| 1. |
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- 2019
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Journal article (peer-reviewed)
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| 2. |
- Chen, Jie, et al.
(author)
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Bidirectional Mendelian Randomisation Analysis Provides Evidence for the Causal Involvement of Dysregulation of CXCL9, CCL11 and CASP8 in the Pathogenesis of Ulcerative Colitis
- 2023
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In: Journal of Crohn's & Colitis. - : Oxford University Press. - 1873-9946 .- 1876-4479. ; 17:5, s. 777-785
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Journal article (peer-reviewed)abstract
- Background and Aims Systemic inflammation is well recognised to be associated with ulcerative colitis [UC], but whether these effects are causal or consequential remains unclear. We aimed to define potential causal relationship of cytokine dysregulation with different tiers of evidence. Methods We first synthesised serum proteomic profiling data from two multicentred observational studies, in which a panel of systemic inflammatory proteins was analysed to examine their associations with UC risk. To further dissect observed associations, we then performed a bidirectional two-sample Mendelian randomisation [TSMR] analysis from both forward and reverse directions using five genome-wide association study [GWAS] summary level data for serum proteomic profiles and the largest GWAS of 28 738 European-ancestry individuals for UC risk. Results Pooled analysis of serum proteomic data identified 14 proteins to be associated with the risk of UC. Forward MR analysis using only cis-acting protein quantitative trait loci [cis-pQTLs] or trans-pQTLs further validated causal associations of two chemokines and the increased risk of UC: C-X-C motif chemokine ligand 9 [CXCL9] [OR 1.45, 95% CI 1.08, 1.95, p = 0.012] and C-C motif chemokine ligand 11 [CCL11] [OR 1.14, 95% CI 1.09, 1.18, p = 3.89 x 10(-10)]. Using both cis- and trans-acting pQTLs, an association of caspase-8 [CASP8] [OR 1.04, 95% CI 1.03, 1.05, p = 7.63 x 10(-19)] was additionally identified. Reverse MR did not find any influence of genetic predisposition to UC on any of these three inflammation proteins. Conclusion Pre-existing elevated levels of CXCL9, CCL11 and CASP8 may play a role in the pathogenesis of UC.
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| 3. |
- Geng, Huifang, et al.
(author)
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Controlled synthesis of highly stable lead-free bismuth halide perovskite nanocrystals : tructures and photophysics
- 2023
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In: SCIENCE CHINA Materials. - : Springer Science and Business Media LLC. - 2095-8226 .- 2199-4501. ; 66:5, s. 2079-2089
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Journal article (peer-reviewed)abstract
- Recently, cesium bismuth halide perovskites have emerged as potential substitutes to their counterparts, cesium lead halide perovskites, owing to their low toxicity. However, the photophysics of cesium-bismuth halides nanocrystals (NCs) have not yet been fully rationalized because their structures remain highly debated. The ultraviolet-visible (UV-vis) absorption along with other photophysical properties such as the nature and lifetime of the excited states vary considerably across the previous reports. Here, we successfully synthesize pure Cs3BiBr6 and Cs3Bi2Br9 NCs via a modified hot-injection method, where the structure can be easily controlled by tuning the reaction temperature. The UV-vis absorption spectrum of the pure Cs3Bi2Br9 NCs features two characteristic peaks originating from the absorption of the first exciton and second exciton, respectively, which ultimately clarifies the debate in the previous reports. Using femtosecond transient absorption spectroscopy, we systematically investigate the excited state dynamics of the Cs3Bi2Br9 NCs and reveal that the photoexcited carriers undergo a self-trapping process within 3 ps after excitation. More intriguingly, the Cs3Bi2Br9 NCs prepared by this method show much better photostability than those prepared by the ligand-assisted reprecipitation process. Photodetectors based on these Cs3Bi2Br9 NCs show a sensitive light response, demonstrating the definite potential for breakthrough optoelectronic applications. [Figure not available: see fulltext.].
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| 4. |
- Horvatovich, Peter, et al.
(author)
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Quest for Missing Proteins : Update 2015 on Chromosome-Centric Human Proteome Project
- 2015
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In: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 14:9, s. 3415-3431
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Journal article (other academic/artistic)abstract
- This paper summarizes the recent activities of the Chromosome-Centric Human Proteome Project (C-HPP) consortium, which develops new technologies to identify yet-to-be annotated proteins (termed "missing proteins") in biological samples that lack sufficient experimental evidence at the protein level for confident protein identification. The C-HPP also aims to identify new protein forms that may be caused by genetic variability, post-translational modifications, and alternative splicing. Proteogenomic data integration forms the basis of the C-HPP's activities; therefore, we have summarized some of the key approaches and their roles in the project. We present new analytical technologies that improve the chemical space and lower detection limits coupled to bioinformatics tools and some publicly available resources that can be used to improve data analysis or support the development of analytical assays. Most of this paper's content has been compiled from posters, slides, and discussions presented in the series of C-HPP workshops held during 2014. All data (posters, presentations) used are available at the C-HPP Wild (http://c-hpp.webhosting.rug.nl/) and in the Supporting Information.
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| 5. |
- Liu, Juan, 1994, et al.
(author)
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Restricting Promiscuity of Plant Flavonoid 3'-Hydroxylase and 4'-O-Methyltransferase Improves the Biosynthesis of (2S)-Hesperetin in E. coli
- 2023
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In: Journal of Agricultural and Food Chemistry. - 0021-8561 .- 1520-5118. ; 71:25, s. 9826-9835
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Journal article (peer-reviewed)abstract
- Enzyme promiscuity is evolutionarily advantageous to plants for gaining new enzyme functions when adapting to environmental challenges. However, this promiscuity can negatively affect the expression of genes encoding for plant enzymes in microorganisms. Here, we show that refining the promiscuity of flavonoid 3'-hydroxylase (F3'H) and 4'-O-methyltransferase (F4'OMT) improves (2S)-hesperetin production in Escherichia coli. First, we employed inverse molecular docking to screen a highly substrate-specific ThF3'H from Tricyrtis hirta, which could selectively convert 100 mg L-1 (2S)-naringenin to (2S)-eriodictyol but not (2S)-isosakuranetin, with a cytochrome P450 reductase from Arabidopsis thaliana. Second, we employed a directed evolution approach to restrict the promiscuity of MpOMT from Mentha x piperita. The strain harboring the MpOMT(S142V) mutant presented a remarkably increased preference for (2S)-eriodictyol. Finally, 27.5 mg L-1 (2S)-hesperetin was produced, while only minor amounts of (2S)-eriodictyol and (2S)-isosakuranetin accumulated as byproducts. This value represents a 14-fold increase in (2S)-hesperetin compared to the parental strain, along with a dramatic reduction in side products. Our work highlights the benefit of alleviating the promiscuity of plant enzymes when engineering production of natural products by microbial cell factories.
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| 6. |
- Liu, Wei, et al.
(author)
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Pickering multiphase materials using plant-based cellulosic micro/nanoparticles
- 2024
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In: Aggregate. - 2692-4560.
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Research review (peer-reviewed)abstract
- Pickering multiphase systems stabilized by solid particles have recently attracted increasing attention due to their excellent stability. Among various solid stabilizers, natural and renewable cellulosic micro/nanoparticles that are derived from agricultural and forestry sources have become promising candidates for Pickering stabilization due to their unique morphological features and tunable surface properties. In this review, recent progress on forming and stabilizing Pickering multiphase systems using cellulosic colloidal particles is summarized, including the physicochemical factors affecting their assembly at the interfaces and the preparation methods suitable for producing Pickering emulsions. In addition, relevant application prospects of corresponding Pickering multiphase materials are outlined. Finally, current challenges and future perspectives of such renewable Pickering multiphase systems are presented. This review aims to encourage the utilization of cellulosic micro/nanoparticles as key components in the development of Pickering systems, leading to enhanced performance and unique functionalities. image
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| 7. |
- Omenn, Gilbert S., et al.
(author)
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Progress Identifying and Analyzing the Human Proteome : 2021 Metrics from the HUPO Human Proteome Project
- 2021
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In: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 20:12, s. 5227-5240
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Journal article (peer-reviewed)abstract
- The 2021 Metrics of the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 357 (92.8%) of the 19 778 predicted proteins coded in the human genome, a gain of 483 since 2020 from reports throughout the world reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 478 to 1421. This represents remarkable progress on the proteome parts list. The utilization of proteomics in a broad array of biological and clinical studies likewise continues to expand with many important findings and effective integration with other omics platforms. We present highlights from the Immunopeptidomics, Glycoproteomics, Infectious Disease, Cardiovascular, MusculoSkeletal, Liver, and Cancers B/D-HPP teams and from the Knowledge-base, Mass Spectrometry, Antibody Profiling, and Pathology resource pillars, as well as ethical considerations important to the clinical utilization of proteomics and protein biomarkers.
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| 8. |
- Omenn, Gilbert S., et al.
(author)
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Progress on Identifying and Characterizing the Human Proteome : 2018 Metrics from the HUPO Human Proteome Project
- 2018
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In: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 17:12, s. 4031-4041
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Journal article (peer-reviewed)abstract
- The Human Proteome Project (HPP) annually reports on progress throughout the field in credibly identifying and characterizing the human protein parts list and making proteomics an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2018-01-17, the baseline for this sixth annual HPP special issue of the Journal of Proteome Research, contains 17 470 PE1 proteins, 89% of all neXtProt predicted PE1-4 proteins, up from 17 008 in release 2017-01-23 and 13 975 in release 2012-02-24. Conversely, the number of neXtProt PE2,3,4 missing proteins has been reduced from 2949 to 2579 to 2186 over the past two years. Of the PEI proteins, 16 092 are based on mass spectrometry results, and 1378 on other kinds of protein studies, notably protein protein interaction findings. PeptideAtlas has 15 798 canonical proteins, up 625 over the past year, including 269 from SUMOylation studies. The largest reason for missing proteins is low abundance. Meanwhile, the Human Protein Atlas has released its Cell Atlas, Pathology Atlas, and updated Tissue Atlas, and is applying recommendations from the International Working Group on Antibody Validation. Finally, there is progress using the quantitative multiplex organ-specific popular proteins targeted proteomics approach in various disease categories.
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| 9. |
- Omenn, Gilbert S., et al.
(author)
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Research on the Human Proteome Reaches a Major Milestone : > 90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project
- 2020
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In: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 19:12, s. 4735-4746
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Journal article (peer-reviewed)abstract
- According to the 2020 Metrics of the HUPO Human Proteome Project (HPP), expression has now been detected at the protein level for >90% of the 19 773 predicted proteins coded in the human genome. The HPP annually reports on progress made throughout the world toward credibly identifying and characterizing the complete human protein parts list and promoting proteomics as an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2020-01 classified 17 874 proteins as PE1, having strong protein-level evidence, up 180 from 17 694 one year earlier. These represent 90.4% of the 19 773 predicted coding genes (all PE1,2,3,4 proteins in neXtProt). Conversely, the number of neXtProt PE2,3,4 proteins, termed the "missing proteins" (MPs), was reduced by 230 from 2129 to 1899 since the neXtProt 2019-01 release. PeptideAtlas is the primary source of uniform reanalysis of raw mass spectrometry data for neXtProt, supplemented this year with extensive data from MassIVE. PeptideAtlas 2020-01 added 362 canonical proteins between 2019 and 2020 and MassIVE contributed 84 more, many of which converted PE1 entries based on non-MS evidence to the MS-based subgroup. The 19 Biology and Disease-driven B/D-HPP teams continue to pursue the identification of driver proteins that underlie disease states, the characterization of regulatory mechanisms controlling the functions of these proteins, their proteoforms, and their interactions, and the progression of transitions from correlation to coexpression to causal networks after system perturbations. And the Human Protein Atlas published Blood, Brain, and Metabolic Atlases.
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| 10. |
- Omenn, Gilbert S., et al.
(author)
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The 2022 Report on the Human Proteome from the HUPO Human Proteome Project
- 2023
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In: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 22:4, s. 1024-1042
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Journal article (peer-reviewed)abstract
- The 2022 Metrics of the Human Proteome from the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 407 (93.2%) of the 19 750 predicted proteins coded in the human genome, a net gain of 50 since 2021 from data sets generated around the world and reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 78 from 1421 to 1343. This represents continuing experimental progress on the human proteome parts list across all the chromosomes, as well as significant reclassifications. Meanwhile, applying proteomics in a vast array of biological and clinical studies continues to yield significant findings and growing integration with other omics platforms. We present highlights from the Chromosome-Centric HPP, Biology and Disease-driven HPP, and HPP Resource Pillars, compare features of mass spectrometry and Olink and Somalogic platforms, note the emergence of translation products from ribosome profiling of small open reading frames, and discuss the launch of the initial HPP Grand Challenge Project, “A Function for Each Protein”.
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| 11. |
- Omenn, Gilbert S., et al.
(author)
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The 2023 Report on the Proteome from the HUPO Human Proteome Project
- 2024
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In: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 23:2, s. 532-549
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Research review (peer-reviewed)abstract
- Since 2010, the Human Proteome Project (HPP), the flagship initiative of the Human Proteome Organization (HUPO), has pursued two goals: (1) to credibly identify the protein parts list and (2) to make proteomics an integral part of multiomics studies of human health and disease. The HPP relies on international collaboration, data sharing, standardized reanalysis of MS data sets by PeptideAtlas and MassIVE-KB using HPP Guidelines for quality assurance, integration and curation of MS and non-MS protein data by neXtProt, plus extensive use of antibody profiling carried out by the Human Protein Atlas. According to the neXtProt release 2023-04-18, protein expression has now been credibly detected (PE1) for 18,397 of the 19,778 neXtProt predicted proteins coded in the human genome (93%). Of these PE1 proteins, 17,453 were detected with mass spectrometry (MS) in accordance with HPP Guidelines and 944 by a variety of non-MS methods. The number of neXtProt PE2, PE3, and PE4 missing proteins now stands at 1381. Achieving the unambiguous identification of 93% of predicted proteins encoded from across all chromosomes represents remarkable experimental progress on the Human Proteome parts list. Meanwhile, there are several categories of predicted proteins that have proved resistant to detection regardless of protein-based methods used. Additionally there are some PE1–4 proteins that probably should be reclassified to PE5, specifically 21 LINC entries and ∼30 HERV entries; these are being addressed in the present year. Applying proteomics in a wide array of biological and clinical studies ensures integration with other omics platforms as reported by the Biology and Disease-driven HPP teams and the antibody and pathology resource pillars. Current progress has positioned the HPP to transition to its Grand Challenge Project focused on determining the primary function(s) of every protein itself and in networks and pathways within the context of human health and disease.
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| 12. |
- Xiao, Zhiqiang, et al.
(author)
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Systematic Engineering of Saccharomyces cerevisiae Chassis for Efficient Flavonoid-7-O-Disaccharide Biosynthesis
- 2023
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In: ACS Synthetic Biology. - 2161-5063. ; 12:9, s. 2740-2749
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Journal article (peer-reviewed)abstract
- Flavonoids are an essential class of secondary metabolites found in plants and possess various nutritional, medicinal, and agricultural properties. However, the poor water solubility of flavonoid aglycones limits their potential applications. To overcome this issue, glycosylation is a promising approach for improving water solubility and bioavailability. In this study, we constructed a flavonoid-7-O-disaccharide biosynthetic pathway with flavonoid aglycones as substrates in Saccharomyces cerevisiae. Subsequently, through metabolic engineering and promoter strategies, we constructed a UDP-rhamnose regeneration system and optimized the UDP-glucose (UDPG) synthetic pathway. The optimized strain produced up to 131.3 mg/L eriocitrin. After this, the chassis cells were applied to other flavonoids, with substrates such as (2S)-naringenin, (2S)-hesperetin, diosmetin, and (2S)-eriodictyol, which resulted in the synthesis of 179.9 mg/L naringin, 276.6 mg/L hesperidin, 249.0 mg/L neohesperidin, 30.4 mg/L diosmin, and 100.7 mg/L neoeriocitrin. To the best of our knowledge, this is the first report on the biosynthesis of flavonoid-7-O-disaccharide.
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| 13. |
- Yu, Xianbin, et al.
(author)
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Photonic-wireless Communication and Sensing in the Terahertz Band
- 2023
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In: 2023 OPTICAL FIBER COMMUNICATIONS CONFERENCE AND EXHIBITION, OFC. - : Institute of Electrical and Electronics Engineers (IEEE).
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Conference paper (peer-reviewed)abstract
- This paper reviews the potential of THz photonics in communication and sensing by presenting our experimental results in the 300-500 GHz. Benefiting from the large available bandwidth in both THz and photonics, THz communications with high speed and THz imaging with high resolution have been achieved.
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| 14. |
- Zhang, Hongqi, et al.
(author)
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Tbit/s Multi-Dimensional Multiplexing THz-Over-Fiber for 6G Wireless Communication
- 2021
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In: Journal of Lightwave Technology. - : Institute of Electrical and Electronics Engineers (IEEE). - 0733-8724 .- 1558-2213. ; 39:18, s. 5783-5790
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Journal article (peer-reviewed)abstract
- Photonics-aided terahertz (THz) wireless systems have been progressively developed to accommodate the forthcoming wireless communication with extremely high data rates in recent years. However, restrained by the obtainable signal-to-noise ratio (SNR) and the dimensions explored in THz photonic wireless systems, achieving data rates of Tbit/s and beyond is still challenging. In this paper, we present a multi-dimensional multiplexing Tbit/s THz-over-Fiber wireless communication system, by efficiently benefiting from the multiplexing gain in both optical wavelength and space domains. Enabled by a combined routine of an optical frequency comb, a low inter-core crosstalk (IC-XT) multi-core fiber and advanced digital signal processing, a line rate of up to 1176 Gbit/s over a wireless distance of 10 m in the 350 GHz band is experimentally demonstrated without any THz amplifiers, resulting in a net data rate of up to 1059 Gbit/s. To the best of our knowledge, this is the first time that beyond Tbit/s wireless data rate is successfully achieved in the THz region above 300 GHz, making a significant contribution to the development of THz-over-Fiber systems for the sixth generation (6G) wireless communication.
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| 15. |
- Zhang, Siqi, et al.
(author)
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Systems Metabolic Engineering of Saccharomyces cerevisiae for the High-Level Production of (2 S )-Eriodictyol
- 2024
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In: Journal of Fungi. - 2309-608X. ; 10:2
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Journal article (peer-reviewed)abstract
- (2S)-eriodictyol (ERD) is a flavonoid widely found in citrus fruits, vegetables, and important medicinal plants with neuroprotective, cardioprotective, antidiabetic, and anti-obesity effects. However, the microbial synthesis of ERD is limited by complex metabolic pathways and often results in a low production performance. Here, we engineered Saccharomyces cerevisiae by fine-tuning the metabolism of the ERD synthesis pathway. The results showed that the ERD titer was effectively increased, and the intermediate metabolites levels were reduced. First, we successfully reconstructed the de novo synthesis pathway of p-coumaric acid in S. cerevisiae and fine-tuned the metabolic pathway using promoter engineering and terminator engineering for the high-level production of (2S)-naringenin. Subsequently, the synthesis of ERD was achieved by introducing the ThF3 ' H gene from Tricyrtis hirta. Finally, by multiplying the copy number of the ThF3 ' H gene, the production of ERD was further increased, reaching 132.08 mg L-1. Our work emphasizes the importance of regulating the metabolic balance to produce natural products in microbial cell factories.
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