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Article: Yeast for virus research.

Zhao, Richard Yuqi

2017 Volume 4, Issue 10, Page(s) 311–330

Abstract: Budding yeast ( ...

Abstract	Budding yeast (
Keywords	covid19
Language	English
Publishing date	2017-09-18
Publishing country	Austria
Document type	Journal Article ; Review
ZDB-ID	2814756-X
ISSN	2311-2638
ISSN	2311-2638
DOI	10.15698/mic2017.10.592
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: [The application of waterless empirical taste test（WETT

Zhao, Bingjie / Wang, Yutong / She, Ningning / Yuan, Yuqi / Zhang, Cui / Qin, Qing / Richard, L Doty / Ren, Xiaoyong / Chen, Jingguo

Lin chuang er bi yan hou tou jing wai ke za zhi = Journal of clinical otorhinolaryngology, head, and neck surgery

2022 Volume 37, Issue 1, Page(s) 13–19

Abstract: Objective: ...

Abstract	Objective:
MeSH term(s)	Aged ; Middle Aged ; Male ; Humans ; Female ; Taste ; Healthy Volunteers ; East Asian People ; Taste Perception
Language	Chinese
Publishing date	2022-12-22
Publishing country	China
Document type	English Abstract ; Journal Article
ISSN	2096-7993
ISSN	2096-7993
DOI	10.13201/j.issn.2096-7993.2023.01.003
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Article ; Online: Yeast for virus research

Richard Yuqi Zhao

Microbial Cell, Vol 4, Iss 10, Pp 311-

2017 Volume 364

Abstract: Budding yeast (Saccharomyces cerevisiae) and fission yeast (Schizosaccharomyces pombe) are two popular model organisms for virus research. They are natural hosts for viruses as they carry their own indige-nous viruses. Both yeasts have been used for ... ...

Abstract	Budding yeast (Saccharomyces cerevisiae) and fission yeast (Schizosaccharomyces pombe) are two popular model organisms for virus research. They are natural hosts for viruses as they carry their own indige-nous viruses. Both yeasts have been used for studies of plant, animal and human viruses. Many positive sense (+) RNA viruses and some DNA viruses replicate with various levels in yeasts, thus allowing study of those viral ac-tivities during viral life cycle. Yeasts are single cell eukaryotic organisms. Hence, many of the fundamental cellular functions such as cell cycle regula-tion or programed cell death are highly conserved from yeasts to higher eu-karyotes. Therefore, they are particularly suited to study the impact of those viral activities on related cellular activities during virus-host interactions. Yeasts present many unique advantages in virus research over high eukary-otes. Yeast cells are easy to maintain in the laboratory with relative short doubling time. They are non-biohazardous, genetically amendable with small genomes that permit genome-wide analysis of virologic and cellular func-tions. In this review, similarities and differences of these two yeasts are described. Studies of virologic activities such as viral translation, viral replica-tion and genome-wide study of virus-cell interactions in yeasts are high-lighted. Impacts of viral proteins on basic cellular functions such as cell cycle regulation and programed cell death are discussed. Potential applications of using yeasts as hosts to carry out functional analysis of small viral genome and to develop high throughput drug screening platform for the discovery of antiviral drugs are presented.
Keywords	Saccharomyces cerevisiae ; Schizosaccharomyces pombe ; virus-host interaction ; viral replication ; cell cycle regulation ; programed cell death ; genome-wide analysis ; high throughput drug screening ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2017-09-01T00:00:00Z
Publisher	Shared Science Publishers OG
Document type	Article ; Online
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Article ; Online: RUNX represses

Science advances

2019 Volume 5, Issue 4, Page(s) eaau8389

Abstract: Patients with neurofibromatosis type 1 (NF1) are predisposed to develop neurofibromas, but the underlying molecular mechanisms of neurofibromagenesis are not fully understood. We showed dual genetic deletion ... ...

Abstract	Patients with neurofibromatosis type 1 (NF1) are predisposed to develop neurofibromas, but the underlying molecular mechanisms of neurofibromagenesis are not fully understood. We showed dual genetic deletion of
MeSH term(s)	Alleles ; Animals ; Base Sequence ; Cell Proliferation ; Cell Survival ; Core Binding Factor Alpha 2 Subunit/metabolism ; Core Binding Factor Alpha 3 Subunit/metabolism ; Core Binding Factor beta Subunit/metabolism ; Female ; Gene Deletion ; Gene Expression Regulation, Neoplastic ; Humans ; Male ; Mice ; Mice, Nude ; Myelin Proteins/metabolism ; Neurofibroma/metabolism ; Promoter Regions, Genetic ; RNA, Small Interfering/metabolism ; Schwann Cells/metabolism ; Signal Transduction ; Transcriptome
Chemical Substances	CBFB protein, human ; Cbfb protein, mouse ; Core Binding Factor Alpha 2 Subunit ; Core Binding Factor Alpha 3 Subunit ; Core Binding Factor beta Subunit ; Myelin Proteins ; PMP22 protein, human ; Pmp22 protein, mouse ; RNA, Small Interfering ; RUNX1 protein, human ; Runx1 protein, mouse ; Runx3 protein, human ; Runx3 protein, mouse
Language	English
Publishing date	2019-04-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.aau8389
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Article: HIV-1 viral protein R (Vpr) & host cellular responses.

Zhao, Richard Yuqi / Bukrinsky, Michael / Elder, Robert T

The Indian journal of medical research

2005 Volume 121, Issue 4, Page(s) 270–286

Abstract: During infection of host cells by HIV-1, active host-pathogen interactions take place. The final balance between these interactions determines the efficiency of viral infection and subsequent disease progression. HIV-infected cells respond to viral ... ...

Abstract	During infection of host cells by HIV-1, active host-pathogen interactions take place. The final balance between these interactions determines the efficiency of viral infection and subsequent disease progression. HIV-infected cells respond to viral invasion with various antiviral strategies such as innate, cellular and humoral immune antiviral defense mechanisms. On the other hand, the virus has also developed tactics to suppress these host cellular responses. Among the many viral offensive strategies, viral protein R (Vpr) plays a particularly active role. Vpr involved in nuclear transport of the viral pre-integration complex, activation of viral transcription, induction of cell cycle G2/M arrest and apoptosis of the host cells. However, specific roles of these Vpr activities in viral pathogenesis and their contribution to disease progression are not fully understood. HIV-1 defective for some or all of these Vpr activities have been associated with slow disease progression in some patients. With regard to the host responses to vpr gene expression, studies show that Vpr is specifically targeted by CD8 T-lymphocytes during acute viral infection and that the host innate immune response may also play a crucial role in suppressing the effects of Vpr on various cellular activities. The effect of host cellular responses to vpr gene expression and its roles in nuclear transport, cell cycle G2/M regulation and induction of apoptosis are discussed in this review. Strategies with potential application for future antiviral therapies directed at suppressing Vpr activities are described.
MeSH term(s)	Apoptosis/physiology ; Cell Division ; Disease Progression ; G2 Phase ; Gene Products, vpr/physiology ; Humans ; Immunity, Cellular
Chemical Substances	Gene Products, vpr
Language	English
Publishing date	2005-04
Publishing country	India
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S. ; Review
ZDB-ID	390883-5
ISSN	0971-5916 ; 0019-5340
ISSN	0971-5916 ; 0019-5340
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Article ; Online: Complex structured beam direct generation by coherent superposition of a complete set of degenerate eigenmodes.

Zhang, Zilong / Zhao, Suyi / Wang, Xin / He, Wei / Wang, Yuqi / Zhao, Changming

Optics express

2023 Volume 31, Issue 10, Page(s) 15514–15522

Abstract: Structured beams have played an important role in many fields due to their rich spatial ...

Abstract	Structured beams have played an important role in many fields due to their rich spatial characteristics. The microchip cavity with a large Fresnel number can directly generate structured beams with complex spatial intensity distribution, which provides convenience for further exploring the formation mechanism of structured beams and realizing low-cost applications. In this article, theoretical and experimental studies are carried out on complex structured beams directly generated by the microchip cavity. It is demonstrated that the complex beams generated by the microchip cavity can be expressed by the coherent superposition of whole transverse eigenmodes within the same order, thus forming the eigenmode spectrum. The mode component analysis of complex propagation-invariant structured beams can be realized by the degenerate eigenmode spectral analysis described in this article.
Language	English
Publishing date	2023-05-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	1491859-6
ISSN	1094-4087 ; 1094-4087
ISSN (online)	1094-4087
ISSN	1094-4087
DOI	10.1364/OE.488812
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Article: Fission yeast homologue of Tip41-like proteins regulates type 2A phosphatases and responses to nitrogen sources.

Fenyvuesvolgyi, Csaba / Elder, Robert T / Benko, Zsigmond / Liang, Dong / Zhao, Richard Yuqi

Biochimica et biophysica acta

2005 Volume 1746, Issue 2, Page(s) 155–162

Abstract: A fission yeast (Schizosaccharomyces pombe) gene encoding a member of the TIP41-like protein family was identified and characterized. Deletion of the fission yeast tip41 gene leads to slower growth when ammonium chloride is the nitrogen source, but the ... ...

Abstract	A fission yeast (Schizosaccharomyces pombe) gene encoding a member of the TIP41-like protein family was identified and characterized. Deletion of the fission yeast tip41 gene leads to slower growth when ammonium chloride is the nitrogen source, but the growth rate is not affected when adenine is the nitrogen source. The tip41 mutant cells also enter the G1 phase of the cell cycle earlier than wild-type cells in response to nitrogen starvation. Overexpression of tip41(+) causes cell death, spherical cell morphology and blocks the shift to G1 phase upon nitrogen starvation. Overexpression of tip41(+) increases the activity of type 2A phosphatase. In a ppa2 deletion strain with reduced PP2A activity, overexpression of tip41(+) no longer blocks the shift to G1 upon nitrogen starvation. These results suggest that fission yeast Tip41 plays a role in cellular responses to nitrogen nutrient conditions at least partly through regulation of type 2A phosphatase activity.
MeSH term(s)	Cloning, Molecular ; G1 Phase ; Genes, Fungal ; Intracellular Signaling Peptides and Proteins/genetics ; Intracellular Signaling Peptides and Proteins/metabolism ; Nitrogen/metabolism ; Phosphoprotein Phosphatases/genetics ; Phosphoprotein Phosphatases/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Schizosaccharomyces/cytology ; Schizosaccharomyces/genetics ; Schizosaccharomyces/metabolism ; Schizosaccharomyces pombe Proteins/genetics ; Schizosaccharomyces pombe Proteins/metabolism ; Sequence Deletion ; Species Specificity
Chemical Substances	Intracellular Signaling Peptides and Proteins ; Saccharomyces cerevisiae Proteins ; Schizosaccharomyces pombe Proteins ; TIP41 protein, S cerevisiae ; Phosphoprotein Phosphatases (EC 3.1.3.16) ; Nitrogen (N762921K75)
Language	English
Publishing date	2005-12-15
Publishing country	Netherlands
Document type	Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	60-7
ISSN	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
ISSN	0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbamcr.2005.09.006
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Article ; Online: Structures and Dynamics of β-Rich Oligomers of ATTR (105-115) Assembly.

Liang, Liqun / Zhang, Yuqi / Zhu, Yanyan / Bai, Juxia / Ni, Yangyang / Wan, Junfeng / Yue, Haiyan / Zhao, Qingjie / Li, Huiyu

ACS chemical neuroscience

2024 Volume 15, Issue 7, Page(s) 1356–1365

Abstract: ... Additionally, interactions between hydrophobic residues L110 and L111 are crucial for the formation of a β-rich ... oligomer formation. These β-rich oligomers may adopt β-barrel conformations, potentially toxic oligomer ... species. Free-energy analysis reveals that β-barrel conformations serve as intermediates for these β-rich ...

Abstract	Transthyretin (TTR) is a tetrameric homologous protein that can dissociate into monomers. Misfolding and aggregation of TTR can lead to amyloid transthyretin amyloidosis (ATTR), which can cause many diseases (e.g., senile systemic amyloidosis, familial amyloid cardiomyopathy, and familial amyloid polyneuropathy). Despite growing evidence indicating that small oligomers play a critical role in regulating cytotoxicity, the structures of these oligomeric intermediates and their conformational transformations are still unclear, impeding our understanding of neurodegenerative mechanisms and the development of therapeutics targeting early aggregation species. The TTR monomer protein consists of various fragments prone to self-aggregation, including the residue 105-115 sequence. Therefore, our study investigated the assembly progress of ATTR (105-115) peptides using all-atom molecular dynamics simulations. The findings indicate that the probability of β-sheet content increases with increasing numbers of peptides. Additionally, interactions between hydrophobic residues L110 and L111 are crucial for the formation of a β-rich oligomer formation. These β-rich oligomers may adopt β-barrel conformations, potentially toxic oligomer species. Free-energy analysis reveals that β-barrel conformations serve as intermediates for these β-rich oligomers. Our insights into the structural ensemble dynamics of ATTR (105-115) contribute to understanding the physical mechanisms underlying the β-barrel oligomers of ATTR. These findings may shed light on the pathological role of ATTR in neurodegenerative diseases and offer potential therapeutic targets.
MeSH term(s)	Prealbumin ; Amyloid/metabolism ; Molecular Dynamics Simulation ; Amyloidogenic Proteins ; Peptides/chemistry ; Entropy ; Amyloid Neuropathies, Familial
Chemical Substances	Prealbumin ; Amyloid ; Amyloidogenic Proteins ; Peptides
Language	English
Publishing date	2024-03-14
Publishing country	United States
Document type	Journal Article
ISSN	1948-7193
ISSN (online)	1948-7193
DOI	10.1021/acschemneuro.3c00574
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Article: Fermented Wheat Germ Alleviates Depression-like Behavior in Rats with Chronic and Unpredictable Mild Stress.

Hu, Zheyuan / Zhao, Penghui / Liao, Aimei / Pan, Long / Zhang, Jie / Dong, Yuqi / Huang, Jihong / He, Weiwei / Ou, Xingqi

Foods (Basel, Switzerland)

2023 Volume 12, Issue 5

Abstract: ... an inexpensive raw material that is rich in bioactive ingredients. For example, gamma-aminobutyric acid (GABA) is ...

Abstract	Depression is a chronic mental illness with devastating effects on a person's physical and mental health. Studies have reported that food fermentation with probiotics can enrich the nutritional values of food and produce functional microorganisms that can alleviate depression and anxiety. Wheat germ is an inexpensive raw material that is rich in bioactive ingredients. For example, gamma-aminobutyric acid (GABA) is reported to have antidepressant effects. Several studies concluded that
Language	English
Publishing date	2023-02-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704223-6
ISSN	2304-8158
ISSN	2304-8158
DOI	10.3390/foods12050920
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Article ; Online: Taiyi: a bilingual fine-tuned large language model for diverse biomedical tasks.

Luo, Ling / Ning, Jinzhong / Zhao, Yingwen / Wang, Zhijun / Ding, Zeyuan / Chen, Peng / Fu, Weiru / Han, Qinyu / Xu, Guangtao / Qiu, Yunzhi / Pan, Dinghao / Li, Jiru / Li, Hao / Feng, Wenduo / Tu, Senbo / Liu, Yuqi / Yang, Zhihao / Wang, Jian / Sun, Yuanyuan /

Lin, Hongfei

Journal of the American Medical Informatics Association : JAMIA

2024

Abstract: ... potential for bilingual biomedical multitasking.: Conclusion: Leveraging rich high-quality biomedical ...

Abstract	Objective: Most existing fine-tuned biomedical large language models (LLMs) focus on enhancing performance in monolingual biomedical question answering and conversation tasks. To investigate the effectiveness of the fine-tuned LLMs on diverse biomedical natural language processing (NLP) tasks in different languages, we present Taiyi, a bilingual fine-tuned LLM for diverse biomedical NLP tasks. Materials and methods: We first curated a comprehensive collection of 140 existing biomedical text mining datasets (102 English and 38 Chinese datasets) across over 10 task types. Subsequently, these corpora were converted to the instruction data used to fine-tune the general LLM. During the supervised fine-tuning phase, a 2-stage strategy is proposed to optimize the model performance across various tasks. Results: Experimental results on 13 test sets, which include named entity recognition, relation extraction, text classification, and question answering tasks, demonstrate that Taiyi achieves superior performance compared to general LLMs. The case study involving additional biomedical NLP tasks further shows Taiyi's considerable potential for bilingual biomedical multitasking. Conclusion: Leveraging rich high-quality biomedical corpora and developing effective fine-tuning strategies can significantly improve the performance of LLMs within the biomedical domain. Taiyi shows the bilingual multitasking capability through supervised fine-tuning. However, those tasks such as information extraction that are not generation tasks in nature remain challenging for LLM-based generative approaches, and they still underperform the conventional discriminative approaches using smaller language models.
Language	English
Publishing date	2024-02-29
Publishing country	England
Document type	Journal Article
ZDB-ID	1205156-1
ISSN	1527-974X ; 1067-5027
ISSN (online)	1527-974X
ISSN	1067-5027
DOI	10.1093/jamia/ocae037
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