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Gene expression, transcription factor binding and histone modification predict leaf adaxial-abaxial polarity related genes

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Horticultural Plant Journal 2024年第4期10卷 971-982页

作者： Wei Sun Zhicheng Zhang Guusje Bonnema Xiaowu Wang Aalt Dirk Jan van Dijk State Key laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural Sciences Sino-Dutch Joint lab of Vegetable Genomics Bioinformatics group Wageningen University and Research Plant Breeding Wageningen University and Research biosystems Data Analysis Swammerdam Institute for Life SciencesUniversity of Amsterdam

Leaf adaxial-abaxial(ad-abaxial) polarity is crucial for leaf morphology and function, but the genetic machinery governing this process remains unclear. To uncover critical genes involved in leaf ad-abaxial patterning, we applied a combination of in silico prediction using machine learning(ML) and experimental analysis. A Random Forest model was trained using genes known to influence ad-abaxial polarity as ground truth.Gene expression data from various tissues and conditions as well as promoter regulation data derived from transcription factor chromatin immunoprecipitation sequencing(chip-seq) was used as input, enabling the prediction of novel ad-abaxial polarity-related genes and additional transcription factors. Parallel to this, available and newly-obtained transcriptome data enabled us to identify genes differentially expressed across leaf ad-abaxial sides. Based on these analyses, we obtained a set of 111 novel genes which are involved in leaf ad-abaxial specialization. To explore implications for vegetable crop breeding, we examined the conservation of expression patterns between Arabidopsis and Brassica rapa using single-cell transcriptomics. The results demonstrated the utility of our computational approach for predicting candidate genes in crop species. Our findings expand the understanding of the genetic networks governing leaf ad-abaxial differentiation in agriculturally important vegetables,enhancing comprehension of natural variation impacting leaf morphology and development, with demonstrable breeding applications.

关键词： Machine learning Leaf polarity Arabidopsis thaliana Brassica rapa Transcription factor

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Systematic characterization of cleanroom-free fabricated macrovalves,demonstrating pumps and mixers for automated fluid handling tuned for organ-on-chip applications

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Microsystems & Nanoengineering 2022年第3期8卷 163-176页

作者： Elsbeth G.B.M.Bossink Anke R.Vollertsen Joshua T.Loessberg-Zahl Andries D.van der Meer Loe l.Segerink Mathieu Odijk bios lab on a chip group MESA+instituteTechnical Medical CenterMax Planck Institute for Complex Fluid DynamicsUniversity of TwenteEnschedeThe Netherlands Applied Stem Cell Technologies group Technical Medical CenterUniversity of TwenteEnschedeThe Netherlands

Integrated valves enable automated control in microfuidic systems,as they can be applied for mixing,pumping and compartmentalization purposes.Such automation would be highly valuable for applications in organ-on-chip(OoC)systems.However,OoC systems typically have channel dimensions in the range of hundreds of micrometers,which is an order of magnitude larger than those of typical microfluidic valves.The most-used fabrication process for integrated,normally open polydimethylsiloxane(PDMS)valves requires a reflow photoresist that limits the achievable channel height.In addition,the low stroke volumes of these valves make it challenging to achieve flow rates of microliters per minute,which are typically required in OoC systems.Herein,we present a mechanical'macrovalve'fabricated by multilayer soft lithography using micromilled direct molds.We demonstrate that these valves can close off rounded channels of up to 700μm high and 1000μm wide.Furthermore,we used these macrovalves to create a peristaltic pump with a pumping rate of up to 48μL/min and a mixing and metering device that can achieve the complete mixing of a volume of 6.4μL within only 17 s.An initial cell culture experiment demonstrated that a device with integrated macrovalves is biocompatible and allows the cell culture of endothelial cells over multiple days under continuous perfusion and automated medium refreshment.

关键词： pumping mixer pump

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From chip-in-a-lab to lab-on-a-chip:a portable Coulter counter using a modular platform

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Microsystems & Nanoengineering 2018年第1期4卷 57-64页

作者： Stefan Dekker Pelin Kubra Isgor Tobias Feijten Loes I.Segerink Mathieu Odijk bios lab on chip group MESA+Institute for NanotechnologyUniversity of Twente7500 AE EnschedeNetherlands

The field of microfluidics has been struggling to obtain widespread market penetration.In order to overcome this struggle,a standardized and modular platform is introduced and applied.By providing easy-to-fabricate modular building blocks which are compatible with mass manufacturing,we decrease the gap from lab-to-fab.These standardized blocks are used in combination with an application-specific fluidic circuit board.On this board,electrical and fluidic connections are demonstrated by implementing an alternating current Coulter counter.This multipurpose building block is reusable in many applications.In this study,it identifies and counts 6 and 11μm beads.The system is kept in a credit card-sized footprint,as a result of in-house-developed electronics and standardized building blocks.We believe that this easy-to-fabricate,credit card-sized,modular,and standardized prototype brings us closer to clinical and veterinary applications,because it provides an essential stepping stone to fully integrated point-of-care devices.

关键词： sized portable closer

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Droplet microreactor for high-throughput fluorescence-based measurements of single catalyst particle acidity

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Microsystems & Nanoengineering 2023年第2期9卷 101-111页

作者： Jeroen C.Vollenbroek Anne-Eva Nieuwelink Johan G.Bomer Roald M.Tiggelar Albert van den Berg Bert M.Weckhuysen Mathieu Odijko bios lab on a chip group MESA+InstituteUniversity of TwenteHallenweg 157522 NH EnschedeThe Netherlands inorganic Chemistry and Catalysis Debye Institute for Nanomaterials ScienceUtrecht UniversityUniversiteitsweg 993584 CG UtrechtThe Netherlands Nanolab Cleanroom MESA+InstituteUniversity of TwenteHallenweg 157522 NH EnschedeThe Netherlands

The particles of heterogeneous catalysts differ greatly in size,morphology,and most importantly,in activity.Studying these catalyst particles in batch typically results in ensemble averages,without any information at the level of individual catalyst particles.To date,the study of individual catalyst particles has been rewarding but is stll rather slow and often cumbersomel.Furthermore,these valuable in-depth studies at the single particle level lack statistical relevance.Here,we report the development of a droplet microreactor for high-throughput fluorescence-based measurements of the acidities of individual particles in fluid catalytic cracking(FCC)equilibrium catalysts(ECAT).This method combines systematic screening of single catalyst particles with statistical relevance.An oligomerization reaction of 4-methoxystyrene,catalyzed by the Bronsted acid sites inside the zeolite domains of the ECAT particles,Was performed on-chip at 95 ℃.The fluorescence signal generated by the reaction products inside the ECAT particles was detected near the outlet of the microreactor.The high-throughput acidity screening platform was capable of detecting~1000 catalyst particles at a rate of 1 catalyst particle every 2.4 s.The number of detected catalyst particles was representative of the overall catalyst particle population with a confidence level of 95%.The measured fluorescence intensities showed a clear acidity distribution among the catalyst particles,with the majority(96.1%)showing acidity levels belonging to old,deactivated catalyst particles and a minority(3.9%)exhibiting high acidity levels.The latter are potentially of high interest,as they reveal interesting new physicochemical properties indicating why the particles were still highly acidic and reactive.

关键词： catalyst acidity particle

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Exploiting biased reptation for continuous flow preparative DNA fractionation in a versatile microfluidic platform

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Microsystems & Nanoengineering 2017年第1期3卷 294-301页

作者： Burcu Gumuscu Johan G.Bomer Hans L.de Boer Albert van den Berg Jan C.T.Eijkel bios lab-on-a-chip group MESA+Institute for NanotechnologyMIRA Institute for Biomedical Technology and Technical MedicineUniversity of Twente7500 AE EnschedeThe Netherlands

A new approach is presented for preparative,continuous flow fractionation of sub-10-kbp DNA fragments,which exploits the variation in the field-dependent mobility of the DNA molecules based on their length.Orthogonally pulsed electric fields of significantly different magnitudes are applied to a microchip filled with a sieving matrix of 1.2% agarose gel.Using this method,we demonstrate a high-resolution separation of 0.5,1,2,5,and 10 kbp DNA fragments within 2 min.During the separation,DNA fragments are also purified from other ionic species.Preparative fractionation of sub-10-kbp DNA molecules plays an important role in second-generation sequencing.The presented device performs rapid high-resolution fractionation and it can be reliably manufactured with simple microfabrication procedures.

关键词： agarose gel biased reptation continuous flow DNA separation DNA purification preparative fractionation

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Large-scale fabrication of highly ordered sub-20 nm noble metal nanoparticles on silica substrates without metallic adhesion layers

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Microsystems & Nanoengineering 2018年第1期4卷 380-389页

作者： Hai Le-The Erwin Berenschot Roald M.Tiggelaar Niels R.Tas Albert van den Berg Jan C.T.Eijkel bios lab-on-a-chip group MESA+Institute for NanotechnologyMIRA Institute for Biomedical Technology and Technical MedicineMax Planck Center for Complex Fluid DynamicsUniversity of TwenteEnschede 7522 NBThe Netherlands Mesoscale Chemical Systems group MESA+Institute for NanotechnologyUniversity of TwenteEnschede 7522 NBThe Netherlands Nanolab Cleanroom MESA+Institute for NanotechnologyUniversity of TwenteEnschede 7522 NBThe Netherlands

Periodic noble metal nanoparticles offer a wide spectrum of applications including chemical and biological sensors,optical devices,and model catalysts due to their extraordinary properties.For sensing purposes and catalytic studies,substrates made of glass or fused-silica are normally required as supports,without the use of metallic adhesion layers.However,precise patterning of such uniform arrays of silica-supported noble metal nanoparticles,especially at sub-100 nm in diameter,is challenging without adhesion layers.In this paper,we report a robust method to large-scale fabricate highly ordered sub-20 nm noble metal nanoparticles,i.e.,gold and platinum,supported on silica substrates without adhesion layers,combining displacement Talbot lithography(DTL)with dry-etching techniques.Periodic photoresist nanocolumns at diameters of~110 nm are patterned on metal-coated oxidized silicon wafers using DTL,and subsequently transferred at a 1:1 ratio into anti-reflection layer coating(BARC)nanocolumns with the formation of nano-sharp tips,using nitrogen plasma etching.These BARC nanocolumns are then used as a mask for etching the deposited metal layer using inclined argon ion-beam etching.We find that increasing the etching time results in coneshaped silica features with metal nanoparticles on the tips at diameters ranging from 100 nm to sub-30 nm,over large areas of 3×3 cm^(2).Moreover,subsequent annealing these sub-30 nm metal nanoparticle arrays at high-temperature results in sub-20 nm metal nanoparticle arrays with~10^(10) uniform particles.

关键词： metallic ordered columns

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Modular operation of microfluidic chips for highly parallelized cell culture and liquid dosing via a fluidic circuit board

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Microsystems & Nanoengineering 2020年第1期6卷 106-121页

作者： A.R.Vollertsen D.de Boer S.Dekker B.A.M.Wesselink R.Haverkate H.S.Rho R.J.Boom M.Skolimowski M.Blom R.Passier A.van den Berg A.D.van der Meer M.Odijk bios lab on chip group MESA+Institute for NanotechnologyUniversity of TwenteEnschedeThe Netherlands Mesoscale Chemical Systems MESA+Institute for NanotechnologyUniversity of TwenteEnschedeThe Netherlands Institute for Technology-Inspired Regenerative Medicine Maastricht UniversityMaastrichtThe Netherlands Micronit Microtechnologies EnschedeThe Netherlands Applied Stem Cell Technologies TechMed CentreUniversity of TwenteEnschedeThe Netherlands

Microfluidic systems enable automated and highly parallelized cell culture with low volumes and defined liquid dosing.To achieve this,systems typically integrate all functions into a single,monolithic device as a“one size fits all”solution.However,this approach limits the end users’(re)design flexibility and complicates the addition of new functions to the system.To address this challenge,we propose and demonstrate a modular and standardized plug-and-play fluidic circuit board(FCB)for operating microfluidic building blocks(MFBBs),whereby both the FCB and the MFBBs contain integrated valves.A single FCB can parallelize up to three MFBBs of the same design or operate MFBBs with entirely different architectures.The operation of the MFBBs through the FCB is fully automated and does not incur the cost of an extra external footprint.We use this modular platform to control three microfluidic large-scale integration(mLSI)MFBBs,each of which features 64 microchambers suitable for cell culturing with high spatiotemporal control.We show as a proof of principle that we can culture human umbilical vein endothelial cells(HUVECs)for multiple days in the chambers of this MFBB.Moreover,we also use the same FCB to control an MFBB for liquid dosing with a high dynamic range.Our results demonstrate that MFBBs with different designs can be controlled and combined on a single FCB.Our novel modular approach to operating an automated microfluidic system for parallelized cell culture will enable greater experimental flexibility and facilitate the cooperation of different chips from different labs.

关键词： FCB operation culture

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Wafer-scale 3D shaping of high aspect ratio structures by multistep plasma etching and corner lithography

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Microsystems & Nanoengineering 2020年第1期6卷 1176-1186页

作者： Shu Ni Erwin J.W.Berenschot Pieter J.Westerik Meint Jde Boer Rene Wolf Hai Le-The Han J.G.E.Gardeniers Niels R.Tas Mesoscale Chemical System group MESA+InstituteUniversity of Twente7522 NB EnschedeThe Netherlands Inorganic Materials Science group MESA+InstituteUniversity of Twente7522 NB EnschedeThe Netherlands Nanolab Cleanroom MESA+InstituteUniversity of Twente7522 NB EnschedeThe Netherlands Physics of Fluids group MESA+Institute&Max Planck Center for Complex Fluid DynamicsUniversity of Twente7522 NB EnschedeThe Netherlands bios lab-on-a-chip group MESA+Institute&Max Planck Center for Complex Fluid DynamicsUniversity of Twente7522 NB EnschedeThe Netherlands

The current progress of system miniaturization relies extensively on the development of 3D machining techniques to increase the areal structure density.In this work,a wafer-scale out-of-plane 3D silicon(Si)shaping technology is reported,which combines a multistep plasma etching process with corner lithography.The multistep plasma etching procedure results in high aspect ratio structures with stacked semicircles etched deep into the sidewall and thereby introduces corners with a proper geometry for the subsequent corner lithography.Due to the geometrical contrast between the gaps and sidewall,residues are left only inside the gaps and form an inversion mask inside the semicircles.Using this mask,octahedra and donuts can be etched in a repeated manner into Si over the full wafer area,which demonstrates the potential of this technology for constructing high-density 3D structures with good dimensional control in the bulk of Si wafers.

关键词： lithography high structures

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Separation of spermatozoa fromerythrocytes using their tumblingmechanism in a pinch flow fractionationdevice

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Microsystems & Nanoengineering 2019年第1期5卷 474-480页

作者： Johanna T.W.Berendsen Jan C.T.Eijkel Alex M.Wetzels Loes I.Segerink bios lab on a chip group MESA+Institute for NanotechnologyTechnical Medical CentreUniversity of TwenteEnschedeThe Netherlands Department of Obstetrics and Gynaecology Radboud University Nijmegen Medical CentreNijmegenThe Netherlands

Men suffering from azoospermia can father a child,by extracting spermatozoa from a testicular biopsy sample.The main complication in this procedure is the presence of an abundance of erythrocytes.Currently,the isolation of the few spermatozoa from the sample is manually performed due to ineffectiveness of filtering methods,making it time consuming and labor intensive.The spermatozoa are smaller in both width and height than any other cell type found in the sample,with a very small difference compared with the erythrocyte for the smallest,making this not the feature to base the extraction on.However,the length of the spermatozoon is 5×larger than the diameter of an erythrocyte and can be utilized.Here we propose a microfluidic chip,in which the tumbling behavior of spermatozoa in pinched flow fractionation is utilized to separate them from the erythrocytes.We show that we can extract 95%of the spermatozoa from a sample containing 2.5%spermatozoa,while removing around 90%of the erythrocytes.By adjusting the flow rates,we are able to increase the collection efficiency while slightly sacrificing the purity,tuning the solution for the available sample in the clinic.

关键词： erythrocytes flow utilized

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Fabrication of freestanding Pt nanowires for use as thermal anemometry probes in turbulence measurements

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Microsystems & Nanoengineering 2021年第2期7卷 155-165页

作者： Hai Le-The Christian Küchler Albert van den Berg Eberhard Bodenschatz Detlef Lohse Dominik Krug Physics of Fluids group MESA+InstituteUniversity of Twente7522 NBEnschedeThe Netherlands bios lab-on-a-chip group MESA+InstituteUniversity of Twente7522 NBEnschedeThe Netherlands Max Planck-University of Twente Center for Complex Fluid Dynamics GöttingenGermany Max Planck Institute for Dynamics and Self-Organization 37077GöttingenGermany

We report a robust fabrication method for patterning freestanding Pt nanowires for use as thermal anemometry probes for small-scale turbulence measurements.Using e-beam lithography,high aspect ratio Pt nanowires(~300 nm width,~70µm length,~100 nm thickness)were patterned on the surface of oxidized silicon(Si)wafers.Combining wet etching processes with dry etching processes,these Pt nanowires were successfully released,rendering them freestanding between two silicon dioxide(SiO2)beams supported on Si cantilevers.Moreover,the unique design of the bridge holding the device allowed gentle release of the device without damaging the Pt nanowires.The total fabrication time was minimized by restricting the use of e-beam lithography to the patterning of the Pt nanowires,while standard photolithography was employed for other parts of the devices.We demonstrate that the fabricated sensors are suitable for turbulence measurements when operated in constant-current mode.A robust calibration between the output voltage and the fluid velocity was established over the velocity range from 0.5 to 5 m s−1 in a SF6 atmosphere at a pressure of 2 bar and a temperature of 21°C.The sensing signal from the nanowires showed negligible drift over a period of several hours.Moreover,we confirmed that the nanowires can withstand high dynamic pressures by testing them in air at room temperature for velocities up to 55 m s−1.

关键词： nanowires turbulence thermal

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