High-throughput Investigation Research Articles

Evaluation of Primers Targeting the Diazotroph Functional Gene and Development of NifMAP - A Bioinformatics Pipeline for Analyzing nifH Amplicon Data.

Diazotrophic microorganisms introduce biologically available nitrogen (N) to the global N cycle through the activity of the nitrogenase enzyme. The genetically conserved dinitrogenase reductase (nifH) gene is phylogenetically distributed across four clusters (I–IV) and is widely used as a marker gene for N2 fixation, permitting investigators to study the genetic diversity of diazotrophs in nature and target potential participants in N2 fixation. To date there have been limited, standardized pipelines for analyzing the nifH functional gene, which is in stark contrast to the 16S rRNA gene. Here we present a bioinformatics pipeline for processing nifH amplicon datasets – NifMAP (“NifH MiSeq Illumina Amplicon Analysis Pipeline”), which as a novel aspect uses Hidden-Markov Models to filter out homologous genes to nifH. By using this pipeline, we evaluated the broadly inclusive primer pairs (Ueda19F–R6, IGK3–DVV, and F2–R6) that target the nifH gene. To evaluate any systematic biases, the nifH gene was amplified with the aforementioned primer pairs in a diverse collection of environmental samples (soils, rhizosphere and roots samples, biological soil crusts and estuarine samples), in addition to a nifH mock community consisting of six phylogenetically diverse members. We noted that all primer pairs co-amplified nifH homologs to varying degrees; up to 90% of the amplicons were nifH homologs with IGK3–DVV in some samples (rhizosphere and roots from tall oat-grass). In regards to specificity, we observed some degree of bias across the primer pairs. For example, primer pair F2–R6 discriminated against cyanobacteria (amongst others), yet captured many sequences from subclusters IIIE and IIIL-N. These aforementioned subclusters were largely missing by the primer pair IGK3–DVV, which also tended to discriminate against Alphaproteobacteria, but amplified sequences within clusters IIIC (affiliated with Clostridia) and clusters IVB and IVC. Primer pair Ueda19F–R6 exhibited the least bias and successfully captured diazotrophs in cluster I and subclusters IIIE, IIIL, IIIM, and IIIN, but tended to discriminate against Firmicutes and subcluster IIIC. Taken together, our newly established bioinformatics pipeline, NifMAP, along with our systematic evaluations of nifH primer pairs permit more robust, high-throughput investigations of diazotrophs in diverse environments.

High-Throughput Investigation of Contractile and Electrophysiological Properties of Optically Stimulated hiPSC-CM Monolayers

High-Throughput Investigation of Contractile and Electrophysiological Properties of Optically Stimulated hiPSC-CM Monolayers

Celiac disease microarray analysis based on System Biology Approach.

Aim of this study is screen of the large numbers of related genes of CD to find the key ones. Celiac disease (CD) is known as a gluten sensitive and immune system dependent disease. There are several high throughput investigations about CD but it is necessary to clarify new molecular aspects mechanism of celiac. Whole-genome profile (RNA) of the human peripheral blood mononuclear cells (PBMCs) as Gene expression profile GSE113469 was retrieved Gene Expression Omnibus (GEO) database. The significant genes were selected and analyzed via protein-protein interaction (PPI) network by Cytoscape software. The key genes were introduced and enriched via ClueGO to find the related biochemical pathways. Among 250 significant genes 47 genes with expressed change above 2 fold change (FC) were interacted and the constructed network were analyzed. The network characterized by poor connections so it was promoted by addition 50 related nodes and 18 crucial nodes were introduced. Two clusters of biochemical pathways were identified and discussed. There is an obvious conflict between microarray finding and the well-known related genes of CD. This problem can be solve by more attention to the interpretation of PPI ntwork analysis results.

Functional Genomics in Murine Macrophages.

In this chapter, we describe methods for functional genomics studies in mouse macrophages. In particular, we describe complementary methods for gene inhibition using RNA interference (RNAi) and gene overexpression. These methods are readily amenable to medium- and high-throughput functional genomics investigations. These complementary loss-of-function and gain-of-function genomic approaches provide a rapid means of investigating the function of candidate genes prior to initiating more cumbersome studies in vivo.

Next-Generation Sequencing and Mutational Analysis: Implications for Genes Encoding LINC Complex Proteins.

Targeted panel, whole exome, or whole genome DNA sequencing using next-generation sequencing (NGS) allows for extensive high-throughput investigation of molecular machines/systems such as the LINC complex. This includes the identification of genetic variants in humans that cause disease, as is the case for some genes encoding LINC complex proteins. The relatively low cost and high speed of the sequencing process results in large datasets at various stages of analysis and interpretation. For those not intimately familiar with the process, interpretation of the data might prove challenging. This review lays out the most important and most commonly used materials and methods of NGS. It also discusses data analysis and potential pitfalls one might encounter because of peculiarities of the laboratory methodology or data analysis pipelines.

Multivariable extrapolation of grand canonical free energy landscapes.

We derive an approach for extrapolating the free energy landscape of multicomponent systems in the grand canonical ensemble, obtained from flat-histogram Monte Carlo simulations, from one set of temperature and chemical potentials to another. This is accomplished by expanding the landscape in a Taylor series at each value of the order parameter which defines its macrostate phase space. The coefficients in each Taylor polynomial are known exactly from fluctuation formulas, which may be computed by measuring the appropriate moments of extensive variables that fluctuate in this ensemble. Here we derive the expressions necessary to define these coefficients up to arbitrary order. In principle, this enables a single flat-histogram simulation to provide complete thermodynamic information over a broad range of temperatures and chemical potentials. Using this, we also show how to combine a small number of simulations, each performed at different conditions, in a thermodynamically consistent fashion to accurately compute properties at arbitrary temperatures and chemical potentials. This method may significantly increase the computational efficiency of biased grand canonical Monte Carlo simulations, especially for multicomponent mixtures. Although approximate, this approach is amenable to high-throughput and data-intensive investigations where it is preferable to have a large quantity of reasonably accurate simulation data, rather than a smaller amount with a higher accuracy.

Flexible and Accessible Automated Operation of Miniature Chromatography Columns on a Liquid Handling Station.

The High Throughput (HT) investigation of chromatographic separations is an important element of downstream bioprocess development due to the importance of chromatography as a technique for achieving stringent regulatory requirements on product purity. Various HT formats for chromatography exist, but the miniature column approach has characteristics resembling large scale packed bed column chromatography the most. The operation of such columns on robotic stations can be automated, but this is not always a straightforward procedure; the robotic manipulations are highly dependent on the settings of each experiment and the standard commands of the supporting software may not provide readily the required flexibility and accessibility for "plug and play" functionality. These can limit the potential of this technique in laboratories engaging on HT activities. In this work, we present an application which aims to overcome this challenge by providing end-users with a flexible operation of the miniature column technique on an automated liquid handler. The application includes a script which is written on Freedom EVOware, and is supplemented by custom compiled executables. Here, the manipulations carried out by the application are described in detail and its functionality is demonstrated through typical experiments based on bind and elute miniature column chromatography. The application is shown to allow for the unsupervised "on-the-fly" programming of the robotic station and to ultimately make the technique accessible to non-automation experts. This application is therefore well suited to simplifying development activities based on the robotic deployment of the miniature column chromatography technique.

Heat-Responsive Photosynthetic and Signaling Pathways in Plants: Insight from Proteomics.

Heat stress is a major abiotic stress posing a serious threat to plants. Heat-responsive mechanisms in plants are complicated and fine-tuned. Heat signaling transduction and photosynthesis are highly sensitive. Therefore, a thorough understanding of the molecular mechanism in heat stressed-signaling transduction and photosynthesis is necessary to protect crop yield. Current high-throughput proteomics investigations provide more useful information for underlying heat-responsive signaling pathways and photosynthesis modulation in plants. Several signaling components, such as guanosine triphosphate (GTP)-binding protein, nucleoside diphosphate kinase, annexin, and brassinosteroid-insensitive I-kinase domain interacting protein 114, were proposed to be important in heat signaling transduction. Moreover, diverse protein patterns of photosynthetic proteins imply that the modulations of stomatal CO2 exchange, photosystem II, Calvin cycle, ATP synthesis, and chlorophyll biosynthesis are crucial for plant heat tolerance.

Bacterial artificial chromosomes as recombinant reporter constructs to investigate gene expression and regulation in echinoderms.

Genome sequences contain all the necessary information-both coding and regulatory sequences-to construct an organism. The developmental process translates this genomic information into a three-dimensional form. One interpretation of this translation process can be described using gene regulatory network (GRN) models, which are maps of interactions among regulatory gene products in time and space. As high throughput investigations reveal increasing complexity within these GRNs, it becomes apparent that efficient methods are required to test the necessity and sufficiency of regulatory interactions. One of the most complete GRNs for early development has been described in the purple sea urchin, Strongylocentrotus purpuratus. This work has been facilitated by two resources: a well-annotated genome sequence and transgenes generated in bacterial artificial chromosome (BAC) constructs. BAC libraries played a central role in assembling the S. purpuratus genome sequence and continue to serve as platforms for generating reporter constructs for use in expression and regulatory analyses. Optically transparent echinoderm larvae are highly amenable to transgenic approaches and are therefore particularly well suited for experiments that rely on BAC-based reporter transgenes. Here, we discuss the experimental utility of BAC constructs in the context of understanding developmental processes in echinoderm embryos and larvae.

High-throughput direct measurement of magnetocaloric effect based on lock-in thermography technique

We demonstrate a high-throughput direct measurement method for the magnetocaloric effect (MCE) by means of a lock-in thermography (LIT) technique. This method enables systematic measurements of the magnetic-field and operation-frequency dependences of the temperature change induced by the MCE. This is accomplished in a shorter time compared to conventional adiabatic temperature measurement methods. The direct measurement based on LIT is free from any possible miscalculations and errors arising from indirect measurements using thermodynamic relations. Importantly, the LIT technique makes simultaneous MCE measurements of multiple materials possible without increasing the measurement time, realizing high-throughput investigations of the MCE. By applying this method to Gd, we obtain the MCE-induced temperature change of 1.84 ± 0.11 K under a modulation field of 1.0 T and modulation frequency of 0.5 Hz at a temperature of 300.5 ± 0.5 K, offering evidence that the LIT method gives quantitative results.

High-throughput investigation of orientations effect on nanoscale magnetization reversal in cobalt ferrite thin films induced by electric field

The magnetoelectric device concept which enables the non-volatile electric field control of magnetism needs to be investigated for the development of practical information storage devices. In this aspect, the emerging field of magneto-ionics based on the modulation of magnetism by field-driven ion migration is promising because it only requires a simple sample structure in the solid state and has good cyclability. However, the degree of ion migration within the magnetic structure is strongly dependent on the crystal orientations. Since the epitaxial films growing on the commercial single crystal substrates have limited orientations, the ability of magnetism modulated by field-driven ion migration cannot be optimized and understood by using these data. In this work, we utilized the high-throughput synthesis approach, namely, combinatorial substrate epitaxy, which utilizes a polycrystalline substrate. This provides a platform to develop and understand the degree of ionic migration in different orientations of the model system CoFe2O4 (CFO) films. The library of electric driven nanoscale magnetization reversal data of CFO with different orientations was obtained by applying the electric field in the same region of known CFO grain orientations. It was determined from the analysis that the [110] crystal direction exhibits the maximum nanoscale magnetization reversal ratio. This is mainly attributed to the ease Co2+ migration in the [110] direction under the electric field assisted by a Fe3+ and oxygen vacancies.

TiO2 Photocatalysis-DESI-MS Rotating Array Platform for High-Throughput Investigation of Oxidation Reactions.

We present a new high-throughput platform for studying titanium dioxide (TiO2) photocatalytic oxidation reactions by performing reactions on a TiO2-coated surface, followed by direct analysis of oxidation products from the surface by desorption electrospray ionization mass spectrometry (DESI-MS). For this purpose, we coated a round glass wafer with photocatalytically active anatase-phase TiO2 using atomic layer deposition. Approximately 70 aqueous 1 μL samples can be injected onto the rim of the TiO2-coated glass wafer, before the entire wafer is exposed to UV irradiation. After evaporation of water, the oxidation products can be directly analyzed from the sample spots by DESI-MS, using a commercial rotating sample platform. The method was shown to provide fast photocatalytic oxidation reactions and analysis with throughput of about four samples per minute. The feasibility of the method was examined for mimicking phase I metabolism reactions of amodiaquine, buspirone and verapamil. Their main photocatalytic reaction products were mostly similar to the products observed earlier in TiO2 photocatalysis and in in vitro phase I metabolism assays performed using human liver microsomes.

Optimization of Monte Carlo particle transport parameters and validation of a novel high throughput experimental setup to measure the biological effects of particle beams.

Accurate modeling of the relative biological effectiveness (RBE) of particle beams requires increased systematic invitro studies with human cell lines with care towards minimizing uncertainties in biologic assays as well as physical parameters. In this study, we describe a novel high-throughput experimental setup and an optimized parameterization of the Monte Carlo (MC) simulation technique that is universally applicable for accurate determination of RBE of clinical ion beams. Clonogenic cell-survival measurements on a human lung cancer cell line (H460) are presented using proton irradiation. Experiments were performed at the Heidelberg Ion Therapy Center (HIT) with support from the Deutsches Krebsforschungszentrum (DKFZ) in Heidelberg, Germany using a mono-energetic horizontal proton beam. A custom-made variable range selector was designed for the horizontal beam line using the Geant4 MC toolkit. This unique setup enabled a high-throughput clonogenic assay investigation of multiple, well defined dose and linear energy transfer (LETs) per irradiation for human lung cancer cells (H460) cultured in a 96-well plate. Sensitivity studies based on application of different physics lists in conjunction with different electromagnetic constructors and production threshold values to the MC simulations were undertaken for accurate assessment of the calculated dose and the dose-averaged LET (LETd ). These studies were extended to helium and carbon ion beams. Sensitivity analysis of the MC parameterization revealed substantial dependence of the dose and LETd values on both the choice of physics list and the production threshold values. While the dose and LETd calculations using FTFP_BERT_LIV, FTFP_BERT_EMZ, FTFP_BERT_PEN and QGSP_BIC_EMY physics lists agree well with each other for all three ions, they show large differences when compared to the FTFP_BERT physics list with the default electromagnetic constructor. For carbon ions, the dose corresponding to the largest LETd value is observed to differ by as much as 78% between FTFP_BERT and FTFP_BERT_LIV. Furthermore, between the production threshold of 700μm and 5μm, proton dose varies by as much as 19% corresponding to the largest LETd value sampled in the current investigation. Based on the sensitivity studies, the FTFP_BERT physics list with the low energy Livermore electromagnetic constructor and a production threshold of 5μm was employed for determining accurate dose and LETd . The optimized MC parameterization results in a different LETd dependence of the RBE curve for 10% SF of the H460 cell line irradiated with proton beam when compared with the results from a previous study using the same cell line. When the MC parameters are kept consistent between the studies, the proton RBE results agree well with each other within the experimental uncertainties. A custom high-throughput, high-accuracy experimental design for accurate invitro cell survival measurements was employed at a horizontal beam line. High sensitivity of the physics-based optimization establishes the importance of accurate MC parameterization and hence the conditioning of the MC system on a case-by-case basis. The proton RBE results from current investigations are observed to agree with a previous measurement made under different experimental conditions. This establishes the consistency of our experimental findings across different experiments and institutions.

Multiplexed sgRNA Expression Allows Versatile Single Nonrepetitive DNA Labeling and Endogenous Gene Regulation.

The CRISPR/Cas9 system has made significant contributions to genome editing, gene regulation and chromatin studies in recent years. High-throughput and systematic investigations into the multiplexed biological systems require simultaneous expression and coordinated functioning of multiple sgRNAs. However, current cotransfection based sgRNA coexpression systems remain inefficient, and virus-based transfection approaches are relatively costly and labor intensive. Here we established a vector-independent method allowing multiple sgRNA expression cassettes to be assembled in series into a single plasmid. This synthetic biology-based strategy excels in its efficiency, controllability and scalability. Taking the flexibility advantage of this all-in-one sgRNA expressing system, we further explored its applications in single nonrepetitive genomic locus imaging as well as coordinated gene regulation in live cells. With its full potency, our method will facilitate the research in understanding genome structure, function and dynamics.

The gymnastics of epigenomics in rice.

Epigenomics is represented by the high-throughput investigations of genome-wide epigenetic alterations, which ultimately dictate genomic, transcriptomic, proteomic and metabolomic dynamism. Rice has been accepted as the global staple crop. As a result, this model crop deserves significant importance in the rapidly emerging field of plant epigenomics. A large number of recently available data reveal the immense flexibility and potential of variable epigenomic landscapes. Such epigenomic impacts and variability are determined by a number of epigenetic regulators and several crucial inheritable epialleles, respectively. This article highlights the correlation of the epigenomic landscape with growth, flowering, reproduction, non-coding RNA-mediated post-transcriptional regulation, transposon mobility and even heterosis in rice. We have also discussed the drastic epigenetic alterations which are reported in rice plants grown from seeds exposed to the extraterrestrial environment. Such abiotic conditions impose stress on the plants leading to epigenomic modifications in a genotype-specific manner. Some significant bioinformatic databases and in silico approaches have also been explained in this article. These softwares provide important interfaces for comparative epigenomics. The discussion concludes with a unified goal of developing epigenome editing to promote biological hacking of the rice epigenome. Such a cutting-edge technology if properly standardized, can integrate genomics and epigenomics together with the generation of high-yielding trait in several cultivars of rice.

Organosilane Chemical Gradients: Progress, Properties, and Promise.

Chemical gradients play an important role in nature, driving many different phenomena critical to life, including the transport of chemical species across membranes and the transport, attachment, and assembly of cells. Taking a cue from these natural processes, scientists and engineers are now working to develop synthetic chemical gradients for use in a broad range of applications, such as in high-throughput investigations of surface properties, as means to guide the motions and/or assembly of liquid droplets, vesicles, nanoparticles, and cells and as new media for stationary-phase-gradient chemical separations. Our groups have been working to develop new methods for preparing chemical gradients from organoalkoxysilane and organochlorosilane precursors and to obtain a better understanding of their properties on macroscopic to microscopic length scales. This review highlights our recent work on the development of controlled-rate infusion and infusion-withdrawal dip-coating methods for the preparation of gradients on planar glass and silicon substrates, on thin-layer chromatography plates, and in capillaries and monoliths for liquid chromatography. We also cover the new knowledge gained from the characterization of our gradients using sessile drop and Wilhelmy plate dynamic water contact angle measurements, X-ray photoelectron spectroscopy mapping, and single-molecule tracking and spectroscopy. Our studies reveal important evidence of phase separation and cooperative interactions occurring along multicomponent gradients. Emerging concepts and new directions in the preparation and characterization of organosilane-based chemical gradients are also discussed.

Shape Memory Micro- and Nanowire Libraries for the High-Throughput Investigation of Scaling Effects.

The scaling behavior of Ti-Ni-Cu shape memory thin-film micro- and nanowires of different geometry is investigated with respect to its influence on the martensitic transformation properties. Two processes for the high-throughput fabrication of Ti-Ni-Cu micro- to nanoscale thin film wire libraries and the subsequent investigation of the transformation properties are reported. The libraries are fabricated with compositional and geometrical (wire width) variations to investigate the influence of these parameters on the transformation properties. Interesting behaviors were observed: Phase transformation temperatures change in the range from 1 to 72 °C (austenite finish, (Af), 13 to 66 °C (martensite start, Ms) and the thermal hysteresis from -3.5 to 20 K. It is shown that a vanishing hysteresis can be achieved for special combinations of sample geometry and composition.

How Chemical Composition Alone Can Predict Vibrational Free Energies and Entropies of Solids

Computing vibrational free energies (Fvib) and entropies (Svib) has posed a long-standing challenge to the high-throughput ab initio investigation of finite temperature properties of solids. Here, we use machine-learning techniques to efficiently predict Fvib and Svib of crystalline compounds in the Inorganic Crystal Structure Database. Using descriptors based simply on the chemical formula and using a training set of only 300 compounds, mean absolute errors of less than 0.04 meV/K/atom (15 meV/atom) are achieved for Svib (Fvib), whose values are distributed within a range of 0.9 meV/K/atom (300 meV/atom.) In addition, for training sets containing fewer than 2000 compounds, the chemical formula alone is shown to perform as well as, if not better than, four other more complex descriptors previously used in the literature. The accuracy and simplicity of the approach means that it can be advantageously used for fast screening of chemical reactions at finite temperatures.

Oblique Colloidal Lithography for the Fabrication of Nonconcentric Features.

Herein, we describe the development of oblique colloidal lithography (OCL) and establish a systematic patterning strategy for creating libraries of nanosized nonconcentric plasmonic structures. This strategy combines OCL, capillary force lithography, and several wet and ion etching steps. Hexagonal arrays of nonconcentric gold features were created on glass substrates with highly controllable geometric parameters. The size, geometry, and eccentricity of the gold features could be independently tuned by controlling the experimental conditions. Gaps within surface elements could be shrunk to as small as 30 nm, while the total patterned area was about l cm2. The goal was to devise a method that offers a high degree of control over the resolution and morphology of asymmetric structures without the need to resort to electron beam lithography. This technique also enabled the development of numerous surface patterns through the stepwise fabrication of separate elements. Complex features, including dots-surrounded nonconcentric targets, nonconcentric hexagram-disks, and nonconcentric annular aperture arrays, were demonstrated, and their optical properties were characterized. Indeed, spectroscopic studies and FDTD simulations demonstrated that Fano resonances could readily be generated by the nonconcentric gold features. Consequently, our patterning strategy should enable the high-throughput investigation of plasmonic coupling and Fano resonances as a function of the physical parameters of the elements within the nanopattern array.

Evaluation of anticancer drug in a polymer 3D cell chip

Three-dimensional (3D) models play an important role in understanding the behavior of a tumor in a well-defined microenvironment, because some aspects of tumor characteristics cannot be fully recapitulated in cell monolayers. In this study, a novel method is presented for the culture of tumor spheroids and for in vivo 3D cell growth simulation of a tumor on a 3D cell chip fabricated in the 3rd floor structure. Scanning electron microscopy and confocal imaging show that, soon after the adjacent tumor adheres to the micropatterned pillar sidewalls, they are subsequently pulled between the pillars in a suspended position. The half maximal inhibitory concentration (IC50) values of mitroxanthrone in the two-dimensional (2D) plate were at the concentration of 345.65 µg/ml. In contrast, the IC50 value of 3D mitroxanthrone in the 3D cell chip was not detected at the system. Our results indicated that 3D spheroids are generated in uniformly fabricated cancer cell chips, and large numbers of morphologically homogenous spheroids are easily produced. The result showed that the 3D cancer cell chip is more resistant to anticancer agents than 2D plate cell culture. Thus, the 3D cancer cell chip could be used for high-throughput investigations of the efficacy vs. toxicity of drugs or numerous other cancer spheroid cellular and biochemical assays.