Roots are the primary site of interaction between plants and microorganisms. To meet food demands in changing climates, improved yields and stress resistance are increasingly important, stimulating ...efforts to identify factors that affect plant productivity. The role of bacterial endophytes that reside inside plants remains largely unexplored, because analysis of their specific functions is impeded by difficulties in cultivating most prokaryotes. Here, we present the first metagenomic approach to analyze an endophytic bacterial community resident inside roots of rice, one of the most important staple foods. Metagenome sequences were obtained from endophyte cells extracted from roots of field-grown plants. Putative functions were deduced from protein domains or similarity analyses of protein-encoding gene fragments, and allowed insights into the capacities of endophyte cells. This allowed us to predict traits and metabolic processes important for the endophytic lifestyle, suggesting that the endorhizosphere is an exclusive microhabitat requiring numerous adaptations. Prominent features included flagella, plant-polymer-degrading enzymes, protein secretion systems, iron acquisition and storage, quorum sensing, and detoxification of reactive oxygen species. Surprisingly, endophytes might be involved in the entire nitrogen cycle, as protein domains involved in N(2)-fixation, denitrification, and nitrification were detected and selected genes expressed. Our data suggest a high potential of the endophyte community for plant-growth promotion, improvement of plant stress resistance, biocontrol against pathogens, and bioremediation, regardless of their culturability.
Significance Influenza A viruses (IAVs) are a cause of major morbidity in the human population. Being RNA viruses, replication is error prone, and proteins such as viral envelope hemagglutinin ...rapidly mutate. Current vaccines stimulate antibodies targeting exposed virion proteins but require annual reformation due to constant sequence variation. In contrast, vaccines that stimulate CD8 T cells directed at conserved peptides from internal proteins would offer stable immunity if these peptides are displayed by HLA proteins on infected cells. Currently, functional readouts infer the IAV peptides displayed. Using new MS technology, epitopes on infected human HLA-A2 ⁺ lung epithelium are identified and abundances characterized. The data show interconnections between viral evasion, immunodominance, and stealth responses that will aid in developing cellular vaccines against influenza.
Vaccines eliciting immunity against influenza A viruses (IAVs) are currently antibody-based with hemagglutinin-directed antibody titer the only universally accepted immune correlate of protection. To investigate the disconnection between observed CD8 T-cell responses and immunity to IAV, we used a Poisson liquid chromatography data-independent acquisition MS method to physically detect PR8/34 (H1N1), X31 (H3N2), and Victoria/75 (H3N2) epitopes bound to HLA-A*02:01 on human epithelial cells following in vitro infection. Among 32 PR8 peptides (8–10mers) with predicted IC ₅₀ < 60 nM, 9 were present, whereas 23 were absent. At 18 h postinfection, epitope copies per cell varied from a low of 0.5 for M1 ₃–₁₁ to a high of >500 for M1 ₅₈–₆₆ with PA, HA, PB1, PB2, and NA epitopes also detected. However, aside from M1 ₅₈–₆₆, natural CD8 memory responses against conserved presented epitopes were either absent or only weakly observed by blood Elispot. Moreover, the functional avidities of the immunodominant M1 ₅₈–₆₆/HLA-A*02:01-specific T cells were so poor as to be unable to effectively recognize infected human epithelium. Analysis of T-cell responses to primary PR8 infection in HLA-A*02:01 transgenic B6 mice underscores the poor avidity of T cells recognizing M1 ₅₈–₆₆. By maintaining high levels of surface expression of this epitope on epithelial and dendritic cells, the virus exploits the combination of immunodominance and functional inadequacy to evade HLA-A*02:01-restricted T-cell immunity. A rational approach to CD8 vaccines must characterize processing and presentation of pathogen-derived epitopes as well as resultant immune responses. Correspondingly, vaccines may be directed against “stealth” epitopes, overriding viral chicanery.
This section summarizes several strategies for a more complete understanding of carbohydrate structure with a focus on glycolipids and glycoprotein glycans. The techniques include periodate oxidation ...to impart greater molecular specificity to isomeric glycans, methylation to improve sensitivity and the information content within CID spectra, electrospray for "soft" and efficient ionization, and CID to obtain structural detail. The lipophilicity of the products following derivatization contributes to product cleanup by solvent extraction and enhances sensitivity during ES. When combined with CID information, this yields sequence, linkage, and branching information. Oxidation and reduction preceding methylation augments CID analysis with an altered structure that can be profiled at the same sensitivity. Within the context of established motifs, these contrasting profiles corroborate glycan structure and specifically identify isobaric elements transparent in the initial profile. An earlier report indicating ring-opening fragments were essentially absent in low-energy collisions of methylated and natriated oligosaccharides contrasts our observations. However, as this report used a methylated oligomer containing an internal N-acetylhexose as an illustration, the conclusion is plausible (cf., Figure 9). The poor ionization efficiency of FAB and the high matrix background limit the dynamic range in the CID spectrum and, thereby, the ability to unambiguously identify weaker peaks. It would be expected that high-energy CID affords a broader range of fragment types, including ring-opening fragments. In terms of a structural methodology, this is ambivalent since the increase in fragmentation pathways also applies to small molecule eliminations which are usually less informative. In ES-CID-MS, the carbohydrate chemist has a powerful new tool in hand for structural elucidations that can be conducted at the low-picomole level. Parallel developments can be expected to continue for other ionization methods, in particular matrix-assisted desorption/ionization on linear and reflectron time of flight mass spectrometers, and improvement in the performance and sensitivity of high-resolution mass analyzers through the use of focal plane detectors and more sophisticated hardware and software for Fourier transform ion cyclotron resonance mass measurements. These have, as yet, only begun to be applied to carbohydrate structural analysis but should add still more versatility to experimental design in the future.
The human CD1b protein presents lipid antigens to T cells, but the molecular mechanism is unknown. Identification of mycobacterial glucose monomycolate (GMM) as a CD1b-presented glycolipid allowed ...determination of the structural requirements for its recognition by T cells. Presentation of GMM to CD1b-restricted T cells was not affected by substantial variations in its lipid tails, but was extremely sensitive to chemical alterations in its carbohydrate or other polar substituents. These findings support the view that the recently demonstrated hydrophobic CD1 groove binds the acyl chains of lipid antigens relatively nonspecifically, thereby positioning the hydrophilic components for highly specific interactions with T cell antigen receptors.
The local efficiency of lamellar shaped Cu(In,Ga)Se
solar cells has been investigated using scanning near-field optical microscopy (SNOM). Topographic and photocurrent measurements have been ...performed simultaneously with a 100 nm tip aperture. The lamellar shaped solar cell with monolithic interconnects (P scribe) has been investigated on a nanometre scale for the first time at different regions using SNOM. It was found that, the cell region between P1 and P2 significantly contributes to the solar cells overall photocurrent generation. The photocurrent produced depends locally on the sample topography and it is concluded that it is mainly due to roughness changes of the ZnO:Al/i-ZnO top electrode. Regions lying under large grains of ZnO produce significantly less current than regions under small granules. The observed photocurrent features were allocated primarily to the ZnO:Al/i-ZnO top electrode. They were found to be independent of the wavelength of the light used (532 nm and 633 nm).
Summary
The local efficiency of lamellar shaped Cu(In,Ga)Se2 solar cells has been investigated using scanning near‐field optical microscopy (SNOM). Topographic and photocurrent measurements have been ...performed simultaneously with a 100 nm tip aperture. The lamellar shaped solar cell with monolithic interconnects (P scribe) has been investigated on a nanometre scale for the first time at different regions using SNOM. It was found that, the cell region between P1 and P2 significantly contributes to the solar cells overall photocurrent generation. The photocurrent produced depends locally on the sample topography and it is concluded that it is mainly due to roughness changes of the ZnO:Al/i‐ZnO top electrode. Regions lying under large grains of ZnO produce significantly less current than regions under small granules. The observed photocurrent features were allocated primarily to the ZnO:Al/i‐ZnO top electrode. They were found to be independent of the wavelength of the light used (532 nm and 633 nm).
Lay description
Copper–indium–gallium–selenide (CIGSe for short) is one of the most interesting materials in solar technology. CIGSe based solar cells are made of thin films of CIGSe deposited on a surface made of glass. The CIGSe film is inserted between two layers of conductive materials, called electrodes, which are used to extract the electricity produced by the cell.
We investigated the behaviour of the photogenerated current in a nanometre scale for the first time in a lamellar shaped CIGSe solar cell with monolithic interconnects. We have measured the topography and the related produced current using a microscope called scanning near‐field optical microscope. This technique implies scanning of a probe, usually a tapered then aluminium‐coated optical fibre, across a surface leading to the illumination of very tiny area lying directly under the probe aperture. The results show that the different scribes contribute to the cell overall photogenerated current. We have also studied the influence of the morphology of the upper (top) electrode on the local performance of CIGSe solar cells. The measurements show that the current produced by the solar device depends locally on the topographic features of the top electrode, made of aluminium–zinc oxide. The performance of the device is significantly weak in the regions that contain large grains, whereas the regions containing smaller particles exhibit better performance. This behaviour was found to be independent of the colour of the light used in this experiment (green and red).
In a previous study the linkage region between chitin and beta (1 arrow right 3)-glucan was solubilized and isolated in the form of oligosaccharides, after digestion of yeast cell walls with beta (1 ...arrow right 3)-glucanase, reduction with borotritide, and subsequent incubation with chitinase. In addition to the oligosaccharides, the solubilized fraction contained tritium-labeled high molecular weight material. We have now investigated the nature of this material and found that it represents areas in which all four structural components of the cell wall, beta (1 arrow right 3)-glucan, beta (1 arrow right 6)-glucan, chitin, and mannoprotein are linked together. Mannoprotein, with a protein moiety about 100 kDa in apparent size, is attached to beta (1 arrow right 6)-glucan through a remnant of a glycosylphosphatidylinositol anchor containing five alpha -linked mannosyl residues. The beta (1 arrow right 6)-glucan has some beta (1 arrow right 3)-linked branches, and it is to these branches that the reducing terminus of chitin chains appears to be attached in a beta (1 arrow right 4) or beta (1 arrow right 2) linkage. Finally, the reducing end of beta (1 arrow right 6)-glucan is connected to the nonreducing terminal glucose of beta (1 arrow right 3)-glucan through a linkage that remains to be established. A fraction of the isolated material has three of the main components but lacks mannoprotein. From these results and previous findings on the linkage between mannoproteins and beta (1 arrow right 6)-glucan, it is concluded that the latter polysaccharide has a central role in the organization of the yeast cell wall. The possible mechanism of synthesis and physiological significance of the cross-links is discussed.
The detailed structure of the symbiotically important exopolysaccharide succinoglycan from Rhizobium meliloti Rm1021 was determined by mass spectrometry with electrospray ionization and ...collision-induced dissociation of the octameric oligosaccharide repeating unit. Previously undetermined locations of the succinyl and acetyl modifications were determined, in respect to both the residue locations within the octamer and the carbon positions within the pyranose ring. Glycosidic linkages determined previously by methylation analysis were also verified
To study the mortality among morbidly obese patients qualifying for bariatric surgery. Mortality from bariatric surgery for morbid obesity has been widely reported; however, little is known about the ...mortality in morbidly obese patients who defer surgery.
Consecutive patients evaluated for bariatric surgery with an initial encounter between 1997 and 2004 were identified. The Social Security Death Index and office records were used to identify mortality through 2006. We conducted telephone interviews to determine whether the 305 patients who did not undergo bariatric surgery at our institution had undergone the surgery elsewhere. Using Cox proportional hazards models, we compared the mortality in patients undergoing surgery with that of those who did not. To evaluate bias resulting from missing data, we conducted analyses assuming that all patients with missing data had (1) undergone surgery and (2) not undergone surgery.
A total of 908 patients underwent bariatric surgery (880 patients at our institution and 28 patients elsewhere). A total of 112 patients did not undergo surgery. Data regarding surgery on 165 patients could not be obtained. The mortality in those patients who did not undergo surgery was 14.3% compared with 2.9% for those who did undergo surgery. Adjusting for age, gender, and body mass index, patients who had undergone surgery had an 82% reduction in mortality (hazard ratio 0.18, 95% confidence interval 0.09-0.35, P <.0001). Sensitivity analysis, assuming that all patients with missing data received surgery resulted in an 85% mortality reduction (P <.001) and assuming that patients did not receive surgery resulted in a 50% mortality reduction (P = .04).
Mortality among morbidly obese patients without surgery was 14.3% during the study period. Surgical intervention offered a 50%-85% mortality reduction benefit.
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