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111.
Reed canary grass (RCG, Phalaris arundinacea L.) is a suitable energy crop for cultivation in northern peatlands. However, the atmospheric impact of RCG cultivation as influenced by harvest frequency and fertilization is not clear. Here, we compared the biomass yield and greenhouse gas (GHG) balance for RCG cultivation in peatlands affected by cutting frequency and fertilizer managements. The managements included one-cut (OC) and two-cut (TC) systems that were either fertilized (TC-F) or unfertilized (TC-U) after the first cut in summer. Biomass yield of OC, TC-F and TC-U were 12, 16 and 11 Mg dry biomass per hectare per year, respectively. GHG fluxes of CO2, N2O and CH4 were measured with closed chamber techniques in the period between first and second (final) harvest of the TC managements, i.e. from 15 June to 23 September 2011. In the GHG monitoring period of 100 days, all systems were net sources of CO2 corresponding to 64?±?3, 217?±?15 and 50?±?23 g?CO2-C?m?2 (mean?±?standard error, n?=?3) from the OC, TC-F and TC-U systems, respectively. In the same period, emissions of N2O from TC-F were ten times higher as compared to OC and TC-U. Emissions of CH4 were negligible from all systems. The TC systems could not improve the GHG balance during cultivation (271, 663 and 210 g CO2e-C?m?2 emissions from the OC, TC-F and TC-U systems, respectively), but in a broader GHG life cycle perspective, the increased biomass yield by TC-F could replace more fossil fuel and offset at least some of the higher emissions from the system. 相似文献
112.
Richard R. Stein Vanni Bucci Nora C. Toussaint Charlie G. Buffie Gunnar R?tsch Eric G. Pamer Chris Sander Jo?o B. Xavier 《PLoS computational biology》2013,9(12)
The intestinal microbiota is a microbial ecosystem of crucial importance to human health. Understanding how the microbiota confers resistance against enteric pathogens and how antibiotics disrupt that resistance is key to the prevention and cure of intestinal infections. We present a novel method to infer microbial community ecology directly from time-resolved metagenomics. This method extends generalized Lotka–Volterra dynamics to account for external perturbations. Data from recent experiments on antibiotic-mediated Clostridium difficile infection is analyzed to quantify microbial interactions, commensal-pathogen interactions, and the effect of the antibiotic on the community. Stability analysis reveals that the microbiota is intrinsically stable, explaining how antibiotic perturbations and C. difficile inoculation can produce catastrophic shifts that persist even after removal of the perturbations. Importantly, the analysis suggests a subnetwork of bacterial groups implicated in protection against C. difficile. Due to its generality, our method can be applied to any high-resolution ecological time-series data to infer community structure and response to external stimuli. 相似文献
113.
Annalisa Nuccitelli C. Daniela Rinaudo Barbara Brogioni Roberta Cozzi Mario Ferrer-Navarro Daniel Yero John L. Telford Guido Grandi Xavier Daura Martin Zacharias Domenico Maione 《PLoS computational biology》2013,9(6)
The pilus 2a backbone protein (BP-2a) is one of the most structurally and functionally characterized components of a potential vaccine formulation against Group B Streptococcus. It is characterized by six main immunologically distinct allelic variants, each inducing variant-specific protection. To investigate the molecular determinants driving the variant immunogenic specificity of BP-2a, in terms of single residue contributions, we generated six monoclonal antibodies against a specific protein variant based on their capability to recognize the polymerized pili structure on the bacterial surface. Three mAbs were also able to induce complement-dependent opsonophagocytosis killing of live GBS and target the same linear epitope present in the structurally defined and immunodominant domain D3 of the protein. Molecular docking between the modelled scFv antibody sequences and the BP-2a crystal structure revealed the potential role at the binding interface of some non-conserved antigen residues. Mutagenesis analysis confirmed the necessity of a perfect balance between charges, size and polarity at the binding interface to obtain specific binding of mAbs to the protein antigen for a neutralizing response. 相似文献
114.
115.
Swati Kaushik Eshita Mutt Ajithavalli Chellappan Sandhya Sankaran Narayanaswamy Srinivasan Ramanathan Sowdhamini 《PloS one》2013,8(2)
Background
Development of sensitive sequence search procedures for the detection of distant relationships between proteins at superfamily/fold level is still a big challenge. The intermediate sequence search approach is the most frequently employed manner of identifying remote homologues effectively. In this study, examination of serine proteases of prolyl oligopeptidase, rhomboid and subtilisin protein families were carried out using plant serine proteases as queries from two genomes including A. thaliana and O. sativa and 13 other families of unrelated folds to identify the distant homologues which could not be obtained using PSI-BLAST.Methodology/Principal Findings
We have proposed to start with multiple queries of classical serine protease members to identify remote homologues in families, using a rigorous approach like Cascade PSI-BLAST. We found that classical sequence based approaches, like PSI-BLAST, showed very low sequence coverage in identifying plant serine proteases. The algorithm was applied on enriched sequence database of homologous domains and we obtained overall average coverage of 88% at family, 77% at superfamily or fold level along with specificity of ∼100% and Mathew’s correlation coefficient of 0.91. Similar approach was also implemented on 13 other protein families representing every structural class in SCOP database. Further investigation with statistical tests, like jackknifing, helped us to better understand the influence of neighbouring protein families.Conclusions/Significance
Our study suggests that employment of multiple queries of a family for the Cascade PSI-BLAST searches is useful for predicting distant relationships effectively even at superfamily level. We have proposed a generalized strategy to cover all the distant members of a particular family using multiple query sequences. Our findings reveal that prior selection of sequences as query and the presence of neighbouring families can be important for covering the search space effectively in minimal computational time. This study also provides an understanding of the ‘bridging’ role of related families. 相似文献116.
Nathanael Lapidus Xavier de Lamballerie Nicolas Salez Michel Setbon Rosemary M. Delabre Pascal Ferrari Nanikaly Moyen Marie-Lise Gougeon Frédéric Vely Marianne Leruez-Ville Laurent Andreoletti Simon Cauchemez Pierre-Yves Bo?lle éric Vivier Laurent Abel Micha?l Schwarzinger Michèle Legeas Pierre Le Cann Antoine Flahault Fabrice Carrat 《PloS one》2013,8(4)
The CoPanFlu-France cohort of households was set up in 2009 to study the risk factors for infection by the pandemic influenza virus (H1N1pdm) in the French general population. The authors developed an integrative data-driven approach to identify individual, collective and environmental factors associated with the post-seasonal serological H1N1pdm geometric mean titer, and derived a nested case-control analysis to identify risk factors for infection during the first season. This analysis included 1377 subjects (601 households). The GMT for the general population was 47.1 (95% confidence interval (CI): 45.1, 49.2). According to a multivariable analysis, pandemic vaccination, seasonal vaccination in 2009, recent history of influenza-like illness, asthma, chronic obstructive pulmonary disease, social contacts at school and use of public transports by the local population were associated with a higher GMT, whereas history of smoking was associated with a lower GMT. Additionally, young age at inclusion and risk perception of exposure to the virus at work were identified as possible risk factors, whereas presence of an air humidifier in the living room was a possible protective factor. These findings will be interpreted in light of the longitudinal analyses of this ongoing cohort. 相似文献
117.
Changes to the nucleolus, the site of ribosome production, have long been linked to cancer, and mutations in several ribosomal proteins (RPs) have been associated with an increased risk for cancer in human diseases. Relevantly, a number of RPs have been shown to bind to MDM2 and inhibit MDM2 E3 ligase activity, leading to p53 stabilization and cell cycle arrest, thus revealing a RP-Mdm2-p53 signaling pathway that is critical for ribosome biogenesis surveillance. Here, we have identified RPL37, RPS15, and RPS20 as RPs that can also bind Mdm2 and activate p53. We found that each of the aforementioned RPs, when ectopically expressed, can stabilize both co-expressed Flag-tagged Mdm2 and HA-tagged p53 in p53-null cells as well as endogenous p53 in a p53-containing cell line. For each RP, the mechanism of Mdm2 and p53 stabilization appears to be through inhibiting the E3 ubiquitin ligase activity of Mdm2. Interestingly, although they are each capable of inducing cell death and cell cycle arrest, these RPs differ in the p53 target genes that are regulated upon their respective introduction into cells. Furthermore, each RP can downregulate MdmX levels but in distinct ways. Thus, RPL37, RPS15 and RPS20 regulate the Mdm2-p53-MdmX network but employ different mechanisms to do so. 相似文献
118.
Xavier Fioramonti Adam Deak Srinidhi Deshpande Lionel Carneiro Chunxue Zhou Nazish Sayed Branly Orban Joshua R. Berlin Luc Pénicaud Corinne Leloup Annie Beuve Vanessa H. Routh 《PloS one》2013,8(7)
Aims
Hypoglycemia is a severe side effect of intensive insulin therapy. Recurrent hypoglycemia (RH) impairs the counter-regulatory response (CRR) which restores euglycemia. During hypoglycemia, ventromedial hypothalamus (VMH) production of nitric oxide (NO) and activation of its receptor soluble guanylyl cyclase (sGC) are critical for the CRR. Hypoglycemia also increases brain reactive oxygen species (ROS) production. NO production in the presence of ROS causes protein S-nitrosylation. S-nitrosylation of sGC impairs its function and induces desensitization to NO. We hypothesized that during hypoglycemia, the interaction between NO and ROS increases VMH sGC S-nitrosylation levels and impairs the CRR to subsequent episodes of hypoglycemia. VMH ROS production and S-nitrosylation were quantified following three consecutive daily episodes of insulin-hypoglycemia (RH model). The CRR was evaluated in rats in response to acute insulin-induced hypoglycemia or via hypoglycemic-hyperinsulinemic clamps. Pretreatment with the anti-oxidant N-acetyl-cysteine (NAC) was used to prevent increased VMH S-nitrosylation.Results
Acute insulin-hypoglycemia increased VMH ROS levels by 49±6.3%. RH increased VMH sGC S-nitrosylation. Increasing VMH S-nitrosylation with intracerebroventricular injection of the nitrosylating agent S-nitroso-L-cysteine (CSNO) was associated with decreased glucagon secretion during hypoglycemic clamp. Finally, in RH rats pre-treated with NAC (0.5% in drinking water for 9 days) hypoglycemia-induced VMH ROS production was prevented and glucagon and epinephrine production was not blunted in response to subsequent insulin-hypoglycemia.Conclusion
These data suggest that NAC may be clinically useful in preventing impaired CRR in patients undergoing intensive-insulin therapy. 相似文献119.
Neal N. Padte Mar Boente-Carrera Chasity D. Andrews Jenny McManus Brooke F. Grasperge Agegnehu Gettie Jordana G. Coelho-dos-Reis Xiangming Li Douglass Wu Joseph T. Bruder Martha Sedegah Noelle Patterson Thomas L. Richie Chi-Huey Wong David D. Ho Sandhya Vasan Moriya Tsuji 《PloS one》2013,8(10)
A key strategy to a successful vaccine against malaria is to identify and develop new adjuvants that can enhance T-cell responses and improve protective immunity. Upon co-administration with a rodent malaria vaccine in mice, 7DW8-5, a recently identified novel analog of α-galactosylceramide (α-GalCer), enhances the level of malaria-specific protective immune responses more strongly than the parent compound. In this study, we sought to determine whether 7DW8-5 could provide a similar potent adjuvant effect on a candidate human malaria vaccine in the more relevant non-human primate (NHP) model, prior to committing to clinical development. The candidate human malaria vaccine, AdPfCA (NMRC-M3V-Ad-PfCA), consists of two non-replicating recombinant adenoviral (Ad) vectors, one expressing the circumsporozoite protein (CSP) and another expressing the apical membrane antigen-1 (AMA1) of Plasmodium falciparum. In several phase 1 clinical trials, AdPfCA was well tolerated and demonstrated immunogenicity for both humoral and cell-mediated responses. In the study described herein, 25 rhesus macaques received prime and boost intramuscular (IM) immunizations of AdPfCA alone or with an ascending dose of 7DW8-5. Our results indicate that 7DW8-5 is safe and well-tolerated and provides a significant enhancement (up to 9-fold) in malaria-specific CD8+ T-cell responses after both priming and boosting phases, supporting further clinical development. 相似文献
120.
Jean-Emmanuel Bibault Sylvain Dewas Claire Vautravers-Dewas Antoine Hollebecque Hajer Jarraya Thomas Lacornerie Eric Lartigau Xavier Mirabel 《PloS one》2013,8(10)