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Article: Development of an Immunochromatographic Test Based on Rhoptry Protein 14 for Serological Detection of

Yang, Yimin / Huang, Yechuan / Zhao, Xianfeng / Lin, Mi / Chen, Lulu / Zhao, Mingxiu / Chen, Xueqiu / Yang, Yi / Ma, Guangxu / Yao, Chaoqun / Huang, Siyang / Du, Aifang

Animals : an open access journal from MDPI

2022 Volume 12, Issue 15

Abstract: Toxoplasma ... ...

Abstract	Toxoplasma gondii
Language	English
Publishing date	2022-07-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606558-7
ISSN	2076-2615
ISSN	2076-2615
DOI	10.3390/ani12151929
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A comprehensive analysis and resource to use CRISPR-Cas13 for broad-spectrum targeting of RNA viruses.

Lin, Xueqiu / Liu, Yanxia / Chemparathy, Augustine / Pande, Tara / La Russa, Marie / Qi, Lei S

Cell reports. Medicine

2021 Volume 2, Issue 4, Page(s) 100245

Abstract: The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) and variants has led to significant mortality. We recently reported that an RNA-targeting CRISPR-Cas13 system, called prophylactic ... ...

Abstract	The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) and variants has led to significant mortality. We recently reported that an RNA-targeting CRISPR-Cas13 system, called prophylactic antiviral CRISPR in human cells (PAC-MAN), offered an antiviral strategy against SARS-CoV-2 and influenza A virus. Here, we expand
MeSH term(s)	COVID-19/pathology ; COVID-19/virology ; CRISPR-Cas Systems/genetics ; Humans ; RNA Virus Infections/pathology ; RNA Virus Infections/virology ; RNA Viruses/genetics ; RNA Viruses/isolation & purification ; RNA, Guide, CRISPR-Cas Systems/metabolism ; RNA, Viral/metabolism ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification ; Species Specificity
Chemical Substances	RNA, Guide, CRISPR-Cas Systems ; RNA, Viral
Language	English
Publishing date	2021-03-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2666-3791
ISSN (online)	2666-3791
DOI	10.1016/j.xcrm.2021.100245
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Willingness to use acupuncture: Knowledge, attitudes, beliefs, and practices among allergic rhinitis patients.

Cao, Xueqiu / Liao, Yong / Wu, Xiaohui / Yang, Qiang / Zhao, Junhui / Gong, Cheng / Xiang, Lin / Tang, Yao

Medicine

2023 Volume 102, Issue 39, Page(s) e35297

Abstract: This study aims to assess knowledge, attitudes, beliefs, and practices (KABP) among China mainland allergic rhinitis (AR) participants regarding their willingness to use acupuncture. Little is known about the understanding, attitudes, beliefs and ... ...

Abstract	This study aims to assess knowledge, attitudes, beliefs, and practices (KABP) among China mainland allergic rhinitis (AR) participants regarding their willingness to use acupuncture. Little is known about the understanding, attitudes, beliefs and practices of people with AR in China. A questionnaire was designed and administered to AR participants in mainland China to gather information about KABP regarding acupuncture use. A total of 324 valid questionnaires were collected from 30 provinces on the Chinese mainland. We recorded basic information and data about AR. The questionnaire designed according to KABP theory and with excellent reliability (Cronbach α coefficient: 0.725) and validity (KMO: 0.819). Knowledge: Fifty-five percent (179) of respondents reported knowing about acupuncture. The majority (172) knew that acupuncture was used for AR; 119 had received acupuncture for AR, and about 66% were aware of acupuncture. Attitudes and beliefs: Seventy percent of patients were willing to recommend acupuncture for AR to family and friends. Practice: Approximately 75% of respondents were willing to undergo acupuncture if they knew it was effective for AR. Approximately 25% of the respondents answered "Do it a few times and see how it works," "Do several treatments depending on how much they can afford," or "It is up to the doctor to decide". Correlation analysis: Those who identified with traditional Chinese medicine showed a robust willingness to recommend acupuncture for treating other diseases to family and friends (R = 0.718, P < .01) and a robust willingness to recommend acupuncture for AR to their families and friends (R = 0.564, P < .01). Acupuncture for AR has shown excellent awareness, recommendation and acceptance in mainland China. Efficacy, affordability, and trust in doctors were the 3 key factors that led respondents to choose acupuncture for their AR. Identification with traditional Chinese medicine culture significantly influenced attitudes, leading to AR recommendations and acceptance of acupuncture.
MeSH term(s)	Humans ; Health Knowledge, Attitudes, Practice ; Reproducibility of Results ; Rhinitis, Allergic/therapy ; Acupuncture Therapy ; Medicine, Chinese Traditional
Language	English
Publishing date	2023-09-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	80184-7
ISSN	1536-5964 ; 0025-7974
ISSN (online)	1536-5964
ISSN	0025-7974
DOI	10.1097/MD.0000000000035297
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A comprehensive analysis and resource to use CRISPR-Cas13 for broad-spectrum targeting of RNA viruses

Xueqiu Lin / Yanxia Liu / Augustine Chemparathy / Tara Pande / Marie La Russa / Lei S. Qi

Cell Reports Medicine, Vol 2, Iss 4, Pp 100245- (2021)

2021

Abstract: Summary: The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) and variants has led to significant mortality. We recently reported that an RNA-targeting CRISPR-Cas13 system, called ... ...

Abstract	Summary: The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) and variants has led to significant mortality. We recently reported that an RNA-targeting CRISPR-Cas13 system, called prophylactic antiviral CRISPR in human cells (PAC-MAN), offered an antiviral strategy against SARS-CoV-2 and influenza A virus. Here, we expand in silico analysis to use PAC-MAN to target a broad spectrum of human- or livestock-infectious RNA viruses with high specificity, coverage, and predicted efficiency. Our analysis reveals that a minimal set of 14 CRISPR RNAs (crRNAs) is able to target >90% of human-infectious viruses across 10 RNA virus families. We predict that a set of 5 experimentally validated crRNAs can target new SARS-CoV-2 variant sequences with zero mismatches. We also build an online resource (crispr-pacman.stanford.edu) to support community use of CRISPR-Cas13 for broad-spectrum RNA virus targeting. Our work provides a new bioinformatic resource for using CRISPR-Cas13 to target diverse RNA viruses to facilitate the development of CRISPR-based antivirals.
Keywords	CRISPR ; Cas13 ; SARS-CoV-2 ; COVID-19 ; antiviral ; RNA virus ; Medicine (General) ; R5-920
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The first apicoplast tRNA thiouridylase plays a vital role in the growth of

Yang, Yimin / Lin, Mi / Chen, Xueqiu / Zhao, XianFeng / Chen, Lulu / Zhao, Mingxiu / Yao, Chaoqun / Sheng, Kaiyin / Yang, Yi / Ma, Guangxu / Du, Aifang

Frontiers in cellular and infection microbiology

2022 Volume 12, Page(s) 947039

Abstract: Toxoplasmosis caused by the ... ...

Abstract	Toxoplasmosis caused by the protozoan
MeSH term(s)	Animals ; Apicoplasts/genetics ; Apicoplasts/metabolism ; Humans ; Mice ; Mice, Knockout ; Protozoan Proteins/genetics ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Toxoplasma ; Toxoplasmosis/parasitology
Chemical Substances	Protozoan Proteins ; RNA, Transfer (9014-25-9)
Language	English
Publishing date	2022-08-15
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2619676-1
ISSN	2235-2988 ; 2235-2988
ISSN (online)	2235-2988
ISSN	2235-2988
DOI	10.3389/fcimb.2022.947039
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A benchmark of algorithms for the analysis of pooled CRISPR screens.

Bodapati, Sunil / Daley, Timothy P / Lin, Xueqiu / Zou, James / Qi, Lei S

Genome biology

2020 Volume 21, Issue 1, Page(s) 62

Abstract: Genome-wide pooled CRISPR-Cas-mediated knockout, activation, and repression screens are powerful tools for functional genomic investigations. Despite their increasing importance, there is currently little guidance on how to design and analyze CRISPR- ... ...

Abstract	Genome-wide pooled CRISPR-Cas-mediated knockout, activation, and repression screens are powerful tools for functional genomic investigations. Despite their increasing importance, there is currently little guidance on how to design and analyze CRISPR-pooled screens. Here, we provide a review of the commonly used algorithms in the computational analysis of pooled CRISPR screens. We develop a comprehensive simulation framework to benchmark and compare the performance of these algorithms using both synthetic and real datasets. Our findings inform parameter choices of CRISPR screens and provide guidance to researchers on the design and analysis of pooled CRISPR screens.
MeSH term(s)	Algorithms ; CRISPR-Cas Systems ; Computer Simulation ; RNA, Small Interfering ; Sequence Analysis
Chemical Substances	RNA, Small Interfering
Language	English
Publishing date	2020-03-09
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-020-01972-x
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Article ; Online: A benchmark of algorithms for the analysis of pooled CRISPR screens

Sunil Bodapati / Timothy P. Daley / Xueqiu Lin / James Zou / Lei S. Qi

Genome Biology, Vol 21, Iss 1, Pp 1-

2020 Volume 13

Abstract: Abstract Genome-wide pooled CRISPR-Cas-mediated knockout, activation, and repression screens are powerful tools for functional genomic investigations. Despite their increasing importance, there is currently little guidance on how to design and analyze ... ...

Abstract	Abstract Genome-wide pooled CRISPR-Cas-mediated knockout, activation, and repression screens are powerful tools for functional genomic investigations. Despite their increasing importance, there is currently little guidance on how to design and analyze CRISPR-pooled screens. Here, we provide a review of the commonly used algorithms in the computational analysis of pooled CRISPR screens. We develop a comprehensive simulation framework to benchmark and compare the performance of these algorithms using both synthetic and real datasets. Our findings inform parameter choices of CRISPR screens and provide guidance to researchers on the design and analysis of pooled CRISPR screens.
Keywords	CRISPR screen ; CRISPR knockoout ; CRISPR interference ; CRISPR activation ; Benchmarking ; Screen algorithms ; Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
Language	English
Publishing date	2020-03-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: A benchmark of algorithms for the analysis of pooled CRISPR screens

Bodapati, Sunil / Daley, Timothy P / Lin, Xueqiu / Zou, James / Qi, Lei S

Genome biology. 2020 Dec., v. 21, no. 1

2020

Abstract	Genome-wide pooled CRISPR-Cas-mediated knockout, activation, and repression screens are powerful tools for functional genomic investigations. Despite their increasing importance, there is currently little guidance on how to design and analyze CRISPR-pooled screens. Here, we provide a review of the commonly used algorithms in the computational analysis of pooled CRISPR screens. We develop a comprehensive simulation framework to benchmark and compare the performance of these algorithms using both synthetic and real datasets. Our findings inform parameter choices of CRISPR screens and provide guidance to researchers on the design and analysis of pooled CRISPR screens.
Keywords	CRISPR-Cas systems ; algorithms ; gene editing ; genomics
Language	English
Dates of publication	2020-12
Size	p. 62.
Publishing place	BioMed Central
Document type	Article
Note	Review
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6906
ISSN (online)	1474-760X
ISSN	1465-6906
DOI	10.1186/s13059-020-01972-x
Database	NAL-Catalogue (AGRICOLA)

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Article: Development of an Immunochromatographic Test Based on Rhoptry Protein 14 for Serological Detection of Toxoplasma gondii Infection in Swine

Yang, Yimin / Huang, Yechuan / Zhao, Xianfeng / Lin, Mi / Chen, Lulu / Zhao, Mingxiu / Chen, Xueqiu / Yang, Yi / Ma, Guangxu / Yao, Chaoqun / Huang, Siyang / Du, Aifang

Animals. 2022 July 28, v. 12, no. 15

2022

Abstract: Toxoplasma gondii, a worldwide distributed apicomplexan protozoan, can infect almost all warm-blooded animals and may cause toxoplasmosis. In order to provide a point-of-care detection method for T. gondii infection, an immunochromatographic test (ICT) ... ...

Abstract	Toxoplasma gondii, a worldwide distributed apicomplexan protozoan, can infect almost all warm-blooded animals and may cause toxoplasmosis. In order to provide a point-of-care detection method for T. gondii infection, an immunochromatographic test (ICT) was established. The proposed test uses recombinant T. gondii rhoptry protein 14 (ROP14) conjugated with 20 nm gold particles, recombinant protein A as the detection line and monoclonal antibody TgROP14-5D5 as the control line. The specificity, sensitivity, positive predictive value, negative predictive value and stability of this new ICT were evaluated. rTgROP14 was specifically recognized by positive serum of T. gondii but not negative serum. mAb TgROP14-5D5 showed higher specific recognition of T. gondii antigens and was therefore selected for subsequent colloidal gold strip construction. The new ICT based on TgROP14 exhibited good diagnostic performance with high specificity (86.9%) and sensitivity (90.9%) using IHA as a “reference standard”. Among 436 field porcine sera, ICT and IHA detected 134 (30.7%) and 99 (22.7%) positive samples, respectively. The relative agreement was 87.8%. These data indicate that this new ICT based on TgROP14 is a suitable candidate for routine testing of T. gondii in the field.
Keywords	Protozoa ; Toxoplasma gondii ; blood serum ; gold ; immunoaffinity chromatography ; monoclonal antibodies ; point-of-care systems ; recombinant proteins ; rhoptry ; swine ; toxoplasmosis
Language	English
Dates of publication	2022-0728
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2606558-7
ISSN	2076-2615
ISSN	2076-2615
DOI	10.3390/ani12151929
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Development of an Immunochromatographic Test Based on Rhoptry Protein 14 for Serological Detection of Toxoplasma gondii Infection in Swine

Yimin Yang / Yechuan Huang / Xianfeng Zhao / Mi Lin / Lulu Chen / Mingxiu Zhao / Xueqiu Chen / Yi Yang / Guangxu Ma / Chaoqun Yao / Siyang Huang / Aifang Du

Animals, Vol 12, Iss 1929, p

2022 Volume 1929

Abstract: Toxoplasma gondii , a worldwide distributed apicomplexan protozoan, can infect almost all warm-blooded animals and may cause toxoplasmosis. In order to provide a point-of-care detection method for T. gondii infection, an immunochromatographic test (ICT) ... ...

Abstract	Toxoplasma gondii , a worldwide distributed apicomplexan protozoan, can infect almost all warm-blooded animals and may cause toxoplasmosis. In order to provide a point-of-care detection method for T. gondii infection, an immunochromatographic test (ICT) was established. The proposed test uses recombinant T. gondii rhoptry protein 14 (ROP14) conjugated with 20 nm gold particles, recombinant protein A as the detection line and monoclonal antibody TgROP14-5D5 as the control line. The specificity, sensitivity, positive predictive value, negative predictive value and stability of this new ICT were evaluated. rTgROP14 was specifically recognized by positive serum of T. gondii but not negative serum. mAb TgROP14-5D5 showed higher specific recognition of T. gondii antigens and was therefore selected for subsequent colloidal gold strip construction. The new ICT based on TgROP14 exhibited good diagnostic performance with high specificity (86.9%) and sensitivity (90.9%) using IHA as a “reference standard”. Among 436 field porcine sera, ICT and IHA detected 134 (30.7%) and 99 (22.7%) positive samples, respectively. The relative agreement was 87.8%. These data indicate that this new ICT based on TgROP14 is a suitable candidate for routine testing of T. gondii in the field.
Keywords	Toxoplasma gondii ; immunochromatographic test ; TgROP14 ; swine ; Veterinary medicine ; SF600-1100 ; Zoology ; QL1-991
Subject code	630
Language	English
Publishing date	2022-07-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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