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961.
Sabrina Backhaus Juergen Kreyling Kerstin Grant Carl Beierkuhnlein Julia Walter Anke Jentsch 《Ecosystems》2014,17(6):1068-1081
The frequency and magnitude of extreme weather events such as drought are expected to increase in the future. At present, plant responses to recurrent extreme events have been sparsely examined and the role of stress history on subsequent stress response has been widely neglected. In a long-term field experiment, we investigated the response of grassland and heath communities to a very severe drought event, which exceeded the duration of projected drought scenarios. During the preceding 6 years, the plant communities experienced scenarios of varying water supply, including annually recurring drought, heavy rain, regular watering, and natural drought periods. Single species and plant communities that were regularly watered in the preceding years revealed the highest tissue die-back under a very severe drought when compared to plants that experienced mild or severe drought stress before. Contrary to expectations, the root to shoot ratio did not increase due to previous recurrent drought occurrences. Furthermore, pre-exposure effects on Vaccinium myrtillus and Plantago lanceolata tissue die-back and reproductive biomass (P. lanceolata) were altered by community composition. Recurrent mild drought stress seems to improve drought resistance of plant communities and species. Potential reasons could be epigenetic changes or soil biotic legacies. Morphological legacies such as altered root to shoot ratio did not play a role in our study. Imprinting events which trigger this ecological stress memory do not have to be extreme themselves. Thresholds, longevity of effects, and the role of biodiversity shown by the importance of community composition require further attention. 相似文献
962.
Non‐native acylated homoserine lactones reveal that LuxIR quorum sensing promotes symbiont stability
Jessica S. Ho Grant D. Geske Helen E. Blackwell Edward G. Ruby 《Environmental microbiology》2014,16(8):2623-2634
Quorum sensing, a group behaviour coordinated by a diffusible pheromone signal and a cognate receptor, is typical of bacteria that form symbioses with plants and animals. LuxIR‐type N‐acyl L‐homoserine (AHL) quorum sensing is common in Gram‐negative Proteobacteria, and many members of this group have additional quorum‐sensing networks. The bioluminescent symbiont Vibrio fischeri encodes two AHL signal synthases: AinS and LuxI. AinS‐dependent quorum sensing converges with LuxI‐dependent quorum sensing at the LuxR regulatory element. Both AinS‐ and LuxI‐mediated signalling are required for efficient and persistent colonization of the squid host, Euprymna scolopes. The basis of the mutualism is symbiont bioluminescence, which is regulated by both LuxI‐ and AinS‐dependent quorum sensing, and is essential for maintaining a colonization of the host. Here, we used chemical and genetic approaches to probe the dynamics of LuxI‐ and AinS‐mediated regulation of bioluminescence during symbiosis. We demonstrate that both native AHLs and non‐native AHL analogues can be used to non‐invasively and specifically modulate induction of symbiotic bioluminescence via LuxI‐dependent quorum sensing. Our data suggest that the first day of colonization, during which symbiont bioluminescence is induced by LuxIR, is a critical period that determines the stability of the V. fischeri population once symbiosis is established. 相似文献
963.
Christian B Matranga Kristian G Andersen Sarah Winnicki Michele Busby Adrianne D Gladden Ryan Tewhey Matthew Stremlau Aaron Berlin Stephen K Gire Eleina England Lina M Moses Tarjei S Mikkelsen Ikponmwonsa Odia Philomena E Ehiane Onikepe Folarin Augustine Goba S Humarr Kahn Donald S Grant Anna Honko Lisa Hensley Christian Happi Robert F Garry Christine M Malboeuf Bruce W Birren Andreas Gnirke Joshua Z Levin Pardis C Sabeti 《Genome biology》2014,15(11)
We have developed a robust RNA sequencing method for generating complete de novo assemblies with intra-host variant calls of Lassa and Ebola virus genomes in clinical and biological samples. Our method uses targeted RNase H-based digestion to remove contaminating poly(rA) carrier and ribosomal RNA. This depletion step improves both the quality of data and quantity of informative reads in unbiased total RNA sequencing libraries. We have also developed a hybrid-selection protocol to further enrich the viral content of sequencing libraries. These protocols have enabled rapid deep sequencing of both Lassa and Ebola virus and are broadly applicable to other viral genomics studies.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-014-0519-7) contains supplementary material, which is available to authorized users. 相似文献964.
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Li Ping Chung Svetlana Baltic Manuel Ferreira Suzanna Temple Grant Waterer Philip J. Thompson 《PloS one》2014,9(4)
Background
β2 adrenergic receptor (ADRβ2) polymorphisms including ADRβ2+46G>A have been reported to cause adverse outcomes in mild asthmatics. The extent to which ADRβ2 polymorphisms and in particular their haplotypes contribute to severe asthma is unknown.Objective
To determine the association of ADRβ2 polymorphisms and haplotypes with asthma severity.Methods
Caucasians (n = 2979) were genotyped for 11 ADRβ2 polymorphisms. The cohort (mean age 39.6, 60% female) included 2296 non-asthmatics, 386 mild asthmatics, 172 moderate asthmatics and 125 severe asthmatics. Haplotype frequency and haplotype pair for each subject was determined using the PHASE algorithm.Results
The three asthmatic cohorts were comparable in age and gender but were distinguishable from each other in terms of symptoms, spirometry, medication use and health care utilisation (p <0.001). None of the polymorphisms showed a genotypic or allelic association with asthma diagnosis or severity. Nine haplotypes were identified and no association was found with asthma diagnosis or severity per se. Haplotype pair 2/4 was associated with asthma severity (Trend Test, OR 1.42, p = 0.0008) but not with asthma per se. Prevalence of haplotype pair 2/2 appeared to decrease with asthma severity (Trend Test, OR 0.78, p = 0.067). Two new haplotypes were identified, occurring exclusively in asthmatics at a frequency of ≥ 1%. In addition, a positive association between carriage of ADRβ2 +523*C and increased risk of atopy was discovered.Conclusions
ADRβ2 haplotype pair 2/4 is associated with severe asthma and is consistent with findings of poor bronchodilator response in mild asthmatics who are also haplotype 2/4. 相似文献969.
Jason Li Maria A. Doyle Isaam Saeed Stephen Q. Wong Victoria Mar David L. Goode Franco Caramia Ken Doig Georgina L. Ryland Ella R. Thompson Sally M. Hunter Saman K. Halgamuge Jason Ellul Alexander Dobrovic Ian G. Campbell Anthony T. Papenfuss Grant A. McArthur Richard W. Tothill 《PloS one》2014,9(4)
Targeted resequencing by massively parallel sequencing has become an effective and affordable way to survey small to large portions of the genome for genetic variation. Despite the rapid development in open source software for analysis of such data, the practical implementation of these tools through construction of sequencing analysis pipelines still remains a challenging and laborious activity, and a major hurdle for many small research and clinical laboratories. We developed TREVA (Targeted REsequencing Virtual Appliance), making pre-built pipelines immediately available as a virtual appliance. Based on virtual machine technologies, TREVA is a solution for rapid and efficient deployment of complex bioinformatics pipelines to laboratories of all sizes, enabling reproducible results. The analyses that are supported in TREVA include: somatic and germline single-nucleotide and insertion/deletion variant calling, copy number analysis, and cohort-based analyses such as pathway and significantly mutated genes analyses. TREVA is flexible and easy to use, and can be customised by Linux-based extensions if required. TREVA can also be deployed on the cloud (cloud computing), enabling instant access without investment overheads for additional hardware. TREVA is available at http://bioinformatics.petermac.org/treva/. 相似文献
970.
Jing Zhang Lisa Carnduff Grant Norman Tyson Josey Yushan Wang Thomas W. Sawyer Christopher J. Martyniuk Valerie S. Langlois 《PloS one》2014,9(8)
With wide adoption of explosive-dependent weaponry during military activities, Blast-induced neurotrauma (BINT)-induced traumatic brain injury (TBI) has become a significant medical issue. Therefore, a robust and accessible biomarker system is in demand for effective and efficient TBI diagnosis. Such systems will also be beneficial to studies of TBI pathology. Here we propose the mammalian hair follicles as a potential candidate. An Advanced Blast Simulator (ABS) was developed to generate shock waves simulating traumatic conditions on brains of rat model. Microarray analysis was performed in hair follicles to identify the gene expression profiles that are associated with shock waves. Gene set enrichment analysis (GSEA) and sub-network enrichment analysis (SNEA) were used to identify cell processes and molecular signaling cascades affected by simulated bomb blasts. Enrichment analyses indicated that genes with altered expression levels were involved in central nervous system (CNS)/peripheral nervous system (PNS) responses as well as signal transduction including Ca2+, K+-transportation-dependent signaling, Toll-Like Receptor (TLR) signaling and Mitogen Activated Protein Kinase (MAPK) signaling cascades. Many of the pathways identified as affected by shock waves in the hair follicles have been previously reported to be TBI responsive in other organs such as brain and blood. The results suggest that the hair follicle has some common TBI responsive molecular signatures to other tissues. Moreover, various TBI-associated diseases were identified as preferentially affected using a gene network approach, indicating that the hair follicle may be capable of reflecting comprehensive responses to TBI conditions. Accordingly, the present study demonstrates that the hair follicle is a potentially viable system for rapid and non-invasive TBI diagnosis. 相似文献