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High-Throughput, Volume 8, Issue 4 (December 2019) – 5 articles

Cover Story (view full-size image): The determination and measurement of grape metabolites can be achieved using NIR spectroscopy. This method is by excellence one of the most versatile high throughput techniques. View this paper.

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27 pages, 9083 KiB

Open AccessFeature PaperArticle

Descriptors for High Throughput in Structural Materials Development

by Matthias Steinbacher, Gabriela Alexe, Michael Baune, Ilya Bobrov, Ingmar Bösing, Brigitte Clausen, Tobias Czotscher, Jérémy Epp, Andreas Fischer, Lasse Langstädtler, Daniel Meyer, Sachin Raj Menon, Oltmann Riemer, Heike Sonnenberg, Arne Thomann, Anastasiya Toenjes, Frank Vollertsen, Nicole Wielki and Nils Ellendt

High-Throughput 2019, 8(4), 22; https://doi.org/10.3390/ht8040022 - 5 Dec 2019

Cited by 17 | Viewed by 6283

Abstract

The development of novel structural materials with increasing mechanical requirements is a very resource-intense process if conventional methods are used. While there are high-throughput methods for the development of functional materials, this is not the case for structural materials. Their mechanical properties are determined by their microstructure, so that increased sample volumes are needed. Furthermore, new short-time characterization techniques are required for individual samples which do not necessarily measure the desired material properties, but descriptors which can later be mapped on material properties. While universal micro-hardness testing is being commonly used, it is limited in its capability to measure sample volumes which contain a characteristic microstructure. We propose to use alternative and fast deformation techniques for spherical micro-samples in combination with classical characterization techniques such as XRD, DSC or micro magnetic methods, which deliver descriptors for the microstructural state. Full article

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9 pages, 862 KiB

Open AccessFeature PaperReview

From the Laboratory to The Vineyard—Evolution of The Measurement of Grape Composition using NIR Spectroscopy towards High-Throughput Analysis

by Aoife Power, Vi Khanh Truong, James Chapman and Daniel Cozzolino

High-Throughput 2019, 8(4), 21; https://doi.org/10.3390/ht8040021 - 30 Nov 2019

Cited by 23 | Viewed by 4337

Abstract

Compared to traditional laboratory methods, spectroscopic techniques (e.g., near infrared, hyperspectral imaging) provide analysts with an innovative and improved understanding of complex issues by determining several chemical compounds and metabolites at once, allowing for the collection of the sample “fingerprint”. These techniques have the potential to deliver high-throughput options for the analysis of the chemical composition of grapes in the laboratory, the vineyard and before or during harvest, to provide better insights of the chemistry, nutrition and physiology of grapes. Faster computers, the development of software and portable easy to use spectrophotometers and data analytical methods allow for the development of innovative applications of these techniques for the analyses of grape composition. Full article

(This article belongs to the Special Issue Shining the Light on High-Throughput—the Forgotten Role of Vibrational Spectroscopy)

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18 pages, 5163 KiB

Open AccessArticle

Comparative Analysis of Strategies for De Novo Transcriptome Assembly in Prokaryotes: Streptomyces clavuligerus as a Case Study

by Carlos Caicedo-Montoya, Laura Pinilla, León F. Toro, Jeferyd Yepes-García and Rigoberto Ríos-Estepa

High-Throughput 2019, 8(4), 20; https://doi.org/10.3390/ht8040020 - 30 Nov 2019

Cited by 1 | Viewed by 6424

Abstract

The performance of software tools for de novo transcriptome assembly greatly depends on the selection of software parameters. Up to now, the development of de novo transcriptome assembly for prokaryotes has not been as remarkable as that for eukaryotes. In this contribution, Rockhopper2 was used to perform a comparative transcriptome analysis of Streptomyces clavuligerus exposed to diverse environmental conditions. The study focused on assessing the incidence of software parameters on software performance for the identification of differentially expressed genes as a final goal. For this, a statistical optimization was performed using the Transrate Assembly Score (TAS). TAS was also used for evaluating the software performance and for comparing it with related tools, e.g., Trinity. Transcriptome redundancy and completeness were also considered for this analysis. Rockhopper2 and Trinity reached a TAS value of 0.55092 and 0.58337, respectively. Trinity assembles transcriptomes with high redundancy, with 55.6% of transcripts having some duplicates. Additionally, we observed that the total number of differentially expressed genes (DEG) and their annotation greatly depends on the method used for removing redundancy and the tools used for transcript quantification. To our knowledge, this is the first work aimed at assessing de novo assembly software for prokaryotic organisms. Full article

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12 pages, 1185 KiB

Open AccessFeature PaperArticle

Investigation of RNA Editing Sites within Bound Regions of RNA-Binding Proteins

by Tyler Weirick, Giuseppe Militello, Mohammed Rabiul Hosen, David John, Joseph B. Moore IV and Shizuka Uchida

High-Throughput 2019, 8(4), 19; https://doi.org/10.3390/ht8040019 - 29 Nov 2019

Cited by 3 | Viewed by 3826

Abstract

Studies in epitranscriptomics indicate that RNA is modified by a variety of enzymes. Among these RNA modifications, adenosine to inosine (A-to-I) RNA editing occurs frequently in the mammalian transcriptome. These RNA editing sites can be detected directly from RNA sequencing (RNA-seq) data by examining nucleotide changes from adenosine (A) to guanine (G), which substitutes for inosine (I). However, a careful investigation of such nucleotide changes must be conducted to distinguish sequencing errors and genomic mutations from the genuine editing sites. Building upon our recent introduction of an easy-to-use bioinformatics tool, RNA Editor, to detect RNA editing events from RNA-seq data, we examined the extent by which RNA editing events affect the binding of RNA-binding proteins (RBP). Through employing bioinformatic techniques, we uncovered that RNA editing sites occur frequently in RBP-bound regions. Moreover, the presence of RNA editing sites are more frequent when RNA editing islands were examined, which are regions in which RNA editing sites are present in clusters. When the binding of one RBP, human antigen R [HuR; encoded by ELAV-like protein 1 (ELAV1)], was quantified experimentally, its binding was reduced upon silencing of the RNA editing enzyme adenosine deaminases acting on RNA (ADAR) compared to the control—suggesting that the presence of RNA editing islands influence HuR binding to its target regions. These data indicate RNA editing as an important mediator of RBP–RNA interactions—a mechanism which likely constitutes an additional mode of post-transcription gene regulation in biological systems. Full article

(This article belongs to the Special Issue Emerging Topics in Epitranscriptomics (RNA Modifications))

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18 pages, 3701 KiB

Open AccessArticle

Expression Profiling of Candidate Genes in Sugar Beet Leaves Treated with Leonardite-Based Biostimulant

by Hanifeh Seyed Hajizadeh, Bahram Heidari, Giovanni Bertoldo, Maria Cristina Della Lucia, Francesco Magro, Chiara Broccanello, Andrea Baglieri, Ivana Puglisi, Andrea Squartini, Giovanni Campagna, Giuseppe Concheri, Serenella Nardi and Piergiorgio Stevanato

High-Throughput 2019, 8(4), 18; https://doi.org/10.3390/ht8040018 - 11 Oct 2019

Cited by 7 | Viewed by 3478

Abstract

Leonardite-based biostimulants are a large class of compounds, including humic acid substances. Foliar application of biostimulants at field level improves plant growth, yield and quality through metabolic changes and stimulation of plant proton pumps. The present study aimed at identifying optimum dosage of BLACKJAK, a humic acid-based substance, which is able to modify genes involved in sugar beet growth. Thirty-three genes belonging to various biochemical pathway categories were tested in leaves of treated sugar beet (Beta vulgaris L.) samples to assess gene expression profiling in response to BLACKJAK. Seedlings of a diploid and multigerm variety were grown in plastic pots and sprayed with two dilutions of BLACKJAK (dilution 1:500–1.0 mg C L⁻¹ and dilution 1:1000–0.5 mg C L⁻¹). Leaf samples were collected after 24, 48, and 72 h treatment with BLACKJAK for each dilution. RNA was extracted and the quantification of gene expression was performed while using an OpenArray platform. Results of analysis of variance demonstrated that, 15 genes out of a total of 33 genes tested with OpenArray qPCR were significantly affected by treatment and exposure time. Analysis for annotation of gene products and pathways revealed that genes belonging to the mitochondrial respiratory pathways, nitrogen and hormone metabolisms, and nutrient uptake were up-regulated in the BLACKJAK treated samples. Among the up-regulated genes, Bv_PHT2;1 and Bv_GLN1 expression exerted a 2-fold change in 1:1000 and 1:500 BLACKJAK concentrations. Overall, the gene expression data in the BLACKJAK treated leaves demonstrated the induction of plant growth–related genes that were contributed almost to amino acid and nitrogen metabolism, plant defense system, and plant growth. Full article

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