| 1. |
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| 2. |
- Chen, Hai-Xia, et al.
(författare)
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A comparative study of nemertean complete mitochondrial genomes, including two new ones for Nectonemertes cf. mirabilis and Zygeupolia rubens, may elucidate the fundamental pattern for the phylum Nemertea
- 2012
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Ingår i: Bmc Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Background: The mitochondrial genome is important for studying genome evolution as well as reconstructing the phylogeny of organisms. Complete mitochondrial genome sequences have been reported for more than 2200 metazoans, mainly vertebrates and arthropods. To date, from a total of about 1275 described nemertean species, only three complete and two partial mitochondrial DNA sequences from nemerteans have been published. Here, we report the entire mitochondrial genomes for two more nemertean species: Nectonemertes cf. mirabilis and Zygeupolia rubens. Results: The sizes of the entire mitochondrial genomes are 15365 bp for N. cf. mirabilis and 15513 bp for Z. rubens. Each circular genome contains 37 genes and an AT-rich non-coding region, and overall nucleotide composition is AT-rich. In both species, there is significant strand asymmetry in the distribution of nucleotides, with the coding strand being richer in T than A and in G than C. The AT-rich non-coding regions of the two genomes have some repeat sequences and stem-loop structures, both of which may be associated with the initiation of replication or transcription. The 22 tRNAs show variable substitution patterns in nemerteans, with higher sequence conservation in genes located on the H strand. Gene arrangement of N. cf. mirabilis is identical to that of Paranemertes cf. peregrina, both of which are Hoplonemertea, while that of Z. rubens is the same as in Lineus viridis, both of which are Heteronemertea. Comparison of the gene arrangements and phylogenomic analysis based on concatenated nucleotide sequences of the 12 mitochondrial protein-coding genes revealed that species with closer relationships share more identical gene blocks. Conclusion: The two new mitochondrial genomes share many features, including gene contents, with other known nemertean mitochondrial genomes. The tRNA families display a composite substitution pathway. Gene order comparison to the proposed ground pattern of Bilateria and some lophotrochozoans suggests that the nemertean ancestral mitochondrial gene order most closely resembles the heteronemertean type. Phylogenetic analysis proposes a sister-group relationship between Hetero- and Hoplonemertea, which supports one of two recent alternative hypotheses of nemertean phylogeny.
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| 3. |
- Grimsholm, Ola, 1979, et al.
(författare)
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Absence of surrogate light chain results in spontaneous autoreactive germinal centres expanding V(H)81X-expressing B cells
- 2015
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Random recombination of antibody heavy- and light-chain genes results in a diverse B-cell receptor (BCR) repertoire including self-reactive BCRs. However, tolerance mechanisms that prevent the development of self-reactive B cells remain incompletely understood. The absence of the surrogate light chain, which assembles with antibody heavy chain forming a pre-BCR, leads to production of antinuclear antibodies (ANAs). Here we show that the naive follicular B-cell pool is enriched for cells expressing prototypic ANA heavy chains in these mice in a non-autoimmune background with a broad antibody repertoire. This results in the spontaneous formation of T-cell-dependent germinal centres that are enriched with B cells expressing prototypic ANA heavy chains. However, peripheral tolerance appears maintained by selection thresholds on cells entering the memory B-cell and plasma cell pools, as exemplified by the exclusion of cells expressing the intrinsically self-reactive V(H)81X from both pools.
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| 4. |
- Hu, Hai-Xi, et al.
(författare)
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Structural insights into HetR-PatS interaction involved in cyanobacterial pattern formation
- 2015
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- The one-dimensional pattern of heterocyst in the model cyanobacterium Anabaena sp. PCC 7120 is coordinated by the transcription factor HetR and PatS peptide. Here we report the complex structures of HetR binding to DNA, and its hood domain (HetR(Hood)) binding to a PatS-derived hexapeptide (PatS6) at 2.80 and 2.10 angstrom, respectively. The intertwined HetR dimer possesses a couple of novel HTH motifs, each of which consists of two canonical alpha-helices in the DNA-binding domain and an auxiliary alpha-helix from the flap domain of the neighboring subunit. Two PatS6 peptides bind to the lateral clefts of HetR(Hood), and trigger significant conformational changes of the flap domain, resulting in dissociation of the auxiliary alpha-helix and eventually release of HetR from the DNA major grove. These findings provide the structural insights into a prokaryotic example of Turing model.
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| 5. |
- Ji, Zhong-Hai, et al.
(författare)
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High-throughput screening and machine learning for the efficient growth of high-quality single-wall carbon nanotubes
- 2021
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Ingår i: Nano Reseach. - : Tsinghua University Press. - 1998-0124 .- 1998-0000. ; 14, s. 4610-4615
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Tidskriftsartikel (refereegranskat)abstract
- It has been a great challenge to optimize the growth conditions toward structure-controlled growth of single-wall carbon nanotubes (SWCNTs). Here, a high-throughput method combined with machine learning is reported that efficiently screens the growth conditions for the synthesis of high-quality SWCNTs. Patterned cobalt (Co) nanoparticles were deposited on a numerically marked silicon wafer as catalysts, and parameters of temperature, reduction time and carbon precursor were optimized. The crystallinity of the SWCNTs was characterized by Raman spectroscopy where the featured G/D peak intensity (IG/ID) was extracted automatically and mapped to the growth parameters to build a database. 1,280 data were collected to train machine learning models. Random forest regression (RFR) showed high precision in predicting the growth conditions for high-quality SWCNTs, as validated by further chemical vapor deposition (CVD) growth. This method shows great potential in structure-controlled growth of SWCNTs. [Figure not available: see fulltext.].
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| 6. |
- Nie, Shuai, et al.
(författare)
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Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color
- 2023
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Ingår i: Horticulture Research. - : Oxford University Press. - 2662-6810 .- 2052-7276. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea breeding. Gapless genome assembly was generated for the yellow-flowered azalea, Rhododendron molle. Comparative genomics found recent proliferation of long terminal repeat retrotransposons (LTR-RTs), especially Gypsy, has resulted in a 125 Mb (19%) genome size increase in species-specific regions, and a significant amount of dispersed gene duplicates (13 402) and pseudogenes (17 437). Metabolomic assessment revealed that yellow flower coloration is attributed to the dynamic changes of carotenoids/flavonols biosynthesis and chlorophyll degradation. Time-ordered gene co-expression networks (TO-GCNs) and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct flower pigmentation. B3 and ERF TFs were found dominating the gene regulation of carotenoids/flavonols characterized pigmentation in R. molle, while WRKY, ERF, WD40, C2H2, and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-flowered R simsii. This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.
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| 7. |
- Ren, Bo, et al.
(författare)
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A Carbohydrate- Anion Recognition System in Aprotic Solvents
- 2014
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Ingår i: Chemistry - An Asian Journal. - : Wiley. - 1861-4728 .- 1861-471X. ; 9:5, s. 1298-1304
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Tidskriftsartikel (refereegranskat)abstract
- A carbohydrate-anion recognition system in nonpolar solvents is reported, in which complexes form at the B-faces of -D-pyranosides with H1-, H3-, and H5-cis patterns similar to carbohydrate- interactions. The complexation effect was evaluated for a range of carbohydrate structures; it resulted in either 1:1 carbohydrate-anion complexes, or 1:2 complex formation depending on the protection pattern of the carbohydrate. The interaction was also evaluated with different anions and solvents. In both cases it resulted in significant binding differences. The results indicate that complexation originates from van der Waals interactions or weak CHA(-) hydrogen bonds between the binding partners and is related to electron-withdrawing groups of the carbohydrates as well as increased hydrogen-bond-accepting capability of the anions.
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| 8. |
- Ren, Bo, et al.
(författare)
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An Iron(III) Catalyst with Unusually Broad Substrate Scope in Regioselective Alkylation of Diols and Polyols
- 2016
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Ingår i: Chemistry - A European Journal. - : Wiley-VCH Verlagsgesellschaft. - 0947-6539 .- 1521-3765. ; 22:7, s. 2481-2486
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Tidskriftsartikel (refereegranskat)abstract
- In this study, [Fe(dibm)(3)] (dibm=diisobutyrylmethane) is shown to have unusually broad scope as a catalyst for the selective monoalkylation of a diverse set of 1,2- and 1,3-diol-containing structures. The mechanism is proposed to proceed via a cyclic dioxolane-type intermediate, formed between the iron(III) species and two adjacent hydroxyl groups. This approach represents the first transition-metal catalysts that are able to replace stoichiometric amounts of organotin reagents in regioselective alkylation. The reactions generally lead to very high regioselectivities and high yields, on par with, or better than, previous methods used for regioselective alkylation.
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| 9. |
- Ren, Bo, et al.
(författare)
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Regioselective Acetylation of Diols and Polyols by Acetate Catalysis: Mechanism and Application.
- 2014
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Ingår i: Journal of Organic Chemistry. - : American Chemical Society (ACS). - 0022-3263 .- 1520-6904. ; 79:17, s. 8134-8142
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Tidskriftsartikel (refereegranskat)abstract
- We propose a principle for H-bonding activation in acylation of hydroxyl groups, where the acylation is activated by the formation of hydrogen bonds between hydroxyl groups and anions. With the guidance of this principle, we demonstrate a method for the selective acylation of carbohydrates. By this method, diols and polyols are regioselectively acetylated in high yields under mild conditions using catalytic amts. of acetate. In comparison to other methods involving reagents such as organotin, organoboron, organosilicon, organobase, and metal salts, this method is more environmentally friendly, convenient, and efficient and is also assocd. with higher regioselectivity. We have performed a thorough quantum chem. study to decipher the mechanism, which suggests that acetate first forms a dual H-bond complex with a diol, which enables subsequent monoacylation by acetic anhydride under mild conditions. The regioselectivity appears to originate from the inherent structure of the diols and polyols and their specific interactions with the coordinating acetate catalyst. [on SciFinder(R)]
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| 10. |
- Ren, Lin-Ling, et al.
(författare)
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Subcellular relocalization and positive selection play key Roles in the retention of duplicate genes of populus class III peroxidase family
- 2014
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Ingår i: The Plant Cell. - : Oxford University Press (OUP). - 1040-4651 .- 1532-298X. ; 26:6, s. 2404-2419
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Tidskriftsartikel (refereegranskat)abstract
- Gene duplication is the primary source of new genes and novel functions. Over the course of evolution, many duplicate genes lose their function and are eventually removed by deletion. However, some duplicates have persisted and evolved diverse functions. A particular challenge is to understand how this diversity arises and whether positive selection plays a role. In this study, we reconstructed the evolutionary history of the class III peroxidase (PRX) genes from the Populus trichocarpa genome. PRXs are plant-specific enzymes that play important roles in cell wall metabolism and in response to biotic and abiotic stresses. We found that two large tandem-arrayed clusters of PRXs evolved from an ancestral cell wall type PRX to vacuole type, followed by tandem duplications and subsequent functional specification. Substitution models identified seven positively selected sites in the vacuole PRXs. These positively selected sites showed significant effects on the biochemical functions of the enzymes. We also found that positive selection acts more frequently on residues adjacent to, rather than directly at, a critical active site of the enzyme, and on flexible regions rather than on rigid structural elements of the protein. Our study provides new insights into the adaptive molecular evolution of plant enzyme families.
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| 11. |
- Ren, Weicheng, et al.
(författare)
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Complete genome sequence of acute viral necrosis virus associated with massive mortality outbreaks in the Chinese scallop, Chlamys farreri.
- 2013
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Ingår i: Virology journal. - 1743-422X. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Acute viral necrosis virus (AVNV) is the causative agent of a serious disease resulting in high mortality in cultured Chinese scallops, Chlamys farreri. We have sequenced and analyzed the complete genome of AVNV. RESULTS: The AVNV genome is a linear, double-stranded DNA molecule of 210,993 bp with a nucleotide composition of 38.5% G + C. A total of 123 open reading frames were predicted to encode functional proteins, ranging from 41 to 1,878 amino acid residues. The DNA sequence of AVNV is 97% identical to that of ostreid herpesvirus 1 (OsHV-1), and the amino acid sequences of the encoded proteins of these two viruses are 94-100% identical. The genomic organization of AVNV is similar to that of OsHV-1, and consists of two unique regions (170.4 kb and 3.4 kb, respectively), each flanked by two inverted repeats (7.6 kb and 10.2 kb, respectively), with a third unique region (1.5 kb) situated between the two internal repeats. CONCLUSIONS: Our results indicate that AVNV is a variant of OsHV-1. The AVNV genome sequence provides information useful for understanding the evolution and divergence of OsHV-1 in marine molluscs.
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| 12. |
- Shi, Tian-Le, et al.
(författare)
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High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar
- 2024
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Ingår i: Plant Physiology. - : Oxford University Press. - 0032-0889 .- 1532-2548. ; 195:1, s. 652-670
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Tidskriftsartikel (refereegranskat)abstract
- Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid “84K” (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.
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| 13. |
- Wang, Faming, et al.
(författare)
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Coastal blue carbon in China as a nature-based solution toward carbon neutrality
- 2023
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Ingår i: INNOVATION. - 2666-6758. ; 4:5
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Forskningsöversikt (refereegranskat)abstract
- To achieve the Paris Agreement, China pledged to become "Carbon Neutral" by the 2060s. In addition to massive decarbonization, this would require significant changes in ecosystems toward negative CO2 emissions. The ability of coastal blue carbon ecosystems (BCEs), including mangrove, salt marsh, and seagrass meadows, to sequester large amounts of CO2 makes their conservation and restoration an important "nature-based solution (NbS)" for climate adaptation and mitigation. In this review, we examine how BCEs in China can contribute to climate mitigation. On the national scale, the BCEs in China store up to 118 Tg C across a total area of 1,440,377 ha, including over 75% as unvegetated tidal flats. The annual sedimental C burial of these BCEs reaches up to 2.06 Tg C year(-1) , of which most occurs in salt marshes and tidal flats. The lateral C flux of mangroves and salt marshes contributes to 1.17 Tg C year(-1) along the Chinese coastline. Conservation and restoration of BCEs benefit climate change mitigation and provide other ecological services with a value of $32,000 ha(-1) year(-1). The potential practices and technologies that can be implemented in China to improve BCE C sequestration, including their constraints and feasibility, are also outlined. Future directions are suggested to improve blue carbon estimates on aerial extent, carbon stocks, sequestration, and mitigation potential. Restoring and preserving BCEs would be a cost-effective step to achieve Carbon Neutral by 2060 in China despite various barriers that should be removed.
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| 14. |
- Yuan-Biao, Qiao, et al.
(författare)
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Antifungal resistance-modifying multiplexing action of Momordica charantia protein and phosphorylated derivatives on the basis of growth-dependent gene coregulation in Candida albicans
- 2021
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Ingår i: Medical Mycology. - : Oxford University Press. - 1369-3786 .- 1460-2709. ; 59:6, s. 515-527
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Tidskriftsartikel (refereegranskat)abstract
- Fungal growth-dependent gene coregulation is strongly implicated in alteration of gene-encoding target proteases ruling with an antifungal resistance niche and biology of resistant mutants. On the basis of multialterative processes in this platform, the resistance-modifying strategy is designed in ketoconazole resistant Candida albicans and evaluated with less selective Momordica charantia protein and allosterically phosphorylated derivatives at the Thr102, Thr24 and Thr255 sites, respectively. We demonstrate absolutely chemosensitizing efficacy regarding stepwise-modifying resistance in sensitivity, by a load of only 26.23-40.00 mu g/l agents in Sabouraud's dextrose broth. Five successive modifying-steps realize the decreasing of ketoconazole E-test MIC50 from 11.10 to a lower level than 0.10 mg/l. With the ketoconazole resistance-modifying, colony undergoes a high-frequency morphological switch between high ploidy (opaque) and small budding haploid (white). A cellular event in the first modifying-step associates with relatively slow exponential growth (ie, a 4-h delay)-dependent action, mediated by agents adsorption. Moreover, multiple molecular roles are coupled with intracellularly and extracellularly binding to ATP-dependent RNA helicase dbp6; the 0.08-2.45 fold upregulation of TATA-box-binding protein, rRNA-processing protein and translation initiation factor 5A; and the 7.52-55.33% decrease of cytochrome P450 lanosterol 14 alpha-demethylase, glucan 1, 3-beta glucosidase, candidapepsin-1 and 1-acylglycerol-3-phosphate O-acyltransferase. Spatial and temporal gene coregulation, in the transcription and translation initiation stages with rRNA-processing, is a new coprocessing platform enabling target protease attenuations for resistance-impairing. An updated resistance-modifying measure of these agents in the low-dose antifungal strategic design may provide opportunities to a virtually safe therapy that is in high dose-dependency.
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| 15. |
- Zhao, Shi-Wei, et al.
(författare)
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Haplotype-resolved genome assembly of Coriaria nepalensis a non-legume nitrogen-fixing shrub
- 2023
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Ingår i: Scientific Data. - : Springer Nature. - 2052-4463. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Coriaria nepalensis Wall. (Coriariaceae) is a nitrogen-fixing shrub which forms root nodules with the actinomycete Frankia. Oils and extracts of C. nepalensis have been reported to be bacteriostatic and insecticidal, and C. nepalensis bark provides a valuable tannin resource. Here, by combining PacBio HiFi sequencing and Hi-C scaffolding techniques, we generated a haplotype-resolved chromosome-scale genome assembly for C. nepalensis. This genome assembly is approximately 620 Mb in size with a contig N50 of 11 Mb, with 99.9% of the total assembled sequences anchored to 40 pseudochromosomes. We predicted 60,862 protein-coding genes of which 99.5% were annotated from databases. We further identified 939 tRNAs, 7,297 rRNAs, and 982 ncRNAs. The chromosome-scale genome of C. nepalensis is expected to be a significant resource for understanding the genetic basis of root nodulation with Frankia, toxicity, and tannin biosynthesis.
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| 16. |
- Zhou, Guoyi, et al.
(författare)
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Climate and litter C/N ratio constrain soil organic carbon accumulation
- 2019
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Ingår i: National Science Review. - : Oxford University Press (OUP). - 2095-5138 .- 2053-714X. ; 6:4, s. 746-757
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Tidskriftsartikel (refereegranskat)abstract
- Soil organic carbon (SOC) plays critical roles in stabilizing atmospheric CO2 concentration, but the mechanistic controls on the amount and distribution of SOC on global scales are not well understood. In turn, this has hampered the ability to model global C budgets and to find measures to mitigate climate change. Here, based on the data from a large field survey campaign with 2600 plots across China's forest ecosystems and a global collection of published data from forested land, we find that a low litter carbon-to-nitrogen ratio (C/N) and high wetness index (P/PET, precipitation-to-potential-evapotranspiration ratio) are the two factors that promote SOC accumulation, with only minor contributions of litter quantity and soil texture. The field survey data demonstrated that high plant diversity decreased litter C/N and thus indirectly promoted SOC accumulation by increasing the litter quality. We conclude that any changes in plant-community composition, plant-species richness and environmental factors that can reduce the litter C/N ratio, or climatic changes that increase wetness index, may promote SOC accumulation. The study provides a guideline for modeling the carbon cycle of various ecosystem scales and formulates the principle for land-based actions for mitigating the rising atmospheric CO2 concentration.
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| 17. |
- Zhou, Yixuan, et al.
(författare)
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H-Bonding Activation in Highly Regioselective Acetylation of Diols.
- 2013
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Ingår i: Journal of Organic Chemistry. - : American Chemical Society (ACS). - 0022-3263 .- 1520-6904. ; 78:22, s. 11618-11622
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Tidskriftsartikel (refereegranskat)abstract
- H-bonding activation in the regioselective acetylation of vicinal and 1,3-diols is presented. Herein, the acetylation of the hydroxyl group with acetic anhydride can be activated by the formation of H-bonds between the hydroxyl group and anions. The reaction exhibits high regioselectivity when a catalytic amt. of tetrabutylammonium acetate is employed. Mechanistic studies indicated that acetate anion forms dual H-bonding complexes with the diol, which facilitates the subsequent regioselective monoacetylation. [on SciFinder(R)]
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