Stable Reference Gene Selection for RT-qPCR Analysis in Nonviruliferous and Viruliferous \u3cem\u3eFrankliniella occidentalis\u3c/em\u3e

Reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) is a reliable technique for measuring and evaluating gene expression during variable biological processes. To facilitate gene expression studies, normalization of genes of interest relative to stable reference genes is crucial. The western flower thrips Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), the main vector of tomato spotted wilt virus (TSWV), is a destructive invasive species. In this study, the expression profiles of 11 candidate reference genes from nonviruliferous and viruliferous F. occidentalis were investigated. Five distinct algorithms, geNorm, NormFinder, BestKeeper, the ΔCt method, and RefFinder, were used to determine the performance of these genes. geNorm, NormFinder, BestKeeper, and RefFinder identified heat shock protein 70 (HSP70), heat shock protein 60 (HSP60), elongation factor 1 α, and ribosomal protein l32 (RPL32) as the most stable reference genes, and the ΔCt method identified HSP60, HSP70, RPL32, and heat shock protein 90 as the most stable reference genes. Additionally, two reference genes were sufficient for reliable normalization in nonviruliferous and viruliferous F. occidentalis. This work provides a foundation for investigating the molecular mechanisms of TSWV and F. occidentalis interactions

The roles of SMYD4 in epigenetic regulation of cardiac development in zebrafish

SMYD4 belongs to a family of lysine methyltransferases. We analyzed the role of smyd4 in zebrafish development by generating a smyd4 mutant zebrafish line (smyd4L544Efs*1) using the CRISPR/Cas9 technology. The maternal and zygotic smyd4L544Efs*1 mutants demonstrated severe cardiac malformations, including defects in left-right patterning and looping and hypoplastic ventricles, suggesting that smyd4 was critical for heart development. Importantly, we identified two rare SMYD4 genetic variants in a 208-patient cohort with congenital heart defects. Both biochemical and functional analyses indicated that SMYD4(G345D) was pathogenic. Our data suggested that smyd4 functions as a histone methyltransferase and, by interacting with HDAC1, also serves as a potential modulator for histone acetylation. Transcriptome and bioinformatics analyses of smyd4L544Efs*1 and wild-type developing hearts suggested that smyd4 is a key epigenetic regulator involved in regulating endoplasmic reticulum-mediated protein processing and several important metabolic pathways in developing zebrafish hearts

Metal-Organic-Framework-based nanofiltration membranes for selective multi-cationic recovery from seawater and brines

Nanofiltration (NF) is gaining a role of increasing importance in Zero Liquid Discharge (ZLD)/Minimal Liquid Discharge (MLD) systems, enhancing the efficiency of downstream technologies to recover valuable minerals from seawater and brines. However, often the purity of the recovered minerals does not meet market specifications, making ZLD/MLD currently economically unfeasible. To such end, in this study, a novel positively charged NF membrane was developed to enhance magnesium and calcium selectivity. The membrane comprised: (i) an ultrafiltration substrate and (ii) an active layer that incorporated NH2-MIL-101(Al) and ZnO nanoparticles in a chitosan matrix. The influence of different loadings of NH2-MIL-101(Al) and ZnO on membrane structure, selectivity and water permeability was investigated. Initial filtration tests with single-salt solutions at 1000 ppm (NaCl, Na2SO4, MgCl2, CaCl2) showed that the membrane with 35%wt of ZnO presented the highest rejections of MgCl2 (90.10%) and CaCl2 (86.49%). Selectivity towards MgCl2 and CaCl2 was higher than those of commercial membranes (NF90 and NF270) and the positively charged membranes introduced in recent literature. The novel synthesized membrane in this work was also tested with synthetic seawater and brine at a trans-membrane pressure of 30 bar. Results highlighted the intriguing competitiveness of the novel membrane in terms of magnesium and calcium selectivity with NF90 and NF270 within the field of both seawater and brine valorization.The authors would like to acknowledge that parts of the research activities were carried out within the framework of "Programma Operativo Nazionale Ricerca e Innovazione2014-2020 (CCI 2014IT16M2OP005), Fondo Sociale Europeo, Azione I.1 “Dottorati Innovativi con caratterizzazione Industriale”, Code: DOT204NJ79, CUP: B73D20005110001. J. López research was developed under the Margarita Salas postdoctoral fellowship from Ministerio de Universidades (MIU) and founded by the European Union-NextGenerationEU. Moreover, J.L. Cortina received support for the research through the “ICREA Academia” recognition for excellence in research funded by the Generalitat de Catalunya.Peer ReviewedPostprint (published version

The genome sequence of the wisent (Bison bonasus)

This work was supported by the Youth Science and Technology Innovation Team of Sichuan Province (2014TD003), Shenzhen Industrial Designation Services Cloud Platform (GGJS20150429172906635), International Collaboration 111 Projects of China, Fundamental Research Funds for the Central Universities, 985 and 211 Projects of Sichuan University.The wisent, also known as the European bison, was rescued from extinction approximately 80 years ago through the conservation of 12 individuals. Here, we present the draft genome sequence of a male wisent individual descended from this founding stock. A total of 366 billion base pairs (Gb) of raw reads from whole-genome sequencing of this wisent were generated using the Illumina HiSeq2000 platform. The final genome assembly (2.58 Gb) is composed of 29,074 scaffolds with an N50 of 4.7 Mb. 47.3% of the genome is composed of repetitive elements. We identified 21,542 genes and 58,385 non-coding RNAs. A phylogenetic tree based on nuclear genomes indicated sister relationships between bison and wisent and between the wisent-bison clade and yak. For 75 genes we obtained evidence of positive evolution in the wisent lineage. We provide the first genome sequence and gene annotation for the wisent. The availability of these resources will be of value for the future conservation of this endangered large mammal and for reconstructing the evolutionary history of the Bovini tribe.Publisher PDFPeer reviewe

Generation of ESTs for Flowering Gene Discovery and SSR Marker Development in Upland Cotton

BACKGROUND: Upland cotton, Gossypium hirsutum L., is one of the world's most important economic crops. In the absence of the entire genomic sequence, a large number of expressed sequence tag (EST) resources of upland cotton have been generated and used in several studies. However, information about the flower development of this species is rare. METHODOLOGY/PRINCIPAL FINDINGS: To clarify the molecular mechanism of flower development in upland cotton, 22,915 high-quality ESTs were generated and assembled into 14,373 unique sequences consisting of 4,563 contigs and 9,810 singletons from a normalized and full-length cDNA library constructed from pooled RNA isolated from shoot apexes, squares, and flowers. Comparative analysis indicated that 5,352 unique sequences had no high-degree matches to the cotton public database. Functional annotation showed that several upland cotton homologs with flowering-related genes were identified in our library. The majority of these genes were specifically expressed in flowering-related tissues. Three GhSEP (G. hirsutum L. SEPALLATA) genes determining floral organ development were cloned, and quantitative real-time PCR (qRT-PCR) revealed that these genes were expressed preferentially in squares or flowers. Furthermore, 670 new putative microsatellites with flanking sequences sufficient for primer design were identified from the 645 unigenes. Twenty-five EST-simple sequence repeats were randomly selected for validation and transferability testing in 17 Gossypium species. Of these, 23 were identified as true-to-type simple sequence repeat loci and were highly transferable among Gossypium species. CONCLUSIONS/SIGNIFICANCE: A high-quality, normalized, full-length cDNA library with a total of 14,373 unique ESTs was generated to provide sequence information for gene discovery and marker development related to upland cotton flower development. These EST resources form a valuable foundation for gene expression profiling analysis, functional analysis of newly discovered genes, genetic linkage, and quantitative trait loci analysis