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1.
Joran Martijn Anders E. Lind Max E. Schön Ian Spiertz Lina Juzokaite Ignas Bunikis Olga V. Pettersson Thijs J. G. Ettema 《Environmental microbiology》2019,21(7):2485-2498
Amplicon sequencing of the 16S rRNA gene is the predominant method to quantify microbial compositions and to discover novel lineages. However, traditional short amplicons often do not contain enough information to confidently resolve their phylogeny. Here we present a cost-effective protocol that amplifies a large part of the rRNA operon and sequences the amplicons with PacBio technology. We tested our method on a mock community and developed a read-curation pipeline that reduces the overall read error rate to 0.18%. Applying our method on four environmental samples, we captured near full-length rRNA operon amplicons from a large diversity of prokaryotes. The method operated at moderately high-throughput (22286–37,850 raw ccs reads) and generated a large amount of putative novel archaeal 23S rRNA gene sequences compared to the archaeal SILVA database. These long amplicons allowed for higher resolution during taxonomic classification by means of long (∼1000 bp) 16S rRNA gene fragments and for substantially more confident phylogenies by means of combined near full-length 16S and 23S rRNA gene sequences, compared to shorter traditional amplicons (250 bp of the 16S rRNA gene). We recommend our method to those who wish to cost-effectively and confidently estimate the phylogenetic diversity of prokaryotes in environmental samples at high throughput. 相似文献
2.
Dorina Ibi Manon Boot Martijn E.T. Dollé J. Wouter Jukema Frits R. Rosendaal Constantinos Christodoulides Matt J. Neville Robert Koivula Patrick C.N. Rensen Fredrik Karpe Raymond Noordam Ko Willems van Dijk 《Journal of lipid research》2022,63(5):100193
Triglyceride (TG)-lowering LPL variants in combination with genetic LDL-C-lowering variants are associated with reduced risk of coronary artery disease (CAD). Genetic variation in the APOA5 gene encoding apolipoprotein A-V also strongly affects TG levels, but the potential clinical impact and underlying mechanisms are yet to be resolved. Here, we aimed to study the effects of APOA5 genetic variation on CAD risk and plasma lipoproteins through factorial genetic association analyses. Using data from 309,780 European-ancestry participants from the UK Biobank, we evaluated the effects of lower TG levels as a result of genetic variation in APOA5 and/or LPL on CAD risk with or without a background of reduced LDL-C. Next, we compared lower TG levels via APOA5 and LPL variation with over 100 lipoprotein measurements in a combined sample from the Netherlands Epidemiology of Obesity study (N = 4,838) and the Oxford Biobank (N = 6,999). We found that lower TG levels due to combined APOA5 and LPL variation and genetically-influenced lower LDL-C levels afforded the largest reduction in CAD risk (odds ratio: 0.78 (0.73–0.82)). Compared to patients with genetically-influenced lower TG via LPL, genetically-influenced lower TG via APOA5 had similar and independent, but notably larger, effects on the lipoprotein profile. Our results suggest that lower TG levels as a result of APOA5 variation have strong beneficial effects on CAD risk and the lipoprotein profile, which suggest apo A-V may be a potential novel therapeutic target for CAD prevention. 相似文献
3.
Peter L Hagedoorn Martijn C.P.F Driessen Marieke van den Bosch Ilse Landa Wilfred R Hagen 《FEBS letters》1998,440(3):6683
The redox chemistry of Pyrococcus furiosus rubredoxin and ferredoxin has been studied as a function of temperature in direct voltammetry and in EPR monitored bulk titrations. The Ems of both proteins, measured with direct voltammetry, have a normal (linear) temperature dependence and show no pH dependence. EPR monitoring is not a reliable method to determine the temperature dependence of the Em: upon rapid freezing the proteins take their conformation corresponding to the freezing point of the solution. 相似文献
4.
Background
Mitochondria are highly complex, membrane-enclosed organelles that are essential to the eukaryotic cell. The experimental elucidation of organellar proteomes combined with the sequencing of complete genomes allows us to trace the evolution of the mitochondrial proteome. 相似文献5.
Dimitry Y. Sorokin Martijn Diender Alexander Y. Merkel Michel Koenen Nicole J. Bale Martin Pabst Jaap S. Sinninghe Damsté Diana Z. Sousa 《Environmental microbiology》2021,23(7):3460-3476
An anaerobic enrichment with CO from sediments of hypersaline soda lakes resulted in a methane-forming binary culture, whereby CO was utilized by a bacterium and not the methanogenic partner. The bacterial isolate ANCO1 forms a deep-branching phylogenetic lineage at the level of a new family within the class ‘Natranaerobiia’. It is an extreme haloalkaliphilic and moderate thermophilic acetogen utilizing CO, formate, pyruvate and lactate as electron donors and thiosulfate, nitrate (reduced to ammonia) and fumarate as electron acceptors. The genome of ANCO1 encodes a full Wood–Ljungdahl pathway allowing for CO oxidation and acetogenic conversion of pyruvate. A locus encoding Nap nitrate reductase/NrfA ammonifying nitrite reductase is also present. Thiosulfate respiration is encoded by a Phs/Psr-like operon. The organism obviously relies on Na-based bioenergetics, since the genome encodes for the Na+-Rnf complex, Na+-F1F0 ATPase and Na+-translocating decarboxylase. Glycine betaine serves as a compatible solute. ANCO1 has an unusual membrane polar lipid composition dominated by diethers, more common among archaea, probably a result of adaptation to multiple extremophilic conditions. Overall, ANCO1 represents a unique example of a triple extremophilic CO-oxidizing anaerobe and is classified as a novel genus and species Natranaerofaba carboxydovora in a novel family Natranaerofabacea. 相似文献
6.
María B. Birkisdttir Dick Jaarsma Renata M. C. Brandt Sander Barnhoorn Nicole van Vliet Sandra Imholz Conny T. van Oostrom Bhawani Nagarajah Eliana Portilla Fernndez Anton J. M. Roks Ype Elgersma Harry van Steeg Jos A. Ferreira Jeroen L. A. Pennings Jan H. J. Hoeijmakers Wilbert P. Vermeij Martijn E. T. Doll 《Aging cell》2021,20(2)
7.
Joyce S. F. D. de Almeida Teobaldo R. Cuya Guizado Ana P. Guimarães Teodorico C. Ramalho Arlan S. Gonçalves Martijn C. de Koning 《Journal of biomolecular structure & dynamics》2016,34(12):2632-2642
In the present work, we performed docking and molecular dynamics simulations studies on two groups of long-tailored oximes designed as peripheral site binders of acetylcholinesterase (AChE) and potential penetrators on the blood brain barrier. Our studies permitted to determine how the tails anchor in the peripheral site of sarin-inhibited human AChE, and which aminoacids are important to their stabilization. Also the energy values obtained in the docking studies corroborated quite well with the experimental results obtained before for these oximes. 相似文献
8.
Olaf Binsch Ellen S. Wilschut Martijn Arns Charelle Bottenheft Pierre J. L. Valk Eric H. G. J. M. Vermetten 《Applied psychophysiology and biofeedback》2018,43(1):37-47
There is a growing interest in the application of psychophysiological signals in more applied settings. Unidirectional sensory motor rhythm-training (SMR) has demonstrated consistent effects on sleep. In this study the main aim was to analyze to what extent participants could gain voluntary control over sleep-related parameters and secondarily to assess possible influences of this training on sleep metrics. Bidirectional training of SMR as well as heart rate variability (HRV) was used to assess the feasibility of training these parameters as possible brain computer interfaces (BCI) signals, and assess effects normally associated with unidirectional SMR training such as the influence on objective and subjective sleep parameters. Participants (n?=?26) received between 11 and 21 training sessions during 7 weeks in which they received feedback on their personalized threshold for either SMR or HRV activity, for both up- and down regulation. During a pre- and post-test a sleep log was kept and participants used a wrist actigraph. Participants were asked to take an afternoon nap on the first day at the testing facility. During napping, sleep spindles were assessed as well as self-reported sleep measures of the nap. Although the training demonstrated successful learning to increase and decrease SMR and HRV activity, no effects were found of bidirectional training on sleep spindles, actigraphy, sleep diaries, and self-reported sleep quality. As such it is concluded that bidirectional SMR and HRV training can be safely used as a BCI and participants were able to improve their control over physiological signals with bidirectional training, whereas the application of bidirectional SMR and HRV training did not lead to significant changes of sleep quality in this healthy population. 相似文献
9.
Lennard van der Woude Markus Piotrowski Gruson Klaasse Judith K. Paulus Daniel Krahn Sabrina Ninck Farnusch Kaschani Markus Kaiser Ondřej Novák Karin Ljung Suzanne Bulder Marcel van Verk Basten L. Snoek Martijn Fiers Nathaniel I. Martin Renier A. L. van der Hoorn Stéphanie Robert Sjef Smeekens Martijn van Zanten 《The Plant journal : for cell and molecular biology》2021,106(6):1523-1540
Temperature passively affects biological processes involved in plant growth. Therefore, it is challenging to study the dedicated temperature signalling pathways that orchestrate thermomorphogenesis, a suite of elongation growth-based adaptations that enhance leaf-cooling capacity. We screened a chemical library for compounds that restored hypocotyl elongation in the pif4-2–deficient mutant background at warm temperature conditions in Arabidopsis thaliana to identify modulators of thermomorphogenesis. The small aromatic compound ‘Heatin’, containing 1-iminomethyl-2-naphthol as a pharmacophore, was selected as an enhancer of elongation growth. We show that ARABIDOPSIS ALDEHYDE OXIDASES redundantly contribute to Heatin-mediated hypocotyl elongation. Following a chemical proteomics approach, the members of the NITRILASE1-subfamily of auxin biosynthesis enzymes were identified among the molecular targets of Heatin. Our data reveal that nitrilases are involved in promotion of hypocotyl elongation in response to high temperature and Heatin-mediated hypocotyl elongation requires the NITRILASE1-subfamily members, NIT1 and NIT2. Heatin inhibits NIT1-subfamily enzymatic activity in vitro and the application of Heatin accordingly results in the accumulation of NIT1-subfamily substrate indole-3-acetonitrile in vivo. However, levels of the NIT1-subfamily product, bioactive auxin (indole-3-acetic acid), were also significantly increased. It is likely that the stimulation of hypocotyl elongation by Heatin might be independent of its observed interaction with NITRILASE1-subfamily members. However, nitrilases may contribute to the Heatin response by stimulating indole-3-acetic acid biosynthesis in an indirect way. Heatin and its functional analogues present novel chemical entities for studying auxin biology. 相似文献
10.