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21.
Wenhao Xu Yu Lin Keliang Zhao Haimeng Li Yinping Tian Jacob Njaramba Ngatia Yue Ma Sunil Kumar Sahu Huabing Guo Xiaosen Guo Yan Chun Xu Huan Liu Karsten Kristiansen Tianming Lan Xinying Zhou 《Ecology and evolution》2021,11(1):390-401
Ancient DNA research has developed rapidly over the past few decades due to improvements in PCR and next‐generation sequencing (NGS) technologies, but challenges still exist. One major challenge in relation to ancient DNA research is to recover genuine endogenous ancient DNA sequences from raw sequencing data. This is often difficult due to degradation of ancient DNA and high levels of contamination, especially homologous contamination that has extremely similar genetic background with that of the real ancient DNA. In this study, we collected whole‐genome sequencing (WGS) data from 6 ancient samples to compare different mapping algorithms. To further explore more effective methods to separate endogenous DNA from homologous contaminations, we attempted to recover reads based on ancient DNA specific characteristics of deamination, depurination, and DNA fragmentation with different parameters. We propose a quick and improved pipeline for separating endogenous ancient DNA while simultaneously decreasing homologous contaminations to very low proportions. Our goal in this research was to develop useful recommendations for ancient DNA mapping and for separation of endogenous DNA to facilitate future studies of ancient DNA. 相似文献
22.
Lisa Kolden Midtb? Mohammad Madani Ibrahim Lene Secher Myrmel Ulrike Liisberg Aune Anita R?yneberg Alvheim Nina S. Liland Bente E. Torstensen Grethe Rosenlund Bj?rn Liaset Trond Brattelid Karsten Kristiansen Lise Madsen 《PloS one》2013,8(1)
Background
To ensure sustainable aquaculture, fish derived raw materials are replaced by vegetable ingredients. Fatty acid composition and contaminant status of farmed Atlantic salmon (Salmo salar L.) are affected by the use of plant ingredients and a spillover effect on consumers is thus expected. Here we aimed to compare the effects of intake of Atlantic salmon fed fish oil (FO) with intake of Atlantic salmon fed a high proportion of vegetable oils (VOs) on development of insulin resistance and obesity in mice.Methodology/principal findings
Atlantic salmon were fed diets where FO was partly (80%) replaced with three different VOs; rapeseed oil (RO), olive oil (OO) or soy bean oil (SO). Fillets from Atlantic salmon were subsequently used to prepare Western diets (WD) for a mouse feeding trial. Partial replacement of FO with VOs reduced the levels of polychlorinated biphenyls (PCB) and dichloro-diphenyl-tricloroethanes (DDT) with more than 50% in salmon fillets, in WDs containing the fillets, and in white adipose tissue from mice consuming the WDs. Replacement with VOs, SO in particular, lowered the n−3 polyunsaturated fatty acid (PUFA) content and increased n−6 PUFA levels in the salmon fillets, in the prepared WDs, and in red blood cells collected from mice consuming the WDs. Replacing FO with VO did not influence obesity development in the mice, but replacement of FO with RO improved glucose tolerance. Compared with WD-FO fed mice, feeding mice WD-SO containing lower PCB and DDT levels but high levels of linoleic acid (LA), exaggerated insulin resistance and increased accumulation of fat in the liver.Conclusion/Significance
Replacement of FO with VOs in aqua feed for farmed salmon had markedly different spillover effects on metabolism in mice. Our results suggest that the content of LA in VOs may be a matter of concern that warrants further investigation. 相似文献23.
Kasper Worm-Leonhard Thomas Hjelmgaard Rasmus K. Petersen Karsten Kristiansen John Nielsen 《Bioorganic & medicinal chemistry letters》2013,23(14):4162-4165
In this study we present the design, synthesis and biological evaluation of a small, first-generation library of small molecule aromatic amides based on the arylopeptoid skeleton. The compounds were efficiently synthesized using a highly convenient submonomer solid-phase methodology which potentially allows for access to great product diversity. The synthesized compounds were tested for their ability to activate peroxisome proliferator-activated receptors (PPARs) and they all acted as PPARγ agonists in the μM range spanning from 2.5- to 14.7-fold activation of the receptor. This is the first discovery of bioactive molecules based on the arylopeptoid architecture. 相似文献
24.
J⊘rgen Kristiansen 《欧洲藻类学杂志》2013,48(3):231-241
An examination by means of electron microscopy of phytoplankton samples from 23 localities in North Wales and Anglesey yielded 14 species of Synuraceae. Eleven of these have not been recorded previously from this region, and two species are new to Britain, viz. Mallomonas pugio Bradley and Spiniferomonas trioralis Takahashi. 相似文献
25.
Anne-Marie Lundsgaard Jacob B. Holm Kim A. Sjøberg Kirstine N. Bojsen-Møller Lene S. Myrmel Even Fjære Benjamin A.H. Jensen Trine S. Nicolaisen Janne R. Hingst Sine L. Hansen Sophia Doll Philip E. Geyer Atul S. Deshmukh Jens J. Holst Lise Madsen Karsten Kristiansen Jørgen F.P. Wojtaszewski Erik A. Richter Bente Kiens 《Cell metabolism》2019,29(1):50-63.e4
26.
Guangyi Fan Yaolei Zhang Xiaochuan Liu Jiahao Wang Zeguo Sun Shuai Sun He Zhang Jianwei Chen Meiqi Lv Kai Han Xiaoxuan Tan Jie Hu Rui Guan Yuanyuan Fu Shanshan Liu Xi Chen Qiwu Xu Yating Qin Longqi Liu Jie Bai Ou Wang Jingbo Tang Haorong Lu Zhouchun Shang Bo Wang Guohai Hu Xia Zhao Yan Zou Ao Chen Meihua Gong Wenwei Zhang Simon M.‐Y. Lee Songhai Li Junnian Liu Zhen Li Yishan Lu Jamal S. M. Sabir Mumdooh J. Sabir Muhummadh Khan Nahid H. Hajrah Ye Yin Karsten Kristiansen Huanming Yang Jian Wang Xun Xu Xin Liu 《Molecular ecology resources》2019,19(4):944-956
Marine mammals are important models for studying convergent evolution and aquatic adaption, and thus reference genomes of marine mammals can provide evolutionary insights. Here, we present the first chromosome‐level marine mammal genome assembly based on the data generated by the BGISEQ‐500 platform, for a stranded female sperm whale (Physeter macrocephalus). Using this reference genome, we performed chromosome evolution analysis of the sperm whale, including constructing ancestral chromosomes, identifying chromosome rearrangement events and comparing with cattle chromosomes, which provides a resource for exploring marine mammal adaptation and speciation. We detected a high proportion of long interspersed nuclear elements and expanded gene families, and contraction of major histocompatibility complex region genes which were specific to sperm whale. Using comparisons with sheep and cattle, we analysed positively selected genes to identify gene pathways that may be related to adaptation to the marine environment. Further, we identified possible convergent evolution in aquatic mammals by testing for positively selected genes across three orders of marine mammals. In addition, we used publicly available resequencing data to confirm a rapid decline in global population size in the Pliocene to Pleistocene transition. This study sheds light on the chromosome evolution and genetic mechanisms underpinning sperm whale adaptations, providing valuable resources for future comparative genomics. 相似文献
27.
Venkata N. Are Ashwani Kumar Venuka Durani Goyal Siddhant S. Gotad Biplab Ghosh Rekha Gadre Sahayog N. Jamdar Ravindra D. Makde 《Proteins》2019,87(3):212-225
M24B peptidases cleaving Xaa-Pro bond in dipeptides are prolidases whereas those cleaving this bond in longer peptides are aminopeptidases-P. Bacteria have small aminopeptidases-P (36-39 kDa), which are diverged from canonical aminopeptidase-P of Escherichia coli (50 kDa). Structure-function studies of small aminopeptidases-P are lacking. We report crystal structures of small aminopeptidases-P from E. coli and Deinococcus radiodurans, and report substrate-specificities of these proteins and their ortholog from Mycobacterium tuberculosis. These are aminopeptidases-P, structurally close to small prolidases except for absence of dipeptide-selectivity loop. We noticed absence of this loop and conserved arginine in canonical archaeal prolidase (Maher et al., Biochemistry. 43, 2004, 2771-2783) and questioned its classification. Our enzymatic assays show that this enzyme is an aminopeptidase-P. Further, our mutagenesis studies illuminate importance of DXRY sequence motif in bacterial small aminopeptidases-P and suggest common evolutionary origin with human XPNPEP1/XPNPEP2. Our analyses reveal sequence/structural features distinguishing small aminopeptidases-P from other M24B peptidases. 相似文献
28.
The present study shows that freezing of freeze-tolerant larvae of the wood fly Xylophagus cinctus caused Na(+), K(+) and Mg(++) to move to electrochemical equilibrium across the cell membranes. Na(+) and Mg(++) moved from the haemolymph into the cells, while K(+) moved the opposite way. The original distribution of ions was restored after the larvae were thawed. The transmembrane fluxes of ions were of the same magnitude in the frozen and thawed larvae. The redistribution of ions in the frozen larvae did not give rise to any apparent change in the volume of cells and haemolymph upon thawing, i.e. the redistribution of solutes appeared to be osmotically neutral. 相似文献
29.
Hagemeister JJ Grave M Kristiansen TB Assaad F Hellung-Larsen P 《The Journal of eukaryotic microbiology》1999,46(1):6-11
ABSTRACT We have previously shown that the cell death of Tetrahymena thermophila in low inocula cultures in a chemically-defined medium is not apoptotic. The death is caused by a cell lysis occurring at the medium-air interface and can be prevented by the addition of insulin or Pluronic F-68. Here, we report that cell death can also be caused by the medium. The specific effects of several medium constituents were tested in the presence and absence of an interface. Four of the 19 amino acids (arginine, aspartic acid, glutamic acid, and histidine in millimolar concentration) as well as Ca2+ (68 μM) and Mg2+ (2 mM) and trace metal ions (micromolar concentrations) are all sufficient to induce the interface-mediated death. The effect of the amino acids and the salt ions Ca2+ and Mg2+ can be abolished by the addition of insulin (10-6 M) or Pluronic F-68 (0.01% w/v), whereas insulin/Pluronic F-68 only postpones the death induced by trace metal ions. On the basis of our findings, a new recipe for a chemically-defined medium has been formulated. Single cells can grow in this medium in the presence of medium-air interface without any supplements. 相似文献
30.
Kristiansen LV Marques FA Soroka V Ronn LC Kiselyov V Pedersen N Berezin V Bock E 《FEBS letters》1999,464(1-2):30-34
The cell adhesion molecules NCAM and L1 are considered to play key roles in neuronal development and plasticity. L1 has been shown to interact with NCAM, possibly through NCAM binding to oligomannosidic glycans present in L1. We investigated the effect of recombinant immunoglobulin (Ig) modules of NCAM involved in homophilic NCAM binding, on L1 induced neurite outgrowth from PC12-E2 cells and found a complete inhibition of L1 induced neurite outgrowth after addition of Ig-modules 1, 2 and 3 of NCAM, suggesting that the ligation state of NCAM is crucial for normal L1 signaling. 相似文献