Alternative Plant Vitrification Solution A3-80% and Initial Ammonium-Free Regrowth Medium Enable Cryobanking of Chrysanthemum Germplasm.

Cryopreservation, storing biological material in liquid nitrogen (LN, -196 °C), offers a valuable option for the long-term conservation of non-orthodox seeds and vegetatively propagated species in the sector of agrobiodiversity and wild flora. Although large-scale cryobanking of germplasm collections has been increasing worldwide, the wide application of cryopreservation protocol is hampered by a lack of universal cryopreservation protocols, among others. This study established a systematic approach to developing a droplet-vitrification cryopreservation procedure for chrysanthemum shoot tips. The standard procedure includes two-step preculture with 10% sucrose for 31 h and with 17.5% sucrose for 16 h, osmoprotection with loading solution C4-35% (17.5% glycerol + 17.5% sucrose, w/v) for 40 min, cryoprotection with alternative plant vitrification solution A3-80% (33.3% glycerol + 13.3% dimethyl sulfoxide + 13.3% ethylene glycol + 20.1% sucrose, w/v) at 0 °C for 60 min, and cooling and rewarming using aluminum foil strips. After unloading, a three-step regrowth procedure starting with an ammonium-free medium with 1 mg L-1 gibberellic acid (GA3) and 1 mg L-1 benzyl adenine (BA) followed by an ammonium-containing medium with and without growth regulators was essential for the development of normal plantlets from cryopreserved shoot tips. A pilot cryobanking of 154 accessions of chrysanthemum germplasm initiated with post-cryopreservation regeneration of 74.8%. This approach will facilitate the cryobanking of the largest Asteraceae family germplasm as a complementary long-term conservation method.

Metabolite Profiling to Evaluate Metabolic Changes in Genetically Modified Protopanaxadiol-Enriched Rice.

Event DS rice producing protopanaxadiol (PPD) has been previously developed by inserting Panax ginseng dammarenediol-II synthase gene (PgDDS) and PPD synthase gene (CYP716A47). We performed a gas chromatography-mass spectrometry (GC-MS)-based metabolomics of the DS rice to identify metabolic alterations as the effects of genetic engineering by measuring the contents of 65 metabolites in seeds and 63 metabolites in leaves. Multivariate analysis and one-way analysis of variance between DS and non-genetically modified (GM) rice showed that DS rice accumulated fewer tocotrienols, tocopherols, and phytosterols than non-GM rice. These results may be due to competition for the same precursors because PPDs in DS rice are synthesized from the same precursors as those of phytosterols. In addition, multivariate analysis of metabolic data from rice leaves revealed that composition differed by growth stage rather than genetic modifications. Our results demonstrate the potential of metabolomics for identifying metabolic alterations in response to genetic modifications.

Hetero-Integration of Silicon Nanomembranes with 2D Materials for Bioresorbable, Wireless Neurochemical System.

Although neurotransmitters are key substances closely related to evaluating degenerative brain diseases as well as regulating essential functions in the body, many research efforts have not been focused on direct observation of such biochemical messengers, rather on monitoring relatively associated physical, mechanical, and electrophysiological parameters. Here, a bioresorbable silicon-based neurochemical analyzer incorporated with 2D transition metal dichalcogenides is introduced as a completely implantable brain-integrated system that can wirelessly monitor time-dynamic behaviors of dopamine and relevant parameters in a simultaneous mode. An extensive range of examinations of molybdenum/tungsten disulfide (MoS2 /WS2 ) nanosheets and catalytic iron nanoparticles (Fe NPs) highlights the underlying mechanisms of strong chemical and target-specific responses to the neurotransmitters, along with theoretical modeling tools. Systematic characterizations demonstrate reversible, stable, and long-term operational performances of the degradable bioelectronics with excellent sensitivity and selectivity over those of non-dissolvable counterparts. A complete set of in vivo experiments with comparative analysis using carbon-fiber electrodes illustrates the capability for potential use as a clinically accessible tool to associated neurodegenerative diseases.

Multipath Lightweight Deep Network Using Randomly Selected Dilated Convolution.

Robot vision is an essential research field that enables machines to perform various tasks by classifying/detecting/segmenting objects as humans do. The classification accuracy of machine learning algorithms already exceeds that of a well-trained human, and the results are rather saturated. Hence, in recent years, many studies have been conducted in the direction of reducing the weight of the model and applying it to mobile devices. For this purpose, we propose a multipath lightweight deep network using randomly selected dilated convolutions. The proposed network consists of two sets of multipath networks (minimum 2, maximum 8), where the output feature maps of one path are concatenated with the input feature maps of the other path so that the features are reusable and abundant. We also replace the 3×3 standard convolution of each path with a randomly selected dilated convolution, which has the effect of increasing the receptive field. The proposed network lowers the number of floating point operations (FLOPs) and parameters by more than 50% and the classification error by 0.8% as compared to the state-of-the-art. We show that the proposed network is efficient.

Metabolomic Variability of Different Soybean Genotypes: ß-Carotene-Enhanced (Glycine max), Wild (Glycine soja), and Hybrid (Glycine max × Glycine soja) Soybeans.

We obtained a new hybrid soybean (Hybrid) by hybridizing ß-carotene-enhanced soybean (BCE; Glycine max L.) containing the phytoene synthase-2A-carotene desaturase gene and wild-type soybean (Wild; Glycine soja). To investigate metabolic changes between variants, we performed metabolic profiling of leaves (three growth stages) and seeds. Multivariate analyses revealed significant metabolic differences between genotypes in seeds and leaves, with seeds showing accumulation of phytosterols, tocopherols, and carotenoids (BCE only), indicating co-induction of the methylerythritol 4-phosphate and mevalonic acid pathways. Additionally, Hybrid produced intermediate levels of carotenoids and high levels of amino acids. Principal component analysis revealed metabolic discrimination between growth stages of soybean leaves and identified differences in leaf groups according to different genotypes at 8, 12, and 16 weeks, with Wild showing higher levels of environmental stress-related compounds relative to BCE and Hybrid leaves. The metabolic profiling approach could be a useful tool to identify metabolic links in various soybean cultivars.

Optimization of a Cryopreservation Method for the Endangered Korean Species Pogostemon yatabeanus Using a Systematic Approach: The Key Role of Ammonium and Growth Regulators.

Cryopreservation provides a secure long-term conservation option for rare and endangered plant species with non-orthodox or limitedly available seeds. Wide application of cryopreservation to biobank wild flora is hampered by the need to re-optimize nearly all protocol steps for every new species. We applied a systematic approach to simplify optimization of a multi-stage droplet-vitrification method for the endangered wetland Korean species, Pogostemon yatabeanus. This approach consisted of a standard procedure pre-selected based on material type and size, which was complemented with 11 additional treatments to reveal the most impactful conditions. Effect of ammonium nitrate at various protocol steps was also tested. The highest shoot tip survival (92%) and plant regeneration (90%) after cryopreservation were achieved using preculture with 10% sucrose followed by 40 min osmoprotection and 60 min treatment with vitrification solution A3-80% (33.3% glycerol + 13.3% dimethyl sulfoxide + 13.3% ethylene glycol + 20.1% sucrose) on ice. A three-step regrowth procedure starting with ammonium-free medium with 1 mg/L GA3 and 1 mg/L BA followed by ammonium-containing medium with and without growth regulators was essential for the development of healthy plants from cryopreserved shoot tips. This approach enables fast optimization of the cryopreservation procedure for new osmotic stress-sensitive plant species.

Three-Dimensional Vascularized Lung Cancer-on-a-Chip with Lung Extracellular Matrix Hydrogels for In Vitro Screening.

Recent advances in immunotherapies and molecularly targeted therapies have led to an increased interest in exploring the field of in vitro tumor mimetic platforms. An increasing need to understand the mechanisms of anti-cancer therapies has led to the development of natural tumor tissue-like in vitro platforms capable of simulating the tumor microenvironment. The incorporation of vascular structures into the in vitro platforms could be a crucial factor for functional investigation of most anti-cancer therapies, including immunotherapies, which are closely related to the circulatory system. Decellularized lung extracellular matrix (ldECM), comprised of ECM components and pro-angiogenic factors, can initiate vascularization and is ideal for mimicking the natural microenvironment. In this study, we used a ldECM-based hydrogel to develop a 3D vascularized lung cancer-on-a-chip (VLCC). We specifically encapsulated tri-cellular spheroids made from A549 cells, HUVECs, and human lung fibroblasts, for simulating solid type lung cancer. Additionally, two channels were incorporated in the hydrogel construct to mimic perfusable vessel structures that resemble arterioles or venules. Our study highlights how a more effective dose-dependent action of the anti-cancer drug Doxorubicin was observed using a VLCC over 2D screening. This observation confirmed the potential of the VLCC as a 3D in vitro drug screening tool.

Metabolic Analysis of Root, Stem, and Leaf of Scutellaria baicalensis Plantlets Treated with Different LED Lights.

Light emitting diodes (LEDs) have recently been considered an efficient artificial light source in plant factories for enhancing plant growth and nutritional quality. Accordingly, this study aimed to review blue, red, and white LED light sources for efficiency and length of the growing period to produce seedlings of Scutellaria baicalensis with high nutritional value. The roots, stems, and leaves of S. baicalensis seedlings were grown under different LED lights and harvested after two and four weeks, and analyzed using high-performance liquid chromatography and gas chromatography time-of-flight mass spectrometry to identify and quantify primary and secondary metabolites. Roots, particularly in the seedlings treated with white LEDs were determined to contain the greatest concentrations of the representative compounds present in S. baicalensis: baicalin, baicalein, and wogonin, which show highly strong biological properties compared to the other plant organs. A total of 50 metabolites (amino acids, sugars, sugar alcohols, organic acids, phenolic acids, and amines) were detected in the roots, stems, and leaves of S. baicalensis seedlings, and the concentrations of primary and secondary metabolites were generally decreased with the increasing duration of LED illumination. Therefore, this study suggests that white LED light and a 2-week growing period are the most efficient conditions for the production of baicalin, baicalein, and wogonin.

Highly Sensitive On-Skin Temperature Sensors Based on Biocompatible Hydrogels with Thermoresponsive Transparency and Resistivity.

The development of electrically responsive sensors that interact directly with human skin and at the same time produce a visual indication of the temperature is in great demand. Here, we report a highly sensitive electronic skin (E-skin) sensor that measures and visualizes skin temperature simultaneously using a biocompatible hydrogel displaying thermoresponsive transparency and resistivity resulting from a temperature dependence of the strength of the hydrogen bonding between its components. This thermoresponsive hydrogel (TRH) showed a temperature dependence of not only the proton conductivity but also of its transmittance of light through a change in polymer conformation. We were able to use our TRH temperature sensor (TRH-TS) to measure temperature in a wide range of temperatures based on a change in its intrinsic resistivity (-0.0289 °C-1 ) and to visualize the temperature due to its thermoresponsive transmittance (from 7% to 96%). The TRH-TS exhibited high reliability upon multiple cycles of heating and cooling. The on-skin TRH-TS patch is also shown to successfully produce changes in its impedance and optical transparency as a result of changes in skin temperature during cardiovascular exercise. This work has shown that our biocompatible TRH-TS is potentially suitable as wearable E-skin for various emerging flexible healthcare monitoring applications.

Information Measure in Terms of the Hazard Function and Its Estimate.

It is well-known that some information measures, including Fisher information and entropy, can be represented in terms of the hazard function. In this paper, we provide the representations of more information measures, including quantal Fisher information and quantal Kullback-leibler information, in terms of the hazard function and reverse hazard function. We provide some estimators of the quantal KL information, which include the Anderson-Darling test statistic, and compare their performances.

Changes in taste and food preferences in breast cancer patients receiving chemotherapy: a pilot study.

PURPOSE: Cancer treatment may relate to appetite reduction and malnutrition. We investigated taste alterations and dish-type preferences during chemo- and/or radiation therapy in breast cancer patients. METHODS: Breast cancer patients (BC, n = 59) scheduled to receive cancer therapy and healthy subjects (control group or CTRL, n = 49) were voluntarily recruited. Taste detection thresholds (DTs) and recognition thresholds (RT) were compared between pre-treatment BC patients and CTRL for sweet (sucrose), salty (NaCl), bitter (caffeine), and sour (citric acid) solutions. Changes in taste thresholds and dish preferences during treatment were monitored in the BC group. Blood chemistry and anthropometric data were collected. RESULTS: At baseline, BC patients demonstrated lower sweet and salty DTs and RTs and a higher sour RT compared to CTRL. Bitter DT and RT were similar in both groups. Mild/soft dishes were preferred over fried/oily dishes by BC patients. Throughout treatment in BC patients, sweet thresholds significantly declined, while salty, bitter, and sour DTs and RTs were not affected, and there was no increase in preference for a dish. However, preference towards mild/soft dishes remained. While sweet-sour fruits and sweetened nuts were not favored during therapy. CONCLUSIONS: Sensitivities to sweet, salty, and sour but not bitter tastes differed between BC patients and CTRL. During treatment, sweet taste sensitivity increased while other tastes were unaffected. BC patients preferred mild/soft dishes over fried and sweetened dishes compared to CTRL. Our findings may contribute to developing dishes for breast cancer patients to increase food intake and thereby lower the risk of malnutrition.

Estimation of functional components of Chinese cabbage leaves grown in a plant factory using diffuse reflectance spectroscopy.

BACKGROUND: In recent years, protected crop production using plant factories to produce high-value crops with greater functional components has become more popular in many countries. The quantification of the components, however, is mainly conducted by laboratory analyses, which are both time- and labor-consuming. The present study aimed to investigate the potential of a non-destructive diffuse reflectance spectroscopy technique for estimating functional components (i.e. glucosinolates, amino acids, sugars and carotenoids) in the leaves of Chinese cabbage grown in a plant factory. RESULTS: From the overall analysis, better estimations were obtained using the partial least square regression procedure. The important wavelengths for each functional component were identified mainly in the ultraviolet-visible regions. Identified wavelengths were 317, 390, 888 and 940 nm for sugars; 520 and 960 nm for amino acids; 385, 860 and 945 nm for glucosinolates; and 454, 472 and 530 nm for carotenoids. CONCLUSION: Optical reflectance spectroscopy shows potential as a tool for the estimation of functional components in the leaves of Chinese cabbage. The results of the present study provide useful information for the design and application of sensors with respect to on-site quantification of the functional components. © 2018 Society of Chemical Industry.

Highly selective retrieval of accurate DNA utilizing a pool of in situ-replicated DNA from multiple next-generation sequencing platforms.

Scalable and cost-effective production of error-free DNA is critical to meet the increased demand for such DNA in the field of biological science. Methods based on 'Dial-out PCR' have enabled the high-throughput error-free DNA synthesis from a microarray-synthesized DNA pool by labeling with retrieval PCR tags, and retrieving error-free DNA of which the sequence is identified via next generation sequencing (NGS). However, most of the retrieved products contain byproducts due to background amplification of redundantly labeled DNAs. Here, we present a highly selective retrieval method of desired DNA from a pool of millions of DNA clones from NGS platforms. Our strategy is based on replicating entire sequence-verified DNA molecules from NGS plates to obtain population-controlled DNA pool. Using the NGS-replica pool, we could perform improved and selective retrieval of desired DNA from the replicated DNA pool compared to other dial-out PCR based methods. To evaluate the method, we tested this strategy by using 454, Illumina, and Ion Torrent platforms for producing NGS-replica pool. As a result, we observed a highly selective retrieval yield of over 95%. We anticipate that applications based on this method will enable the preparation of high-fidelity sequenced DNA from heterogeneous collections of DNA molecules.

Overexpression of a tartary buckwheat R2R3-MYB transcription factor gene, FtMYB9, enhances tolerance to drought and salt stresses in transgenic Arabidopsis.

Tartary buckwheat (Fagopyrum tataricum) is a traditional coarse cereal that exhibits strong plasticity in its adaptation to harsh and complicated environmental stresses. In an attempt to study the strong tolerance of tartary buckwheat, the FtMYB9 gene, which encodes an R2R3-MYB transcription factor protein, was functionally investigated. FtMYB9 expression was rapidly and strongly induced by ABA, cold, salt, and drought treatments in the seedling stage. A yeast one-hybrid system assay indicated that FtMYB9 is an activator of transcriptional activity, consistent with its roles as a transcription factor. Its overexpression in plants resulted in increased sensitivity to ABA at the germination and seedling stages compared to wild type. The overexpression of FtMYB9 increased tolerance to drought and salt stresses by the activation of some stress-related genes from both ABA-independent and ABA-dependent pathways in transgenic Arabidopsis. Furthermore, enhanced proline content and the activation of the P5CS1 gene implied that FtMYB9 may be involved in proline synthesis in plants. Collectively, these results suggest that FtMYB9 functions as a novel R2R3-MYB TF which plays positive roles in salt and drought tolerance by regulating different stress-responsive signaling pathways.

Identification, isolation and expression analysis of eight stress-related R2R3-MYB genes in tartary buckwheat (Fagopyrum tataricum).

KEY MESSAGE: Eight R2R3 - MYB genes in tartary buckwheat were identified, and their expression patterns were comprehensively analyzed, which reveals role in plant response to abiotic stresses. The proteins of the R2R3-MYB superfamily play key roles in the growth and development processes as well as defense responses in plants. However, their characteristics and functions have not been fully investigated in tartary buckwheat (Fagopyrum tataricum), a strongly abiotic resistant coarse cereal. In this article, eight tartary buckwheat R2R3-MYB genes were isolated with full-length cDNA and DNA sequences. Phylogenetic analysis of the members of the R2R3-MYB superfamily between Arabidopsis and tartary buckwheat revealed that the assumed functions of the eight tartary buckwheat R2R3-MYB proteins are divided into five Arabidopsis functional subgroups that are involved in abiotic stress. Expression analysis during abiotic stress and exogenous phytohormone treatments identified that the eight R2R3-MYB genes responded to one or more treatments. This study is the first comprehensive analysis of the R2R3-MYB gene family in tartary buckwheat under abiotic stress.

De novo assembly and next-generation sequencing to analyse full-length gene variants from codon-barcoded libraries.

Interpreting epistatic interactions is crucial for understanding evolutionary dynamics of complex genetic systems and unveiling structure and function of genetic pathways. Although high resolution mapping of en masse variant libraries renders molecular biologists to address genotype-phenotype relationships, long-read sequencing technology remains indispensable to assess functional relationship between mutations that lie far apart. Here, we introduce JigsawSeq for multiplexed sequence identification of pooled gene variant libraries by combining a codon-based molecular barcoding strategy and de novo assembly of short-read data. We first validate JigsawSeq on small sub-pools and observed high precision and recall at various experimental settings. With extensive simulations, we then apply JigsawSeq to large-scale gene variant libraries to show that our method can be reliably scaled using next-generation sequencing. JigsawSeq may serve as a rapid screening tool for functional genomics and offer the opportunity to explore evolutionary trajectories of protein variants.

Development of vitrification protocol in Rubia akane (nakai) hairy roots using a systematic approach.

BACKGROUND: A solution-based vitrification protocol is a process of sequentially changing-solutions from which both influx of cryoprotectants (loading) and efflux of water (dehydration) were accomplished before cryo-exposure. Hence, we need to properly control the concentration /composition of the cryoprotectant solutions. OBJECTIVE: The study was, using a systematic approach, to develop a protocol for Rubia akane hairy roots, a very sensitive material to cytotoxicity of vitrification solutions. METHODS: Due to the poor response of 10-year in vitro maintained R. akane hairy roots to already established cryopreservation protocols, the following sets of experiments were designed: 1) combinational effect of preculture, osmoprotection and cryoprotection with PVS2-based (A3-70%) and PVS3-based (B5-80%) vitrification solutions; 2) different cooling/warming rates and warming temperature; 3) varying unloading solutions (25%, 35%and 45% sucrose) and durations (7 min and 30 min) with or without changing the unloading solutions. RESULTS: Preculture and osmoprotection treatments were necessary to acquire cytotoxicity tolerance in both vitrification solutions tested and osmoprotection treatment was more critical, especially in B5-80%. A sequential osmoprotection treatment (C10-50%) following conventional osmoprotection (C4-35%) was needed to increase the post-cryopreservation regrowth. Aluminum foil strips were superior to cryovials, but the warming temperature tested (20 degree C and 40 degree C) did not affect post-cryopreservation recovery. In the unloading procedure, a longer duration (30 min) with a higher sucrose solution (S-45%) was harmful, possibly due to osmotic stress. CONCLUSION: R. akane hairy roots are very sensitive to cytotoxicity (both osmotic stress and chemical toxicity) and thus a proper process (preculture, osmoprotection, cryoprotection and unloading) is necessary for higher post-cryopreservation recovery.

Characterization of two tartary buckwheat R2R3-MYB transcription factors and their regulation of proanthocyanidin biosynthesis.

Tartary buckwheat (Fagopyrum tataricum Gaertn.) contains high concentrations of flavonoids. The flavonoids are mainly represented by rutin, anthocyanins and proanthocyanins in tartary buckwheat. R2R3-type MYB transcription factors (TFs) play key roles in the transcriptional regulation of the flavonoid biosynthetic pathway. In this study, two TF genes, FtMYB1 and FtMYB2, were isolated from F. tataricum and characterized. The results of bioinformatic analysis indicated that the putative FtMYB1 and FtMYB2 proteins belonged to the R2R3-MYB family and displayed a high degree of similarity with TaMYB14 and AtMYB123/TT2. In vitro and in vivo evidence both showed the two proteins were located in the nucleus and exhibited transcriptional activation activities. During florescence, both FtMYB1 and FtMYB2 were more highly expressed in the flowers than any other organ. The overexpression of FtMYB1 and FtMYB2 significantly enhanced the accumulation of proanthocyanidins (PAs) and showed a strong effect on the target genes' expression in Nicotiana tabacum. The expression of dihydroflavonol-4-reductase (DFR) was upregulated to 5.6-fold higher than that of control, and the expression level was lower for flavonol synthase (FLS). To our knowledge, this is the first functional characterization of two MYB TFs from F. tataricum that control the PA pathway.

Characterization of developmental- and stress-mediated expression of cinnamoyl-CoA reductase in kenaf (Hibiscus cannabinus L.).

Cinnamoyl-CoA reductase (CCR) is an important enzyme for lignin biosynthesis as it catalyzes the first specific committed step in monolignol biosynthesis. We have cloned a full length coding sequence of CCR from kenaf (Hibiscus cannabinus L.), which contains a 1,020-bp open reading frame (ORF), encoding 339 amino acids of 37.37 kDa, with an isoelectric point (pI) of 6.27 (JX524276, HcCCR2). BLAST result found that it has high homology with other plant CCR orthologs. Multiple alignment with other plant CCR sequences showed that it contains two highly conserved motifs: NAD(P) binding domain (VTGAGGFIASWMVKLLLEKGY) at N-terminal and probable catalytic domain (NWYCYGK). According to phylogenetic analysis, it was closely related to CCR sequences of Gossypium hirsutum (ACQ59094) and Populus trichocarpa (CAC07424). HcCCR2 showed ubiquitous expression in various kenaf tissues and the highest expression was detected in mature flower. HcCCR2 was expressed differentially in response to various stresses, and the highest expression was observed by drought and NaCl treatments.

Molecular characterization of ferulate 5-hydroxylase gene from kenaf (Hibiscus cannabinus L.).

The purpose of this study is to clone and characterize the expression pattern of a F5H gene encoding ferulate 5-hydroxylase in the phenylpropanoid pathway from kenaf (Hibiscus cannabinus L.). Kenaf is a fast-growing dicotyledonous plant valued for its biomass. F5H, a cytochrome P450-dependent monooxygenase (CYP84), is a key enzyme for syringyl lignin biosynthesis. The full length of the F5H ortholog was cloned and characterized. The full-length F5H ortholog consists of a 1,557-bp open reading frame (ORF) encoding 518 amino acids (GenBank Accession number JX524278). The deduced amino acid sequence showed that kenaf F5H had the highest similarity (78%) with that of Populus trichocarpa. Transcriptional analysis of F5H ortholog was conducted using quantitative real-time PCR during the developmental stages of various tissues and in response to various abiotic stresses. The highest transcript level of the F5H ortholog was observed in immature flower tissues and in early stage (6 week-old) of stem tissues, with a certain level of expression in all tissues tested. The highest transcript level of F5H ortholog was observed at the late time points after treatments with NaCl (48 h), wounding (24 h), cold (24 h), abscisic acid (24 h), and methyl jasmonate (24 h).