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Background JAZ subfamily plays crucial roles in growth and development, stress, and hormone responses in various plant species. Despite its importance, the structural and functional analyses of the JAZ subfamily in Brassica napus are still limited. Results Comparing to the existence of 12 JAZ genes (AtJAZ1-AtJAZ12) in Arabidopsis, there are 28, 31, and 56 JAZ orthologues in the reference genome of B. rapa, B. oleracea, and B. napus, respectively, in accordance with the proven triplication events during the evolution of Brassicaceae. The phylogenetic analysis showed that 127 JAZ proteins from A. thaliana, B. rapa, B. oleracea, and B. napus could fall into five groups. The structure analysis of all 127 JAZs showed that these proteins have the common motifs of TIFY and Jas, indicating their conservation in Brassicaceae species. In addition, the cis-element analysis showed that the main motif types are related to phytohormones, biotic and abiotic stresses. The qRT-PCR of the representative 11 JAZ genes in B. napus demonstrated that different groups of BnJAZ individuals have distinct patterns of expression under normal conditions or treatments with distinctive abiotic stresses and phytohormones. Especially, the expression of BnJAZ52 (BnC08.JAZ1-1) was significantly repressed by abscisic acid (ABA), gibberellin (GA), indoleacetic acid (IAA), polyethylene glycol (PEG), and NaCl treatments, while induced by methyl jasmonate (MeJA), cold and waterlogging. Expression pattern analysis showed that BnC08.JAZ1-1 was mainly expressed in the vascular bundle and young flower including petal, pistil, stamen, and developing ovule, but not in the stem, leaf, and mature silique and seed. Subcellular localization showed that the protein was localized in the nucleus, in line with its orthologues in Arabidopsis. Overexpression of BnC08.JAZ1-1 in Arabidopsis resulted in enhanced seed weight, likely through regulating the expression of the downstream response genes involved in the ubiquitin–proteasome pathway and phospholipid metabolism pathway. Conclusions The systematic identification, phylogenetic, syntenic, and expression analyses of BnJAZs subfamily improve our understanding of their roles in responses to stress and phytohormone in B. napus. In addition, the preliminary functional validation of BnC08.JAZ1-1 in Arabidopsis demonstrated that this subfamily might also play a role in regulating seed weight.

Background Yield is the most important and complex trait that is influenced by numerous relevant traits with very complicated interrelations. While there are a large number of studies on the phenotypic relationship and genetic basis of yield traits, systematic studies with further dissection focusing on yield are limited. Therefore, there is still lack of a comprehensive and in-depth understanding of the determination of yield. Results In this study, yield was systematically dissected at the phenotypic, genetic to molecular levels in oilseed rape (Brassica napus L.). The analysis of correlation, network, and principal component for 21 traits in BnaZN-RIL population showed that yield was determined by a complex trait network with key contributors. The analysis of the constructed high-density single nucleotide polymorphism (SNP) linkage map revealed the concentrated distribution of distorted and heterozygous markers, likely due to selection on genes controlling the growth period and yield heterosis. A total of 134 consensus quantitative trait loci (QTL) were identified for 21 traits, of which all were incorporated into an interconnecting QTL network with dozens of hub-QTL. Four representative hub-QTL were further dissected to the target or candidate genes that governed the causal relationships between the relevant traits. Conclusions The highly consistent results at the phenotypic, genetic, and molecular dissecting demonstrated that yield was determined by a multilayer composite network that involved numerous traits and genes showing complex up/down-stream and positive/negative regulation. This provides a systematic view, further insight, and exact roadmap for yield determination, which represents a significant advance toward the understanding and dissection of complex traits.

Background Many viruses depend on the extensive membranous network of the endoplasmic reticulum (ER) for their translation, replication, and packaging. Certain membrane modifications of the ER can be a trigger for ER stress, as well as the accumulation of viral protein in the ER by viral infection. Then, unfolded protein response (UPR) is activated to alleviate the stress. Zika virus (ZIKV) is a mosquito-borne flavivirus and its infection causes microcephaly in newborns and serious neurological complications in adults. Here, we investigated ER stress and the regulating model of UPR in ZIKV-infected neural cells in vitro and in vivo. Methods Mice deficient in type I and II IFN receptors were infected with ZIKV via intraperitoneal injection and the nervous tissues of the mice were assayed at 5 days post-infection. The expression of phospho-IRE1, XBP1, and ATF6 which were the key markers of ER stress were analyzed by immunohistochemistry assay in vivo. Additionally, the nuclear localization of XBP1s and ATF6n were analyzed by immunohistofluorescence. Furthermore, two representative neural cells, neuroblastoma cell line (SK-N-SH) and astrocytoma cell line (CCF-STTG1), were selected to verify the ER stress in vitro. The expression of BIP, phospho-elF2α, phospho-IRE1, and ATF6 were analyzed through western blot and the nuclear localization of XBP1s was performed by confocal immunofluorescence microscopy. RT-qPCR was also used to quantify the mRNA level of the UPR downstream genes in vitro and in vivo. Results ZIKV infection significantly upregulated the expression of ER stress markers in vitro and in vivo. Phospho-IRE1 and XBP1 expression significantly increased in the cerebellum and mesocephalon, while ATF6 expression significantly increased in the mesocephalon. ATF6n and XBP1s were translocated into the cell nucleus. The levels of BIP, ATF6, phospho-elf2α, and spliced xbp1 also significantly increased in vitro. Furthermore, the downstream genes of UPR were detected to investigate the regulating model of the UPR during ZIKV infection in vitro and in vivo. The transcriptional levels of atf4, gadd34, chop, and edem-1 in vivo and that of gadd34 and chop in vitro significantly increased. Conclusion Findings in this study demonstrated that ZIKV infection activates ER stress in neural cells. The results offer clues to further study the mechanism of neuropathogenesis caused by ZIKV infection.

The structure of the replum was studied in 64 rapeseed lines and in an F2 population derived from a cross between a high pod shattering resistance line, zy72360, and a susceptible line, R1. The dimensions of the replum close to the pedicel in lines with high silique shattering resistance index (SSRI) were greater than those with low SSRI. The replum-valve joint area index (RJAI) was used to investigate the relationship between the replum size and pod shattering. In the 64 accessions, RJAI displayed wide variation (0.50-4.12 mm(2)), with a variance coefficient of 45.4%. There were highly significant positive correlations between SSRI and RJAI, with a correlation coefficient of 0.6140. Analysis of RJAI in 276 F2 individuals further validated the positive correlations between SSRI and RJAI. These results revealed that replum structure was highly associated with pod shattering, and that a thick replum structure could produce high pod shatter resistance. The replum-valve joint area offers a good method to screen high resistance materials beneficial for breeding.

Pandemic influenza A virus (H1N1) 2009 poses a serious public-health challenge worldwide. To characterize the neutralizing epitopes of this virus, we generated a panel of eight monoclonal antibodies (mAbs) against the HA of the A/California/07/2009 virus. The antibodies were specific for the 2009 pdm H1N1 HA, as the antibodies displayed HA-specific ELISA, hemagglutination inhibition (HAI) and neutralization activity. One mAb (mAb12) showed significantly higher HAI and neutralizing titers than the other mAbs. We mapped the antigenic epitopes of the HA by characterizing escape mutants of a 2009 H1N1 vaccine strain (NYMC X-179A). The amino acid changes suggested that these eight mAbs recognized HA antigenic epitopes located in the Sa, Sb, Ca1 and Ca2 sites. Passive immunization with mAbs showed that mAb12 displayed more efficient neutralizing activity in vivo than the other mAbs. mAb12 was also found to be protective, both prophylactically and therapeutically, against a lethal viral challenge in mice. In addition, a single injection of 10 mg/kg mAb12 outperformed a 5-day course of treatment with oseltamivir (10 mg/kg/day by gavage) with respect to both prophylaxis and treatment of lethal viral infection. Taken together, our results showed that mouse-origin mAbs displayed neutralizing effectiveness in vitro and in vivo. One mAb in particular (mAb12) recognized an epitope within the Sb site and demonstrated outstanding neutralizing effectiveness.

Background Adenoviruses are important pathogens with the potential for interspecies transmission between humans and non-human primates. Although many adenoviruses have been identified in monkeys, the knowledge of these viruses from the Colobinae members is quite limited. Findings We conducted a surveillance of viral infection in endangered golden snub-nosed monkeys (Rhinopithecus roxellana) in the subfamily Colobinae in China, and found that 5.1% of sampled individuals were positive for adenovirus. One of the adenoviruses (SAdV-WIV19) was successfully isolated and its full-length genome was sequenced. The full-length genome of WIV19 is 33,562 bp in size, has a G + C content of 56.2%, and encodes 35 putative genes. Sequence analysis revealed that this virus represents a novel species in the genus Mastadenovirus. Diverse cell lines, including those of human origin, were susceptible to WIV19. Conclusion We report the first time the isolation and full-length genomic characterization of an adenovirus from the subfamily Colobinae. Electronic supplementary material The online version of this article (doi:10.1186/s12985-016-0648-6) contains supplementary material, which is available to authorized users.

Background Tick-borne encephalitis virus (TBEV) is one of the most important flaviviruses that targets the central nervous system (CNS) and causes encephalitides in humans. Although neuroinflammatory mechanisms may contribute to brain tissue destruction, the induction pathways and potential roles of specific chemokines in TBEV-mediated neurological disease are poorly understood. Methods BALB/c mice were intracerebrally injected with TBEV, followed by evaluation of chemokine and cytokine profiles using protein array analysis. The virus-infected mice were treated with the CC chemokine antagonist Met-RANTES or anti-RANTES mAb to determine the role of RANTES in affecting TBEV-induced neurological disease. The underlying signaling mechanisms were delineated using RANTES promoter luciferase reporter assay, siRNA-mediated knockdown, and pharmacological inhibitors in human brain-derived cell culture models. Results In a mouse model, pathological features including marked inflammatory cell infiltrates were observed in brain sections, which correlated with a robust up-regulation of RANTES within the brain but not in peripheral tissues and sera. Antagonizing RANTES within CNS extended the survival of mice and reduced accumulation of infiltrating cells in the brain after TBEV infection. Through in vitro studies, we show that virus infection up-regulated RANTES production at both mRNA and protein levels in human brain-derived cell lines and primary progenitor-derived astrocytes. Furthermore, IRF-3 pathway appeared to be essential for TBEV-induced RANTES production. Site mutation of an IRF-3-binding motif abrogated the RANTES promoter activity in virus-infected brain cells. Moreover, IRF-3 was activated upon TBEV infection as evidenced by phosphorylation of TBK1 and IRF-3, while blockade of IRF-3 activation drastically reduced virus-induced RANTES expression. Conclusions Our findings together provide insights into the molecular mechanism underlying RANTES production induced by TBEV, highlighting its potential importance in the process of neuroinflammatory responses to TBEV infection. Electronic supplementary material The online version of this article (doi:10.1186/s12974-016-0665-9) contains supplementary material, which is available to authorized users.

Three strains of H6N6 subtype avian influenza virus (AIV) were isolated from live-poultry markets of central China during 2009-2010. A phylogenetic analysis showed that these isolates originated from gene reassortment among different virus lineages of the H6 subtype. In an experimental infection of animals, the selected isolate was non-pathogenic for chickens and low-pathogenic for mice. The wild-type isolate was capable of replication in mouse lung without prior adaptation, and the virulence to mice increased rapidly during adaption in mouse lung. The genomes of viruses of passage 0 (P0), P4, and P8 were sequenced and compared, and virulence-related amino acid substitutions were found in multiple sites during mouse lung passage.

Our previous studies have proven the adjuvanticity of chitosan in mice when administered with inactivated and subunit influenza vaccine. In this study, we investigated the adjuvant effect of chitosan on the immunogenicity and protective efficacy of a live attenuated influenza vaccine. Mice were inoculated intranasally with live attenuated influenza vaccine plus chitosan and then challenged with a high, lethal dose of homologous or heterologous virus. Antibody responses, secretion of IFN-γ by spleen cells, body weight loss, survival rates, and residual lung virus titers were tested. The results demonstrated that live attenuated influenza vaccine with chitosan adjuvant not only protected mice completely against challenge with the homologous virus but also provided good cross-protection against a heterologous virus. In addition, chitosan as adjuvant could significantly increase the levels of antigen-specific antibodies and the population of IFN-γ-secreting T cells. These results reveal the potential of chitosan as a candidate adjuvant for use in a live attenuated influenza vaccine.

The complete nucleotide sequence of the rapeseed (Brassica napus L.) chloroplast genome (cpDNA) was determined. The 152,860 bp cpDNA contained a pair of 26,035 bp inverted repeat regions (IR), which are separated by small and large single copy regions (SSC and LSC) of 83,030 and 17,760 bp, respectively. The major portion (56.4%) of the B. napus cpDNA consists of gene coding regions, while intergenic spacers make up 43.6% of the complete genome. The average AT content of the B. napus cpDNA is 63.7% and for the LSC, SSC and IR region is 65.9, 70.8 and 57.7%, respectively. Fifteen genes contained one intron, while three genes had two introns. In total, 86 simple sequence repeats were identified. The detailed comparison of the B. napus with one of its putative parents, B. rapa L. cpDNA indicated that the two species were highly similar. The entire gene pool and relative positions of 113 individual genes were identical to those of B. rapa cpDNA. The sequence divergence analysis of B. napus and B. rapa showed only 0.133% in the coding regions, 0.275% in the intron regions, and 0.348% in the intergenic spacer regions. The phylogenies based on 61 protein coding genes from 48 cpDNA sequences provided strong support for monophyly of many major classes of angiosperms and provided support that Amborella could be a sister to all other angiosperms. Our analysis also supported that B. napus is the closest species to B. rapa and B. rapa could be the mathernal parent of B. napus cv. zy036.

High oil content is one of the most important characteristics of rapeseed (Brassica napus L.) breeding. In order to understand the genetic basis of seed oil content, a series of reciprocal crosses between rapeseed parents with high oil content (53110, 61616 and 6F313), medium-oil content (Zhongshuang 9) and low oil content (51070 and 93275) were conducted. It was found that the oil content of F1 hybrid seeds in rapeseed was mainly controlled by the maternal genotype. The maternal effect value of oil content was estimated to be 0.86. The pollen parent had a xenia effect on oil content, estimated to be 0.14 which changed the mean value by 1.86 percent. The inheritance of oil content was studied in a set of 8 × 8 diallel crosses of different varieties. The results indicated that the inheritance of oil content could be explained by an additive-dominant-epistasis model. Although the dominant and additive effects played major roles and accounted for more than 70% of the total variance, there was also a small epistatic effect. The broad and narrow sense heritability of oil content was 83.88 and 36.94%, respectively. Based on the oil content differences between the reciprocal crosses in the same offspring generation (F1 and F2) in rapeseed, it could be concluded that there were significant cytoplasmic effects on oil content. In this study, two lines with significantly cytoplasmic effects, either positive or negative, were selected.

Mustard (Brassicajuncea) is an important crop in both ancient and modern world. It has a broad resource of genetic diversity that is used primarily as oilseed but as vegetables, condiment and medicines also. Its superior tolerance to adverse environments, e.g., drought, high temperature and low fertility suggests its better adaptability in future possible harsh environments. Chinese vegetable mustard displays a wide spectrum of morphotypes. A collection of 95 accessions of B. juncea representing oil and vegetable mustards from China, France, India, Pakistan, and Japan were assessed to determine diversity at the molecular level using sequence-related amplified polymorphism (SRAP). Eight SRAP primer combinations identified a total of 326 scorable fragments of which 161 were polymorphic (49.39%). The percentage of polymorphism for each primer combination varied from 21.88 to 66.67%. Both Shannon-Weaver and Simpson genetic diversity index indicated that the level of genetic diversity within vegetable mustard is much higher than within oil mustard, and also winter oil mustards are genetically more diverse than spring oil mustards. Based on the Cluster and Principal Coordinates analysis, which were conducted on the similarity matrix of SRAP marker data, vegetable, spring oil and winter oil mustard were clearly divided into three distinct groups and among these three groups, spring and winter oil mustard are geneticlly closer than vegetable mustard. This suggests that bilateral gene exchange between oil and vegetable gene pools in the breeding program will effectively elevate the genetic potential in developing higher yields, more disease resistance, better quality and better adapted lines.

Rapeseed cultivars exhibit a wide range of oil content in the mature seeds. Little is known about the relationship between the oilbody structures and the differences in oil contents of Brassica napus cultivars. In the present study, the oilbody morphology and its fate during the embryo development and seedling growth in several cultivars with oil contents ranging from 33.4 to 49.8% were studied. Cultivars with low oil contents (LO), some of the oilbodies were in similar size to those in cultivars with high oil content (HO), while some oilbodies in the LO cultivars were several times bigger (over 5.0 μm). These are much larger than the average size of B. napus seed oilbodies that were previously reported (Mantese et al. Ann Bot 97:999–1010, 2006). The oleosin protein levels and oleosin1 gene transcript abundances in the HO cultivars were clearly higher than in the LO cultivars. The shapes of oilbodies were similar during early stages of embryo development in both HO and LO cultivars, while as the embryos matured, the unusually large oilbodies were generated in the LO cells. After germination, the oilbodies in LO cultivars were consumed more slowly than in HO, and the seed germination rates of LO cultivars were less than those of HO cultivars. The low accumulation of oleosins results in the forming of unusually large oilbodies in LO cultivars.

In this study, the correlations among these characters were investigated in 18 rapeseed (Brassica napus L.) accessions with different seed coat color. The results indicated that seed water uptake and flooding tolerance were significantly correlated with seed color and melanin pigment content of testa. The red or black-seeded accessions had higher melanin content in testa, showed slower water uptake and lower leakage and higher flooding tolerance. The majority of yellow-seeded rapeseed accessions which had low melanin pigments content in testa showed a rapid water uptake and higher leakage than the red or black-seeded, which led to imbibition damage and lower flooding tolerance. The results suggest that the yellow-seeded cultivars experienced poor field emergence and more serious pre-harvest sprouting in raining weather than the dark-seeded cultivars. Some yellow-seeded accessions showed a slow imbibition behavior and relative high flooding tolerance, indicated these accessions can be used as a genetic resource to improve the flooding tolerance and reduce imbibition damage for the yellow-seeded B. napus L.

Problems involving coupled multiple space and time scales offer a real challenge for conventional frameworks of either particle or continuum mechanics. In this paper, four cases studies (shear band formation in bulk metallic glasses, spallation resulting from stress wave, interaction between a probe tip and sample, the simulation of nanoindentation with molecular statistical thermodynamics) are provided to illustrate the three levels of trans-scale problems (problems due to various physical mechanisms at macro-level, problems due to micro-structural evolution at macro/micro-level, problems due to the coupling of atoms/molecules and a finite size body at micro/nano-level) and their formulations. Accordingly, non-equilibrium statistical mechanics, coupled trans-scale equations and simultaneous solutions, and trans-scale algorithms based on atomic/molecular interaction are suggested as the three possible modes of trans-scale mechanics.

A putative basic DNA-binding protein (BDBP) gene was identified in the fragment EcoRI-K of the Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus (HearNPV) genome. The ORF is 330 nucleotides long encoding a basic protein of 109 amino acids with a molecular mass of 11.6 kDa. It is the first BDBP identified in single nucleocapsid NPVs and a homologue of Autographa californica MNPV (AcMNPV) P6.9. A consensus late transcription motif, ATAAG, was found at 57 nt upstream of the translational start codon and a polyadenylation signal was observed at 172 nt downstream of the stop codon. A major transcript of 620 nt was first observed in HearNPV-infected Hz2e5 cells 16 h post infection. Primer extension analysis revealed that this transcript initiated from the first residue of the consensus ATAAG late transcription start motif. Comparison with other baculoviral BDBPs showed that they all contained two conserved cAMP- and cGMP-dependent protein kinase phosphorylation motifs, R-R-R-S. The HearNPV P6.9 homologue is the longest BDBP found so far in baculoviruses.

Background The highly conserved nucleoprotein (NP) is an internal protein of influenza virus and is capable of inducing cross-protective immunity against different influenza A viruses, making it a main target of universal influenza vaccine. In current study, we characterized the immune response induced by DNA prime-intranasal protein boost strategy based on NP (A/PR/8/34, H1N1) in mouse model, and evaluated its protection ability against a lethal dose challenge of influenza virus. Results The intranasal boost with recombinant NP (rNP) protein could effectively enhance the pre-immune response induced by the NP DNA vaccine in mice. Compared to the vaccination with NP DNA or rNP protein alone, the prime-boost strategy increased the level of NP specific serum antibody, enhanced the T cell immune response, and relatively induced more mucosal IgA antibody. The overall immune response induced by this heterologous prime-boost regimen was Th-1-biased. Furthermore, the immune response in mice induced by this strategy provided not only protection against the homologous virus but also cross-protection against a heterosubtypic H9N2 strain. Conclusions The NP DNA prime-intranasal protein boost strategy may provide an effective strategy for universal influenza vaccine development.