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51.
Loman NJ Misra RV Dallman TJ Constantinidou C Gharbia SE Wain J Pallen MJ 《Nature biotechnology》2012,30(5):434-439
Three benchtop high-throughput sequencing instruments are now available. The 454 GS Junior (Roche), MiSeq (Illumina) and Ion Torrent PGM (Life Technologies) are laser-printer sized and offer modest set-up and running costs. Each instrument can generate data required for a draft bacterial genome sequence in days, making them attractive for identifying and characterizing pathogens in the clinical setting. We compared the performance of these instruments by sequencing an isolate of Escherichia coli O104:H4, which caused an outbreak of food poisoning in Germany in 2011. The MiSeq had the highest throughput per run (1.6 Gb/run, 60 Mb/h) and lowest error rates. The 454 GS Junior generated the longest reads (up to 600 bases) and most contiguous assemblies but had the lowest throughput (70 Mb/run, 9 Mb/h). Run in 100-bp mode, the Ion Torrent PGM had the highest throughput (80–100 Mb/h). Unlike the MiSeq, the Ion Torrent PGM and 454 GS Junior both produced homopolymer-associated indel errors (1.5 and 0.38 errors per 100 bases, respectively). 相似文献
52.
Microevolution and maternal effects on tadpole Rana temporaria growth and development rate 总被引:2,自引:0,他引:2
Jon Loman 《Journal of Zoology》2002,257(1):93-99
53.
54.
Jon Loman 《Biodiversity and Conservation》2003,12(7):1467-1479
Great tit breeding performance in small habitat islands in an agricultural landscape was compared to that in large deciduous woods. Clutch size was similar in both habitats, but more nestlings starved and fledgling weight was lower in the small habitat islands. The area of wooded habitat in the territories of tits breeding in the small habitat islands was less than what is common to encounter in optimum habitat, deciduous woods. I suggest that this may be responsible, ultimately or proximately, for the poor performance in the small habitat islands. Two possible mechanisms for this effect are discussed. It is possible that the small habitat islands were perceived as inferior by the tits and used by competitively inferior individuals that also were less successful in raising a brood. However, the results were obtained even when female age and weight were controlled for. Therefore, the competitive ability (and probably also young raising competence) may be the same for tits breeding in small habitat islands as for those breeding in optimum habitat. Such a pattern is conceivable if tits have been selected for maintaining a large territory as a response to the close presence of other tits and not as a means of securing a large feeding area. Historically, territories large enough to reduce predation or mate competition (or any cause of territoriality) may always have contained ample food. The presence of small islands, without close neighbours but with insufficient food, may be evolutionarily new. It is probably typical of modern agricultural landscape. 相似文献
55.
Maja Radulovic Eva Maria Wenzel Sania Gilani Lya KK Holland Alf Hkon Lystad Santosh Phuyal Vesa M Olkkonen Andreas Brech Marja Jttel Kenji Maeda Camilla Raiborg Harald Stenmark 《The EMBO journal》2022,41(24)
Lysosome integrity is essential for cell viability, and lesions in lysosome membranes are repaired by the ESCRT machinery. Here, we describe an additional mechanism for lysosome repair that is activated independently of ESCRT recruitment. Lipidomic analyses showed increases in lysosomal phosphatidylserine and cholesterol after damage. Electron microscopy demonstrated that lysosomal membrane damage is rapidly followed by the formation of contacts with the endoplasmic reticulum (ER), which depends on the ER proteins VAPA/B. The cholesterol‐binding protein ORP1L was recruited to damaged lysosomes, accompanied by cholesterol accumulation by a mechanism that required VAP–ORP1L interactions. The PtdIns 4‐kinase PI4K2A rapidly produced PtdIns4P on lysosomes upon damage, and knockout of PI4K2A inhibited damage‐induced accumulation of ORP1L and cholesterol and led to the failure of lysosomal membrane repair. The cholesterol–PtdIns4P transporter OSBP was also recruited upon damage, and its depletion caused lysosomal accumulation of PtdIns4P and resulted in cell death. We conclude that ER contacts are activated on damaged lysosomes in parallel to ESCRTs to provide lipids for membrane repair, and that PtdIns4P generation and removal are central in this response. 相似文献
56.
RC Pritchett AM Al-Nawaiseh KK Pritchett V Nethery PA Bishop JM Green 《Biology of sport / Institute of Sport》2015,32(3):249-254
Sweat production is crucial for thermoregulation. However, sweating can be problematic for individuals with spinal cord injuries (SCI), as they display a blunting of sudomotor and vasomotor responses below the level of the injury. Sweat gland density and eccrine gland metabolism in SCI are not well understood. Consequently, this study examined sweat lactate (S-LA) (reflective of sweat gland metabolism), active sweat gland density (SGD), and sweat output per gland (S/G) in 7 SCI athletes and 8 able-bodied (AB) controls matched for arm ergometry VO2peak. A sweat collection device was positioned on the upper scapular and medial calf of each subject just prior to the beginning of the trial, with iodine sweat gland density patches positioned on the upper scapular and medial calf. Participants were tested on a ramp protocol (7 min per stage, 20 W increase per stage) in a common exercise environment (21±1°C, 45-65% relative humidity). An independent t-test revealed lower (p<0.05) SGD (upper scapular) for SCI (22.3 ±14.8 glands · cm−2) vs. AB. (41.0 ± 8.1 glands · cm−2). However, there was no significant difference for S/G between groups. S-LA was significantly greater (p<0.05) during the second exercise stage for SCI (11.5±10.9 mmol · l−1) vs. AB (26.8±11.07 mmol · l−1). These findings suggest that SCI athletes had less active sweat glands compared to the AB group, but the sweat response was similar (SLA, S/G) between AB and SCI athletes. The results suggest similar interglandular metabolic activity irrespective of overall sweat rate. 相似文献
57.
Matthew D. Johnson James Bell Kim Clarke Rachel Chandler Prachi Pathak Yandong Xia Robert L. Marshall George M. Weinstock Nicholas J. Loman Peter J. Winn Peter A. Lund 《Molecular microbiology》2014,93(5):911-927
Laboratory‐based evolution and whole‐genome sequencing can link genotype and phenotype. We used evolution of acid resistance in exponential phase Escherichia coli to study resistance to a lethal stress. Iterative selection at pH 2.5 generated five populations that were resistant to low pH in early exponential phase. Genome sequencing revealed multiple mutations, but the only gene mutated in all strains was evgS, part of a two‐component system that has already been implicated in acid resistance. All these mutations were in the cytoplasmic PAS domain of EvgS, and were shown to be solely responsible for the resistant phenotype, causing strong upregulation at neutral pH of genes normally induced by low pH. Resistance to pH 2.5 in these strains did not require the transporter GadC, or the sigma factor RpoS. We found that EvgS‐dependent constitutive acid resistance to pH 2.5 was retained in the absence of the regulators GadE or YdeO, but was lost if the oxidoreductase YdeP was also absent. A deletion in the periplasmic domain of EvgS abolished the response to low pH, but not the activity of the constitutive mutants. On the basis of these results we propose a model for how EvgS may become activated by low pH. 相似文献
58.
M V Lafleur M van Heuvel J Woldhuis H Loman 《International journal of radiation biology and related studies in physics, chemistry, and medicine》1978,33(3):273-281
Single-stranded phiX174 DNA in aqueous solutions has been irradiated in the absence of oxygen, under conditions in which only H radicals react with the DNA. It was shown that H radical reactions result in breaks, which contribute approximately 10 per cent inactivation. Further, two types of alkali-labile sites are formed. One is lethal and gives rise to single-strand breaks by alkali and is most probably identical with post-irradiation heat damage and contributes about 33 per cent to the inactivation mentioned above. The other consists of non-lethal damage, partly dihydropyrimidine derivatives, and is converted to lethal damage by alkali. This follows from experiments in which the DNA was treated with osmium-tetroxide, which oxidizes thymine to 5,6-dihydroxy-dihydrothymine. Treatment with alkali of this DNA gives the same temperature dependence as found for the non-lethal alkali-labile sites in irradiated DNA. A similar temperature dependence is found for dihydrothymine and irradiated pyrimidines with alkali. 相似文献
59.
The tricorn protease is an archaeal protease that forms massive proteasome-like capsids with a hollow chamber. beta-Propeller and PDZ domains are thought to play a role in substrate selection. By analysis of predicted proteins from novel bacterial genome sequences, we have identified four new bacterial tricorn-like proteases, complete with similar beta-propeller, PDZ and catalytic domains. We propose various hypotheses as to the function of these domains that can now be tested in the laboratory. 相似文献
60.
Lotte Heimans Kirsten VC Wevers-de Boer KK Michel Koudijs Karen Visser Yvonne P Goekoop-Ruiterman Joop B Harbers Gerda M Steup-Beekman Leroy R Lard Bernard AM Grillet Tom WJ Huizinga Cornelia F Allaart 《Arthritis research & therapy》2013,15(5):R173