Genome wide transcriptional profile analysis of Vitis amurensis and Vitis vinifera in response to cold stress

Grape is one of the most important fruit crops worldwide. The suitable geographical locations and productivity of grapes are largely limited by temperature. Vitis amurensis is a wild grapevine species with remarkable cold-tolerance, exceeding that of Vitis vinifera, the dominant cultivated species of grapevine. However, the molecular mechanisms that contribute to the enhanced freezing tolerance of V. amurensis remain unknown. Here we used deep sequencing data from restriction endonuclease-generated cDNA fragments to evaluate the whole genome wide modification of transcriptome of V. amurensis under cold treatment. Vitis vinifera cv. Muscat of Hamburg was used as control to help investigate the distinctive features of V. amruensis in responding to cold stress. Approximately 9 million tags were sequenced from non-cold treatment (NCT) and cold treatment (CT) cDNA libraries in each species of grapevine sampled from shoot apices. Alignment of tags into V. vinifera cv. Pinot noir (PN40024) annotated genome identified over 15,000 transcripts in each library in V. amruensis and more than 16,000 in Muscat of Hamburg. Comparative analysis between NCT and CT libraries indicate that V. amurensis has fewer differential expressed genes (DEGs, 1314 transcripts) than Muscat of Hamburg (2307 transcripts) when exposed to cold stress. Common DEGs (408 transcripts) suggest that some genes provide fundamental roles during cold stress in grapes. The most robust DEGs (more than 20-fold change) also demonstrated significant differences between two kinds of grapevine, indicating that cold stress may trigger species specific pathways in V. amurensis. Functional categories of DEGs indicated that the proportion of up-regulated transcripts related to metabolism, transport, signal transduction and transcription were more abundant in V. amurensis. Several highly expressed transcripts that were found uniquely accumulated in V. amurensis are discussed in detail. This subset of unique candidate transcripts may contribute to the excellent cold-hardiness of V. amurensis.

Comprehensive analysis of NAC domain transcription factor gene family in Vitis vinifera

KEY MESSAGE : Genome-wide identification of grapevine NAC domain genes and investigation of their chromosome locations, gene structures, duplication, evolution, phylogeny and expression profiles. Grapevine is a widely used fruit crop. NAC (NAM, ATAF1/2 and CUC2) domain genes are plant-specific transcription factors (TFs) that comprise a conserved NAM domain in the N-terminus. Members of this gene family have been reported to contribute to plant development. During this study, 74 NAC genes were identified from 12× assembled grapevine genomic sequences. The duplication patterns, genomic structures and phylogeny of these 74 grapevine NAC genes were investigated. To understand the roles of VvNAC during grapevine development, their expression profiles in different tissues including leaf, tendril, inflorescence, stem, root and veraison berry skin were tested using quantitative real-time PCR. Analysis revealed expression diversity of various VvNAC genes among different grapevine tissues. To identify candidate grapevine NAC genes with a role in response to stress, publicly available microarray data were obtained to calculate their expression change under abiotic and biotic treatments, with a number of VvNAC genes displaying up-regulation after stress induction. Therefore, this study has uncovered more knowledge relating to the gene structures, chromosome organizations, evolution, expression profiles and functions of VvNAC genes.

Multiphoton ionization as a clock to reveal molecular dynamics with intense short x-ray free electron laser pulses

We investigate molecular dynamics of multiple ionization in N2 through multiple core-level photoabsorption and subsequent Auger decay processes induced by intense, short x-ray free electron laser pulses. The timing dynamics of the photoabsorption and dissociation processes is mapped onto the kinetic energy of the fragments. Measurements of the latter allow us to map out the average internuclear separation for every molecular photoionization sequence step and obtain the average time interval between the photoabsorption events. Using multiphoton ionization as a tool of the multiple-pulse pump-probe scheme, we demonstrate the modification of the ionization dynamics as we vary the x-ray laser pulse duration.

Catalyst-free growth of millimeter-long topological insulator Bi₂Se₃ nanoribbons and the observation of the π-Berry phase

We report the growth of single-crystalline Bi(2)Se(3) nanoribbons with lengths up to several millimeters via a catalyst-free physical vapor deposition method. Scanning transmission electron microscopy analysis reveals that the nanoribbons grow along the (112̅0) direction. We obtain a detailed characterization of the electronic structure of the Bi(2)Se(3) nanoribbons from measurements of Shubnikov-de Haas (SdH) quantum oscillations. Angular dependent magneto-transport measurements reveal a dominant two-dimensional contribution originating from surface states. The catalyst-free synthesis yields high-purity nanocrystals enabling the observation of a large number of SdH oscillation periods and allowing for an accurate determination of the π-Berry phase, one of the key features of Dirac fermions in topological insulators. The long-length nanoribbons open the possibility for fabricating multiple nanoelectronic devices on a single nanoribbon.

Mitochondrial bioenergetic deficits in the hippocampi of rats with chronic ischemia-induced vascular dementia

Vascular dementia (VD), defined as a loss of memory and cognitive function resulting from vascular lesions in the brain, is the second-most-common cause of dementia in the elderly, after Alzheimer's disease. In recent years, research has focused on the pathogenesis of VD, and mitochondrial bioenergetic deficits have been suggested to contribute to VD onset. To further investigate the role of mitochondria in VD, we used a rat model of VD, which involved permanent bilateral occlusion of the common carotid arteries (with a 1-week interval between artery occlusion to avoid an abrupt reduction in cerebral blood flow) leading to chronic cerebral hypoperfusion. Prior to occlusion, male Wistar rats underwent 7 days of Morris water maze training. Only animals that could swim and passed the Morris water maze test were chosen for the study. After 5 days of Morris water maze training, mitochondria from the hippocampi of rats, which were randomly selected from animals that could complete the Morris water maze test, were isolated for functional assessment. Mitochondria isolated from the hippocampi of rats from the ischemia group had decreased pyruvate dehydrogenase protein levels, and increased oxidative stress, as manifested by increased hydrogen peroxide production. The ischemia group mitochondria also exhibited decreased respiration coupled to decreased expression and activity of the electron transport chain complex IV (cytochrome c oxidase). These results indicate that the mitochondrial oxidative metabolism is inhibited in the hippocampi of rats following chronic ischemia-induced VD. As the mitochondrial oxidative metabolism deficits, namely mitochondrial bioenergetic deficits directly affect the functions of neurons, it may contribute to VD onset.

Occurrence of Phoma macdonaldii, the Causal Agent of Sunflower Black Stem Disease, in Sunflower Fields in China

Phoma macdonaldii Boerma is the pathogen of sunflower black stem disease, causing dark black, oval to long lesions on stems of sunflower plants. Infection during early growth stages can reduce yield by 10 to 30% (3). This fungal disease is distributed mainly in North and South America and Europe. In China, the first case was reported in Xinjiang in 2008 (1), and was believed to be introduced as a result of hybrid sunflower seeds being imported from abroad. The Chinese government included this fungus into its quarantine pests list in 2010 (2). Since China imports a great number of sunflower seeds to grow in its Northern provinces from epidemic areas such as the United States, Argentina, and France, monitoring the disease occurrence in planting areas became crucial. During 2010 and 2011 growing seasons, surveys were conducted in 37 commercial farms or individual households in 12 counties of five areas (Xinjiang, Inner Mongolia, Ningxia, Hebei, and Beijing). A total of 185 suspicious samples of sunflower black stem disease were collected and all were found from imported hybrid seed fields. The presence of P. macdonaldii was confirmed as following: 4 mm² tissue pieces cut from lesion margins were disinfected with 1% NaOCl, plated on APDA (acid potato dextrose agar, 4.5 to 5.0 pH adjusted with lactic acid), and incubated at 25°C with 12L:12D photoperiod. After 3 days of incubation, colonies were opalescent or ivory in color, and fluffy or flocculent in appearance. After 4 to 6 days, a large number of spherical or oblate black-brown pycnidia were formed separately or in clusters with thin wall and papillate ostiole in diameter of 135 to 324 μm (average 178 μm). A light pink or opalescent gelatinous substance (pycnidiospores) exuded from the ostiole. Pycnidiospores were single celled, oval or kidney-shaped and hyaline both with and without oil balls, and 1.5 to 3.0 μm × 3.0 to 6.5 μm (average 2.0 × 4.7 μm). Sequences of ITS1-5.8S- ITS2 rDNA fragment of all isolates (GenBank Accession No. JQ979487, JQ979488) were identical and had 100% homology with P. macdonaldii isolates from Xinjiang (HM003206) and Australia (DQ351823, DQ351825) and 99% homology with isolates from the former Yugoslavia (DQ351821, DQ351822) in GenBank. Pathogenicity studies of the isolate were performed by injecting 10 × 10⁶/ml spore suspension into the hypocotyl of four true leaves of sunflower seedlings with a syringe. Sterile water was injected as control. After being inoculated in a plastic bag in the shade at room temperature for 48 h, the plastic bag was removed and the seedlings were grown under natural light. Symptoms of black stem disease were observed in all P. macdonaldii inoculated seedlings and the fungus was reisolated from the lesions for confirmation. The current survey found that 105 of 185 suspicious samples were P. macdonaldii positive and were all from four counties in Xinjiang, suggesting that the disease has not spread to other areas since its introduction. The monitoring of sunflower black stem disease is continuing, as is the research for measuring P. macdonaldii adaptability in China and the development of rapid molecular detection technology. References: (1) W. M. Chen et al. J. Yunnan Agric. Univ. 23:609, 2008. (2) J. Luo et al. Australas. Plant Pathol. 40:504, 2011. (3) E. Miric et al. Aust. J. Agr. Res. 50:325, 1999.

Reactions between bacterial exopolymers and goethite: A combined macroscopic and spectroscopic investigation

The adsorption to goethite of extracellular polymeric substances (EPS) isolated from Pseudomonas putida was investigated using batch adsorption experiments, electrophoretic mobility (EM) measurements, Fourier transform infrared (FTIR) spectroscopy, isothermal titration calorimetry (ITC) and X-ray absorption fine structure (XAFS) spectroscopy. The adsorption of EPS decreased the point of zero charge of goethite from 7.6 to 3.2, suggesting the formation of negatively charged inner-sphere surface complexes. The adsorption isotherms of EPS on goethite conformed to the Langmuir equation. The adsorption energy constant (K) of EPS on goethite was in the sequence of EPS phosphate-containing moieties > nitrogen-containing moieties > carbon-containing moieties, indicating those containing phosphate were the most strongly adsorbed. FTIR showed ligand exchange of phosphate groups of EPS with surface hydroxyls on goethite. Extended X-ray absorption fine structure (EXAFS) and X-ray absorption near edge structure (XANES) spectroscopy results further demonstrated phosphate groups of EPS can form monodentate inner-sphere complexes at lower pH 3.0, while form bidentate inner-sphere complexes at higher pH 9.0. The oxidation state of iron in goethite was not changed after the reaction with EPS at different pH values. The information obtained in this study is of fundamental significance for the understanding of the interaction mechanisms between bacteria and minerals in soil and aquatic environments.

Epidemic trend of measles in Shandong Province, China, 1963-2005

OBJECTIVES

Although measles is a vaccine-preventable infectious disease and the measles vaccine is safe and effective, it still poses a serious threat to the health of children and susceptible populations in China every year. This study aimed to investigate the epidemiological characteristics of measles in Shandong Province, China, including its spatial distribution pattern, in order to have a precise prediction of measles epidemics for better public health strategic planning and resource allocation.

STUDY DESIGN

Longitudinal data study.

METHODS

This study was based on the surveillance data set of measles from all 17 regions (cities) in Shandong Province between 1963 and 2005. Geographical Information Systems and piecewise exponential smoothing of logarithmic transformed data were applied with consideration of the spatial and temporal features of the data. The parameters of epidemic peaks were estimated by filtering off the drifting long-term trends.

RESULTS

Measles presented in almost all regions in Shandong Province with different spatial distribution over the 43-year study period. The incidence of measles was very high in the pre-vaccination period, with an average incidence of 617.61/100,000 population in 1963. With the implementation of vaccination, the average incidence of measles decreased to 3.63/100,000 population in 2005, the periodicity died out and the trend remained at a stable low level. Outbreaks have been reported recently.

CONCLUSIONS

This study identified the effects of different strategies on the incidence of measles observed in Shandong, China, and will provide valuable information to assist local and national public health policy making. There are still some challenges to improve vaccination coverage and efficacy in order to eliminate measles in China. Strengthening surveillance will be essential in the framework of the anticipated global elimination campaign for measles.

The association between RhEPO and FN expression in glomerular mesangial cells

AIM

Erythropoietin (rhEPO) is increasingly being used in the treatment of anemia caused by miscellaneous reasons. The aim of our research is to investigate the effects of recombinant human erythropoietin (rhEPO) on cellular growth and fibronectin (FN) expression in glomerular mesangial cells.

METHODS

Western blot was used to detect the expression of FN induced by rhEPO (1, 10, 100 and 1000U/mL). In vivo studies, male CD-1 mice were administered rhEPO subcutaneously at a single dose of 1000U/Kg. The cellular hypertrophy was quantified by counting cell number and calculating the ratio of cell protein to cell number.

RESULTS

1) Compared with the control group, the results of mesangial cells' growth stimulated by rhEPO were not significantly different; 2) RhEPO lead to hypertrophy of mesangial cells; 3) rhEPO induced FN expression of mesangial cell in a dose-dependent way. Compared to control, 100U/mL rhEPO enhanced the expression of FN significantly; 4) indirect immunofluorescence showed that rhEPO induced large amount deposition of FN in the intercellular space of mesangial cells; 5) in vivo studies, there were markedly increase of FN expression in mice received the injection of rhEPO.

CONCLUSION

RhEPO could up-regulated the expression of FN and induced glomerular mesangial cells hypertrophy. These results suggested rhEPO could induce dysfunction of renal glomerulus through its influence on the function of mesangial cells.

Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

BACKGROUND

Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development.

RESULTS

An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations.

CONCLUSIONS

The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison.

Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

BACKGROUND

Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development.

RESULTS

An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations.

CONCLUSIONS

The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison.