| 1. |
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| 2. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
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| 4. |
- Feng, Shaohong, et al.
(författare)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 5. |
- Daneshjou, Roxana, et al.
(författare)
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Working toward precision medicine : Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges
- 2017
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Ingår i: Human Mutation. - : Hindawi Limited. - 1059-7794 .- 1098-1004. ; 38:9, s. 1182-1192
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Tidskriftsartikel (refereegranskat)abstract
- Precision medicine aims to predict a patient's disease risk and best therapeutic options by using that individual's genetic sequencing data. The Critical Assessment of Genome Interpretation (CAGI) is a community experiment consisting of genotype-phenotype prediction challenges; participants build models, undergo assessment, and share key findings. For CAGI 4, three challenges involved using exome-sequencing data: Crohn's disease, bipolar disorder, and warfarin dosing. Previous CAGI challenges included prior versions of the Crohn's disease challenge. Here, we discuss the range of techniques used for phenotype prediction as well as the methods used for assessing predictive models. Additionally, we outline some of the difficulties associated with making predictions and evaluating them. The lessons learned from the exome challenges can be applied to both research and clinical efforts to improve phenotype prediction from genotype. In addition, these challenges serve as a vehicle for sharing clinical and research exome data in a secure manner with scientists who have a broad range of expertise, contributing to a collaborative effort to advance our understanding of genotype-phenotype relationships.
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| 6. |
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| 7. |
- Peng, Ningxin, et al.
(författare)
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Platelet mitochondrial DNA methylation : A novel biomarker for myocardial infarction – A preliminary study
- 2023
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Ingår i: International Journal of Cardiology. - 0167-5273.
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Tidskriftsartikel (refereegranskat)abstract
- Background: Platelet activation and thrombus formation play critical roles in the pathogenesis of myocardial infarction (MI). In addition to their role in energy production, platelet mitochondria also regulate cellular functions related to apoptosis, oxidative stress, and inflammation. Epigenetic modifications of platelet mitochondrial DNA (mtDNA) may influence platelet function and are believed to be an important factor in MI. Therefore, the aim of this study was to investigate the differences in platelet mtDNA methylation levels between MI patients and controls. Methods: The present study utilized propensity score matching to generate 45 multivariate matched apparently healthy controls for 45 patients with newly-onset acute MI. Platelet mtDNA methylation levels were assessed through bisulfite-PCR pyrosequencing and compared between the two groups, with further adjustments made in the sensitivity analysis. Results: Among the measured mitochondrial genes (MT-COX1, MT-COX2, MT-COX3, MT-ND5, MT-ATP6 and tRNA_Leu), patients with MI exhibited statistically significant differences in mtDNA methylation levels as compared to matched controls. Specifically, higher levels of mtDNA methylation were observed in MT-COX1, MT-COX3, and tRNA_Leu, while a lower level was observed in MT-ATP6 (all p < 0.0001). These results remained robust in the sensitivity analysis. Conclusion: Our study demonstrated significant variations in platelet mtDNA methylation levels between patients with MI and controls. Platelet mtDNA methylation may serve as a novel biomarker for MI. This observation also provided some insights into the etiology of MI.
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| 8. |
- Sun, Fengbo, et al.
(författare)
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1,5-Diiodocycloctane: a cyclane solvent additive that can extend the exciton diffusion length in thick film organic solar cells
- 2024
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Ingår i: Energy and Environmental Sciences. - 1754-5692 .- 1754-5706. ; 17:5, s. 1916-1930
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Tidskriftsartikel (refereegranskat)abstract
- The short exciton diffusion length associated with most state-of-the-art organic semiconductors used in organic solar cells (OSCs) imposes severe limits on the exciton transport in the larger donor/acceptor domains and the exciton dissociation at the interface, which hinder further improvements in the power conversion efficiencies (PCE) of the thick-film devices. In this study, a new cyclane, 1,5-diiodocycloctane (DICO), was employed as a solvent additive to effectively extend the exciton LD within the bulk-heterojunction blend, which can function with the multiple photovoltaic materials system. Due to the great enhancement of molecular stacking and exclusively large domain sizes of photovoltaic materials with the assistance of the DICO additive, the trap density in devices is significantly reduced, thereby nearly doubling the LD in the thick film OSCs. Notably, the DICO-processed PM6/L8-BO-based OSC showed high thickness tolerance for the bulk-heterojunction (BHJ) layer, delivering a high PCE of 19.1% in the case of a 110 nm thick film and still maintaining an excellent PCE of 17.2% in the case of a 300 nm thick film. Crucially, a noticeably increased stability of the multiple materials system was observed in the DICO-processed OSCs. These findings enrich the additive family with new cyclane systems to extend the exciton LD in thick film OSCs with high performance.
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| 9. |
- Tu, Yongming, et al.
(författare)
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Nanoscale insights into NASH under high-velocity fluids erosion: A molecular dynamics study
- 2024
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Ingår i: Journal of Building Engineering. - : Elsevier. - 2352-7102. ; 94
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Tidskriftsartikel (refereegranskat)abstract
- The poor durability of geopolymer is a major factor hindering its application, and erosion from high-velocity fluids exacerbates this drawback. This study aimed to characterize the microstructural features of geopolymer under high-velocity fluids erosion and investigate the influence of harmful ions on erosion damage. Models of geopolymer/water solution and geopolymer/NaCl solution were constructed to simulate the erosion of geopolymer by high-velocity fluids. The results indicated that under high-velocity fluids erosion, most of the atoms on the surface of the geopolymer experienced leaching, indicating destruction of the substrate. Additionally, water molecules in solution were able to form hydrogen bonds to the substrate surface, accelerating its degradation. Under NaCl solution erosion, Na ions interacted with the exposed bridging oxygen in the geopolymer, and ion exchange occurred between Na ions and the substrate, making the substrate more unstable and leaching more pronounced. The findings of this study provide nanoscale insights into the erosion resistance of geopolymer that could guide the development of new erosion-resistant materials and methods.
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| 10. |
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| 11. |
- Chen, Gang, et al.
(författare)
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EDF-VD Scheduling of Flexible Mixed-Criticality System With Multiple-Shot Transitions
- 2018
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Ingår i: IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. - 0278-0070 .- 1937-4151. ; 37:11, s. 2393-2403
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Tidskriftsartikel (refereegranskat)abstract
- The existing mixed-criticality (MC) real-time task models assume that once any high-criticality task overruns, all high-criticality jobs execute up to their most pessimistic WCET estimations simultaneously in a one-shot manner. This is very pessimistic in the sense of unnecessary resource overbooking. In this paper, we propose a more generalized mixed-critical real-time task model, called flexible MC model with multiple-shot transitions (FMC-MST), to address this problem. In FMC-MST, high-criticality tasks can transit multiple intermediate levels to handle less pessimistic overruns independently and to nonuni-formly scale the deadline on each level. We develop a run-time schedulability analysis for FMC-MST under EDF-VD scheduling, in which a better tradeoff between the penalties of low-criticality tasks and the overruns of high-criticality tasks is achieved to improve the service quality of low-criticality tasks. We also develop a resource optimization technique to find resource-efficient level-insertion configurations for FMC-MST task systems under MC timing constraints. Experiments demonstrate the effectiveness of FMC-MST compared with the state-of-the-art techniques.
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| 12. |
- Deng, Biao, et al.
(författare)
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Effects of Austenitizing Temperature on Tensile and Impact Properties of a Martensitic Stainless Steel Containing Metastable Retained Austenite
- 2021
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Ingår i: Materials. - : MDPI AG. - 1996-1944 .- 1996-1944. ; 14:4
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Tidskriftsartikel (refereegranskat)abstract
- Austenitizing temperature is one decisive factor for the mechanical properties of medium carbon martensitic stainless steels (MCMSSs). In the present work, the effects of austenitizing temperature (1000, 1020, 1040 and 1060 degrees C) on the microstructure and mechanical properties of MCMSSs containing metastable retained austenite (RA) were investigated by means of electron microscopy, X-ray diffraction (XRD), as well as tensile and impact toughness tests. Results suggest that the microstructure including an area fraction of undissolved M23C6, carbon and chromium content in matrix, prior austenite grain size (PAGS), fraction and composition of RA in studied MCMSSs varies with employed austenitizing temperature. By optimizing austenitizing temperature (1060 degrees C for 40 min) and tempering (250 degrees C for 30 min) heat treatments, the MCMSS demonstrates excellent mechanical properties with the ultimate tensile strength of 1740 +/- 8 MPa, a yield strength of 1237 +/- 19 MPa, total elongation (ductility) of 10.3 +/- 0.7% and impact toughness of 94.6 +/- 8.0 Jcm(-2) at room temperature. The increased ductility of alloys is mainly attributed to the RA with a suitable stability via a transformation-induced plasticity (TRIP) effect, and a matrix containing reduced carbon and chromium content. However, the impact toughness of MCMSSs largely depends on M23C6 carbides.
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| 13. |
- Ekblom, Robert, Docent, 1976-, et al.
(författare)
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Development of transcriptome genetic markers for the great snipe (Gallinago media)
- 2017
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Ingår i: Conservation Genetics Resources. - : SPRINGER. - 1877-7252 .- 1877-7260. ; 9:4, s. 643-645
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Tidskriftsartikel (refereegranskat)abstract
- We sequenced the transcriptomes of 14 great snipe (Gallinago media) males from the Gavalia study population (central Norway) using Roche 454 technology. The assembled transcriptome sequences (RNA-Seq) was used to identify 140 microsatellite repeat sequences with sufficient flanking sequence information for primer design. In addition several 1000 single nucleotide polymorphisms in the transcriptome were identified, and a small subset of these were verified by independent genotyping.
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| 14. |
- Gu, Shi-Ran, et al.
(författare)
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Phylogeny and re-circumscription of Cheniella (Leguminosae: Cercidoideae) based on plastome data and morphology, with description of three new species
- 2024
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Ingår i: TAXON. - 0040-0262 .- 1996-8175. ; 73:2, s. 475-502
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Tidskriftsartikel (refereegranskat)abstract
- Subfamily Cercidoideae is an early-diverging lineage of Leguminosae, within which the number and classification of genera have been controversial. Cheniella is a recently described genus in the Cercidoideae which requires revision and testing of its monophyly and circumscription. Here we infer the phylogenetic position and infrageneric relationships of Cheniella as well as the intergeneric relationships of Cercidoideae using 48 newly sequenced plastid genomes, including 34 individuals representing all species of Cheniella. Our phylogenetic analyses yield a well-resolved tree of Cercidoideae with robust support at most nodes. We also present morphological studies through field work and herbarium studies to re-assess the classification and circumscription of the genus. Based on the results of molecular analyses and morphological studies combined with distribution data, we broaden the circumscription of Cheniella to comprise a total of 15 species and 3 subspecies, including three new species (C. hechiensis, C. longistaminea, C. pubicarpa), one new combination (C. tianlinensis) and one new status and combination (C. longipes).
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| 15. |
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| 16. |
- Höglund, Jacob, et al.
(författare)
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Blood transcriptomes and de novo identification of candidate loci for mating success in lekking great snipe (Gallinago media)
- 2017
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 26:13, s. 3458-3471
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Tidskriftsartikel (refereegranskat)abstract
- We assembled the great snipe blood transcriptome using data from fourteen lekking males, in order to de novo identify candidate genes related to sexual selection, and determined the expression profiles in relation to mating success. The three most highly transcribed genes were encoding different haemoglobin subunits. All tended to be overexpressed in males with high mating success. We also called single nucleotide polymorphisms (SNPs) from the transcriptome data and found considerable genetic variation for many genes expressed during lekking. Among these, we identified 14 polymorphic candidate SNPs that had a significant genotypic association with mating success (number of females mated with) and/or mating status (mated or not). Four of the candidate SNPs were found in HBAA (encoding the haemoglobin a-chain). Heterozygotes for one of these and one SNP in the gene PABPC1 appeared to enjoy higher mating success compared to males homozygous for either of the alleles. In a larger data set of individuals, we genotyped 38 of the identified SNPs but found low support for consistent selection as only one of the zygosities of previously identified candidate SNPs and none of their genotypes were associated with mating status. However, candidate SNPs generally showed lower levels of spatial genetic structure compared to noncandidate markers. We also scored the prevalence of avian malaria in a subsample of birds. Males infected with avian malaria parasites had lower mating success in the year of sampling than noninfected males. Parasite infection and its interaction with specific genes may thus affect performance on the lek.
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| 17. |
- Höglund, Jacob, et al.
(författare)
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Phylogeography of willow grouse (Lagopus lagopus) in the Arctic : taxonomic discordance as inferred from molecular data
- 2013
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Ingår i: Biological Journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4066 .- 1095-8312. ; 110:1, s. 77-90
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Tidskriftsartikel (refereegranskat)abstract
- Using independently segregating nuclear single nucleotide polymorphisms (SNPs) and mitochondrial control region sequences, we found an east-west division among sampled willow grouse Lagopus lagopus subspecies. This division cut across the range of the subspecies with the largest distribution (lagopus) and thus contradicted existing taxonomic classifications. Russian Lagopus lagopus lagopus tended to cluster with North American willow grouse partly classified as other subspecies. Scandinavian willow grouse (L.l. lagopus) clustered with red grouse from Britain and Ireland (Lagopus lagopus scoticus and Lagopus lagopus hibernicus) but substructuring confirmed the monophyly of the latter. In North America, we could not detect any major genetic divisions apart from two birds described as alexandrae from the Heceta Island (Alaska) when using mitochondrial sequences. Other samples from North America were intermingled regardless of whether they were described as muriei, alexandrae or lagopus. A specimen described as alexandrae was to some extent distinct when analysing the SNP data. The genetic analyses indicated some concordance between genetics and taxonomy but not complete congruence. This is particularly evident for mitochondrial DNA network analyses. We suggest that the taxonomy of this species would benefit by a careful re-examination of the available evidence for subspecies. It appears as if subspecies status is a poor proxy for assigning evolutionary significant units and management units in this species.
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| 18. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
- 2008
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Ingår i: Autophagy. - : Landes Bioscience. - 1554-8627 .- 1554-8635. ; 4:2, s. 151-175
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Forskningsöversikt (refereegranskat)abstract
- Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.
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| 19. |
- Liu, Yang, et al.
(författare)
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Genome Assembly of the Common Pheasant Phasianus colchicus : A Model for Speciation and Ecological Genomics
- 2019
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Ingår i: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653 .- 1759-6653. ; 11:12, s. 3326-3331
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Tidskriftsartikel (refereegranskat)abstract
- The commonpheasant (Phasianus colchicus) in the order Galliformes and the family Phasianidae, has 30 subspecies distributed across its native range in the Palearctic realm and has been introduced to Europe, NorthAmerica, and Australia. It is an important game bird often subjected to wildlife management as well as a model species to study speciation, biogeography, and local adaptation. However, the genomic resources for the commonpheasant are generally lacking. We sequenced a male individual of the subspecies torquatus of the common pheasant with the Illumina HiSeq platform. We obtained 94.88Gb of usable sequences by filtering out low-quality reads of the raw data generated. This resulted in a 1.02Gb final assembly, which equals the estimated genome size. BUSCO analysis using chicken as a model showed that 93.3% of genes were complete. The contig N50 and scaffold N50 sizes were 178 kb and 10.2 Mb, respectively. All these indicate that we obtained a high-quality genome assembly. We annotated 16,485 protein-coding genes and 123.3 Mb (12.05% of the genome) of repetitive sequences by ab initio and homology-based prediction. Furthermore, we applied a RAD-sequencing approach for another 45 individuals of seven representative subspecies in China and identified 4,376,351 novel single nucleotide polymorphism (SNPs) markers. Using this unprecedented data set, we uncovered the geographic population structure and genetic introgression among common pheasants in China. Our results provide the first high-quality reference genome for the common pheasant and a valuable genome-wide SNP database for studying population genomics and demographic history.
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| 20. |
- Morales, Hernan E., et al.
(författare)
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Neutral and selective drivers of colour evolution in a widespread Australian passerine
- 2017
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Ingår i: Journal of Biogeography. - : WILEY-BLACKWELL. - 0305-0270 .- 1365-2699. ; 44:3, s. 522-536
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Tidskriftsartikel (refereegranskat)abstract
- AimRump plumage coloration of the Eastern Yellow Robin (Eopsaltria australis), a widespread Australian songbird, varies from bright yellow in the tropical north to olive-green in the temperate south. Here, we test whether colour variation: (1) correlates most strongly with neutral genetic variation and so is best explained by historical processes, (2) reflects selection associated with different visual environments (dense versus open habitats) and/or (3) reflects selection associated with climatic variation. LocationEastern Australia. MethodsWe quantified colour variation using reflectance spectrometry and visual models. We performed geographical cline analysis of colour and neutral genetic variation (genome-wide single nucleotide polymorphisms). We tested for correlations of colour variation with climate, vegetation density, geographical location and genetic variation. We accounted for covariation and spatial autocorrelation, and conducted analyses at continental and regional spatial scales. ResultsClinal variation of colour traits and neutral genetic markers were largely concordant. At the continental scale, colour variation was strongly associated with neutral genetic structure and geography, and to a lesser extent with environment. At the regional scale, environmental variation was a better predictor of colour variation than it was at the larger scale. Main conclusionAt the continental scale, colour variation is strongly associated with large-scale population history. In contrast, at the regional scale, where the influence of history and geography is weaker, environmental variation has a role in facilitating the maintenance of colour variation. Our results highlight the need to assess selective and neutral alternatives at multiple spatial scales when studying geographical variation.
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| 21. |
- Quintela, Maria, et al.
(författare)
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Genetic diversity and differentiation among Lagopus lagopus populations in Scandinavia and Scotland : evolutionary significant units confirmed by SNP markers
- 2010
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 19:12, s. 2380-2393
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Tidskriftsartikel (refereegranskat)abstract
- Single Nucleotide Polymorphism in four Scandinavian populations of willow grouse (Lagopus lagopus) and two Scottish populations of red grouse (Lagopus lagopus scoticus) were assessed at 13 protein-coding loci. We found high levels of diversity, with one substitution every 55 bp as an average and a total of 76 unlinked parsimony informative SNPs. Different estimators of genetic diversity such as: number of synonymous and non-synonymous sites, average number of alleles, number and percentage of polymorphic loci, mean nucleotide diversity (pi(s), pi(a)) and gene diversity at synonymous and non-synonymous sites showed higher diversity in the northern populations compared to southern ones. Strong levels of purifying selection found in all the populations together with neutrality tests conforming to neutral expectations agree with large effective population sizes. Assignment tests reported a clear distinction between Scandinavian and Scottish grouse suggesting the existence of two different evolutionary significant units. The divergence time between willow and red grouse ranging between 12 500 and 125 000 years, in conjunction with the presence of 'specific' markers for each subspecies prompt a reassessment of the taxonomical status of the Scottish red grouse.
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| 22. |
- Song, Luying, et al.
(författare)
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Intra- and Inter-Self-Assembly of Identical Supramolecules on Silver Surfaces
- 2022
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Ingår i: Journal of Physical Chemistry Letters. - : AMER CHEMICAL SOC. - 1948-7185 .- 1948-7185. ; 13:38, s. 8902-8907
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Tidskriftsartikel (refereegranskat)abstract
- Self-assembly of identical organometallic supra -molecules into ordered superstructures is of great interest in both chemical science and nanotechnology due to its potential to generate neoteric properties through collective effects. In this work, we demonstrate that large-scale self-organization of atomically precise organometallic supramolecules can be achieved through cascaded on-surface chemical reactions, by the combination of intra-and inter-supramolecular interactions. Supramolecules with defined size and shape are first built through intramolecular reaction and intermolecular metal coordination, followed by the formation of well-ordered two-dimensional arrays with the assistance of Br atoms by-C-HmiddotmiddotmiddotBr interactions. The mechanism of this process has been investigated from the perspectives of thermodynamics and kinetics.
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| 23. |
- Song, Luying, et al.
(författare)
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Synthesis of Two-Dimensional Metal-Organic Frameworks via Dehydrogenation Reactions on a Cu(111) Surface
- 2020
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Ingår i: The Journal of Physical Chemistry C. - : AMER CHEMICAL SOC. - 1932-7447 .- 1932-7455. ; 124:23, s. 12390-12396
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Tidskriftsartikel (refereegranskat)abstract
- Metal-organic frameworks prepared on surfaces (SMOFs) have been considered to have potential applications in various research fields. Traditionally, the SMOFs are prepared by coadsorbing organic ligands and metal atoms on surfaces. In this article, we successfully construct the SMOFs via the dehydrogenation reactions of aromatic amines on the Cu(111) surfaces. The dehydrogenated nitrogen radicals interact with the copper adatoms, forming the N-Cu-N bonds. Combining with the scanning tunneling microscopy and the density functional theory calculations, we obtain the structural models of the SMOFs.
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| 24. |
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| 25. |
- Strand, Tanja, et al.
(författare)
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Evolutionary history of black grouse major histocompatibility complex class IIB genes revealed through single locus sequence-based genotyping
- 2013
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Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 14, s. 29-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Gene duplications are frequently observed in the Major Histocompatibility Complex (MHC) of many species, and as a consequence loci belonging to the same MHC class are often too similar to tell apart. In birds, single locus genotyping of MHC genes has proven difficult due to concerted evolution homogenizing sequences at different loci. But studies on evolutionary history, mode of selection and heterozygosity correlations on the MHC cannot be performed before it is possible to analyse duplicated genes separately. In this study we investigate the architecture and evolution of the MHC class IIB genes in black grouse. We developed a sequence-based genotyping method for separate amplification of the two black grouse MHC class IIB genes BLB1 and BLB2. Based on this approach we are able to study differences in structure and selection between the two genes in black grouse and relate these results to the chicken MHC structure and organization. Results: Sequences were obtained from 12 individuals and separated into alleles using the software PHASE. We compared nucleotide diversity measures and employed selection tests for BLB1 and BLB2 to explore their modes of selection. Both BLB1 and BLB2 are transcribed and display classic characteristics of balancing selection as predicted for expressed MHC class IIB genes. We found evidence for both intra- and interlocus recombination or gene conversion, as well as indication for positive but differential selection at both loci. Moreover, the two loci appear to be linked. Phylogenetic analyses revealed orthology of the black grouse MHC class IIB genes to the respective BLB loci in chicken. Conclusions: The results indicate that the duplication of the BLB gene occurred before the species divergence into black grouse, chicken and pheasant. Further, we conclude that BLB1 and BLB2 in black grouse are subjected to homogenizing concerted evolution due to interlocus genetic exchange after species divergence. The loci are in linkage disequilibrium, which is in line with the theory of tightly coevolving genes within the MHC under the minimal essential MHC hypothesis. Our results support the conclusion that MHC form and function in birds derived from studies on the domesticated chicken are not artefacts of the domestication process.
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| 26. |
- Trybel, Florian, et al.
(författare)
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Absence of proton tunneling during the hydrogen-bond symmetrization in delta-AlOOH
- 2021
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Ingår i: Physical Review B. - : American Physical Society. - 2469-9950 .- 2469-9969. ; 104:10
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Tidskriftsartikel (refereegranskat)abstract
- delta-AlOOH is of significant crystallochemical interest due to a subtle structural transition near 10 GPa from a P2(1) nm to a Pnnm structure, the nature and origin of hydrogen disorder, the symmetrization of the O-H center dot center dot center dot O hydrogen bond and their interplay. We perform a series of density functional theory-based simulations in combination with high-pressure nuclear magnetic resonance (NMR) experiments on delta-AlOOH up to 40 GPa with the goal to better characterize the hydrogen potential and therefore the nature of hydrogen disorder. Simulations predict a phase transition in agreement with our NMR experiments at 10 - 11 GPa and hydrogen bond symmetrization at 14.7 GPa. Calculated hydrogen potentials do not show any double-well character and there is no evidence for proton tunneling in our NMR data.
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| 27. |
- Wang, Biao
(författare)
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Development and Application of Genomic Resources in Non-model Bird Species
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Understanding the genetic basis of biological processes is a fundamental component of modern ecology and evolutionary biology studies. With the recent advent of next generation sequencing (NGS) technologies, it is now possible to perform large genome and transcriptome projects for ecologically important non-model species. In this thesis, I focused on the development and application of genomic resources of two non-model bird species, the black grouse (Tetrao tetrix) and the great snipe (Gallinago media). Using the chicken genome as a reference, I developed a reference guided NGS pipeline to assemble the complete draft genome of black grouse. The draft genome has a good coverage of the main 29 chromosomes of the chicken genome. The genome was used to develop a vast number of genetic markers. Comparing this genome with that of other species, I identified the genomic regions which were important for the lineage specific evolution of black grouse. I also sequenced and characterised the spleen transcriptome of the black grouse. I identified and validated a large number of gene-based microsatellite markers from the transcriptome and identified and confirmed the expression of immune related genes. Using a similar RNA-Seq approach, I also sequenced the blood transcriptomes of 14 great snipe males with different mating success. I identified genes and single nucleotide polymorphisms (SNPs) which might be related to male mating success in this species, both in terms of gene expression levels and genetic variation structure. For the immunologically important major histocompatibility complex (MHC) gene region of black grouse, I constructed a fosmid library and used it to sequence the complete core MHC region of this species. This resource allowed me to perform a comprehensive comparative genomics analysis of the galliform MHC, by which I found that some genes in this region were affected by selective forces. I was also able to develop a single locus genotyping protocol for the duplicated MHC BLB (class IIB) genes and found that the two black grouse BLB loci followed different evolutionary trajectories. This thesis set an example of developing genomic resources in non-model species and applying them in addressing questions relevant to ecology and evolutionary biology.
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| 28. |
- Wang, Biao, et al.
(författare)
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Sequencing of the core MHC region of black grouse (Tetrao tetrix) and comparative genomics of the galliform MHC
- 2012
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 13, s. 553-
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Tidskriftsartikel (refereegranskat)abstract
- Background: The MHC, which is regarded as the most polymorphic region in the genomes of jawed vertebrates, plays a central role in the immune system by encoding various proteins involved in the immune response. The chicken MHC-B genomic region has a highly streamlined gene content compared to mammalian MHCs. Its core region includes genes encoding Class I and Class IIB molecules but is only similar to 92Kb in length. Sequences of other galliform MHCs show varying degrees of similarity as that of chicken. The black grouse (Tetrao tetrix) is a wild galliform bird species which is an important model in conservation genetics and ecology. We sequenced the black grouse core MHC-B region and combined this with available data from related species (chicken, turkey, gold pheasant and quail) to perform a comparative genomics study of the galliform MHC. This kind of analysis has previously been severely hampered by the lack of genomic information on avian MHC regions, and the galliformes is still the only bird lineage where such a comparison is possible. Results: In this study, we present the complete genomic sequence of the MHC-B locus of black grouse, which is 88,390 bp long and contains 19 genes. It shows the same simplicity as, and almost perfect synteny with, the corresponding genomic region of chicken. We also use 454-transcriptome sequencing to verify expression in 17 of the black grouse MHC-B genes. Multiple sequence inversions of the TAPBP gene and TAP1-TAP2 gene block identify the recombination breakpoints near the BF and BLB genes. Some of the genes in the galliform MHC-B region also seem to have been affected by selective forces, as inferred from deviating phylogenetic signals and elevated rates of non-synonymous nucleotide substitutions. Conclusions: We conclude that there is large synteny between the MHC-B region of the black grouse and that of other galliform birds, but that some duplications and rearrangements have occurred within this lineage. The MHC-B sequence reported here will provide a valuable resource for future studies on the evolution of the avian MHC genes and on links between immunogenetics and ecology of black grouse.
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| 29. |
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| 30. |
- Wang, Biao, et al.
(författare)
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Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development
- 2012
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Ingår i: Open Biology. - : The Royal Society. - 2046-2441. ; 2, s. 120054-
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Tidskriftsartikel (refereegranskat)abstract
- The black grouse (Tetrao tetrix) is a galliform bird species that is important forboth ecological studies and conservation genetics. Here, we report the sequencing of the spleen transcriptome of black grouse using 454 GS FLX Titanium sequencing. We performed a large-scale gene discovery analysis with a focus on genes that might be related to fitness in this species and also identified a large set of microsatellites. In total, we obtained 182 179 quality-filtered sequencing reads that we assembled into 9035 contigs. Using these contigs and 15 794 length-filtered (greater than 200 bp) singletons, we identified 7762 transcripts that appear to be homologues of chicken genes. A specific BLAST search with an emphasis on immune genes found 308 homologous chicken genes that have immune function, including ten major histocompatibility complex-related genes located on chicken chromosome 16. We also identified 1300 expressed sequence tag microsatellites and were able to design suitable flanking primers for 526 of these. A preliminary test of the polymorphism of the microsatellites found 10 polymorphic microsatellites of the 102 tested. Genomic resources generated in this study should greatly benefit future ecological, evolutionary and conservation genetic studies on this species.
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| 31. |
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| 32. |
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| 33. |
- Wang, Gang, et al.
(författare)
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Estimating sea spray volume flux with a laser gauge in a self-consistent system
- 2023
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Ingår i: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Sea spray is one of the drivers of heat, mass, and gas exchange between the ocean and the atmosphere, and its volume flux could be estimated by the record of the laser intensity. In the laboratory experiments, the relationship between sea spray and laser intensity could be established since the returned laser intensity of the observing gauge and spray concentration can be observed instantaneously. However, the difficulty to generalize the laboratory result to field observations is that the measurement of sea spray is usually unavailable on the open seas. Recent studies introduced an environment variable (atmospheric extinction coefficient for instance) to relate the laser intensity to spray volume flux for both laboratory and field observations so that the relationship established in the laboratory experiments could be extended to open seas. These studies however gave estimations of great difference since the relationships between each pair of the variables (spray volume flux, laser intensity, and the atmospheric extinction coefficient) are considered separately. This work established a self-consistent system composed of the three variables, in which the relationship between each pair of the variables in the system is consistent with that deduced from their respective relationships with the third variable. Consistency here we means that if Y=f(X), Y=g(Z) and Z=h(X), then Y=g(h(X))=f(X) is expected. The consistency of the relationships ensures that the estimation of the sea spray volume flux from laser intensity is robust. We established self-consistent relationships for the variables in the system composed of laser intensity, environment variable, and sea spray volume flux, for both laboratory and field experiments. Among them, the relationship between wind speed and spray volume flux is a reasonable reflection of the physical properties in two ways: a threshold value of spray volume flux at low wind speeds and the saturation at strong wind speeds. For a uniform regression of wind speed onto spray volume, a dimensionless parameter concerning wind speed is needed.
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| 34. |
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| 35. |
- Wang, Lina, et al.
(författare)
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Tailoring Alkane Uniaxial Self-Assembly via Polymer Modified Step Edges
- 2019
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Ingår i: The Journal of Physical Chemistry C. - : AMER CHEMICAL SOC. - 1932-7447 .- 1932-7455. ; 123:47, s. 28811-28815
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Tidskriftsartikel (refereegranskat)abstract
- Controlling the orientations of molecules in self-assembled monolayers on surfaces is an effective means to construct high quality organic devices. Herein, we utilize linear polymer-modified step edges as a simple and peculiar template for regulating the subsequent self-assembly of alkane molecules (n-C32H66). With this strategy, all the alkane molecules orientate along the step edge ([011] directions). Combining with systematical DFT calculations, we demonstrated that it is the van der Waals interactions between the molecules that leads to (1) the initially adsorbed alkane monomers lie parallel to the polymers; (2) the adjacent alkane molecules show a parallel configuration. Since the polymers anchor on the surface along an exclusive [011] direction, all the adsorbed molecules in the self-assembly islands are regulated along the [011] directions as well.
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| 36. |
- Wang, Longxin, et al.
(författare)
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Telomere-to-telomere and haplotype-resolved genome assembly of the Chinese cork oak (Quercus variabilis)
- 2023
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- The Quercus variabilis, a deciduous broadleaved tree species, holds significant ecological and economical value. While a chromosome-level genome for this species has been made available, it remains riddled with unanchored sequences and gaps. In this study, we present a nearly complete comprehensive telomere-to-telomere (T2T) and haplotype-resolved reference genome for Q. variabilis. This was achieved through the integration of ONT ultra-long reads, PacBio HiFi long reads, and Hi-C data. The resultant two haplotype genomes measure 789 Mb and 768 Mb in length, with a contig N50 of 65 Mb and 56 Mb, and were anchored to 12 allelic chromosomes. Within this T2T haplotype-resolved assembly, we predicted 36,830 and 36,370 protein-coding genes, with 95.9% and 96.0% functional annotation for each haplotype genome. The availability of the T2T and haplotype-resolved reference genome lays a solid foundation, not only for illustrating genome structure and functional genomics studies but also to inform and facilitate genetic breeding and improvement of cultivated Quercus species.
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| 37. |
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| 38. |
- Yang, Dong, et al.
(författare)
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Air- and Light-Stable P-4 and As-4 within an Anion-Coordination-Based Tetrahedral Cage
- 2017
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Ingår i: Journal of the American Chemical Society. - : AMER CHEMICAL SOC. - 0002-7863 .- 1520-5126. ; 139:16, s. 5946-5951
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Tidskriftsartikel (refereegranskat)abstract
- In contrast to the stable dinitrogen molecule, white phosphorus (P-4) and yellow arsenic (As-4) are very reactive allotropic modifications of these two heavier pnictogen elements, which has greatly hampered the study of their properties and applications. Thus, the safe storage and transport of them is imperative. Supramolecular caged structures are one of the most efficient approaches for the encapsulation and stabilization of reactive species; however, their use in the P-4 and As-4 chemistry is very rare. In the current work, we demonstrate a new design strategy for constructing finite cages and including guests based on anion coordination chemistry. The phosphate-coordination-based tetrahedral cages can readily accommodate the tetrahedral guests P-4 and As-4, which is facilitated by the shape and size complementarity as well as favorable sigma-pi and lone-pair-pi interactions. Moreover, the latter case represents the first example of As-4 inclusion in a well-defined tetrahedral cage.
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| 39. |
- Yang, Dong, et al.
(författare)
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Encapsulation of Halocarbons in a Tetrahedral Anion Cage
- 2015
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Ingår i: Angewandte Chemie International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 54:30, s. 8658-8661
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Tidskriftsartikel (refereegranskat)abstract
- Caged supramolecular systems are promising hosts for guest inclusion, separation, and stabilization. Well-studied examples are mainly metal-coordination-based or covalent architectures. An anion-coordination-based cage that is capable of encapsulating halocarbon guests is reported for the first time. This A(4)L(4)-type (A=anion) tetrahedral cage, [(PO4)(4)L-4](12-), assembled from a C-3-symmetric tris(bisurea) ligand (L) and phosphate ion (PO43-), readily accommodates a series of quasi-tetrahedral halocarbons, such as the Freon components CFCl3, CF2Cl2, CHFCl2, and C(CH3)F-3, and chlorocarbons CH2Cl2, CHCl3, CCl4, C(CH3)Cl-3, C(CH3)(2)Cl-2, and C(CH3)(3)Cl. The guest encapsulation in the solid state is confirmed by crystal structures, while the host-guest interactions in solution were demonstrated by NMR techniques.
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| 40. |
- Yao, Bitao, et al.
(författare)
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Virtual data generation for human intention prediction based on digital modeling of human-robot collaboration
- 2024
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Ingår i: Robotics and Computer-Integrated Manufacturing. - : Elsevier BV. - 0736-5845 .- 1879-2537. ; 87
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Tidskriftsartikel (refereegranskat)abstract
- Human intention prediction is vital for the efficiency of human-robot collaboration (HRC) and is usually modeled based on data-driven methods. However, due to the complexity and diverse nature of HRC, data collection for human intention prediction suffers from low sampling efficiency which restricts the application of HRC in manufacturing. Different from traditional real world data collection, a digital modeling method for HRC is proposed in this paper to generate virtual HRC data. The dynamic musculoskeletal model of human is adopted to simulate the musculoskeletal dynamics of human. The metabolic energy consumption of human is computed and used as an indicator to evaluate the reality of the generated virtual data. The virtual data are used to train human intention prediction model and compared with experimental data. Experimental results show the reality of virtual data and its effectiveness for human intention modeling in human-robot collaborative assembly. The proposed method has potential for reducing the cost of data collection compared with purely experiments.
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| 41. |
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| 42. |
- Yi, Peng, et al.
(författare)
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Circulation of water masses in the Baltic Proper revealed through iodine isotopes
- 2013
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Ingår i: Applied Geochemistry. - : Elsevier BV. - 0883-2927 .- 1872-9134. ; 36, s. 118-124
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Tidskriftsartikel (refereegranskat)abstract
- Tracer technology has been used to understand water circulation in marine systems where the tracer dose is commonly injected into the marine waters through controlled experiments, accidental releases or waste discharges. Anthropogenic discharges of I-129 have been used to trace water circulation in the Arctic and North Atlantic Ocean. Here, I-129, together with I-127, is utilized as a tracer of water pathways and circulation in the Baltic Sea through collection of seawater depth profiles. The results indicate the presence of I-129 signatures which are distinct for each water mass and provide evidence for: (1) inflow water masses through the Drogden Sill that may reach as far as the SW of the Arkona Sea, (2) a portion of North Atlantic water in the bottom of Arkona basin, (3) cyclonic upwelling which breaks through the halocline in a pattern similar to the Baltic haline conveyor belt and (4) more influx of fresher water from the Gulf of Finland and Bothnian Sea in August relative to April. These findings provide advances in labeling and understanding water pathways in the Baltic Sea.
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| 43. |
- Yi, Peng, et al.
(författare)
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Depth profiles of I-129 species in the Bothnian Sea
- 2013
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Ingår i: Journal of Radioanalytical and Nuclear Chemistry. - : Springer Science and Business Media LLC. - 0236-5731 .- 1588-2780. ; 295:2, s. 1459-1463
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Tidskriftsartikel (refereegranskat)abstract
- The Bothnian Sea which is located between Finland and Sweden represents an important source of fresh water to the Baltic Sea. We here present new data on the radioactive isotope I-129 species from water samples collected in December 2009 at different depths in the Bothnian Sea. Concentrations of I-129(-) (iodide) in the Bothnian Sea range from 14 x 10(8) to 32 x 10(8) atoms/L, while (IO3)-I-129 (-) (iodate) concentrations are relatively low and fluctuating at 1 x 10(8) atoms/L. For nutrients data determined in the same samples as I-129, significant correlations could be found between I-129(-) and total P, NO3-N, SiO3-Si, but rather poor with NH4-N. The correlations suggest comparable source pathway of I-129(-) and nutrient parameters, while the source of NH4-N may be different. The small amounts and negligible change of (IO3)-I-129 (-) indicate prevailing extensive reduction of iodate in the Baltic Sea.
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| 44. |
- Yi, Peng, et al.
(författare)
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Model simulation of inflow water to the Baltic Sea based on I-129
- 2013
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Ingår i: Applied Radiation and Isotopes. - : Elsevier BV. - 0969-8043 .- 1872-9800. ; 82, s. 223-231
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Tidskriftsartikel (refereegranskat)abstract
- The semi-enclosed Baltic Sea represents a vital economic and recreational resource for more than 90 million people inhabiting its coasts. Extensive contamination of this sea by a variety of anthropogenic pollutants has raised the concern of the people in the region. Quantifying seawater inflow is crucial for estimating potential environmental risks as well as to find the best remedial strategy. We present here a model to estimate water inflow from the North Sea to the Baltic Sea by utilizing 1291 as a tracer. The results predicted inflow range of 230-450 km(3)/y with best fit value around 330 km(3)/y from the North Sea to the Baltic Sea during 1980-1999. Despite limited time series data on I-129, the model presented here demonstrates a new management tool for the Baltic Sea to calculate inflow water compared to conventional methods (such as salinity, temperature and hydrographic models).
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| 45. |
- Yi, Peng, et al.
(författare)
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Seasonal variation of I-129 species in the Baltic Proper
- 2013
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Ingår i: Journal of Radioanalytical and Nuclear Chemistry. - : Springer Science and Business Media LLC. - 0236-5731 .- 1588-2780. ; 295:3, s. 1797-1801
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Tidskriftsartikel (refereegranskat)abstract
- Iodine speciation plays a significant role in iodine volatilizing into atmosphere from the seas, as well as serving as a biological indicator. Despite this importance, the data on iodine species revealed inconclusive evidence of what factors controlling speciation transformation. We here present new data on profiles of I-129 speciation in the Baltic Proper during November 2009. Along with the two earlier investigations (August 2006 and April 2007), an assessment of seasonal variation of I-129 species is presented. The results show that, due to the anoxic nature of Baltic Proper, presence of (IO3)-I-129 (-) in the Baltic Proper does not follow an obvious seasonal cycle, as the case with I-129(-). Concentrations of I-129(-) in the Baltic Proper exhibit higher values in summer than the other two seasons (spring and winter), which might be associated with degrading of organic matter and release from sediment to water column that is more pronounced during summer. I-129(-) in surface water from the three seasons does not reflect the release function from the reprocessing facilities during the period April 2007 to November 2009. Consequently variability of I-129(-) in surface seawater of the Baltic Proper depends, to some extent, on local physical as well as biochemical conditions.
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| 46. |
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| 47. |
- Yin, Xu-Fei, et al.
(författare)
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Solving independent set problems with photonic quantum circuits
- 2023
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - 0027-8424 .- 1091-6490. ; 120:22
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Tidskriftsartikel (refereegranskat)abstract
- An independent set (IS) is a set of vertices in a graph such that no edge connects any two vertices. In adiabatic quantum computation [E. Farhi, et al., Science 292, 472–475 (2001); A. Das, B. K. Chakrabarti, Rev. Mod. Phys. 80, 1061–1081 (2008)], a given graph G(V, E) can be naturally mapped onto a many-body Hamiltonian , with edges ? being the two-body interactions between adjacent vertices ?. Thus, solving the IS problem is equivalent to finding all the computational basis ground states of . Very recently, non-Abelian adiabatic mixing (NAAM) has been proposed to address this task, exploiting an emergent non-Abelian gauge symmetry of [B. Wu, H. Yu, F. Wilczek, Phys. Rev. A 101, 012318 (2020)]. Here, we solve a representative IS problem ?(8,7) by simulating the NAAM digitally using a linear optical quantum network, consisting of three C-Phase gates, four deterministic two-qubit gate arrays (DGA), and ten single rotation gates. The maximum IS has been successfully identified with sufficient Trotterization steps and a carefully chosen evolution path. Remarkably, we find IS with a total probability of 0.875(16), among which the nontrivial ones have a considerable weight of about 31.4%. Our experiment demonstrates the potential advantage of NAAM for solving IS-equivalent problems.
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| 48. |
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| 49. |
- Zhang, Jing, et al.
(författare)
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Adaptive Laboratory Evolution of Halomonas bluephagenesis Enhances Acetate Tolerance and Utilization to Produce Poly(3-hydroxybutyrate)
- 2022
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Ingår i: Molecules. - : MDPI AG. - 1420-3049 .- 1420-3049. ; 27:9
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Tidskriftsartikel (refereegranskat)abstract
- Acetate is a promising economical and sustainable carbon source for bioproduction, but it is also a known cell-growth inhibitor. In this study, adaptive laboratory evolution (ALE) with acetate as selective pressure was applied to Halomonas bluephagenesis TD1.0, a fast-growing and contamination-resistant halophilic bacterium that naturally accumulates poly(3-hydroxybutyrate) (PHB). After 71 transfers, the evolved strain, B71, was isolated, which not only showed better fitness (in terms of tolerance and utilization rate) to high concentrations of acetate but also produced a higher PHB titer compared with the parental strain TD1.0. Subsequently, overexpression of acetyl-CoA synthetase (ACS) in B71 resulted in a further increase in acetate utilization but a decrease in PHB production. Through whole-genome resequencing, it was speculated that genetic mutations (single-nucleotide variation (SNV) in phaB, mdh, and the upstream of OmpA, and insertion of TolA) in B71 might contribute to its improved acetate adaptability and PHB production. Finally, in a 5 L bioreactor with intermittent feeding of acetic acid, B71 was able to produce 49.79 g/L PHB and 70.01 g/L dry cell mass, which were 147.2% and 82.32% higher than those of TD1.0, respectively. These results highlight that ALE provides a reliable method to harness H. bluephagenesis to metabolize acetate for the production of PHB or other high-value chemicals more efficiently.
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| 50. |
- Zhang, Li, et al.
(författare)
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Characterization of anti-BCG benz[α]anthraquinones and new siderophores from a Xinjiang desert-isolated rare actinomycete Nocardia sp. XJ31
- 2020
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Ingår i: Applied Microbiology and Biotechnology. - : Springer Science and Business Media LLC. - 0175-7598 .- 1432-0614. ; 104:19, s. 8267-8278
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Tidskriftsartikel (refereegranskat)abstract
- The current global demand for novel anti-TB drugs has drawn urgent attention on the discovery of natural product compounds with anti-TB activity. Lots of efforts have emphasized on environmental samples from unexplored or underexplored natural habits and identified numerous rare actinomycete taxa producing structurally diverse bioactive natural products. Herein, we report a survey of the rare actinobacteria diversity in Xinjiang region together with the discovery of anti-TB active natural products from these strains. We have collected 17 soil samples at different sites with different environmental conditions, from which 39 rare actinobacteria were identified by using a selective isolation strategy with 5 media variations. Among those isolated strains, XJ31 was identified as a new Nocardia sp. based on 16S rRNA gene analysis. Through one strain-many compounds (OSMAC) strategy combined with anti-Bacillus Calmette-Guérin bioassay-guided isolation, two groups of compounds were identified. They were twelve siderophores (nocardimicins, 1-12) and two anthraquinones (brasiliquinones, 13 and 14) and ten of them were identified as new compounds. The structures of the purified compounds were elucidated using HR-ESI-MS, 1D NMR, and 2D NMR techniques. The anti-TB bioassays revealed that the two benz[α]anthraquinones have potent activity against BCG (MICs = 25 μM), which can be used as a promising start point for further anti-TB drug development.
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