Search

Larch, a prominent afforestation, and timber species in northeastern China, faces growth limitations due to drought. To further investigate the mechanism of larch's drought resistance, we conducted full-length sequencing on embryonic callus subjected to PEG-simulated drought stress. The sequencing results revealed that the differentially expressed genes (DEGs) primarily played roles in cellular activities and cell components, with molecular functions such as binding, catalytic activity, and transport activity. Furthermore, the DEGs showed significant enrichment in pathways related to protein processing, starch and sucrose metabolism, benzose-glucuronic acid interconversion, phenylpropyl biology, flavonoid biosynthesis, as well as nitrogen metabolism and alanine, aspartic acid, and glutamic acid metabolism. Consequently, the transcription factor T_transcript_77027, which is involved in multiple pathways, was selected as a candidate gene for subsequent drought stress resistance tests. Under PEG-simulated drought stress, the LoMYB8 gene was induced and showed significantly upregulated expression compared to the control. Physiological indices demonstrated an improved drought resistance in the transgenic plants. After 48 h of PEG stress, the transcriptome sequencing results of the transiently transformed LoMYB8 plants and control plants exhibited that genes were significantly enriched in biological process, cellular component and molecular function. Function analyses indicated for the enrichment of multiple KEGG pathways, including energy synthesis, metabolic pathways, antioxidant pathways, and other relevant processes. The pathways annotated by the differential metabolites mainly encompassed signal transduction, carbohydrate metabolism, amino acid metabolism, and flavonoid metabolism. [ABSTRACT FROM AUTHOR]

Nano particle/microsphere TiO2/BiOBr Z-scheme heterojunction is synthesized through an ionic-liquid-hydrothermal method. Flower-like BiOBr are firstly synthesized by an ionic liquid method. Then TiO2 nanoparticles are constructed on BiOBr microspheres through hydrothermal method. The photocatalytic performance of TiO2/BiOBr heterojunction was much better than that of BiOBr or TiO2. 79.33% of tetracycline hydrochloride (TC) is degraded which is 2.23 times and 1.15 times that of the pure BiOBr and TiO2, respectively. Physical and chemical property of the TiO2/BiOBr heterojunctions with varied amount of TiO2 are analyzed by XRD, XPS, FE-SEM, TEM, HRTEM, BET and DRS et. al. The photocatalytic mechanism is also proposed. [ABSTRACT FROM AUTHOR]

The flower-like ZnO self-assembled by nanorods was synthesized by a chemical precipitation method. BiOBr was then covered on the three-dimensional ZnO by hydrothermal method to form coral-like ZnO/BiOBr heterojunctions with high specific surface area. The ZnO/BiOBr heterojunction was investigated by XRD, XPS, FT-IR, FE-SEM, TEM and DRS. The results show that the ZnO/BiOBr heterojunction exhibits significantly enhanced visible-light absorption and carrier transfer capability. It has excellent photocatalytic degradation ability in degradation of Rhodamine B (RhB), tetracycline hydrochloride (TC) and K2Cr2O7. After irradiated for 40 min, 45 min and 100 min, 96.7% RhB, 87.3% TC and 49.8% K2Cr2O7 were degraded, which were 9.3, 1.7 and 41.5 times, respectively, that of the pure ZnO. The photocatalytic mechanism is also proposed. [ABSTRACT FROM AUTHOR]

The NAC transcription factor family is plant-specific with various biological functions. However, there are few studies on the NAC gene involving coniferous species. Bioinformatics research and expression analysis of NAC genes in Larix olgensis can be used to analyse the function of the NAC gene in the future. Screening of excellent genetic materials and molecular breeding have been utilized to cultivate high-quality, stress-resistant larches. According to the transcriptome data for L. olgensis, the genes Unigene81490 and Unigene70699 with complete ORFs (open reading frames) were obtained by conserved domain analysis and named LoNAC1 and LoNAC2, respectively. The cDNAs of LoNAC1 and LoNAC2 were 1971 bp and 1095 bp in length, encoding 656 and 364 amino acids, respectively. The molecular weights of the proteins encoded by the two genes were predicted to be 72.61 kDa and 41.13 kDa, and subcellular localization analysis indicated that the proteins were concentrated in the nucleus. The results of real-time quantitative PCR analysis showed that at different growth stages and in different tissues of L. olgensis, the relative expression levels of the two NAC genes were highest in the stem, and the expression differences were more obvious in non-lignified tissues. After drought, salt and alkali stress and hormone treatment, expression was induced to different degrees. The expression levels of LoNAC1 and LoNAC2 in semi-lignified L. olgensis were higher than in the other two periods (non-lignified and lignified), and expression levels significantly increased under drought and salt stress. Relative expression levels changed under hormone treatment. It is speculated that these two genes may not only be related to drought and salt stress and secondary growth but may also be induced by hormones such as abscisic acid. Overall, LoNAC1 and LoNAC2 are genetic materials that can be used for molecular breeding of larch. [ABSTRACT FROM AUTHOR]

The era of big data has arrived, making it impossible for traditional machine learning algorithms to perform training in a stand-alone computing environment. In this paper, we propose a method for imbalanced binary classification of large-scale datasets based on undersampling and ensemble. More specifically, our method first adaptively partitions the majority class big data into k clusters, followed by undersampling to create k balanced datasets. Subsequently, k base classifiers are trained on each balanced dataset and are combined to perform the final prediction. Existing undersampling methods randomly select a subset of the majority class; thus, important instances may be lost during the process. In contrast, our proposed fuzzy data reduction scheme selects informative instances from each cluster, preventing information loss. Traditional ensemble methods have negative correlations between the base classifiers, whereas our proposed classifier fusion scheme fuses the base classifiers using fuzzy integral to facilitate modeling the relations between the base classifiers. The proposed algorithm is evaluated on six imbalanced large data sets and compared with state-of-the-art undersampling and ensemble methods, including the synthetic minority oversampling technique bagging (SMOTE-Bagging), SMOTE-Boost, and Binary Ensemble Classification for Imbalanced big data based on MapReduce and Upper sampling (BECIMU). Quantitative evaluations and theoretical analysis demonstrate that the proposed method outperforms the three state-of-the-art methods by 1.47%, 2.00% and 2.03%, and by 3.15%, 2.15% and 2.52%, in terms of the average G-mean and AUC-area, respectively. [ABSTRACT FROM AUTHOR]

Class imbalance problems are pervasive in many real-world applications, yet classifying imbalanced data remains to be a very challenging task in machine learning. SMOTE is the most influential oversampling approach. Based on SMOTE, many variants have been proposed. However, SMOTE and its variants have three drawbacks: (1) the probability distribution of the minority class samples is not considered; (2) the generated minority samples lack diversity; (3) the generated minority class samples overlap severely when oversampled many times for balancing with majority class samples. In order to overcome these three drawbacks, a generative adversarial network (GAN) based framework is proposed in this paper. The framework includes an oversampling method and a two-class imbalanced data classification approach. The oversampling method is based on an improved GAN model, and the classification approach is based on classifier fusion via fuzzy integral, which can well model the interactions among the base classifiers trained on the balanced data subsets constructed by the proposed oversampling method. Extensive experiments are conducted to compare the proposed methods with related methods on 5 aspects: MMD-score, Silhouette-score, F-measure, G-means, and AUC-area. The experimental results demonstrate that the proposed methods are more effective and efficient than the compared approaches. [ABSTRACT FROM AUTHOR]

The restricted Boltzmann machine (RBM) is a primary building block of deep learning models. As an efficient representation learning approach, deep RBM can effectively extract sophisticated and informative features from raw data. Little research has been undertaken on using deep RBM to extract features from big data however. In this paper, we investigate this problem, and an ensemble approach for big data classification based on Hadoop MapReduce and fuzzy integral is proposed. The proposed method consists of two stages, map and reduce. In the map stage, multiple RBM-based classifiers used for ensemble are trained in parallel. In the reduce stage, the trained multiple RBM-based classifiers are integrated by fuzzy integral. Experiments on five big data sets show that the proposed approach can outperform other baseline methods to achieve state-of-the-art performance. [ABSTRACT FROM AUTHOR]

Big data are data too big to be handled and analyzed by traditional software tools, big data can be characterized by five V’s features: volume, velocity, variety, value and veracity. However, in the real world, some big data have another feature, i.e., class imbalanced, such as e-health big data, credit card fraud detection big data and extreme weather forecast big data are all class imbalanced. In order to deal with the problem of classifying binary imbalanced big data, based on MapReduce, non-iterative learning, ensemble learning and oversampling, this paper proposed an promising algorithm which includes three stages. Firstly, for each positive instance, its enemy nearest neighbor is found with MapReduce, and p positive instances are randomly generated with uniform distribution in its enemy nearest neighbor hypersphere, i.e., oversampling p positive instances within the hypersphere. Secondly, l balanced data subsets are constructed and l classifiers are trained on the constructed data subsets with an non-iterative learning approach. Finally, the trained classifiers are integrated by fuzzy integral to classify unseen instances. We experimentally compared the proposed algorithm with three related algorithms: SMOTE, SMOTE+RF-BigData and MR-V-ELM, and conducted a statistical analysis on the experimental results. The experimental results and the statistical analysis demonstrate that the proposed algorithm outperforms the other three methods. [ABSTRACT FROM AUTHOR]

Objectives: To establish a recombinase flippase (FLP) and flippase recognition target (FRT) system-mediated protocol for post-integration excision of exogenous DNA fragments in the oleaginous yeast Rhodosporidium toruloides.Results: Binary vectors were constructed to harbor FLP expressing cassette together with the hygromycin-resistance marker. Results showed that R. toruloides transformants produced FLP, but failed to mediate removal of the bleomycin-resistance marker within two FRT sites. When FLP was fused with a native nuclear localization signal (NLS) peptide, the system was found functional. Moreover, R. toruloides recombinant strains expressing the NLS-fused FLP under the control of PADH2, an promoter of alcohol dehydrogenase 2 gene (RHTO_03062), were obtained to realize homologous recombination upon growing in glucose-deficient medium.Conclusions: We have devised a homologous recombination method for R. toruloides based on the FLP/FRT system, which may facilitate further metabolic engineering and designing advanced cell factories for value-added chemicals. [ABSTRACT FROM AUTHOR]

Oleaginous yeast Lipomyces starkeyi, a promising strain of great biotechnical importance, is able to accumulate over 60% of its cell biomass as triacylglycerols (TAGs). It is promising to directly produce the derivatives of TAGs, such as long-chain fatty acid methyl esters and alkanes, in L. starkeyi. However, techniques for genetic modification of this oleaginous yeast are lacking, thus, further research is needed to develop genetic tools and functional elements. Here, we used two exogenous promoters (pGPD and pPGK) from oleaginous yeast Rhodosporidium toruloides to establish a simpler Agrobacterium-mediated transformation (AMT) method for L. starkeyi. Hygromycin-resistant transformants were obtained on antibiotic-contained plate. Mitotic stability test, genotype verification by PCR, and protein expression confirmation all demonstrated the success of this method. Furthermore, the strength of these two promoters was evaluated at the phenotypic level on a hygromycin-gradient plate and at the transcriptional level by real-time quantitative PCR. The PGK promoter strength was 2.2-fold as that of GPD promoter to initiate the expression of the hygromycin-resistance gene. This study provided an easy and efficient genetic manipulation method and elements of the oleaginous yeast L. starkeyi for constructing superior strains to produce advanced biofuels. [ABSTRACT FROM AUTHOR]

Objectives: To target a carotenoid biosynthetic gene in the oleaginous yeast Rhodosporidium toruloides by using the Agrobacterium-mediated transformation (AMT) method. Results: The RHTO_04602 locus of R. toruloides NP11, previously assigned to code the carotenoid biosynthetic gene CRTI, was amplified from genomic DNA and cloned into the binary plasmid pZPK-mcs, resulting in pZPK-CRT. A HYG-expression cassette was inserted into the CRTI sequence of pZPK-CRT by utilizing the restriction-free clone strategy. The resulted plasmid was used to transform R. toruloides cells according to the AMT method, leading to a few white transformants. Sequencing analysis of those transformants confirmed homologous recombination and insertional inactivation of CRTI. When the white variants were transformed with a CRTI-expression cassette, cells became red and produced carotenoids as did the wild-type strain NP11. Conclusions: Successful homologous targeting of the CrtI locus confirmed the function of RHTO_04602 in carotenoids biosynthesis in R. toruloides. It provided valuable information for metabolic engineering of this non-model yeast species. [ABSTRACT FROM AUTHOR]

Aiming at effectively classifying imbalanced large data sets with two classes, this paper proposed a novel algorithm, which consists of four stages: (1) alternately over-sample p times between positive class instances and negative class instances; (2) construct l balanced data subsets based on the generated positive class instances; (3) train l component classifiers with extreme learning machine (ELM) algorithm on the constructed l balanced data subsets; (4) integrate the l ELM classifiers with simple voting approach. Specifically, in first stage, we firstly calculate the center of positive class instances, and then sample instance points along the line between the center and each positive class instance. Next, for each instance point in the new positive class, we firstly find its k nearest neighbors in negative class instances with MapRedcue, and then sample instance points along the line between the instance and its k nearest negative neighbors. The process of over-sampling is repeated p times. In the second stage, we sample instances l times from the negative class with the same size as the generated positive class instances. Each round of sampling, we put positive class and negative class instances together thus obtain l balanced data subsets. The experimental results show that the proposed algorithm can obtain promising speed-up and scalability, and also outperforms three other ensemble algorithms in G-mean. [ABSTRACT FROM AUTHOR]

Two-grid mixed finite element method is proposed based on backward Euler schemes for the unsteady reaction-diffusion equations. The scheme combines with the stabilized mixed finite element scheme by using the lowest equal-order pairs for the velocity and pressure. The space two-grid method is also used to reduce the time consuming. The benefits of this approach are to avoid the higher derivative, but to have more favorable stability, and to get the numerical solution of the two unknown variables simultaneously. Stability analysis and error estimates are given in this work. Finally, the theoretical results are verified by the numerical examples. [ABSTRACT FROM AUTHOR]

Under nutrient-limited conditions, the red yeast Rhodosporidium toruloides can accumulate neutral lipids, of which the compositional fatty acids are mainly saturated and mono-unsaturated ones with 16 or 18 carbon atoms. To improve the linoleic acid content in the lipids, we enabled galactose-inducible expression of the gene encoding Δ12-fatty acid desaturase (FADS) from Mortierella alpina or Fusarium verticillioides by integration of the corresponding expression cassettes into the genome of R. toruloides haploid and diploid strains. The relative linoleic acid content increased up to fivefold and the final linoleic acid titer reached 1.3 g/L under flask culture conditions. Our results suggested that R. toruloides may be further explored as cell factory for production of high-valued lipids and other fatty acid derivatives as bio-based chemicals and fuels. [ABSTRACT FROM AUTHOR]

Odorant binding proteins (OBPs) play important roles in insect olfactory processes. The Chinese pine caterpillar moth, Dendrolimus tabulaeformis (Lepidoptera, Lasiocampidae) is a serious economic pest in China, and the pheromones of this species have been identified to monitor their presence. However, the molecular mechanisms by which D. tabulaeformis perceive pheromones and host volatiles remain unknown. In this study, we identified and characterized three new OBPs, including one pheromone binding protein (PBP1) and two general odor binding proteins (GOBPs), from antennal cDNA of D. tabulaeformis. The deduced amino acid sequences of DtabPBP1, DtabGOBP1, and DtabGOBP2 revealed mature proteins of 140, 147, and 140 amino acids, respectively. Each has six cysteine residues in conserved positions relative to other known OBPs. Amino-acid alignments indicated that the two GOBPs are more conserved (DtabGOBP1 is 52.9-67.4 % identical to orthologs from other Lepidoptera, and DtabGOBP2 is 55.2-81.8 % identical) than the PBP (32.5-46.0 %). Real-time PCR indicated tissue- and sex-specific expression patterns of the three genes. DtabPBP1 was mainly expressed in the antennae of males, whereas female antennae had only 1.09 % the expression in male antennae. Both DtabGOBP1 and DtabGOBP2 were more highly expressed in antennae than in other tissues, while DtabGOBP1 was more abundant in male antennae and DtabGOBP2 in female antennae. In addition, the binding specificities of the three proteins were investigated, and all three OBPs exhibited high binding affinities for the pheromone component (5 Z,7 E)-5,7-dodecadien-1-yl propionate ( Z5, E7-12:OPr). This suggests a role in binding pheromone for GOBPs, as well as PBP1, in D. tabulaeformis. [ABSTRACT FROM AUTHOR]

Early biochemical studies have demonstrated that lipid accumulation by oleaginous yeasts is linked to the activity of the NAD-dependent isocitrate dehydrogenase (Idh). However, molecular study of Idh of oleaginous microorganisms remains limited. Here, we present the cloning of a mitochondrial NAD-specific Idh from Rhodosporidium toruloides (RtIdh), an excellent microbial lipid producer that uses carbohydrates as the carbon source. The evolutionary relationship analyses among RtIdhs and other yeast Idhs revealed that RtIdh had a closer relationship with the Idhs of Ustilago maydis and Schizophyllum commune. We expressed the Rt IDH gene in the yeast Saccharomyces cerevisiae idhΔ mutant. Under the nitrogen-limited condition, the intracellular lipid content and extracellular citrate concentration of the culture of the S. cerevisiae idhΔ carrying the Rt IDH gene increased as the carbon/nitrogen molar ratio of the media increased, while the wild-type S. cerevisiae strain showed no correlation. Our data provided valuable information for elucidating the molecular mechanism of microbial oleaginicity and for engineering microorganisms to produce metabolites of fatty acid pathway. [ABSTRACT FROM AUTHOR]

Sall3 is a member of a gene family with homology to the spalt gene of Drosophila melanogaster, encoding transcription factors, and acts as downstream target of hedgehog. Vertebrate homologues of spalt have been shown to be involved in development of the limbs and nervous system and several organs including the kidney and heart; mutations in the genes are implicated in several human genetic disorders. Recent studies have shown a total loss of olfactory bulb (OB) dopaminergic (DA) neurons in Sall3-null mice. We assume that tyrosine hydroxylase (TH) may be regulated by Sall3 in OB. In this study, we find that Sall3 and TH co-localize in glomerular layer (GL) of OB. Furthermore, we demonstrate a significant induction of the proximal TH promoter transcription activity by Sall3 in dual-luciferase reporter assay and a reduction of TH expression level in Sall3-deficient cell lines. Collectively, these findings support the notion that Sall3 correlates with the expression of TH in mouse OB and may have a role in OB DA neuron development by regulating TH gene expression. The results from this study may advance our understanding of the molecular pathways of OB in the DA neuron development and differentiation. [ABSTRACT FROM AUTHOR]

Here we report an improved method for targeted gene disruption with high efficiency in S. cerevisiae, where the selection markers with long homologous arms are defined by the choice of the primer binding sites at the target locus and the disruption cassettes are constructed by restriction-free (RF) cloning strategy. Three genes, SAM1, IDH1 and IDH2, were disrupted with this method and the disruption efficiencies of SAM1 was improved several folds with much lower false-positive rates compared to the conventional one-step PCR-based gene disruption method. This approach for gene disruption cassettes construction with long flanking homologous arms may be readily applicable to facilitate targeted gene disruption in other non-conventional yeasts and fungi. [ABSTRACT FROM AUTHOR]

Oleaginous yeast Rhodosporidium toruloides is an excellent microbial lipid producer. Therefore, it is important to develop molecular biology tools to understand the basic mechanism for lipid accumulation and further manipulate the microorganism. High-quality RNA extraction from R. toruloides is particularly challenging due to high level of polysaccharides, lipids, and other secondary metabolites. To obtain an optimal protocol for RNA extraction from R. toruloides, four methods were evaluated. Large difference in RNA yield and quality among these protocols was found. The optimum method was modified RNAiso procedure, where RNA was isolated using liquid nitrogen-RNAiso method with salt precipitation and the addition of β-mercaptoethanol. This method consistently recovered RNA in good quality with high yield. Around 297 μg total RNA per gram of cells was obtained with an average purity measured as A/A of 2.09. A titer of 10 cfu/ml could be harvested to construct a full-length cDNA library with the RNA sample in this quality. Electrophoresis gel analysis indicated the fragments ranged from 200 bp to 4.0 kb, with the average size of 1000 bp. Randomly picked clones showed the recombination efficiency at 80%. These results showed that RNA of R. toruloides was successfully extracted for the first time using the modified RNAiso method, and the cDNA library was appropriate for screening the genes related to lipid accumulation. [ABSTRACT FROM AUTHOR]

The malic enzyme-encoding cDNA (GQ372891) from the oleaginous yeast Lipomyces starkeyi AS 2.1560 was isolated, which has an 1719-bp open reading frame flanked by a 290-bp 5′ untranslated sequence and a 92-bp 3′ untranslated sequence. The proposed gene, LsME1, encoded a protein with 572 amino acid residues. The protein presented 58% sequence identity with the malic enzymes from Yarrowia lipolytica CLIB122 and Aspergillus fumigatus Af293 . The LsME1 gene was cloned into the vector pMAL-p4x to express a fusion protein (MBP-LsME1) in Escherichia coli TB1. The fusion protein was purified and then cleaved by Factor Xa to give the recombinant LsME1. This purified enzyme took either NAD+ or NADP+ as the coenzyme but preferred NAD+. The Km values for malic acid, NAD+ and NADP+ were 0.85 ± 0.05 mM, 0.34 ± 0.08 mM, and 7.4 ± 0.32 mM, respectively, at pH 7.3. [ABSTRACT FROM AUTHOR]

Hollow sphere composites were synthesized by a template-free hydrothermal method from MoO3 and In2O3. The spheres have a typical size of 800 ± 50 nm and were characterized by XRD, FESEM, TEM, XPS. Gas sensors based on samples with different Mo/In composite ratios were fabricated and their gas sensing properties were studied. The results show that a Mo:In ratio of 1:1 in the composite gives the highest response, typically at a working temperature of 250 °C. The response increases to 38 when exposed to 100 ppm acetone at 250 °C. This is 13.6 times better than when using pure MoO3. The sensor shows improved selectivity, response, repeatability and long-term stability. Typical features include a large specific surface area, and high levels of chemisorbed oxygen and defective oxygen sites. The N-N heterojunction theory was used to explain the improvement of gas sensing performance. [ABSTRACT FROM AUTHOR]

The successful establishment of bark beetle–fungus symbionts on plants is required to overcome host defenses. However, little is known about how different bark beetle–fungus symbionts adapt to different niches on the same host plant. Here, we investigated the niche partitioning mechanism of two co-occurring bark beetle–fungus symbiotic systems, Ips nitidus–Ophiostoma bicolor and Dendroctonus micans–Endoconidiophora laricicola, on Qinghai spruce (Picea crassifolia) tree. The lower niche of the spruce trunk inhabited by D. micans showed a higher content of monoterpenes than the upper niche of the trunk inhabited by I. nitidus. Dendroctonus micans showed greater tolerance and higher metabolic efficiency toward monoterpenes than I. nitidus. However, both beetle species showed a similar metabolic profile toward α-pinene, albeit with different levels of metabolites. Additionally, O. bicolor, transmitted by I. nitidus, showed a significantly higher tolerance to monoterpenes and pathogenicity to spruce trees than E. laricicola, transmitted by D. micans. In particular, monoterpenoid metabolites were observed to attenuate the inhibitory effect of high-dose α-pinene on E. laricicola, thus increasing its fitness in a high-dose monoterpene microhabitat. These results show that these two bark beetle–fungus symbionts have adapted to different niches, leading to fitness differences in niche distribution that are at least partly related to the different distribution of monoterpene concentration in the spruce trunk. This research provides a novel perspective for understanding the coevolution between bark beetle–fungus symbionts and their host plants. [ABSTRACT FROM AUTHOR]

Hollow sphere composites were synthesized by a template-free hydrothermal method from MoO3 and In2O3. The spheres have a typical size of 800 ± 50 nm and were characterized by XRD, FESEM, TEM, XPS. Gas sensors based on samples with different Mo/In composite ratios were fabricated and their gas sensing properties were studied. The results show that a Mo:In ratio of 1:1 in the composite gives the highest response, typically at a working temperature of 250 °C. The response increases to 38 when exposed to 100 ppm acetone at 250 °C. This is 13.6 times better than when using pure MoO3. The sensor shows improved selectivity, response, repeatability and long-term stability. Typical features include a large specific surface area, and high levels of chemisorbed oxygen and defective oxygen sites. The N-N heterojunction theory was used to explain the improvement of gas sensing performance. [ABSTRACT FROM AUTHOR]