The arabidopsis RCC1 family protein TCF1 regulates freezing tolerance and cold acclimation through modulating lignin biosynthesis

Cell water permeability and cell wall properties are critical to survival of plant cells during freezing, however the underlying molecular mechanisms remain elusive. Here, we report that a specifically cold-induced nuclear protein, Tolerant to Chilling and Freezing 1 (TCF1), interacts with histones H3 and H4 and associates with chromatin containing a target gene, BLUE-COPPER-BINDING PROTEIN (BCB), encoding a glycosylphosphatidylinositol-anchored protein that regulates lignin biosynthesis. Loss of TCF1 function leads to reduced BCB transcription through affecting H3K4me2 and H3K27me3 levels within the BCB gene, resulting in reduced lignin content and enhanced freezing tolerance. Furthermore, plants with knocked-down BCB expression (amiRNA-BCB) under cold acclimation had reduced lignin accumulation and increased freezing tolerance. The pal1pal2 double mutant (lignin content reduced by 30% compared with WT) also showed the freezing tolerant phenotype, and TCF1 and BCB act upstream of PALs to regulate lignin content. In addition, TCF1 acts independently of the CBF (C-repeat binding factor) pathway. Our findings delineate a novel molecular pathway linking the TCF1-mediated cold-specific transcriptional program to lignin biosynthesis, thus achieving cell wall remodeling with increased freezing tolerance

Genome-wide identification of long intergenic non-coding RNAs of responsive to powdery mildew stress in wheat (Triticum aestivum)

Wheat powdery mildew caused by Blumeria graminis f. sp. tritici is one of the most serious foliar diseases of wheat, causing grain yield and quality degradation by affecting plant photosynthesis. It is an effective method to improve the disease resistance of wheat plants by molecular breeding. With the continuous development of sequencing technology, long intergenic noncoding RNAs (lincRNAs) have been discovered in many eukaryotes and act as key regulators of many cellular processes. In this study, 12 sets of RNA-seq data from wheat leaves pre- and post-pathogen infection were analyzed and 2,266 candidate lincRNAs were identified. Consistent with previous findings, lincRNA has shorter length and fewer exons than mRNA. The results of differential expression analysis showed that 486 DE-lincRNAs were selected as lincRNAs that could respond to powdery mildew stress. Since lincRNAs may be functionally related to their adjacent target genes, the target genes of these lincRNAs were predicted, and the GO and KEGG functional annotations of the predicted target genes were performed. Integrating the functions of target genes and the biological processes in which they were involved uncovered 23 lincRNAs that may promote or inhibit the occurrence of wheat powdery mildew. Co-expression patterns of lincRNAs with their adjacent mRNAs showed that some lincRNAs showed significant correlation with the expression patterns of their potential target genes. These suggested an involvement of lincRNAs in pathogen stress response, which will provide a further understanding of the pathogenic mechanism of wheat powdery mildew

Genome Wide Identification and Expression Profiling of Ethylene Receptor Genes during Soybean Nodulation

It has long been known that the gaseous plant hormone ethylene plays a key role in nodulation in legumes. The perception of ethylene by a family of five membrane-localized receptors is necessary to trigger the ethylene signaling pathway, which regulates various biological responses in Arabidopsis. However, a systematic analysis of the ethylene receptors in leguminous plants and their roles in nodule development is lacking. In this study, we performed a characterization of ethylene receptor genes based on the latest Glycine max genome sequence and a public microarray database. Eleven ethylene receptor family genes were identified in soybean through homology searches, and they were divided into two subgroups. Exon–intron analysis showed that the gene structures are highly conserved within each group. Further analysis of their expression patterns showed that these ethylene receptor genes are differentially expressed in various soybean tissues and organs, including functional nodules. Notably, the ethylene receptor genes showed different responses to rhizobial infection and Nod factors, suggesting a possible role for ethylene receptors and ethylene signaling in rhizobia–host cell interactions and nodulation in soybean. Together, these data indicate the functional divergence of ethylene receptor genes in soybean, and that some of these receptors mediate nodulation, including rhizobial infection, nodule development, and nodule functionality. These findings provide a foundation for further elucidation of the molecular mechanism by which the ethylene signaling pathway regulates nodulation in soybean, as well as other legumes

Causative agent distribution and antibiotic therapy assessment among adult patients with community acquired pneumonia in Chinese urban population

<p>Abstract</p> <p>Background</p> <p>Knowledge of predominant microbial patterns in community-acquired pneumonia (CAP) constitutes the basis for initial decisions about empirical antimicrobial treatment, so a prospective study was performed during 2003–2004 among CAP of adult Chinese urban populations.</p> <p>Methods</p> <p>Qualified patients were enrolled and screened for bacterial, atypical, and viral pathogens by sputum and/or blood culturing, and by antibody seroconversion test. Antibiotic treatment and patient outcome were also assessed.</p> <p>Results</p> <p>Non-viral pathogens were found in 324/610 (53.1%) patients among whom <it>M. pneumoniae </it>was the most prevalent (126/610, 20.7%). Atypical pathogens were identified in 62/195 (31.8%) patients carrying bacterial pathogens. Respiratory viruses were identified in 35 (19%) of 184 randomly selected patients with adenovirus being the most common (16/184, 8.7%). The nonsusceptibility of <it>S. pneumoniae </it>to penicillin and azithromycin was 22.2% (Resistance (R): 3.2%, Intermediate (I): 19.0%) and 79.4% (R: 79.4%, I: 0%), respectively. Of patients (312) from whom causative pathogens were identified and antibiotic treatments were recorded, clinical cure rate with β-lactam antibiotics alone and with combination of a β-lactam plus a macrolide or with fluoroquinolones was 63.7% (79/124) and 67%(126/188), respectively. For patients having mixed <it>M. pneumoniae </it>and/or <it>C. pneumoniae </it>infections, a better cure rate was observed with regimens that are active against atypical pathogens (e.g. a β-lactam plus a macrolide, or a fluoroquinolone) than with β-lactam alone (75.8% vs. 42.9%, <it>p </it>= 0.045).</p> <p>Conclusion</p> <p>In Chinese adult CAP patients, <it>M. pneumoniae </it>was the most prevalent with mixed infections containing atypical pathogens being frequently observed. With <it>S. pneumoniae</it>, the prevalence of macrolide resistance was high and penicillin resistance low compared with data reported in other regions.</p

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Colistin and anti-Gram-positive bacterial agents against Acinetobacter baumannii

Introduction Acinetobacter baumannii has attained an alarming level of resistance to antibacterial drugs. Clinicians are now considering the use of older agents or unorthodox combinations of licensed drugs against multidrug-resistant strains to bridge the current treatment gap. We investigated the in vitro activities of combination treatments that included colistin with vancomycin, norvancomycin or linezolid against multidrug-resistant Acinetobacter baumannii. Methods The fractional inhibitory concentration index and time-kill assays were used to explore the combined effects of colistin with vancomycin, norvancomycin or linezolid against 40 clinical isolates of multidrug-resistant Acinetobacter baumannii. Transmission electron microscopy was performed to evaluate the interactions in response to the combination of colistin and vancomycin. Results The minimum inhibitory concentrations (MICs) of vancomycin and norvancomycin for half of the isolates decreased below the susceptibility break point, and the MIC of linezolid for one isolate was decreased to the blood and epithelial lining fluid concentration using the current dosing regimen. When vancomycin or norvancomycin was combined with subinhibitory doses of colistin, the multidrug-resistant Acinetobacter baumannii test samples were eradicated. Transmission electron microscopy revealed that subinhibitory doses of colistin were able to disrupt the outer membrane, facilitating a disruption of the cell wall and leading to cell lysis. Conclusions Subinhibitory doses of colistin significantly enhanced the antibacterial activity of vancomycin, norvancomycin, and linezolid against multidrug-resistant Acinetobacter baumannii

Effects of Land Use/Cover Changes and Urban Forest Configuration on Urban Heat Islands in a Loess Hilly Region: Case Study Based on Yan’an City, China

In this study Yan’an City, a typical hilly valley city, was considered as the study area in order to explain the relationships between the surface urban heat island (SUHI) and land use/land cover (LULC) types, the landscape pattern metrics of LULC types and land surface temperature (LST) and remote sensing indexes were retrieved from Landsat data during 1990–2015, and to find factors contributed to the green space cool island intensity (GSCI) through field measurements of 34 green spaces. The results showed that during 1990–2015, because of local anthropogenic activities, SUHI was mainly located in lower vegetation cover areas. There was a significant suburban-urban gradient in the average LST, as well as its heterogeneity and fluctuations. Six landscape metrics comprising the fractal dimension index, percentage of landscape, aggregation index, division index, Shannon’s diversity index, and expansion intensity of the classified LST spatiotemporal changes were paralleled to LULC changes, especially for construction land, during the past 25 years. In the urban area, an index-based built-up index was the key positive factor for explaining LST increases, whereas the normalized difference vegetation index and modified normalized difference water index were crucial factors for explaining LST decreases during the study periods. In terms of the heat mitigation performance of green spaces, mixed forest was better than pure forest, and the urban forest configuration had positive effects on GSCI. The results of this study provide insights into the importance of species choice and the spatial design of green spaces for cooling the environment

Regeneration of Betula albosinensis in strip clearcut and uncut forests of the Qinling Mountains in China.

To contribute to a better understanding of the regeneration strategy of Betula albosinensis forests and the likely reasons behind either the successful recovery or failure after strip clearcutting, we compared the population structures and spatial patterns of B. albosinensis in eight B. albosinensis stands in Qinling Mountains, China. Four cut and four uncut stands were selected, and each sampled using a single large plot (0.25 ha). Results indicated that, on the one hand, B. albosinensis recruitment was scarce (average of 48 stems ha(-1)) in the uncut stands, relative to the mature population (average of 259 stems ha(-1)), suggesting a failure of recruitment. On the other hand, the subsequent regeneration approximately 50 years after the strip clearcutting showed that the density of the target species seedlings and saplings has increased significantly, and the current average density of seedlings and saplings was 156 stems ha(-1). The clumped spatial pattern of B. albosinensis suggested that their regeneration was highly dependent on canopy disturbance. However, recruitment remained poor in the uncut stands because most gaps were small in scale. The successful regeneration of sunlight-loving B. albosinensis after strip clearcutting was attributed to the exposed land and availability of more sunlight. Bamboo density did not influence B. albosinensis recruitment in the uncut stands. However, stand regeneration was impeded after strip clearcutting; thus, removing bamboo is essential in improving the competitive status of B. albosinensis at the later stage of forest regeneration after clearcutting. The moderate severity of disturbance resulting from strip clearcutting reversed the degeneration trend of primary B. albosinensis stands. This outcome can help strike a balance between forest conservation and the demand for wood products by releasing space and exposing the forested land for recruitment. Life history traits and spatiotemporal disturbance magnitude are important factors to consider in implementing effective B. albosinensis regeneration strategies

Identification of Cold-Responsive miRNAs and Their Target Genes in Nitrogen-Fixing Nodules of Soybean

As a warm climate species, soybean is highly sensitive to chilling temperatures. Exposure to chilling temperatures causes a significant reduction in the nitrogen fixation rate in soybean plants and subsequent yield loss. However, the molecular basis for the sensitivity of soybean to chilling is poorly understood. In this study, we identified cold-responsive miRNAs in nitrogen-fixing nodules of soybean. Upon chilling, the expression of gma-miR397a, gma-miR166u and gma-miR171p was greatly upregulated, whereas the expression of gma-miR169c, gma-miR159b, gma-miR319a/b and gma-miR5559 was significantly decreased. The target genes of these miRNAs were predicted and validated using 5' complementary DNA ends (5'-RACE) experiments, and qPCR analysis identified putative genes targeted by the cold-responsive miRNAs in response to chilling temperatures. Taken together, our results reveal that miRNAs may be involved in the protective mechanism against chilling injury in mature nodules of soybean