Strong Influence of Coadsorbate Interaction on CO Desorption Dynamics on Ru(0001) Probed by Ultrafast X-Ray Spectroscopy and Ab Initio Simulations

We show that coadsorbed oxygen atoms have a dramatic influence on the CO desorption dynamics from Ru(0001). In contrast to the precursor-mediated desorption mechanism on Ru(0001), the presence of surface oxygen modifies the electronic structure of Ru atoms such that CO desorption occurs predominantly via the direct pathway. This phenomenon is directly observed in an ultrafast pump-probe experiment using a soft x-ray free-electron laser to monitor the dynamic evolution of the valence electronic structure of the surface species. This is supported with the potential of mean force along the CO desorption path obtained from density-functional theory calculations. Charge density distribution and frozen-orbital analysis suggest that the oxygen-induced reduction of the Pauli repulsion, and consequent increase of the dative interaction between the CO 5σ and the charged Ru atom, is the electronic origin of the distinct desorption dynamics. Ab initio molecular dynamics simulations of CO desorption from Ru(0001) and oxygen-coadsorbed Ru(0001) provide further insights into the surface bond-breaking process.

A novel system for evaluating drought-cold tolerance of grapevines using chlorophyll fluorescence

BACKGROUND

Grape production in continental climatic regions suffers from the combination of drought and cold stresses during winter. Developing a reliable system to simulate combined drought-cold stress and to determine physiological responses and regulatory mechanisms is important. Evaluating tolerance to combined stress at germplasm level is crucial to select parents for breeding grapevines.

RESULTS

In the present study, two species, namely, Vitis amurensis and V. vinifera cv. 'Muscat Hamburg', were used to develop a reliable system for evaluating their tolerance to drought-cold stress. This system used tissue -cultured grapevine plants, 6% PEG solution, and gradient cooling mode to simulate drought-cold stress. V. amurensis had a significantly lower LT50 value (the temperature of 50% electrolyte leakage) than 'Muscat Hamburg' during simulated drought-cold stress. Thus, the former had higher tolerance than the latter to drought-cold stress based on electrolyte leakage (EL) measurements. Moreover, the chlorophyll fluorescence responses of V. amurensis and 'Muscat Hamburg' were also analyzed under drought-cold stress. The maximum photochemical quantum yield of PS II (Fv/Fm) exhibited a significant linear correlationship with EL. The relationship of EL with Fv/Fm in the other four genotypes of grapevines under drought-cold stress was also detected.

CONCLUSIONS

A novel LT50 estimation model was established, and the LT50 values can be well calculated based on Fv/Fm in replacement of EL measurement. The Fv/Fm-based model exhibits good reliability for evaluating the tolerance of different grapevine genotypes to drought-cold stress.

Impact of commercial housing systems and nutrient and energy intake on laying hen performance and egg quality parameters

The US egg industry is exploring alternative housing systems for laying hens. However, limited published research related to cage-free aviary systems and enriched colony cages exists related to production, egg quality, and hen nutrition. The laying hen's nutritional requirements and resulting productivity are well established with the conventional cage system, but diminutive research is available in regards to alternative housing systems. The restrictions exist with limited availability of alternative housing systems in research settings and the considerable expense for increased bird numbers in a replicate due to alternative housing system design. Therefore, the objective of the current study was to evaluate the impact of nutrient and energy intake on production and egg quality parameters from laying hens housed at a commercial facility. Lohmann LSL laying hens were housed in three systems: enriched colony cage, cage-free aviary, and conventional cage at a single commercial facility. Daily production records were collected along with dietary changes during 15 production periods (28-d each). Eggs were analyzed for shell strength, shell thickness, Haugh unit, vitelline membrane properties, and egg solids each period. An analysis of covariance (ANCOVA) coupled with a principal components analysis (PCA) approach was utilized to assess the impact of nutritional changes on production parameters and monitored egg quality factors. The traits of hen-day production and mortality had a response only in the PCA 2 direction. This finds that as house temperature and Met intake increases, there is an inflection point at which hen-day egg production is negatively effected. Dietary changes more directly influenced shell parameters, vitelline membrane parameters, and egg total solids as opposed to laying hen housing system. Therefore, further research needs to be conducted in controlled research settings on laying hen nutrient and energy intake in the alternative housing systems and resulting impact on egg quality measures.

Environmental assessment of three egg production systems--Part I: Monitoring system and indoor air quality

To comprehensively assess conventional vs. some alternative laying-hen housing systems under U.S. production conditions, a multi-institute and multi-disciplinary project, known as the Coalition for Sustainable Egg Supply (CSES) study, was carried out at a commercial egg production farm in the Midwestern United States over two single-cycle production flocks. The housing systems studied include a conventional cage house (200,000 hen capacity), an aviary house (50,000 hen capacity), and an enriched colony house (50,000 hen capacity). As an integral part of the CSES project, continual environmental monitoring over a 27-month period described in this paper quantifies indoor gaseous and particulate matter concentrations, thermal environment, and building ventilation rate of each house. Results showed that similar indoor thermal environments in all three houses were maintained through ventilation management and environmental control. Gaseous and particulate matter concentrations of the enriched colony house were comparable with those of the conventional cage house. In comparison, the aviary house had poorer indoor air quality, especially in wintertime, resulting from the presence of floor litter (higher ammonia levels) and hens' activities (higher particulate matter levels) in it. Specifically, daily mean indoor ammonia concentrations had the 95% confidence interval values of 3.8 to 4.2 (overall mean of 4.0) ppm for the conventional cage house; 6.2 to 7.2 (overall mean of 6.7) ppm for the aviary house; and 2.7 to 3.0 (overall mean of 2.8) ppm for the enriched colony house. The 95% confidence interval (overall mean) values of daily mean indoor carbon dioxide concentrations were 1997 to 2170 (2083) ppm for the conventional cage house, 2367 to 2582 (2475) ppm for the aviary house, and 2124 to 2309 (2216) ppm for the enriched colony house. Daily mean indoor methane concentrations were similar for all three houses, with 95% confidence interval values of 11.1 to 11.9 (overall mean of 11.5) ppm. The 95% confidence interval values (overall mean) of daily mean PM10 and PM2.5 concentrations, in mg/m3, were, respectively, 0.57 to 0.61 (0.59) and 0.033 to 0.037 (0.035) for the conventional cage house, 3.61 to 4.29 (3.95) and 0.374 to 0.446 (0.410) for the aviary house, and 0.42 to 0.46 (0.44) and 0.054 to 0.059 (0.056) for the enriched colony house. Investigation of mitigation practices to improve indoor air quality of the litter-floor aviary housing system is warranted.

Suggestive value of predilection site and imaging features of pediatric brainstem ganglioglioma including a case report

Brainstem ganglioglioma is rarely reported. Due to its low incidence and atypical site, a brainstem ganglioglioma could easily be misdiagnosed as occurs with other pathological neoplasms radiologically. Here, we report an 8-year-old girl with a brainstem tumor confirmed as a ganglioglioma based on postoperative pathology results. We suggest that when a tumor located in the lower brainstem with benign radiological characteristics occurs in a child with a long-term history, the possibility of brainstem ganglioglioma should be considered in the preoperative diagnosis in addition to other low-grade neoplasms. Early stage diagnosis of brainstem ganglioglioma based on the clinical and imaging features is valuable for clinicians in order to perform effective treatment and achieve a good prognosis.

Identification of cold-inducible microRNAs in grapevine

Low temperature is one of the most important environmental factors that limits the geographical distribution and productivity of grapevine. However, the molecular mechanisms on how grapevine responds to cold stress remains to be elucidated. MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs that play an essential role during plant development and stress responses. Although miRNAs and their targets have been identified in several Vitis species, their participation during cold accumulation in grapevine remains unknown. In this study, two small RNA libraries were generated from micropropagated 'Muscat Hamburg' (V. vinifera) plantlets under normal and low temperatures (4°C). A total of 163 known miRNAs and 67 putative novel miRNAs were detected from two small RNA libraries by Solexa sequencing. Forty-four cold-inducible miRNAs were identified through differentially expressed miRNAs (DEMs) analysis; among which, 13 belonged to upregulated DEMs while 31 belonged downregulated DEMs. The expression patterns of the 13 DEMs were verified by real-time RT-PCR analysis. The prediction of the target genes for DEMs indicated that miRNA may regulate transcription factors, including AP2, SBP, MYB, bHLH, GRAS, and bZIP under cold stress. The 5'-RLM RACE were conducted to verify the cleavage site of predicted targets. Seven predicted target genes for four known and three novel vvi-miRNAs showed specific cleavage sites corresponding to their miRNA complementary sequences. The expression pattern of these seven target genes revealed negative correlation with the expression level of the corresponding vvi-miRNAs. Our results indicated that a diverse set of miRNAs in V. vinifera are cold-inducible and may play an important role in cold stress response.

Lithium-doping inverts the nanoscale electric field at the grain boundaries in Cu2ZnSn(S,Se)4 and increases photovoltaic efficiency

Lithium doping changes the electric field at the GBs and improves DMSO solution processed Cu₂ZnSn(S,Se)₄ solar cell efficiency to 11.8%.

The histological analysis of the anterior cruciate ligament of canine after radiofrequency shrinkage

OBJECTIVE

Radiofrequency (RF) shrinkage has been widely conducted in clinical practice and the anterior cruciate ligament (ACL) laxity is regarded as one of the indications. However, basic researches regarding the postoperative histological changes were still insufficient. The study aimed to investigate postoperative histological changes of different areas of ACL for further identifying the optimal area for RF shrinkage.

MATERIALS AND METHODS

A total of 29 healthy canine (16.5 ± 2.2 kg, 4.1 ± 0.7 years) were recruited, 24 of which were randomly divided into group A and group B. The epiphyseal arrest was confirmed by X-ray examination in all animals. On one canine, an ACL's vascular perfusion model was established by the ink-perfusion method to observe the blood supply of the ACL. The mid-portion of ACL was conducted by RF in group A while the amph-portions of ACL were conducted in group B. Two legs of each canine were sub-divided into fixation group (group A1 and B1) and non-fixation group (group A2 and B2). 8 ACLs were separated from the rest 4 canine. 2 ACLs were sent for the histological examination after RF shrinkage and the rest 6 ACLs were served as blank controls. Masson staining and hematoxylin-eosin (H-E) staining were applied to observe the features of inner fibrous changes of ACL, cell count and vascular density.

RESULTS

According to the Masson staining, collagenous tissues were observed in area after RF shrinkage, which was more evident among group B1 than the others. The cellar density in both group A and B was found lower at 12 weeks postoperatively than that at 6 weeks postoperatively (p < 0.05). In addition, the cellar density in B1 group was found higher than that in A1 group at both 6 and 12 weeks postoperatively (p < 0.05). The density of subsynovial vessel in B1 group was found higher than that in A1 group at 6 weeks postoperatively (p < 0.05) and the density of subsynovial vessel in both A1 and B1 groups was found lower at 12 postoperatively weeks than that at 6 weeks postoperatively (p < 0.05). In both A2 and B2 groups, all ACLs were found ruptured at 12 weeks postoperatively.

CONCLUSIONS

The postoperative revascularization pattern of RF-treated ACL was permeating from the synovium to the RF-treated areas, and the best area for the RF shrinkage treatment was the amph-portions of the ACL. Moreover, the application of postoperative external fixation to restrict the movement of injured limb was necessary.

Vibrational spectroscopic investigation of heat-induced changes in functional groups related to protein structural conformation in camelina seeds and their relationship to digestion in dairy cows

The objective of this study was to use Fourier transform/infrared-attenuated total reflectance (FT/IR-ATR) molecular spectroscopy to quantify the heat-induced changes in feed protein molecular structures in relation to protein digestion in dairy cows. Camelina seeds were evaluated in this study as a model for feed protein. The seeds were either heated in air-draft oven (dry heating) or in autoclave (moist heating) at 120°C for 60 min or kept as raw (control). The parameters evaluated were Cornell net protein and carbohydrate system (CNCPS) subfractions, in situ ruminal degradation kinetics, intestinal digestibility of rumen undegraded protein (RUP) and protein molecular structures. Moist heating decreased (P < 0.05) the content of total rumen degradable (RDP) crude protein (CP) subfractions and increased the content of total RUP subfractions compared with raw seeds, indicating a significant shift at the site of protein digestion from rumen to post-ruminal tract. The decrease in RDP was mainly related to the marked decrease in rapidly solubilised (PA) and degradable (PB1) fractions, whereas the moderately degradable (PB2) and slowly degradable (PB3) fractions increased, suggesting a decrease in degradation rate of RDP. The in situ rumen incubation study revealed that moist heating decreased (P < 0.05) RDP and increased (P < 0.05) RUP and its intestinal digestibility. The molecular spectroscopy study revealed that moist heating altered protein molecular structures. Except PA and lag time, dry heating did not significantly alter any of the CNCPS CP subfraction, in situ ruminal CP degradation parameters, intestinal digestibility of RUP, and protein molecular structures. The correlation analysis showed that the heat-induced changes in protein secondary structures, α-helix-to-β-sheet ratio, were positively correlated (P < 0.05) with the contents PA (r = 0.90), PB1 (r = 0.89), RDP (r = 0.72) and intestinal digestibility (r = 0.91) of RUP, and negatively correlated (P < 0.05) with PB2 (r = –0.90), PB3 (r = –0.85) and RUP (–0.87). These results showed that compared with dry heating, moist heating significantly changed protein subfractions, rumen degradability and intestinal digestibility, and these changes were strongly associated with changes in protein molecular structures.

Myb14, a direct activator of STS, is associated with resveratrol content variation in berry skin in two grape cultivars

High and low resveratrol (Res) contents in two cultivars are correlated with the expression abundance of Myb14 , which could directly activate transcriptional expression of stilbene synthase gene ( STS ). Resveratrol (3,5,4'-trihydroxystilbene) is one of the natural polyphenols produced by secondary metabolism in some plants. Stilbene synthase (STS) is the key enzyme for the final step of precursor formation of resveratrol (Res) in grapevines. In this study, we found that Res contents in ripe berry skin were completely different in two grape cultivars, namely, 'Z168' (Vitis monticola × Vitis riparia) with high-Res and 'Jingzaojing' (Vitis vinifera) with low-Res. Moreover, the level of expression of STS gene was higher in the ripe berry skin of 'Z168' than in that of 'Jingzaojing'. To further investigate the underlying mechanisms, we conducted a co-expression analysis through transcriptomic data. We confirmed that Myb14, an R2R3 Myb transcription factor, is the direct regulator of STS by binding to Box-L5 motif. Moreover, the expression pattern of Myb14 is associated with the variation of Res content. To test this prediction, we conducted a number of experiments in vivo and in vitro. The expression patterns of Myb14 and STS in grapevine leaves were identical under a series of stimulus. Myb14 showed higher expression in the ripe berry skin of 'Z168' than in that of 'Jingzaojing'. Yeast one-hybrid assay indicated that grapevine Myb14 could interact with the promoter of STS in vitro, and the transient overexpression of Myb14 promoted the expression of STS. Furthermore, co-expressing 35S::Myb14 in transgenic Arabidopsis could activate GUS expression promoted by STS promoter. Thus, Myb14 is the direct activator of STS, and its expression pattern is associated with Res content variation in grapes.

Comparative analysis of genome-wide chromosomal histone modification patterns in maize cultivars and their wild relatives

Recent advances demonstrate that epigenome changes can also cause phenotypic diversity and can be heritable across generations, indicating that they may play an important role in evolutionary processes. In this study, we analyzed the chromosomal distribution of several histone modifications in five elite maize cultivars (B73, Mo17, Chang7-2, Zheng58, ZD958) and their two wild relatives (Zea mays L. ssp. parviglumis and Zea nicaraguensis) using a three-dimensional (3D) epigenome karyotyping approach by combining immunostaining and 3D reconstruction with deconvolution techniques. The distribution of these histone modifications along chromosomes demonstrated that the histone modification patterns are conserved at the chromosomal level and have not changed significantly following domestication. The comparison of histone modification patterns between metaphase chromosomes and interphase nuclei showed that some of the histone modifications were retained as the cell progressed from interphase into metaphase, although remodelling existed. This study will increase comprehension of the function of epigenetic modifications in the structure and evolution of the maize genome.

Genome-wide identification of WRKY family genes and their response to cold stress in Vitis vinifera

BACKGROUND

WRKY transcription factors are one of the largest families of transcriptional regulators in plants. WRKY genes are not only found to play significant roles in biotic and abiotic stress response, but also regulate growth and development. Grapevine (Vitis vinifera) production is largely limited by stressful climate conditions such as cold stress and the role of WRKY genes in the survival of grapevine under these conditions remains unknown.

RESULTS

We identified a total of 59 VvWRKYs from the V. vinifera genome, belonging to four subgroups according to conserved WRKY domains and zinc-finger structure. The majority of VvWRKYs were expressed in more than one tissue among the 7 tissues examined which included young leaves, mature leaves, tendril, stem apex, root, young fruits and ripe fruits. Publicly available microarray data suggested that a subset of VvWRKYs was activated in response to diverse stresses. Quantitative real-time PCR (qRT-PCR) results demonstrated that the expression levels of 36 VvWRKYs are changed following cold exposure. Comparative analysis was performed on data from publicly available microarray experiments, previous global transcriptome analysis studies, and qRT-PCR. We identified 15 VvWRKYs in at least two of these databases which may relate to cold stress. Among them, the transcription of three genes can be induced by exogenous ABA application, suggesting that they can be involved in an ABA-dependent signaling pathway in response to cold stress.

CONCLUSIONS

We identified 59 VvWRKYs from the V. vinifera genome and 15 of them showed cold stress-induced expression patterns. These genes represented candidate genes for future functional analysis of VvWRKYs involved in the low temperature-related signal pathways in grape.

Relationship between renal injury and the antagonistic roles of angiotensin-converting enzyme (ACE) and ACE2

Angiotensin-converting enzyme 2 (ACE2), a newly discovered carboxypeptidase in the renin-angiotensin system (RAS), antagonizes ACE activity and plays an active role during tissue injury. Yet the mechanism of its action is not well known. Using a streptozotocin (STZ)-induced renal injury rat model, we investigated the relationship between renal injury and the antagonism between ACE and ACE2. We assayed the levels of urea nitrogen, urine glucose, creatinine, and protein, Ace2, Ace, angiotensin II type 1 receptor (At1) and Mas receptor mRNA, and renal and plasma angiotensin II (Ang II) in STZ-treated and untreated rats. We also used histology and immunohistochemistry to assess glomerular injury and ACE2 glomerular and cortical expression. The amounts of urea nitrogen, urine glucose, creatinine, and protein were significantly higher in STZ-treated rats than in control rats (P < 0.01). There were significant pathological changes in the kidney upon STZ-treatment. Ace2 and Ace mRNA levels were significantly higher in STZ-treated rats than in control rats (P < 0.05 and P = 0.05, respectively). There was no significant difference in the Mas receptor and At1 mRNA levels in the 2 groups, although At1 levels showed an increase upon STZ-treatment. The Ang II level in the renal cortical tissue and plasma of STZ-treated rats was higher than that of control rats (P < 0.05). The increase in Ace mRNA levels was higher than that of Ace2 mRNA levels, leading to an elevated Ace/Ace2 ratio. Together, these data suggest that the ACE-Ang II-AT1 axis is the dominant axis in severe kidney injury.

Immune tolerance of skin allograft transplantation induced by immature dendritic cells of a third party carrying donor antigens in mice

BACKGROUND

Dendritic cells (DCs) are the most powerful antigen-presenting cells in the body. Immature DCs (imDCs) can induce transplantation tolerance. In this study, using a mouse model of skin transplantation. We explored the antigen uptake by imDCs, changes in phenotype and function after antigen loading, as well as survival of skin grafts.

METHODS

Mononuclear cells from C57BL/6 mice mixed with a tritiated leucine ([(3)H]Leu) antigen supernate were incubated with Kunming mice imDC and mature DCs. We recorded the expressions of surface molecules that were detected using flow cytometry, mixed lymphocyte reactions, mean survival times, and postoperative morphological changes in skin grafts.

RESULTS

After the addition of allogeneic antigen supernate, the counts per minute of imDCs were significantly higher than those of mature DCs. The expression rates of I(A)/I(E) and CD80 significantly increased on the cell surface of imDCs. The counts per minute of imDCs in mixed lymphocyte reactions in the presence of allogeneic antigens was significantly higher than those of controls. Comparing mean survival times with controls, skin grafts were significantly longer in the imDCs groups from donors or from a third party carrying donor antigens.

CONCLUSIONS

ImDCs display a strong antigen uptake, gradually maturing in terms of phenotype and function after loading. Complementary application of cytotoxic T-lymphocyte-associated antigen 4 immunoglobulin blocks the immune response of imDCs. Both imDCs from the third party carrying donor antigens and those from the donor strain can establish antigen-specific immune tolerance to allogeneic skin grafts.

Ligand-activated peroxisome proliferator-activated receptor β/δ modulates human endometrial cancer cell survival

Endometrial cancer is the fourth most common malignancy among women and is a major cause of morbidity contributing to approximately 8,200 annual deaths in the USA. Despite advances to the understanding of endometrial cancer, novel interventions for the disease are necessary given that many tumors become refractory to therapy. As a strategy to identify novel therapies for endometrial carcinoma, in this study, we examined the contribution of the peroxisome proliferator-activated receptor β/δ (PPARβ/δ) to endometrial cancer cell proliferation and apoptosis. We found that when activated with the highly selective PPARβ/δ agonists, GW0742 and GW501516, PPARβ/δ inhibited the proliferation and markedly induced the apoptosis of three endometrial cancer cell lines. The specificity of the PPARβ/δ-induced effects on cell proliferation and apoptosis was demonstrated using PPARβ/δ-selective antagonists and PPARβ/δ small interfering RNA in combination with PPARβ/δ-selective agonists. Furthermore, we showed that PPARβ/δ activation increased phosphatase and tensin homolog expression, which led to protein kinase B (AKT) and glycogen synthase kinase-3β (GSK3β) dephosphorylation, and increased β-catenin phosphorylation associated with its degradation. Overall, our data suggest that the antitumorigenic effect of PPARβ/δ activation in endometrial cancer is mediated through the negative regulation of the AKT/GSK3β/β-catenin pathway. These findings warrant further investigation of PPARβ/δ as a therapeutic target in endometrial cancer.

Serum secretory phospholipase A2-IIa (sPLA2-IIA) levels in patients surviving acute myocardial infarction

BACKGROUND

The increase of secretory phospholipase A2-IIa (sPLA2-IIa) in culprit coronary lesions is associated with myocardial infarction, and the increase of sPLA2-IIa in peripheral plasma levels has a significant risk and prognostic value in patients with coronary artery disease. Little is known about the prognostic significance of elevated serum sPLA2-IIa in post-acute myocardial infarction (post-AMI) patients.

OBJECTIVES

The present study is designed to investigate the potential association between serum sPLA2-IIa and prognosis in post-acute myocardial infarction (post-AMI) patients.

PATIENTS AND METHODS

From Oct 1998 to Sep 2008, a total of 964 post-AMI patients with serum samples collected in the convalescent stage were studied. Serum levels of sPLA2-IIa were measured by ELISA. According to the optimal cut-off value for sPLA2-IIa concentration, patients were then divided into 2 groups. Categorical variables were compared between the 2 groups using the χ2 test. All continuous variables are described as mean ± SD and were compared using Student's t-test. Statistical associations between clinicopathological observations and sPLA2-IIa levels were determined using the Mann-Whitney U test. The clinical value of sPLA2-IIa level as a prognostic parameter was evaluated using the Cox's proportional hazards model.

RESULTS

During a median follow-up period of 1,462 days, 123 patients (12.7%) had adverse events (all-cause mortality, n=52; non-fatal MI, n=31; readmission for heart failure [HF], n=40). Patients were divided into 2 groups according to a serum sPLA2-IIa level of 360 ng/dl, which was determined to be the optimal cut-off for discriminating all-cause mortality based on the maximum value of the area under the receiver operating characteristic curve. Patients with elevated sPLA2-IIa (> 360 ng/dl, n=164) had a significantly higher prevalence of death (18.3% [30/164] vs. 2.75% [22/800] p < 0.001) and readmission for HF (14% [23/164/ vs. 2.1% [17/800], p < 0.0001), but not of non-fatal MI (4.88% [8/164]vs. 2.87% [23/800], p = 0.096), compared to those with sPLA2-IIa < 360 ng/dl. Multivariate Cox regression analysis indicated that elevated serum sPLA2-IIa was associated with an increased risk of mortality and readmission for HF.

CONCLUSIONS

Elevated serum sPLA2-IIa during the convalescent stage of AMI predicted long-term mortality and readmission for HF after survival discharge in the post-AMI patients.

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.