Yulong Wei

Yale University

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i-10 index

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Co-Authors

Xuhua Xia

University of Ottawa

Min Xu

Beijing Information Science & Technology University

Aidong Sun

Beijing Forestry University

Zhu Feng Yue

Shanghai Ninth People's Hospital

Ning Yu

Chinese Academy of Inspection and Quarantine

Parisa Aris

University of Ottawa

Yuhang Xiao

Northwest A&F University

Jingyi Hao

Zhengzhou University

Ning Zhu

Peking University

Zhilin Gan

Beijing Forestry University

Cooperative Institutions

Beijing Forestry University

Chinese Academy of Sciences

University of Pennsylvania

Capital Medical University

Shanghai Jiao Tong University

Sun Yat-sen University

Beijing Technology and Business University

Chinese Academy of Medical Sciences & Peking Union Medical College

Northwest A&F University

University of Ottawa

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Research Field

Interferon opens up: HIV-induced inflammation reconfigures 3D chromatin conformation and affects where HIV integrates

Molecular Cell (2022)

Yulong Wei Ya‐Chi Ho

Control reconfiguration

10.1016/j.molcel.2022.11.013

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Citations (3)

The g-Good-Neighbor Conditional Diagnosability of Locally Twisted Cubes

Journal of the Operations Research Society of China (2017)

Yulong Wei Min Xu

Cube (algebra)

10.1007/s40305-017-0166-2

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Citations (19)

5-Heptadecylresorcinol alleviated high-fat diet induced obesity and insulin resistance by activating brown adipose tissue

Food & Function (2023)

Zihui Yang Siqi Yang Ziyuan Wang Yiming Hao Zongwei Wang

The whitening and loss of brown adipose tissue (BAT) during obesity and aging are associated with a higher risk of metabolic syndrome and chronic diseases. 5-Heptadecylresorcinol (AR-C17), the specific biomarker of whole-grain wheat and rye intake, has been proved to have notable health promoting effects, whereas whether AR-C17 could modulate BAT function and the potential mechanism of action remains unclear. In this study, we found that AR-C17 could significantly inhibit body weight gain and insulin resistance in high-fat diet (HFD) induced obese mice. Moreover, AR-C17 treatment improved whole body energy metabolism and alleviated the whitening and loss of BAT compared with the HFD group. RNA sequencing and western-blot analysis indicated that expression of genes and proteins related to BAT energy metabolism was upregulated by AR-C17 administration, including AMPK, UCP-1, ACSL1, CPT1A, and SIRT3. These results suggested that brown adipose tissue might be the target of AR-C17 to prevent obesity and its associated insulin resistance.

10.1039/d3fo00071k

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Citations (1)

The $h$-edge tolerable diagnosability of balanced hypercubes

arXiv (Cornell University) (2019)

Min Xu Yulong Wei

To measure the fault diagnosis capability of a multiprocessor system with faulty links, Zhu et al. [Theoret. Comput. Sci. 758 (2019) 1--8] introduced the $h$-edge tolerable diagnosability. This kind of diagnosability is a generalization of the concept of traditional diagnosability. In this paper, as complement to the results in [Theoret. Comput. Sci. 760 (2019) 1--14], we completely determine the $h$-edge tolerable diagnosability of balanced hypercubes $BH_n$ under the PMC model and the MM$^*$ model. Thus, the traditional diagnosability of $BH_n$ is also determined.

Complement

10.48550/arxiv.1904.07020

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Coronavirus genomes carry the signatures of their habitats

bioRxiv (Cold Spring Harbor Laboratory) (2020)

Yulong Wei Jordan R. Silke Parisa Aris Xuhua Xia

ABSTRACT Coronaviruses such as SARS-CoV-2 regularly infect host tissues that express antiviral proteins (AVPs) in abundance. Understanding how they evolve to adapt or evade host immune responses is important in the effort to control the spread of COVID-19. Two AVPs that may shape viral genomes are the zinc finger antiviral protein (ZAP) and the apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3 protein (APOBEC3). The former binds to CpG dinucleotides to facilitate the degradation of viral transcripts while the latter deaminates C into U residues leading to dysfunctional transcripts. We tested the hypothesis that both APOBEC3 and ZAP may act as primary selective pressures that shape the genome of an infecting coronavirus by considering a comprehensive number of publicly available genomes for seven coronaviruses (SARS-CoV-2, SARS-CoV, MERS, Bovine CoV, Murine MHV, Porcine HEV, and Canine CoV). We show that coronaviruses that regularly infect tissues with abundant AVPs have CpG-deficient and U-rich genomes; whereas viruses that do not infect tissues with abundant AVPs do not share these sequence hallmarks. In SARS-CoV-2, CpG is most deficient in the S protein region to evaded ZAP-mediated antiviral defense during cell entry. Furthermore, over four months of SARS-CoV-2 evolutionary history, we observed a marked increase in C to U substitutions in the 5’ UTR and ORF1ab regions. This suggests that the two regions could be under constant C to U deamination by APOBEC3. The evolutionary pressures exerted by host immune systems onto viral genomes may motivate novel strategies for SARS-CoV-2 vaccine development.

Coronavirus

Viral protein

Antiviral protein

CpG site

10.1101/2020.06.13.149591

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Citations (10)

Barcode ITS2: a useful tool for identifying Trachelospermum jasminoides and a good monitor for medicine market

Scientific Reports (2017)

Ning Yu Yulong Wei Xin Zhang Ning Zhu Yanli Wang

Trachelospermum jasminoides is commonly used in traditional Chinese medicine. However, the use of the plant's local alternatives is frequent, causing potential clinical problems. The T. jasminoides sold in the medicine market is commonly dried and sliced, making traditional identification methods difficult. In this study, the ITS2 region was evaluated on 127 sequences representing T. jasminoides and its local alternatives according to PCR and sequencing rates, intra- and inter-specific divergences, secondary structure, and discrimination capacity. Results indicated the 100% success rates of PCR and sequencing and the obvious presence of a barcoding gap. Results of BLAST 1, nearest distance and neighbor-joining tree methods showed that barcode ITS2 could successfully identify all the texted samples. The secondary structures of the ITS2 region provided another dimensionality for species identification. Two-dimensional images were obtained for better and easier identification. Previous studies on DNA barcoding concentrated more on the same family, genus, or species. However, an ideal barcode should be variable enough to identify closely related species. Meanwhile, the barcodes should also be conservative in identifying distantly related species. This study highlights the application of barcode ITS2 in solving practical problems in the distantly related local alternatives of medical plants.

Barcode

DNA Barcoding

Identification

10.1038/s41598-017-04674-w

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Citations (30)

Applications of Protein Secondary Structure Algorithms in SARS-CoV-2 Research

Journal of Proteome Research (2021)

Alibek Kruglikov Mohan Rakesh Yulong Wei Xuhua Xia

Since the outset of COVID-19, the pandemic has prompted immediate global efforts to sequence SARS-CoV-2, and over 450 000 complete genomes have been publicly deposited over the course of 12 months. Despite this, comparative nucleotide and amino acid sequence analyses often fall short in answering key questions in vaccine design. For example, the binding affinity between different ACE2 receptors and SARS-COV-2 spike protein cannot be fully explained by amino acid similarity at ACE2 contact sites because protein structure similarities are not fully reflected by amino acid sequence similarities. To comprehensively compare protein homology, secondary structure (SS) analysis is required. While protein structure is slow and difficult to obtain, SS predictions can be made rapidly, and a well-predicted SS structure may serve as a viable proxy to gain biological insight. Here we review algorithms and information used in predicting protein SS to highlight its potential application in pandemics research. We also showed examples of how SS predictions can be used to compare ACE2 proteins and to evaluate the zoonotic origins of viruses. As computational tools are much faster than wet-lab experiments, these applications can be important for research especially in times when quickly obtained biological insights can help in speeding up response to pandemics.

Pandemic

Sequence (biology)

Protein sequencing

Sequence homology

Similarity (geometry)

10.1021/acs.jproteome.0c00734

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Citations (3)

Identification of spoilage microorganisms in blueberry juice and their inactivation by a microchip pulsed electric field system

Scientific Reports (2018)

Ning Zhu Ning Yu Zhu Feng Yue Yulong Wei Yanan Hou

Blueberry juice is a healthy and nutritious food that has become increasingly popular worldwide. However, little is known about the microbial groups of this juice that can cause its spoilage. This study aimed to identify the main spoilage microorganisms in blueberry juice and explore whether a microchip pulsed electric field (MPEF) can effectively inactivate them. We performed polymerase chain reaction (PCR) amplification, as well as 16S rDNA, 18S rDNA, internal transcribed spacer (ITS), and 26S rDNA gene sequence analyses. Nine species belonging to eight genera, including Pantoea, Burkholderia, Pichia, Meyerozyma, Cryptococcus, Aureobasidium, Cladosporium, and Penicillium were identified as spoilage microorganisms. Cryptococcus sp., Meyerozyma sp., and Pichia sp. were specific spoilage organisms (SSO) owing to their rising numbers throughout spoilage progression. The effect of MPEF on the potential inactivation of these microorganisms was to induce significant inactivation of viable Cryptococcus sp., Meyerozyma sp., and Pichia sp. This research provides a theoretical basis for the application of MPEF in improving the quality of blueberry juice.

Pichia

10.1038/s41598-018-26513-2

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Citations (10)

Author response for "EGFR signaling is required for maintaining adult cartilage homeostasis and attenuating osteoarthritis progression"

Yulong Wei Xiaoyuan Ma Hao Sun Tao Gui Jun Li

Homeostasis

10.1002/jbmr.4531/v2/response1

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The characteristic polynomials of uniform hypercycles with length four

arXiv (Cornell University) (2023)

Cunxiang Duan Ligong Wang Yulong Wei

Let $C_{m}$ be a cycle with length $m.$ The $k$-uniform hypercycle with length $m$ obtained by adding $k-2$ new vertices in every edge of $C_{m},$ denoted by $C_{m,k}.$ In this paper, we obtain some trace formulas of uniform hypercycles with length four. Moreover, we give the characteristic polynomials of uniform hypercycles with length four.

TRACE (psycholinguistics)

10.48550/arxiv.2309.02830

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