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Article ; Online: Programming bacteria for multiplexed DNA detection

Yu-Yu Cheng / Zhengyi Chen / Xinyun Cao / Tyler D. Ross / Tanya G. Falbel / Briana M. Burton / Ophelia S. Venturelli

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 11

Abstract: Abstract DNA is a universal and programmable signal of living organisms. Here we develop cell-based DNA sensors by engineering the naturally competent bacterium Bacillus subtilis (B. subtilis) to detect specific DNA sequences in the environment. The DNA ... ...

Abstract	Abstract DNA is a universal and programmable signal of living organisms. Here we develop cell-based DNA sensors by engineering the naturally competent bacterium Bacillus subtilis (B. subtilis) to detect specific DNA sequences in the environment. The DNA sensor strains can identify diverse bacterial species including major human pathogens with high specificity. Multiplexed detection of genomic DNA from different species in complex samples can be achieved by coupling the sensing mechanism to orthogonal fluorescent reporters. We also demonstrate that the DNA sensors can detect the presence of species in the complex samples without requiring DNA extraction. The modularity of the living cell-based DNA-sensing mechanism and simple detection procedure could enable programmable DNA sensing for a wide range of applications.
Keywords	Science ; Q
Language	English
Publishing date	2023-04-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: A monolithic column based on covalent cross-linked polymer gels for online extraction and analysis of trace aflatoxins in food sample

Wei, Tianfu / Zhengyi Chen / Gongke Li / Zhuomin Zhang

Journal of chromatography. 2018 May 04, v. 1548

2018

Abstract: Aflatoxins are highly toxic mycotoxin contamination, which pose serious food safety incidents. It is very important to precisely and rapidly determine trace aflatoxins in food. In this study, we designed porous monolithic column based on covalent cross- ... ...

Abstract	Aflatoxins are highly toxic mycotoxin contamination, which pose serious food safety incidents. It is very important to precisely and rapidly determine trace aflatoxins in food. In this study, we designed porous monolithic column based on covalent cross-linked polymer gels for online extraction and analysis of trace aflatoxins in food samples with complicated matrices coupled with high-performance liquid chromatography-ultraviolet detector (HPLC-UV). The prepared monolithic column showed excellent enrichment performance due to its good permeability, good reproducibility and long life span. The study of adsorption mechanism suggested that the excellent enrichment performance of this monolithic column was attributed to the multiple effect of π-π stacking interaction, hydrophobic effect and steric effect. When the online analytical method was applied for the determine of trace aflatoxins in real food samples, aflatoxins G1 and aflatoxins B1 could be actually found in one positive bean sauce sample and quantified to be 32.8 and 26.4 μg/kg, respectively. Aflatoxins G1 in one bean sample could be also found and quantified to be 25.9 μg/kg. The low detection limits of the developed method were achieved in range of 0.08-0.2 μg/kg. And the recoveries for spiked samples were in range from 76.1 to 113% with RSDs of 1.1-9.6%. The developed method was proved to be a promising method for online enrichment and analysis of trace aflatoxins in complicated food samples.
Keywords	adsorption ; aflatoxin B1 ; aflatoxin G1 ; beans ; crosslinking ; food contamination ; gels ; high performance liquid chromatography ; hydrophobicity ; liquids ; permeability ; polymers
Language	English
Dates of publication	2018-0504
Size	p. 27-36.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	218139-3
ISSN	0021-9673 ; 0378-4355 ; 0376-737X
ISSN	0021-9673 ; 0378-4355 ; 0376-737X
DOI	10.1016/j.chroma.2018.03.015
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Association of serum irisin concentration with thyroid autoantibody positivity and subclinical hypothyroidism

Zhengyi Chen / Qiao Zhang / Nianchun Peng / Ying Hu / Hong Li / Xi He / Ruoyi Liu / Shujing Xu / Miao Zhang / Lixin Shi

Journal of International Medical Research, Vol

2021 Volume 49

Abstract: Objective This study evaluated the association of serum irisin level with thyroid autoantibody (TAA) positivity and subclinical hypothyroidism (SH). Methods In this cross-sectional study, 334 participants were assigned to one of the following four age- ... ...

Abstract	Objective This study evaluated the association of serum irisin level with thyroid autoantibody (TAA) positivity and subclinical hypothyroidism (SH). Methods In this cross-sectional study, 334 participants were assigned to one of the following four age- and sex-matched groups: TAA plus SH (84 patients), isolated TAA (83 patients), isolated SH (83 patients), or healthy controls (84 individuals). Irisin and creatine kinase (CK) were measured in serum samples. Results Patients with TAA plus SH, isolated TAA, and isolated SH had higher irisin levels compared with the controls. There was a significant increase in the irisin level in the TAA plus SH group compared with the control group. Among all participants, the irisin levels were positively associated with thyroglobulin and thyroid peroxidase antibody titers and high-density lipoprotein cholesterol levels, but negatively associated with waist circumference, glycated hemoglobin levels, and fasting plasma glucose levels. The irisin level was not associated with the thyroid-stimulating hormone, free thyroxine, or CK levels. Irisin levels were independently associated with TAA, with or without SH, but they were not associated with SH alone. Conclusions Irisin level may help to predict the risk of developing TAA with or without SH.
Keywords	Medicine (General) ; R5-920
Subject code	610
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	SAGE Publishing
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: An Efficient Representation-Based Subspace Clustering Framework for Polarized Hyperspectral Images

Zhengyi Chen / Chunmin Zhang / Tingkui Mu / Tingyu Yan / Zeyu Chen / Yanqiang Wang

Remote Sensing, Vol 11, Iss 13, p

2019 Volume 1513

Abstract: Recently, representation-based subspace clustering algorithms for hyperspectral images (HSIs) have been developed with the assumption that pixels belonging to the same land-cover class lie in the same subspace. Polarization is regarded to be a complement ...

Abstract	Recently, representation-based subspace clustering algorithms for hyperspectral images (HSIs) have been developed with the assumption that pixels belonging to the same land-cover class lie in the same subspace. Polarization is regarded to be a complement to spectral information, but related research only focus on the clustering for HSIs without considering polarization, and cannot effectively process large-scale hyperspectral datasets. In this paper, we propose an efficient representation-based subspace clustering framework for polarized hyperspectral images (PHSIs). Combining with spectral information and polarized information, this framework is extensible for most existing representation-based subspace clustering algorithms. In addition, with a sampling-clustering-classification strategy which firstly clusters selected in-sample data into several classes and then matches the out-of-sample data into these classes by collaborative representation-based classification, the proposed framework significantly reduces the computational complexity of clustering algorithms for PHSIs. Some experiments were carried out to demonstrate the accuracy, efficiency and potential capabilities of the algorithms under the proposed framework.
Keywords	hyperspectral images ; polarization ; subspace clustering ; sparse representation ; Science ; Q
Subject code	006
Language	English
Publishing date	2019-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A contamination focused approach for optimizing the single-cell RNA-seq experiment

Deronisha Arceneaux / Zhengyi Chen / Alan J. Simmons / Cody N. Heiser / Austin N. Southard-Smith / Michael J. Brenan / Yilin Yang / Bob Chen / Yanwen Xu / Eunyoung Choi / Joshua D. Campbell / Qi Liu / Ken S. Lau

iScience, Vol 26, Iss 7, Pp 107242- (2023)

2023

Abstract: Summary: Droplet-based single-cell RNA-seq (scRNA-seq) data are plagued by ambient contaminations caused by nucleic acid material released by dead and dying cells. This material is mixed into the buffer and is co-encapsulated with cells, leading to a ... ...

Abstract	Summary: Droplet-based single-cell RNA-seq (scRNA-seq) data are plagued by ambient contaminations caused by nucleic acid material released by dead and dying cells. This material is mixed into the buffer and is co-encapsulated with cells, leading to a lower signal-to-noise ratio. Although there exist computational methods to remove ambient contaminations post-hoc, the reliability of algorithms in generating high-quality data from low-quality sources remains uncertain. Here, we assess data quality before data filtering by a set of quantitative, contamination-based metrics that assess data quality more effectively than standard metrics. Through a series of controlled experiments, we report improvements that can minimize ambient contamination outside of tissue dissociation, via cell fixation, improved cell loading, microfluidic dilution, and nuclei versus cell preparation; many of these parameters are inaccessible on commercial platforms. We provide end-users with insights on factors that can guide their decision-making regarding optimizations that minimize ambient contamination, and metrics to assess data quality.
Keywords	Computational bioinformatics ; Transcriptomics ; Biology experimental methods ; Science ; Q
Subject code	310
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: SELENOP modifies sporadic colorectal carcinogenesis and WNT signaling activity through LRP5/6 interactions

Jennifer M. Pilat / Rachel E. Brown / Zhengyi Chen / Nathaniel J. Berle / Adrian P. Othon / M. Kay Washington / Shruti A. Anant / Suguru Kurokawa / Victoria H. Ng / Joshua J. Thompson / Justin Jacobse / Jeremy A. Goettel / Ethan Lee / Yash A. Choksi / Ken S. Lau / Sarah P. Short / Christopher S. Williams

The Journal of Clinical Investigation, Vol 133, Iss

2023 Volume 13

Abstract: Although selenium deficiency correlates with colorectal cancer (CRC) risk, the roles of the selenium-rich antioxidant selenoprotein P (SELENOP) in CRC remain unclear. In this study, we defined SELENOP’s contributions to sporadic CRC. In human single-cell ...

Abstract	Although selenium deficiency correlates with colorectal cancer (CRC) risk, the roles of the selenium-rich antioxidant selenoprotein P (SELENOP) in CRC remain unclear. In this study, we defined SELENOP’s contributions to sporadic CRC. In human single-cell cRNA-Seq (scRNA-Seq) data sets, we discovered that SELENOP expression rose as normal colon stem cells transformed into adenomas that progressed into carcinomas. We next examined the effects of Selenop KO in a mouse adenoma model that involved conditional, intestinal epithelium-specific deletion of the tumor suppressor adenomatous polyposis coli (Apc) and found that Selenop KO decreased colon tumor incidence and size. We mechanistically interrogated SELENOP-driven phenotypes in tumor organoids as well as in CRC and noncancer cell lines. Selenop-KO tumor organoids demonstrated defects in organoid formation and decreases in WNT target gene expression, which could be reversed by SELENOP restoration. Moreover, SELENOP increased canonical WNT signaling activity in noncancer and CRC cell lines. In defining the mechanism of action of SELENOP, we mapped protein-protein interactions between SELENOP and the WNT coreceptors low-density lipoprotein receptor–related proteins 5 and 6 (LRP5/6). Last, we confirmed that SELENOP-LRP5/6 interactions contributed to the effects of SELENOP on WNT activity. Overall, our results position SELENOP as a modulator of the WNT signaling pathway in sporadic CRC.
Keywords	Gastroenterology ; Medicine ; R
Subject code	570
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	American Society for Clinical Investigation
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Scanning vertical distributions of typical aerosols along the Yangtze River using elastic lidar

Fan, Shidong / Cheng Liu / Guangqiang Fan / Jianguo Liu / Jingbo Duan / Pengfei Zhang / Qihou Hu / Tianshu Zhang / Yunsheng Dong / Zhengyi Chen / Zhouqing Xie

Science of the total environment. 2018 July 01, v. 628-629

2018

Abstract: In recent years, China has experienced heavy air pollution, especially haze caused by particulate matter (PM). The compositions, horizontal distributions, transport, and chemical formation mechanisms of PM and its precursors have been widely investigated ...

Abstract	In recent years, China has experienced heavy air pollution, especially haze caused by particulate matter (PM). The compositions, horizontal distributions, transport, and chemical formation mechanisms of PM and its precursors have been widely investigated in China based on near-ground measurements. However, the understanding of the distributions and physical and chemical processes of PM in the vertical direction remains limited. In this study, an elastic lidar was employed to investigate the vertical profiles of aerosols along the Yangtze River during the Yangtze River Campaign of winter 2015. Some typical aerosols were identified and some events were analyzed in three cases. Dust aerosols can be transported from the Gobi Desert to the Yangtze River basin across a long distance at both low and high altitudes in early December. The transport route was perpendicular to the ship track, suggesting that the dust aerosols may have affected a large area. Moreover, during transport, some dust was also affected by the areas below its transport route since some anthropogenic pollutants were mixed with the dust and changed some of its optical properties. Biomass-burning aerosols covering a distant range along the Yangtze River were identified. This result directly shows the impact areas of biomass-burning aerosols in some agricultural fields. Some directly emitted aerosol plumes were observed, and direct effects of such plumes were limited both temporally and spatially. In addition, an aerosol plume with very low linear depolarization ratios, probably formed through secondary processes, was also observed. These results can help us better understand aerosols in large spatial scales in China and can be useful to regional haze studies.
Keywords	aerosols ; agricultural land ; air pollution ; altitude ; chemical composition ; dust ; lidar ; optical properties ; particulates ; pollutants ; watersheds ; winter ; China ; Gobi Desert ; Yangtze River
Language	English
Dates of publication	2018-0701
Size	p. 631-641.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2018.02.099
Database	NAL-Catalogue (AGRICOLA)

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Article: Novel regenerative large-volume immobilized enzyme reactor: Preparation, characterization and application

Ruan, Guihua / Fuyou Du / Meiping Wei / Rihui Su / Yanjie Zheng / Zhengyi Chen

Journal of Chromatography B. 2014 Sept. 15, v. 967

2014

Abstract: A novel large-volume immobilized enzyme reactor (IMER) on small column was prepared with organicâinorganic hybrid silica particles and applied for fast (10min) and oriented digestion of protein. At first, a thin enzyme support layer was formed in the ... ...

Abstract	A novel large-volume immobilized enzyme reactor (IMER) on small column was prepared with organicâinorganic hybrid silica particles and applied for fast (10min) and oriented digestion of protein. At first, a thin enzyme support layer was formed in the bottom of the small column by polymerization with Î±-methacrylic acid and dimethacrylate. After that, amino SiO2 particles was prepared by the solâgel method with tetraethoxysilane and 3-aminopropyltriethoxysilane. Subsequently, the amino SiO2 particles were activated by glutaraldehyde for covalent immobilization of trypsin. Digestive capability of large-volume IMER for proteins was investigated by using bovine serum albumin (BSA), cytochrome c (Cyt-c) as model proteins. Results showed that although the sequence coverage of the BSA (20%) and Cyt-c (19%) was low, the large-volume IMER could produce peptides with stable specific sequence at 101â105, 156â160, 205â209, 212â218, 229â232, 257â263 and 473â451 of the amino sequence of BSA when digesting 1mg/mL BSA. Eight of common peptides were observed during each of the ten runs of large-volume IMER. Besides, the IMER could be easily regenerated by reactivating with GA and cross-linking with trypsin after breaking the âCNâ bond by 0.01M HCl. The sequence coverage of BSA from regenerated IMER increased to 25% comparing the non-regenerated IMER (17%). 14 common peptides. accounting for 87.5% of first use of IMER, were produced both with IMER and regenerated IMER. When the IMER was applied for ginkgo albumin digestion, the sequence coverage of two main proteins of ginkgo, ginnacin and legumin, was 56% and 55%, respectively. (Reviewer 2) Above all, the fast and selective digestion property of the large-volume IMER indicated that the regenerative IMER could be tentatively used for the production of potential bioactive peptides and the study of oriented protein digestion.
Keywords	bovine serum albumin ; chromatography ; crosslinking ; cytochrome c ; Ginkgo ; glutaraldehyde ; hydrochloric acid ; immobilized enzymes ; legumin ; peptides ; polymerization ; silica ; sol-gel processing ; trypsin
Language	English
Dates of publication	2014-0915
Size	p. 13-20.
Publishing place	Elsevier B.V.
Document type	Article
ISSN	1570-0232
DOI	10.1016/j.jchromb.2014.07.008
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Adult BMI Change and Risk of Colon Cancer in Postmenopausal Women

Lyla Blake-Gumbs / Zhengyi Chen / Cheryl L. Thompson / Nathan A. Berger / Thomas C. Tucker / Li Li

Journal of Obesity, Vol

2012 Volume 2012

Abstract: Purpose. We recently reported an association of adult BMI change with colon cancer risk. Here, we sought to further explore this association with respect to postmenopausal HRT use in a larger study population. Methods. We included 1,457 postmenopausal ... ...

Abstract	Purpose. We recently reported an association of adult BMI change with colon cancer risk. Here, we sought to further explore this association with respect to postmenopausal HRT use in a larger study population. Methods. We included 1,457 postmenopausal women participating in an ongoing population-based case-control study of colon cancer. Results. We confirmed a previously reported association of adulthood weight gain and increased risk of colon cancer: compared to those with <5 kg/m2 change of BMI, women who reported moderate (5–10 kg/m2) and large (>10 kg/m2) BMI changes since their 20s had OR estimates of 1.54 (95% CI = 1.09–2.19) and 1.45 (95% CI = 0.90–2.33), respectively (P for trend = 0.05). Stratified analyses showed that this association was limited to HRT nonusers: ORs were 1.77 (95% CI = 1.02–3.05) and 2.21 (95% CI = 1.09–4.45), respectively (P for trend = 0.03), for BMI changes occurring between the 20s decade and time of recruitment among non-users. Similar associations were observed for BMI changes since the 30s decade. There was no association among HRT users. Conclusion. Our results suggest early adulthood weight gain increases colon cancer risk in postmenopausal women who do not use HRT.
Keywords	Internal medicine ; RC31-1245
Subject code	610
Language	English
Publishing date	2012-01-01T00:00:00Z
Publisher	Hindawi Publishing Corporation
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Adipokines Do Not Mediate the Association of Obesity and Colorectal Adenoma

Heather M. Ochs-Balcom / Rikki Cannioto / Jing Nie / Amy E. Millen / Jo L. Freudenheim / Zhengyi Chen / Cheryl L. Thompson / Russell Tracy / Li Li

Journal of Cancer Epidemiology, Vol

2014 Volume 2014

Abstract: Purpose. The association between obesity and colon neoplasia is well established but the underlying biological mechanisms are not fully understood. Rates of both obesity and colon cancer differ by race. Adipokines have been postulated as contributors to ... ...

Abstract	Purpose. The association between obesity and colon neoplasia is well established but the underlying biological mechanisms are not fully understood. Rates of both obesity and colon cancer differ by race. Adipokines have been postulated as contributors to the observed association; however, few studies have examined the mediating effect of adipokines on the obesity-colon adenoma association with consideration of racial differences. Methods. We determined prediagnostic levels of adiponectin and leptin in Caucasians (217 cases and 650 controls) and African Americans (175 cases and 378 controls) participating in the Case Transdisciplinary Research on Energetics and Cancer Colon Adenoma Study. We evaluated mediating effects of adiponectin and leptin on the association of abdominal adiposity and colon adenoma separately according to race using mediational pathway analysis. Results. We observed differences in circulating adipokine concentrations by race; African Americans had higher levels of leptin and lower levels of adiponectin than Caucasians for both adenoma cases and controls (P values <0.001). Leptin and adiponectin did not mediate the waist-to-hip ratio (WHR) adenoma association in either group (all Sobel P values >0.27). Conclusions. We found no evidence that leptin or adiponectin mediates the abdominal obesity-colorectal adenoma pathway. Larger studies on how these associations vary by race, sex, and obesity are needed.
Keywords	Medicine ; R
Language	English
Publishing date	2014-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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