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101.
Eli K. Moore Laura Villanueva Ellen C. Hopmans W. Irene C. Rijpstra Anchelique Mets Svetlana N. Dedysh Jaap S. Sinninghe Damsté 《Applied and environmental microbiology》2015,81(18):6333-6344
Northern wetlands make up a substantial terrestrial carbon sink and are often dominated by decay-resistant Sphagnum mosses. Recent studies have shown that planctomycetes appear to be involved in degradation of Sphagnum-derived debris. Novel trimethylornithine (TMO) lipids have recently been characterized as abundant lipids in various Sphagnum wetland planctomycete isolates, but their occurrence in the environment has not yet been confirmed. We applied a combined intact polar lipid (IPL) and molecular analysis of peat cores collected from two northern wetlands (Saxnäs Mosse [Sweden] and Obukhovskoye [Russia]) in order to investigate the preferred niche and abundance of TMO-producing planctomycetes. TMOs were present throughout the profiles of Sphagnum bogs, but their concentration peaked at the oxic/anoxic interface, which coincided with a maximum abundance of planctomycete-specific 16S rRNA gene sequences. The sequences detected at the oxic/anoxic interface were affiliated with the Isosphaera group, while sequences present in the anoxic peat layers were related to an uncultured planctomycete group. Pyrosequencing-based analysis identified Planctomycetes as the major bacterial group at the oxic/anoxic interface at the Obukhovskoye peat (54% of total 16S rRNA gene sequence reads), followed by Acidobacteria (19% reads), while in the Saxnäs Mosse peat, Acidobacteria were dominant (46%), and Planctomycetes contributed to 6% of the total reads. The detection of abundant TMO lipids in planctomycetes isolated from peat bogs and the lack of TMO production by cultures of acidobacteria suggest that planctomycetes are the producers of TMOs in peat bogs. The higher accumulation of TMOs at the oxic/anoxic interface and the change in the planctomycete community with depth suggest that these IPLs could be synthesized as a response to changing redox conditions at the oxic/anoxic interface. 相似文献
102.
John R. Gill Payne S. Burks Scott A. Staggenborg Gary N. Odvody Ron W. Heiniger Bisoondat Macoon Ken J. Moore Michael Barrett William L. Rooney 《Bioenergy Research》2014,7(3):1026-1034
Sorghum [Sorghum bicolor (L.) Moench] is one of four herbaceous dedicated bioenergy crops the U.S. Department of Energy identified as critical to annually produce one billion tons of dry biomass. Of these four crops, sorghum is unique as it is a drought-tolerant, annual crop established from seed that is readily tractable to genetic improvement. The purpose of this study was to assess the yield potential and stability of sorghums grown across diverse production environments in the USA. For this study, six sorghum genotypes (one cultivar, five hybrids) were grown in yield trials in seven locations in six states for 5 years (2008–2012). Variation in dry and fresh yield was attributable to not only genotypes, but also to the effects of year, location, and year × location. Even with the highest yielding genotype, environmental conditions were a major factor in determining the yield in a given year. This variability affects the consistency of the biomass supply for ethanol production. In general, the southeastern USA had the highest mean yields for fresh weight and dry weight, indicating that this area may be the most reliable for biomass production. A significant variation was detected among genotypes for fresh weight, dry weight, moisture content, and brix, revealing that sufficient variation within sorghum exists for continued improvement and that certain hybrids are more tractable for biomass/bioenergy production. With dedicated bioenergy sorghum germplasm and proper production environments, sorghum will be a valuable tool in the goal of the sustainable production of one billion tons of dry biomass each year in the USA. 相似文献
103.
104.
Szymon P. Szafranski Melissa L. Wos-Oxley Ramiro Vilchez-Vargas Ruy Jáuregui Iris Plumeier Frank Klawonn Jürgen Tomasch Christa Meisinger Jan Kühnisch Helena Sztajer Dietmar H. Pieper Irene Wagner-D?bler 《Applied and environmental microbiology》2015,81(3):1047-1058
The oral microbiome plays a key role for caries, periodontitis, and systemic diseases. A method for rapid, high-resolution, robust taxonomic profiling of subgingival bacterial communities for early detection of periodontitis biomarkers would therefore be a useful tool for individualized medicine. Here, we used Illumina sequencing of the V1-V2 and V5-V6 hypervariable regions of the 16S rRNA gene. A sample stratification pipeline was developed in a pilot study of 19 individuals, 9 of whom had been diagnosed with chronic periodontitis. Five hundred twenty-three operational taxonomic units (OTUs) were obtained from the V1-V2 region and 432 from the V5-V6 region. Key periodontal pathogens like Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia could be identified at the species level with both primer sets. Principal coordinate analysis identified two outliers that were consistently independent of the hypervariable region and method of DNA extraction used. The linear discriminant analysis (LDA) effect size algorithm (LEfSe) identified 80 OTU-level biomarkers of periodontitis and 17 of health. Health- and periodontitis-related clusters of OTUs were identified using a connectivity analysis, and the results confirmed previous studies with several thousands of samples. A machine learning algorithm was developed which was trained on all but one sample and then predicted the diagnosis of the left-out sample (jackknife method). Using a combination of the 10 best biomarkers, 15 of 17 samples were correctly diagnosed. Training the algorithm on time-resolved community profiles might provide a highly sensitive tool to detect the onset of periodontitis. 相似文献
105.
The uptake of bacteria and picoplankton sized fluorescentlylabelled beads was measured off the west coast of the SouthIsland of New Zealand in winter. Phytoflagellates and heterotrophicflagellates showed similar grazing rates on 0.49 µm beads,with mean clearance rates of 1.1 and 1.8 nl ind.1 h1,respectively. Clearance rates for 1.09 µm beads were 0.9nl ind.1 h1 for heterotrophic flagellates and0.5 nl ind.1 h1 for phytoflagellates. Non-loricateciliates had clearance rates of 1.5 µl ind.1 h1for the picoplankton sized particles. The heterotrophic flagellatesshowed no significant difference between clearance rates of0.49 and 1.09 µm particles. Phytoflagellates, however,showed an apparent preference for the smaller particles. Themeasurement of significant grazing by phytoflagellate populationsin the marine environment is important and indicates that weneed to reassess our concepts of food web structure. 相似文献
106.
Melinda L. Moir Peter A. Vesk Karl E. C. Brennan Lesley Hughes David A. Keith Michael A. McCarthy David J. Coates Sarah Barrett 《Journal of Insect Conservation》2012,16(3):367-377
Translocation of threatened species is a tool used increasingly to conserve biodiversity, but the suite of co-dependent species that use the threatened taxa as hosts can be overlooked. We investigate the preliminary impact of translocating three threatened plant species on insect species and the integrity of insect assemblages that depend on these plants as their hosts. We compare the insect assemblages between natural populations of the threatened species, related non-threatened plant species growing wild near the threatened plants, and threatened plants translocated to another site approximately 40?km away. We used host breadth models and a coextinction risk protocol to determine which insect species are potentially host-specific on the threatened plants, and then assessed these insects?? potential presence at the translocation site. We found that insect assemblages on naturally-occurring threatened plants had more individuals, higher species density and higher species richness than assemblages on translocated plants. For one plant species, Leucopogon gnaphalioides, species composition differed significantly between wild and translocated populations (P?<?0.001). Furthermore, four insect species that were host-specific to Banksia brownii and B. montana were not detected on the translocated plants. Instead, translocated plants supported insect assemblages more similar to those of related plant species from the surrounding area. We conclude that threatened plant translocations that involve seed collection and propagation may have limited benefit for individual dependent species or the supported insect assemblage. Additional conservation actions will be required to maintain the diversity of insect assemblages and host-dependent relationships. 相似文献
107.
Fu G Chumanevich AA Agniswamy J Fang B Harrison RW Weber IT 《Apoptosis : an international journal on programmed cell death》2008,13(11):1291-1302
Caspase-3, -6 and -7 cleave many proteins at specific sites to induce apoptosis. Their recognition of the P5 position in substrates
has been investigated by kinetics, modeling and crystallography. Caspase-3 and -6 recognize P5 in pentapeptides as shown by
enzyme activity data and interactions observed in the crystal structure of caspase-3/LDESD and in a model for caspase-6. In
caspase-3 the P5 main-chain was anchored by interactions with Ser209 in loop-3 and the P5 Leu side-chain interacted with Phe250
and Phe252 in loop-4 consistent with 50% increased hydrolysis of LDEVD relative to DEVD. Caspase-6 formed similar interactions
and showed a preference for polar P5 in QDEVD likely due to interactions with polar Lys265 and hydrophobic Phe263 in loop-4.
Caspase-7 exhibited no preference for P5 residue in agreement with the absence of P5 interactions in the caspase-7/LDESD crystal
structure. Initiator caspase-8, with Pro in the P5-anchoring position and no loop-4, had only 20% activity on tested pentapeptides
relative to DEVD. Therefore, caspases-3 and -6 bind P5 using critical loop-3 anchoring Ser/Thr and loop-4 side-chain interactions,
while caspase-7 and -8 lack P5-binding residues. 相似文献
108.
Jin P Zhang J Sumariwalla PF Ni I Jorgensen B Crawford D Phillips S Feldmann M Shepard HM Paleolog EM 《Arthritis research & therapy》2008,10(4):R73
Introduction
Despite the advent of biological therapies for the treatment of rheumatoid arthritis, there is a compelling need to develop alternative therapeutic targets for nonresponders to existing treatments. Soluble receptors occur naturally in vivo, such as the splice variant of the cell surface receptor for vascular endothelial growth factor (VEGF) – a key regulator of angiogenesis in rheumatoid arthritis. Bioinformatics analyses predict that the majority of human genes undergo alternative splicing, generating proteins – many of which may have regulatory functions. The objective of the present study was to identify alternative splice variants (ASV) from cell surface receptor genes, and to determine whether the novel proteins encoded exert therapeutic activity in an in vivo model of arthritis. 相似文献109.
Modulation of chloride secretory responses and barrier function of intestinal epithelial cells by the Salmonella effector protein SigD 总被引:2,自引:0,他引:2
Bertelsen LS Paesold G Marcus SL Finlay BB Eckmann L Barrett KE 《American journal of physiology. Cell physiology》2004,287(4):C939-C948
The Salmonella effector protein SigD is an inositol phosphate phosphatase that inhibits phosphatidylinositol 3-kinase-dependent signaling. Because epidermal growth factor (EGF) inhibits chloride secretion via phosphatidylinositol 3-kinase, we explored whether Salmonella infection might modify the inhibitory effect of EGF. As expected, EGF inhibited chloride secretion induced by carbachol in T84 epithelial cells. Infection with wild-type (WT) but not sigD mutant S. typhimurium SL1344 decreased CCh-stimulated chloride secretion. Moreover, WT but not sigD Salmonella reduced the inhibitory effect of EGF on carbachol-stimulated chloride secretion. Complementation of sigD restored the ability of mutant Salmonella to reverse the inhibitory effect of EGF. EGF-induced EGF receptor phosphorylation was similar in cells infected with either WT or mutant Salmonella, and neither WT nor sigD Salmonella altered recruitment of the p85 subunit of phosphatidylinositol 3-kinase to EGF receptor, implying that SigD acts downstream of these signaling events. Furthermore, transepithelial resistance fell more rapidly in cells infected with WT vs. sigD Salmonella, indicating an early role for SigD in reducing barrier function, perhaps via activation of protein kinase C. We conclude that the Salmonella bacterial effector protein SigD may play critical roles in the pathogenesis of disease caused by this microorganism. chloride secretion; Salmonella typhimurium; epidermal growth factor 相似文献
110.
Taneja P Boche I Hartmann H Nasheuer HP Grosse F Fanning E Weisshart K 《FEBS letters》2007,581(21):3973-3978
Replication protein A (RPA) is a stable heterotrimeric complex consisting of p70, p32 and p14 subunits. The protein plays a crucial role in SV40 minichromosome replication. Peptides of p70 representing interaction sites for the smaller two subunits, DNA as well as the viral initiator protein large T-antigen (Tag) and the cellular DNA polymerase alpha-primase (Pol) all interfered with the replication process indicating the importance of the different p70 activities in this process. Inhibition by the peptide disrupting protein-protein interactions was observed only during the pre-initiation stage prior to primer synthesis, suggesting the formation of a stable initiation complex between RPA, Tag and Pol at the primer end. 相似文献