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141.
Aurélien Saghaï Samiran Banjeree Florine Degrune Anna Edlinger Pablo García-Palacios Gina Garland Marcel G. A. van der Heijden Chantal Herzog Fernando T. Maestre David S. Pescador Laurent Philippot Matthias C. Rillig Sana Romdhane Sara Hallin 《Environmental microbiology》2022,24(1):341-356
Archaeal communities in arable soils are dominated by Nitrososphaeria, a class within Thaumarchaeota comprising all known ammonia-oxidizing archaea (AOA). AOA are key players in the nitrogen cycle and defining their niche specialization can help predicting effects of environmental change on these communities. However, hierarchical effects of environmental filters on AOA and the delineation of niche preferences of nitrososphaerial lineages remain poorly understood. We used phylogenetic information at fine scale and machine learning approaches to identify climatic, edaphic and geomorphological drivers of Nitrososphaeria and other archaea along a 3000 km European gradient. Only limited insights into the ecology of the low-abundant archaeal classes could be inferred, but our analyses underlined the multifactorial nature of niche differentiation within Nitrososphaeria. Mean annual temperature, C:N ratio and pH were the best predictors of their diversity, evenness and distribution. Thresholds in the predictions could be defined for C:N ratio and cation exchange capacity. Furthermore, multiple, independent and recent specializations to soil pH were detected in the Nitrososphaeria phylogeny. The coexistence of widespread ecophysiological differences between closely related soil Nitrososphaeria highlights that their ecology is best studied at fine phylogenetic scale. 相似文献
142.
Jip J. C. Ramakers Phillip Gienapp Marcel E. Visser 《Evolution; international journal of organic evolution》2019,73(2):175-187
Phenotypic plasticity is an important mechanism for populations to respond to fluctuating environments, yet may be insufficient to adapt to a directionally changing environment. To study whether plasticity can evolve under current climate change, we quantified selection and genetic variation in both the elevation (RNE) and slope (RNS) of the breeding time reaction norm in a long‐term (1973–2016) study population of great tits (Parus major). The optimal RNE (the caterpillar biomass peak date regressed against the temperature used as cue by great tits) changed over time, whereas the optimal RNS did not. Concordantly, we found strong directional selection on RNE, but not RNS, of egg‐laying date in the second third of the study period; this selection subsequently waned, potentially due to increased between‐year variability in optimal laying dates. We found individual and additive genetic variation in RNE but, contrary to previous studies on our population, not in RNS. The predicted and observed evolutionary change in RNE was, however, marginal, due to low heritability and the sex limitation of laying date. We conclude that adaptation to climate change can only occur via micro‐evolution of RNE, but this will necessarily be slow and potentially hampered by increased variability in phenotypic optima. 相似文献
143.
Miao Yu Tiago Castanheira Silva Andries van Opstal Stefan Romeijn Hayley A. Every Wim Jiskoot Geert-Jan Witkamp Marcel Ottens 《Biophysical journal》2019,116(4):595-609
In this study, we developed a microfluidics method, using a so-called H-cell microfluidics device, for the determination of protein diffusion coefficients at different concentrations, pHs, ionic strengths, and solvent viscosities. Protein transfer takes place in the H-cell channels between two laminarly flowing streams with each containing a different initial protein concentration. The protein diffusion coefficients are calculated based on the measured protein mass transfer, the channel dimensions, and the contact time between the two streams. The diffusion rates of lysozyme, cytochrome c, myoglobin, ovalbumin, bovine serum albumin, and etanercept were investigated. The accuracy of the presented methodology was demonstrated by comparing the measured diffusion coefficients with literature values measured under similar solvent conditions using other techniques. At low pH and ionic strength, the measured lysozyme diffusion coefficient increased with the protein concentration gradient, suggesting stronger and more frequent intermolecular interactions. At comparable concentration gradients, the measured lysozyme diffusion coefficient decreased drastically as a function of increasing ionic strength (from zero onwards) and increasing medium viscosity. Additionally, a particle tracing numerical simulation was performed to achieve a better understanding of the macromolecular displacement in the H-cell microchannels. It was found that particle transfer between the two channels tends to speed up at low ionic strength and high concentration gradient. This confirms the corresponding experimental observation of protein diffusion measured via the H-cell microfluidics. 相似文献
144.
Jacob C. Douma Jorad de Vries Erik H. Poelman Marcel Dicke Niels P.R. Anten Jochem B. Evers 《Plant, cell & environment》2019,42(3):1065-1077
Plants balance the allocation of resources between growth and defence to optimize fitness in a competitive environment. Perception of neighbour‐detection cues, such as a low ratio of red to far‐red (R:FR) radiation, activates a suite of shade‐avoidance responses that include stem elongation and upward leaf movement, whilst simultaneously downregulating defence. This downregulation is hypothesized to benefit the plant either by mediating the growth‐defence balance in favour of growth in high plant densities or, alternatively, by mediating defence of individual leaves such that those most photosynthetically productive are best protected. To test these hypotheses, we used a 3D functional–structural plant model of Brassica nigra that mechanistically simulates the interactions between plant architecture, herbivory, and the light environment. Our results show that plant‐level defence expression is a strong determinant of plant fitness and that leaf‐level defence mediation by R:FR can provide a fitness benefit in high densities. However, optimal plant‐level defence expression does not decrease monotonically with plant density, indicating that R:FR mediation of defence alone is not enough to optimize defence between densities. Therefore, assessing the ecological significance of R:FR‐mediated defence is paramount to better understand the evolution of this physiological linkage and its implications for crop breeding. 相似文献
145.
Siyu Wang Stephanie M. Reeve Graham T. Holt Adegoke A. Ojewole Marcel S. Frenkel Pablo Gainza Santosh Keshipeddy Vance G. Fowler Dennis L. Wright Bruce R. Donald 《PLoS computational biology》2022,18(2)
Antimicrobial resistance presents a significant health care crisis. The mutation F98Y in Staphylococcus aureus dihydrofolate reductase (SaDHFR) confers resistance to the clinically important antifolate trimethoprim (TMP). Propargyl-linked antifolates (PLAs), next generation DHFR inhibitors, are much more resilient than TMP against this F98Y variant, yet this F98Y substitution still reduces efficacy of these agents. Surprisingly, differences in the enantiomeric configuration at the stereogenic center of PLAs influence the isomeric state of the NADPH cofactor. To understand the molecular basis of F98Y-mediated resistance and how PLAs’ inhibition drives NADPH isomeric states, we used protein design algorithms in the osprey protein design software suite to analyze a comprehensive suite of structural, biophysical, biochemical, and computational data. Here, we present a model showing how F98Y SaDHFR exploits a different anomeric configuration of NADPH to evade certain PLAs’ inhibition, while other PLAs remain unaffected by this resistance mechanism. 相似文献
146.
Abstract An extensive literature survey of the host-range of Agrobacterium -induced neoplasms has revealed that highly susceptible plant families are accumulators of polyphenolics, whereas families assumed to be non-sensitive to the pathogen seem to lack this property. These and other results might indicate that polyphenolics play a role in the host-pathogen relationship of Agrobacterium -induced neoplasms. This hypothesis will be discussed in the light of the present knowledge of crown gall/hairy root induction and progress in plants. 相似文献
147.
Sandra Bouwhuis Arie J. Van Noordwijk Ben C. Sheldon Simon Verhulst Marcel E. Visser 《Journal of avian biology》2010,41(6):615-620
The process of ageing was long thought to be too infrequent to affect life‐histories in natural populations. Long‐term studies have, however, recently demonstrated ageing to be ubiquitous even in the wild, although confounding factors, such as emigration instead of mortality, or inter‐population variation in rates of ageing have seldom been addressed. Here, we present analyses of female age‐specific reproductive performance in a Dutch island population of great tits Parus major. For this population with limited connectivity to surrounding areas, we show that, between individuals, reproductive lifespan positively co‐varies with recruit production, while within individuals performance improves up to 3 years of age, after which it gradually declines. We also show these patterns to be strikingly similar to those recently found in a less isolated British mainland population of great tits, characterised by different environmental conditions and life‐history strategies, in particular the frequency of multiple breeding. Our results therefore suggest patterns of age‐specific reproductive performance to be robust to both environmental and life‐history variation. 相似文献
148.
McManus DC Scott BR Franklin V Sparks DL Marcel YL 《The Journal of biological chemistry》2001,276(24):21292-21302
We have devised a combined in vivo, ex vivo, and in vitro approach to elucidate the mechanism(s) responsible for the hypoalphalipoproteinemia in heterozygous carriers of a naturally occurring apolipoprotein A-I (apoA-I) variant (Leu(159) to Arg) known as apoA-I Finland (apoA-I(FIN)). Adenovirus-mediated expression of apoA-I(FIN) decreased apoA-I and high density lipoprotein cholesterol concentrations in both wild-type C57BL/6J mice and in apoA-I-deficient mice expressing native human apoA-I (hapoA-I). Interestingly, apoA-I(FIN) was degraded in the plasma, and the extent of proteolysis correlated with the most significant reductions in murine apoA-I concentrations. ApoA-I(FIN) had impaired activation of lecithin:cholesterol acyltransferase in vitro compared with hapoA-I, but in a mixed lipoprotein preparation consisting of both hapoA-I and apoA-I(FIN) there was only a moderate reduction in the activation of this enzyme. Importantly, secretion of apoA-I was also decreased from primary apoA-I-deficient hepatocytes when hapoA-I was co-expressed with apoA-I(FIN) following infection with recombinant adenoviruses, a condition that mimics secretion in heterozygotes. Thus, this is the first demonstration of an apoA-I point mutation that decreases LCAT activation, impairs hepatocyte secretion of apoA-I, and makes apoA-I susceptible to proteolysis leading to dominantly inherited hypoalphalipoproteinemia. 相似文献
149.
Bicelle-based liquid crystals for NMR-measurement of dipolar couplings at acidic and basic pH values 总被引:9,自引:0,他引:9
It is demonstrated that mixtures of ditetradecyl- phosphatidylcholine or didodecyl-phoshatidylcholine and dihexyl- phosphatidylcholine in water form lyotropic liquid crystalline phases under similar conditions as previously reported for bicelles consisting of dimyristoyl-phosphatidylcholine (DMPC) and dihexanoyl- phosphatidylcholine (DHPC). The carboxy-ester bonds present in DMPC and DHPC are replaced by ether linkages in their alkyl analogs, which prevents acid- or base-catalyzed hydrolysis of these compounds. 15N-1H dipolar couplings measured for ubiquitin over the 2.3–10.4pH range indicate that this protein retains a backbone conformation which is very similar to its structure at pH 6.5 over this entire range. 相似文献
150.