate potential RNA quality confounding when comparing expression levels of different brain regions and diagnostic groups beyond schizophrenia. Our approach can therefore improve the interpretation of differential expression analysis of transcriptomic data from the human brain.

By increasing the number of floating electrodes or enlarging the width of single floating electrode, this work provides effective ways to strongly improve the particle trapping performance of induced charge electroosmosis (ICEO). Particle trapping with double or triple separate narrow floating electrodes increases the effective actuating range of ICEO flow and therefore enhance the optimum trapping ability to be 1.63 or 2.34 times of that with single narrow electrode (width of L=200μm), and the ideal trapping frequency is independent of the electrode number due to the mutual independence of electrochemical ion relaxation over each electrode. Furthermore, using a single wide floating electrode with the effective width equal to three separate narrow floating electrodes (L=600μm) instead of a single narrow one slightly lowers the ideal trapping frequency due to an increase in the characteristic polarization length, but the trapping performance is only up to 1.59 times of that with original single narrow electrode, implying that vertical channel confinement effect may severely suppresses the effective actuating range of ICEO flow and renders the trapping performance not as expected. Trapping experiments over wide floating electrode with different channel height were carried out, showing that the trapping performance increases by correctly increasing the channel height.

Differentiating pluripotent cells from fibroblast progenitors is a potentially transformative tool in personalized medicine. We previously identified relatively greater success culturing dura-derived fibroblasts than scalp-derived fibroblasts from postmortem tissue. We hypothesized that these differences in culture success were related to epigenetic differences between the cultured fibroblasts by sampling location, and therefore generated genome-wide DNA methylation and transcriptome data on 11 intrinsically matched pairs of dural and scalp fibroblasts from donors across the lifespan (infant to 85 years). While these cultured fibroblasts were several generations removed from the primary tissue and morphologically indistinguishable, we found widespread epigenetic differences by sampling location at the single CpG (N = 101,989), region (N = 697), “block” (N = 243), and global spatial scales suggesting a strong epigenetic memory of original fibroblast location. Furthermore, many of these epigenetic differences manifested in the transcriptome, particularly at the region-level. We further identified 7,265 CpGs and 11 regions showing significant epigenetic memory related to the age of the donor, as well as an overall increased epigenetic variability, preferentially in scalp-derived fibroblasts—83% of loci were more variable in scalp, hypothesized to result from cumulative exposure to environmental stimuli in the primary tissue. By integrating publicly available DNA methylation datasets on individual cell populations in blood and brain, we identified significantly increased inter-individual variability in our scalp- and other skin-derived fibroblasts on a similar scale as epigenetic differences between different lineages of blood cells. Lastly, these epigenetic differences did not appear to be driven by somatic mutation—while we identified 64 probable de-novo variants across the 11 subjects, there was no association between mutation burden and age of the donor (p = 0.71). These results depict a strong component of epigenetic memory in cell culture from primary tissue, even after several generations of daughter cells, related to cell state and donor age., Author Summary Regenerative medicine specialists have been using a type of cell commonly found in the skin called the fibroblast because it is easily obtained from skin samples, grows well in culture, and can be manipulated in the laboratory to de-differentiate into a primordial state known as the induced pluripotent stem cell. These primitive stem cells can then be transformed into mature tissues, such as liver or pancreas cells. Here we show that fibroblasts, coming from different locations in the same individual, vary significantly in epigenetic marks called DNA methylation, which are involved in the regulation of gene expression. In addition to location-specific patterns of DNA methylation, we also find that fibroblasts from different anatomical locations respond differently in epigenetic patterns related to aging. As the field of regenerative medicine advances, our study demonstrates that deciding upon the source of fibroblasts from an individual to generate new tissues and organs may be an important consideration.

Position-controllable trapping of particles on the surface of a bipolar metal strip by induced-charge electroosmotic (ICEO) flow is presented herein. We demonstrate a nonlinear ICEO slip profile on the electrode surface accounting for stable particle trapping behaviors above the double-layer relaxation frequency, while no trapping occurs in the DC limit as a result of a strong upward fluidic drag induced by a linear ICEO slip profile. By extending an AC-flow field effect transistor from the DC limit to the AC field, we reveal that fixed-potential ICEO exceeding RC charging frequency can adjust the particle trapping position flexibly by generating controllable symmetry breaking in a vortex flow pattern. Our results open up new opportunities to manipulate microscopic objects in modern microfluidic systems by using ICEO.

The purpose of this study was to evaluate the effects of butyrate infusion on rumen epithelial transcriptome. Next-generation sequencing (NGS) and bioinformatics are used to accelerate our understanding of regulation in rumen epithelial transcriptome of cattle in the dry period induced by butyrate infusion at the level of the whole transcriptome. Butyrate, as an essential element of nutrients, is a histone deacetylase (HDAC) inhibitor that can alter histone acetylation and methylation, and plays a prominent role in regulating genomic activities influencing rumen nutrition utilization and function. Ruminal infusion of butyrate was following 0-hour sampling (baseline controls) and continued for 168 hours at a rate of 5.0 L/day of a 2.5 M solution as a continuous infusion. Following the 168-hour infusion, the infusion was stopped, and cows were maintained on the basal lactation ration for an additional 168 hours for sampling. Rumen epithelial samples were serially collected via biopsy through rumen fistulae at 0-, 24-, 72-, and 168-hour (D1, D3, D7) and 168-hour post-infusion (D14). In comparison with pre-infusion at 0 hours, a total of 3513 genes were identified to be impacted in the rumen epithelium by butyrate infusion at least once at different sampling time points at a stringent cutoff of false discovery rate (FDR)

Imprinted genes are vulnerable to environmental influences during early embryonic development, thereby contributing to the onset of disease in adulthood. Monoallelic methylation at several germline imprints has been reported as DNMT1-dependent. However, which of these two epigenetic attributes, DNMT1-dependence or allelic methylation, renders imprinted genes susceptible to environmental stressors has not been determined. Herein, we developed a new approach, referred to as NORED, to identify 2468 DNMT1-dependent DNA methylation patterns in the mouse genome. We further developed an algorithm based on a genetic variation-independent approach (referred to as MethylMosaic) to detect 2487 regions with bimodal methylation patterns. Two approaches identified 207 regions, including known imprinted germline allele-specific methylation patterns (ASMs), that were both NORED and MethylMosaic regions. Examination of methylation in four independent mouse embryonic stem cell lines shows that two regions identified by both NORED and MethylMosaic (Hcn2 and Park7) did not display parent-of-origin-dependent allelic methylation. In these four F1 hybrid cell lines, genetic variation in Cast allele at Hcn2 locus introduces a transcription factor binding site for MTF-1 that may predispose Cast allelic hypomethylation in a reciprocal cross with either C57 or 129 strains. In contrast, each allele of Hcn2 ASM in J1 inbred cell line and Park7 ASM in four F1 hybrid cell lines seems to exhibit similar propensity to be either hypo- or hypermethylated, suggesting a ‘random, switchable’ ASM. Together with published results, our data on ASMs prompted us to propose a hypothesis of regional ‘autosomal chromosome inactivation (ACI)’ that may control a subset of autosomal genes. Therefore, our results open a new avenue to understand monoallelic methylation and provide a rich resource of candidate genes to examine in environmental and nutritional exposure models.

Transcriptome analysis of human brain provides fundamental insight into development and disease, but it largely relies on existing annotation. We sequenced transcriptomes of 72 prefrontal cortex samples across six life stages and identified 50,650 differentially expression regions (DERs) associated with developmental and aging, agnostic of annotation. While many DERs annotated to non-exonic sequence (41.1%), most were similarly regulated in cytosolic mRNA extracted from independent samples. The DERs were developmentally conserved across 16 brain regions and in the developing mouse cortex, and were expressed in diverse cell and tissue types. The DERs were further enriched for active chromatin marks and clinical risk for neurodevelopmental disorders such as schizophrenia. Lastly, we demonstrate quantitatively that these DERs associate with a changing neuronal phenotype related to differentiation and maturation. These data show conserved molecular signatures of transcriptional dynamics across brain development, have potential clinical relevance and highlight the incomplete annotation of the human brain transcriptome.

This paper reports a microfluidic separation device combining 3D electrodes and vaulted obstacles to continuously separate particles experiencing strong positive dielectrophoresis (DEP) from particles experiencing weak positive DEP, or from particles experiencing negative DEP. The separation is achieved by first focusing the particle mixture into a narrow stream by a hydrodynamic focusing flow, and then deviating them into different outlets by AC DEP. The vaulted obstacles facilitate the separation by both increasing the non-uniformity of the electric field, and influencing the particles to move in regions strongly affected by DEP. The 3D electrodes give rise to a spatially non-uniform electric field and extend DEP effect to the channel height. Numerical simulations are performed to investigate the effects of the obstacles on electric field distribution and particle trajectories so as to optimize the obstacle height and compare with the experimental results. The performance of the device is assessed by separating 25 μm gold-coated particles from 10 μm particles in different flow rates by positive DEP and negative DEP, and also separating 25 μm gold-coated particles from yeast cells using only positive DEP. The experimental observation shows a reasonable agreement with numerical simulation results.

Droplet-based microfluidics has provided a means to generate multi-core double emulsions, which are versatile platforms for microreactors in materials science, synthetic biology, and chemical engineering. To provide new opportunities for double emulsion platforms, here, we report a glass capillary microfluidic approach to first fabricate osmolarity-responsive Water-in-Oil-in-Water (W/O/W) double emulsion containing two different inner droplets/cores and to then trigger the coalescence between the encapsulated droplets precisely. To achieve this, we independently control the swelling speed and size of each droplet in the dual-core double emulsion by controlling the osmotic pressure between the inner droplets and the collection solutions. When the inner two droplets in one W/O/W double emulsion swell to the same size and reach the instability of the oil film interface between the inner droplets, core-coalescence happens and this coalescence process can be controlled precisely. This microfluidic methodology enables the generation of highly monodisperse dual-core double emulsions and the osmolarity-controlled swelling behavior provides new stimuli to trigger the coalescence between the encapsulated droplets. Such swelling-caused core-coalescence behavior in dual-core double emulsion establishes a novel microreactor for nanoliter-scale reactions, which can protect reaction materials and products from being contaminated or released.