Influence of Drought Stress on the Rhizosphere Bacterial Community Structure of Cassava (Manihot esculenta Crantz).

Drought presents a significant abiotic stress that threatens crop productivity worldwide. Rhizosphere bacteria play pivotal roles in modulating plant growth and resilience to environmental stresses. Despite this, the extent to which rhizosphere bacteria are instrumental in plant responses to drought, and whether distinct cassava (Manihot esculenta Crantz) varieties harbor specific rhizosphere bacterial assemblages, remains unclear. In this study, we measured the growth and physiological characteristics, as well as the physical and chemical properties of the rhizosphere soil of drought-tolerant (SC124) and drought-sensitive (SC8) cassava varieties under conditions of both well-watered and drought stress. Employing 16S rDNA high-throughput sequencing, we analyzed the composition and dynamics of the rhizosphere bacterial community. Under drought stress, biomass, plant height, stem diameter, quantum efficiency of photosystem II (Fv/Fm), and soluble sugar of cassava decreased for both SC8 and SC124. The two varieties' rhizosphere bacterial communities' overall taxonomic structure was highly similar, but there were slight differences in relative abundance. SC124 mainly relied on Gamma-proteobacteria and Acidobacteriae in response to drought stress, and the abundance of this class was positively correlated with soil acid phosphatase. SC8 mainly relied on Actinobacteria in response to drought stress, and the abundance of this class was positively correlated with soil urease and soil saccharase. Overall, this study confirmed the key role of drought-induced rhizosphere bacteria in improving the adaptation of cassava to drought stress and clarified that this process is significantly related to variety.

Targeted metabolome analysis reveals accumulation of metabolites in testa of four peanut germplasms.

Cultivated peanut (Arachis hypogaea L.) is an important source of edible oil and protein. Peanut testa (seed coat) provides protection for seeds and serves as a carrier for diversity metabolites necessary for human health. There is significant diversity available for testa color in peanut germplasms. However, the kinds and type of metabolites in peanut testa has not been comprehensively investigated. In this study, we performed metabolite profiling using UPLC-MS/MS for four peanut germplasm lines with different testa colors, including pink, purple, red, and white. A total of 85 metabolites were identified in four peanuts. Comparative metabolomics analysis identified 78 differentially accumulated metabolites (DAMs). Some metabolites showed significant correlation with other metabolites. For instance, proanthocyanidins were positively correlated with cyanidin 3-O-rutinoside and malvin, and negatively correlated with pelargonidin-3-glucoside. We observed that the total proanthocyanidins are most abundant in pink peanut variety WH10. The red testa accumulated more isoflavones, flavonols and anthocyanidins compared with that in pink testa. These results provided valuable information about differential accumulation of metabolites in testa with different color, which are helpful for further investigation of the molecular mechanism underlying biosynthesis and accumulation of these metabolites in peanut.

Predicting In-Vitro DNA-Protein Binding With a Spatially Aligned Fusion of Sequence and Shape.

Discovery of transcription factor binding sites (TFBSs) is of primary importance for understanding the underlying binding mechanic and gene regulation process. Growing evidence indicates that apart from the primary DNA sequences, DNA shape landscape has a significant influence on transcription factor binding preference. To effectively model the co-influence of sequence and shape features, we emphasize the importance of position information of sequence motif and shape pattern. In this paper, we propose a novel deep learning-based architecture, named hybridShape eDeepCNN, for TFBS prediction which integrates DNA sequence and shape information in a spatially aligned manner. Our model utilizes the power of the multi-layer convolutional neural network and constructs an independent subnetwork to adapt for the distinct data distribution of heterogeneous features. Besides, we explore the usage of continuous embedding vectors as the representation of DNA sequences. Based on the experiments on 20 in-vitro datasets derived from universal protein binding microarrays (uPBMs), we demonstrate the superiority of our proposed method and validate the underlying design logic.

Rapid detection of two emerging viruses associated with necrotic symptoms in Areca catechu L. by reverse transcription loop-mediated isothermal amplification (RT-LAMP).

Two reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assays were developed for the detection of areca palm necrotic ringspot virus (ANRSV) and areca palm necrotic spindle-spot virus (ANSSV), respectively. These two emerging viruses both induce necrotic symptoms in areca palms. The coat protein (CP) gene of ANRSV and the 9 K gene of ANSSV were used to design the respective RT-LAMP primers for the assays. Each set of four primers designed for each of these viruses was found to be highly specific in the detection of the respective targeted virus. The optimal incubation conditions for the RT-LAMP assays were 63 °C for 40 min for ANRSV and at 61 °C for 40 min for ANSSV. The sensitivity of the RT-LAMP method for each of these viruses was 10-fold greater than that of the corresponding conventional reverse-transcription polymerase chain reaction (RT-PCR). The RT-LAMP assays may be useful for the rapid early detection of ANSSV and ANRSV in commercial areca palm production.

Involvement of abscisic acid-responsive element-binding factors in cassava (Manihot esculenta) dehydration stress response.

Cassava (Manihot esculenta) is a major staple food, animal feed and energy crop in the tropics and subtropics. It is one of the most drought-tolerant crops, however, the mechanisms of cassava drought tolerance remain unclear. Abscisic acid (ABA)-responsive element (ABRE)-binding factors (ABFs) are transcription factors that regulate expression of target genes involved in plant tolerance to drought, high salinity, and osmotic stress by binding ABRE cis-elements in the promoter regions of these genes. However, there is little information about ABF genes in cassava. A comprehensive analysis of Manihot esculenta ABFs (MeABFs) described the phylogeny, genome location, cis-acting elements, expression profiles, and regulatory relationship between these factors and Manihot esculenta betaine aldehyde dehydrogenase genes (MeBADHs). Here we conducted genome-wide searches and subsequent molecular cloning to identify seven MeABFs that are distributed unevenly across six chromosomes in cassava. These MeABFs can be clustered into three groups according to their phylogenetic relationships to their Arabidopsis (Arabidopsis thaliana) counterparts. Analysis of the 5'-upstream region of MeABFs revealed putative cis-acting elements related to hormone signaling, stress, light, and circadian clock. MeABF expression profiles displayed clear differences among leaf, stem, root, and tuberous root tissues under non-stress and drought, osmotic, or salt stress conditions. Drought stress in cassava leaves and roots, osmotic stress in tuberous roots, and salt stress in stems induced expression of the highest number of MeABFs showing significantly elevated expression. The glycine betaine (GB) content of cassava leaves also was elevated after drought, osmotic, or salt stress treatments. BADH1 is involved in GB synthesis. We show that MeBADH1 promoter sequences contained ABREs and that MeBADH1 expression correlated with MeABF expression profiles in cassava leaves after the three stress treatments. Taken together, these results suggest that in response to various dehydration stresses, MeABFs in cassava may activate transcriptional expression of MeBADH1 by binding the MeBADH1 promoter that in turn promotes GB biosynthesis and accumulation via an increase in MeBADH1 gene expression levels and MeBADH1 enzymatic activity. These responses protect cells against dehydration stresses by preserving an osmotic balance that enhances cassava tolerance to dehydration stresses.

Tm3+-Ho3+ codoped tellurite glass microsphere laser in the 1.47 µm wavelength region.

In this Letter, a Tm3+-Ho3+ codoped tellurite glass microsphere laser in the 1.47 µm wavelength region is described. Using a traditional tapered microfiber-microsphere coupling method, multimode and single-mode lasing around the wavelength of 1.47 µm is observed using an 802 nm laser diode as a pump source. This Tm3+-Ho3+ codoped tellurite glass microsphere laser can be used in near-infrared telecommunications, biomedical, and astrophysical applications.

Ultrafast hole transfer mediated by polaron pairs in all-polymer photovoltaic blends.

The charge separation yield at a bulk heterojunction sets the upper efficiency limit of an organic solar cell. Ultrafast charge transfer processes in polymer/fullerene blends have been intensively studied but much less is known about these processes in all-polymer systems. Here, we show that interfacial charge separation can occur through a polaron pair-derived hole transfer process in all-polymer photovoltaic blends, which is a fundamentally different mechanism compared to the exciton-dominated pathway in the polymer/fullerene blends. By utilizing ultrafast optical measurements, we have clearly identified an ultrafast hole transfer process with a lifetime of about 3 ps mediated by photo-excited polaron pairs which has a markedly high quantum efficiency of about 97%. Spectroscopic data show that excitons act as spectators during the efficient hole transfer process. Our findings suggest an alternative route to improve the efficiency of all-polymer solar devices by manipulating polaron pairs.

9.73% Efficiency Nonfullerene All Organic Small Molecule Solar Cells with Absorption-Complementary Donor and Acceptor.

In the last two years, polymer solar cells (PSCs) developed quickly with n-type organic semiconductor (n-OSs) as acceptor. In contrast, the research progress of nonfullerene organic solar cells (OSCs) with organic small molecule as donor and the n-OS as acceptor lags behind. Here, we synthesized a D-A structured medium bandgap organic small molecule H11 with bithienyl-benzodithiophene (BDTT) as central donor unit and fluorobenzotriazole as acceptor unit, and achieved a power conversion efficiency (PCE) of 9.73% for the all organic small molecules OSCs with H11 as donor and a low bandgap n-OS IDIC as acceptor. A control molecule H12 without thiophene conjugated side chains on the BDT unit was also synthesized for investigating the effect of the thiophene conjugated side chains on the photovoltaic performance of the p-type organic semiconductors (p-OSs). Compared with H12, the 2D-conjugated H11 with thiophene conjugated side chains shows intense absorption, low-lying HOMO energy level, higher hole mobility and ordered bimodal crystallite packing in the blend films. Moreover, a larger interaction parameter (χ) was observed in the H11 blends calculated from Hansen solubility parameters and differential scanning calorimetry measurements. These special features combined with the complementary absorption of H11 donor and IDIC acceptor resulted in the best PCE of 9.73% for nonfullerene all small molecule OSCs up to date. Our results indicate that fluorobenzotriazole based 2D conjugated p-OSs are promising medium bandgap donors in the nonfullerene OSCs.

11.4% Efficiency non-fullerene polymer solar cells with trialkylsilyl substituted 2D-conjugated polymer as donor.

Simutaneously high open circuit voltage and high short circuit current density is a big challenge for achieving high efficiency polymer solar cells due to the excitonic nature of organic semdonductors. Herein, we developed a trialkylsilyl substituted 2D-conjugated polymer with the highest occupied molecular orbital level down-shifted by Si-C bond interaction. The polymer solar cells obtained by pairing this polymer with a non-fullerene acceptor demonstrated a high power conversion efficiency of 11.41% with both high open circuit voltage of 0.94 V and high short circuit current density of 17.32 mA cm-2 benefitted from the complementary absorption of the donor and acceptor, and the high hole transfer efficiency from acceptor to donor although the highest occupied molecular orbital level difference between the donor and acceptor is only 0.11 eV. The results indicate that the alkylsilyl substitution is an effective way in designing high performance conjugated polymer photovoltaic materials.

The role of the internal molecular free volume in defining organic porous copolymer properties: tunable porosity and highly selective CO2 adsorption.

A series of novel azo-functionalized copolymerized networks (simply known as NOP-34 series) with tunable permanent microporosity and highly selective carbon dioxide capture are disclosed. The synthesis was accomplished by Zn-induced reductive cross-coupling copolymerization of two nitrobenzene-like building blocks with different 'internal molecular free volumes' (IMFVs), i.e., 2,7,14-trinitrotriptycene and 2,2',7,7'-tetranitro-9,9'-spirobifluorene, with different molar ratios. Increasing the content of spirobifluorene (SBF) segments with a smaller IMFV relative to that of triptycene leads to an unconventional rise-fall pattern in porosity. Unlike most reported porous copolymers whose surface area lies between the corresponding homopolymers, the copolymer NOP-34@7030 with 30% SBF segments unprecedentedly shows the largest Brunauer-Emmett-Teller specific surface area (up to 823 m(2) g(-1)) as well as promoted CO2 uptake abilities (from 2.31 to 3.22 mmol g(-1), at 273 K/1.0 bar). The 100% triptycene(TPC)-derived homopolymer (NOP-34@1000) with a moderate surface area shows the highest CO2/N2 IAST selectivity of 109 (273 K) among the five samples, surpassing most known nanoporous organic polymers. This may contribute significantly to our understanding of the relationship of IMFVs with the properties of copolymerized materials.

Metal Microporous Aromatic Polymers with Improved Performance for Small Gas Storage.

A novel metal-doping strategy was developed for the construction of iron-decorated microporous aromatic polymers with high small-gas-uptake capacities. Cost-effective ferrocene-functionalized microporous aromatic polymers (FMAPs) were constructed by a one-step Friedel-Crafts reaction of ferrocene and s-triazine monomers. The introduction of ferrocene endows the microporous polymers with a regular and homogenous dispersion of iron, which avoids the slow reunion that is usually encountered in previously reported metal-doping procedures, permitting a strong interaction between the porous solid and guest gases. Compared to ferrocene-free analogues, FMAP-1, which has a moderate BET surface area, shows good gas-adsorption capabilities for H2 (1.75 wt % at 77 K/1.0 bar), CH4 (5.5 wt % at 298 K/25.0 bar), and CO2 (16.9 wt % at 273 K/1.0 bar), as well as a remarkably high ideal adsorbed solution theory CO2 /N2 selectivity (107 v/v at 273 K/(0-1.0) bar), and high isosteric heats of adsorption of H2 (16.9 kJ mol(-1) ) and CO2 (41.6 kJ mol(-1) ).

A Luminescent Hypercrosslinked Conjugated Microporous Polymer for Efficient Removal and Detection of Mercury Ions.

A hypercrosslinked conjugated microporous polymer (HCMP-1) with a robustly efficient absorption and highly specific sensitivity to mercury ions (Hg(2+)) is synthesized in a one-step Friedel-Crafts alkylation of cost-effective 2,4,6-trichloro-1,3,5-triazine and dibenzofuran in 1,2-dichloroethane. HCMP-1 has a moderate Brunauer-Emmett-Teller specific surface (432 m(2) g(-1)), but it displays a high adsorption affinity (604 mg g(-1)) and excellent trace efficiency for Hg(2+). The π-π* electronic transition among the aromatic heterocyclic rings endows HCMP-1 a strong fluorescent property and the fluorescence is obviously weakened after Hg(2+) uptake, which makes the hypercrosslinked conjugated microporous polymer a promising fluorescent probe for Hg(2+) detection, owning a super-high sensitivity (detection limit 5 × 10(-8) mol L(-1)).

Bioinformatic identification and expression analysis of banana microRNAs and their targets.

MicroRNAs (miRNAs) represent a class of endogenous non-coding small RNAs that play important roles in multiple biological processes by degrading targeted mRNAs or repressing mRNA translation. Thousands of miRNAs have been identified in many plant species, whereas only a limited number of miRNAs have been predicted in M. acuminata (A genome) and M. balbisiana (B genome). Here, previously known plant miRNAs were BLASTed against the Expressed Sequence Tag (EST) and Genomic Survey Sequence (GSS), a database of banana genes. A total of 32 potential miRNAs belonging to 13 miRNAs families were detected using a range of filtering criteria. 244 miRNA:target pairs were subsequently predicted, most of which encode transcription factors or enzymes that participate in the regulation of development, growth, metabolism, and other physiological processes. In order to validate the predicted miRNAs and the mutual relationship between miRNAs and their target genes, qRT-PCR was applied to detect the tissue-specific expression levels of 12 putative miRNAs and 6 target genes in roots, leaves, flowers, and fruits. This study provides some important information about banana pre-miRNAs, mature miRNAs, and miRNA target genes and these findings can be applied to future research of miRNA functions.

The MaASR gene as a crucial component in multiple drought stress response pathways in Arabidopsis.

Abscisic acid (ABA)-, stress-, and ripening-induced (ASR) proteins are involved in abiotic stress responses. However, the exact molecular mechanism underlying their function remains unclear. In this study, we report that MaASR expression was induced by drought stress and MaASR overexpression in Arabidopsis strongly enhanced drought stress tolerance. Physiological analyses indicated that transgenic lines had higher plant survival rates, seed germination rates, and leaf proline content and lower water loss rates (WLR) and malondialdehyde (MDA) content. MaASR-overexpressing lines also showed smaller leaves and reduced sensitivity to ABA. Further, microarray and chromatin immunoprecipitation-based sequencing (ChIP-seq) analysis revealed that MaASR participates in regulating photosynthesis, respiration, carbohydrate and phytohormone metabolism, and signal transduction to confer plants with enhanced drought stress tolerance. Direct interactions of MaASR with promoters for the hexose transporter and Rho GTPase-activating protein (RhoGAP) genes were confirmed by electrophoresis mobility shift array (EMSA) analysis. Our results indicate that MaASR acts as a crucial regulator of photosynthesis, respiration, carbohydrate and phytohormone metabolism, and signal transduction to mediate drought stress tolerance.

Evaluation of different methods of protein extraction and identification of differentially expressed proteins upon ethylene-induced early-ripening in banana peels.

BACKGROUND: Banana peels (Musa spp.) are a good example of a plant tissue where protein extraction is challenging due to the abundance of interfering metabolites. Sample preparation is a critical step in proteomic research and is critical for good results. RESULTS: We sought to evaluate three methods of protein extraction: trichloroacetic acid (TCA)-acetone precipitation, phenol extraction, and TCA precipitation. We found that a modified phenol extraction protocol was the most optimal method. SDS-PAGE and two-dimensional gel electrophoresis (2-DE) demonstrated good protein separation and distinct spots of high quality protein. Approximately 300 and 550 protein spots were detected on 2-DE gels at pH values of 3-10 and 4-7, respectively. Several spots were excised from the 2-DE gels and identified by mass spectrometry. CONCLUSIONS: The protein spots identified were found to be involved in glycolysis, the tricarboxylic acid cycle, and the biosynthesis of ethylene. Several of the identified proteins may play important roles in banana ripening.

[Parent grouping of 31 elite inbred lines in hot pepper (Capsicum annuum L.)].

Genetic differences were examined among thirty-one elite inbred lines in Capsicum annuum L. Two types of analytic technologies, i.e. SRAP markers and genotypes of traits, were used, and their relative effectiveness was compared. 27 of 30 primer combinations could amplify 310 polymorphic bands among inbred lines, indicating SRAP marker was efficient to detect polymorphism among pepper inbred lines. A dendrogram of 31 inbred lines based on SRAP markers and Yule coefficients could basically separate lines of C. annuum var. grossum and C. annuum var. longum, and reveal the pedigrees of inbred lines. A dendrogram of 31 inbred lines based on genotypes of traits and standardized Euclidean coefficients could separate lines of C. annuum var. grossum and C. annuum var. longum. The SRAP marker genetic distances were correlated with distances based on the genotypes of traits. These results and their application in the development of hot pepper F1 hy-brids were also discussed.