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  1. Article ; Online: Understanding the contemporary high obesity rate from an evolutionary genetic perspective.

    Wu, Tong / Xu, Shuhua

    Hereditas

    2023  Volume 160, Issue 1, Page(s) 5

    Abstract: The topic of obesity is gaining increasing popularity globally. From an evolutionary genetic perspective, it is believed that the main cause of the high obesity rate is the mismatch between environment and genes after people have shifted toward a modern ... ...

    Abstract The topic of obesity is gaining increasing popularity globally. From an evolutionary genetic perspective, it is believed that the main cause of the high obesity rate is the mismatch between environment and genes after people have shifted toward a modern high-calorie diet. However, it has been debated for over 60 years about how obesity-related genes become prevalent all over the world. Here, we review the three most influential hypotheses or viewpoints, i.e., the thrifty gene hypothesis, the drifty gene hypothesis, and the maladaptation viewpoint. In particular, genome-wide association studies in the recent 10 years have provided rich findings and evidence to be considered for a better understanding of the evolutionary genetic mechanisms of obesity. We anticipate this brief review to direct further studies and inspire the future application of precision medicine in obesity treatment.
    MeSH term(s) Humans ; Genome-Wide Association Study ; Obesity/genetics ; Biological Evolution
    Language English
    Publishing date 2023-02-07
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 214294-6
    ISSN 1601-5223 ; 0018-0661
    ISSN (online) 1601-5223
    ISSN 0018-0661
    DOI 10.1186/s41065-023-00268-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Asian-European differentiation of schizophrenia-associated genes driven by admixture and natural selection.

    Chen, Sihan / Tang, Die / Deng, Lian / Xu, Shuhua

    iScience

    2024  Volume 27, Issue 5, Page(s) 109560

    Abstract: The European-centered genome-wide association studies of schizophrenia (SCZ) may not be well applied to non-European populations. We analyzed 1,592 reported SCZ-associated genes using the public genome data and found an overall higher Asian-European ... ...

    Abstract The European-centered genome-wide association studies of schizophrenia (SCZ) may not be well applied to non-European populations. We analyzed 1,592 reported SCZ-associated genes using the public genome data and found an overall higher Asian-European differentiation on the SCZ-associated variants than at the genome-wide level. Notable examples included 15 missense variants, a regulatory variant
    Language English
    Publishing date 2024-03-26
    Publishing country United States
    Document type Journal Article
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2024.109560
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Archaic introgression contributed to the pre-agriculture adaptation of vitamin B1 metabolism in East Asia.

    Ma, Xixian / Xu, Shuhua

    iScience

    2022  Volume 25, Issue 12, Page(s) 105614

    Abstract: Thiamine (vitamin B1) is an essential micronutrient. Genes involved in thiamine metabolisms, such ... ...

    Abstract Thiamine (vitamin B1) is an essential micronutrient. Genes involved in thiamine metabolisms, such as
    Language English
    Publishing date 2022-11-17
    Publishing country United States
    Document type Journal Article
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2022.105614
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Urban traffic regulation and air pollution: A case study of urban motor vehicle restriction policy

    Sun, Chuanwang / Xu, Shuhua / Yang, Mian / Gong, Xu

    Energy policy. 2022 Apr., v. 163

    2022  

    Abstract: Many local governments have taken various regulations to control heavy traffic and alleviate vehicle pollution emissions continuously. In practice, one of the most common and widely used regulations is the motor vehicle restriction policy (MVR policy). ... ...

    Abstract Many local governments have taken various regulations to control heavy traffic and alleviate vehicle pollution emissions continuously. In practice, one of the most common and widely used regulations is the motor vehicle restriction policy (MVR policy). But it is unknown whether a motor vehicle restriction policy can effectively alleviate traffic pollution. Moreover, few studies considered the duration of the policy and distinct the effects of different types of MVR policies. In this paper, we first classify the MVR policies into consecutive and intermittent restrictions policies and analyze their different effects on air pollution based on the difference-in-differences method. Further, we take the Mediation Effect Model to verify the conduction mechanism of the impact. The result shows that both consecutive and intermittent policies can improve air quality, while the latter's effect is more significant. Moreover, as for the impact's conduction mechanism, we find that consecutive policies alleviate pollution by changing driving preference and vehicle purchase. Still, the intermittent policies alleviate pollution by promptly easing traffic jams and avoiding unnecessary vehicle emissions of the idling engine. This founding provides a decision-making basis to the government for more efficient and reasonable regulation policies.
    Keywords air pollution ; air quality ; case studies ; decision making ; energy policy ; models ; traffic ; vehicles (equipment)
    Language English
    Dates of publication 2022-04
    Publishing place Elsevier Ltd
    Document type Article
    ISSN 0301-4215
    DOI 10.1016/j.enpol.2022.112819
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: A protocol for applying low-coverage whole-genome sequencing data in structural variation studies.

    Liu, Qi / Xie, Bo / Gao, Yang / Xu, Shuhua / Lu, Yan

    STAR protocols

    2023  Volume 4, Issue 3, Page(s) 102433

    Abstract: Structural variations (SVs) have a great impact on various biological processes and influence physical traits in many species. Here, we present a protocol for applying the low-coverage next-generation sequencing data of Rhipicephalus microplus to detect ... ...

    Abstract Structural variations (SVs) have a great impact on various biological processes and influence physical traits in many species. Here, we present a protocol for applying the low-coverage next-generation sequencing data of Rhipicephalus microplus to detect high-differentiated SVs accurately. We also outline its use to investigate population/species-specific genetic structures, local adaptation, and transcriptional function. We describe steps for constructing variation maps and SV annotation. We then detail population genetic analysis and differential gene expression analysis. For complete details on the usage and execution of this protocol, please refer to Liu et al. (2023).
    MeSH term(s) Whole Genome Sequencing ; High-Throughput Nucleotide Sequencing
    Language English
    Publishing date 2023-07-10
    Publishing country United States
    Document type Journal Article
    ISSN 2666-1667
    ISSN (online) 2666-1667
    DOI 10.1016/j.xpro.2023.102433
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: The human pangenome reference: the beginning of a new era for genomics.

    Wang, Bo / Dang, Ningxin / Yang, Xiaofei / Xu, Shuhua / Ye, Kai

    Science bulletin

    2023  Volume 68, Issue 14, Page(s) 1484–1487

    MeSH term(s) Humans ; Genomics ; Software
    Language English
    Publishing date 2023-06-16
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2816140-3
    ISSN 2095-9281 ; 2095-9273
    ISSN (online) 2095-9281
    ISSN 2095-9273
    DOI 10.1016/j.scib.2023.06.014
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Detecting archaic introgression and modeling multiple-wave admixture with ArchaicSeeker 2.0.

    Zhang, Rui / Yuan, Kai / Xu, Shuhua

    STAR protocols

    2022  Volume 3, Issue 2, Page(s) 101314

    Abstract: ArchaicSeeker 2.0 is designed to identify the sequences derived from known or unknown archaic hominins and to further model the multiple-wave gene flows. The main functional modules involve seeking introgressed sequences, determining corresponding ... ...

    Abstract ArchaicSeeker 2.0 is designed to identify the sequences derived from known or unknown archaic hominins and to further model the multiple-wave gene flows. The main functional modules involve seeking introgressed sequences, determining corresponding ancestries, and reconstructing the admixture history. The protocol below describes the analytic steps for the application of ArchaicSeeker 2.0 into analysis of example data of the Han Chinese population. For complete details on the use and execution of this protocol, please refer to Yuan et al. (2021).
    MeSH term(s) Animals ; Asians/genetics ; Gene Flow ; Genome, Human ; Hominidae/genetics ; Humans
    Language English
    Publishing date 2022-04-14
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2666-1667
    ISSN (online) 2666-1667
    DOI 10.1016/j.xpro.2022.101314
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: The Peopling and Migration History of the Natives in Peninsular Malaysia and Borneo: A Glimpse on the Studies Over the Past 100 years.

    Hoh, Boon-Peng / Deng, Lian / Xu, Shuhua

    Frontiers in genetics

    2022  Volume 13, Page(s) 767018

    Abstract: Southeast Asia (SEA) has one of the longest records of modern human habitation out-of-Africa. Located at the crossroad of the mainland and islands of SEA, Peninsular Malaysia is an important piece of puzzle to the map of peopling and migration history in ...

    Abstract Southeast Asia (SEA) has one of the longest records of modern human habitation out-of-Africa. Located at the crossroad of the mainland and islands of SEA, Peninsular Malaysia is an important piece of puzzle to the map of peopling and migration history in Asia, a question that is of interest to many anthropologists, archeologists, and population geneticists. This review aims to revisit our understanding to the population genetics of the natives from Peninsular Malaysia and Borneo over the past century based on the chronology of the technology advancement: 1) Anthropological and Physical Characterization; 2) Blood Group Markers; 3) Protein Markers; 4) Mitochondrial and Autosomal DNA Markers; and 5) Whole Genome Analysis. Subsequently some missing gaps of the study are identified. In the later part of this review, challenges of studying the population genetics of natives will be elaborated. Finally, we conclude our review by reiterating the importance of unveiling migration history and genetic diversity of the indigenous populations as a steppingstone towards comprehending disease evolution and etiology.
    Language English
    Publishing date 2022-01-27
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2022.767018
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Population genomics of East Asian ethnic groups.

    Pan, Ziqing / Xu, Shuhua

    Hereditas

    2020  Volume 157, Issue 1, Page(s) 49

    Abstract: East Asia constitutes one-fifth of the global population and exhibits substantial genetic diversity. However, genetic investigations on populations in this region have been largely under-represented compared with European populations. Nonetheless, the ... ...

    Abstract East Asia constitutes one-fifth of the global population and exhibits substantial genetic diversity. However, genetic investigations on populations in this region have been largely under-represented compared with European populations. Nonetheless, the last decade has seen considerable efforts and progress in genome-wide genotyping and whole-genome sequencing of the East-Asian ethnic groups. Here, we review the recent studies in terms of ancestral origin, population relationship, genetic differentiation, and admixture of major East- Asian groups, such as the Chinese, Korean, and Japanese populations. We mainly focus on insights from the whole-genome sequence data and also include the recent progress based on mitochondrial DNA (mtDNA) and Y chromosome data. We further discuss the evolutionary forces driving genetic diversity in East-Asian populations, and provide our perspectives for future directions on population genetics studies, particularly on underrepresented indigenous groups in East Asia.
    MeSH term(s) Asian People/genetics ; Biological Evolution ; Ethnicity/genetics ; Asia, Eastern ; Genetic Variation ; Genetics, Population ; Genomics ; Human Genetics ; Humans ; Selection, Genetic
    Language English
    Publishing date 2020-12-08
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 214294-6
    ISSN 1601-5223 ; 0018-0661
    ISSN (online) 1601-5223
    ISSN 0018-0661
    DOI 10.1186/s41065-020-00162-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Comprehensive RNA-Seq Analysis Pipeline for Non-Model Organisms and Its Application in Schmidtea mediterranea

    Wang, Yanzhi / Li, Sijun / Nong, Baoting / Zhou, Weiping / Xu, Shuhua / Zhou, Songyang / Xiong, Yuanyan

    Genes (Basel). 2023 Apr. 27, v. 14, no. 5

    2023  

    Abstract: RNA sequencing (RNA-seq) is a high-throughput technology that provides in-depth information on transcriptome. The advancement and dropping costs of RNA sequencing, accompanied by more available reference genomes for different species, make transcriptome ... ...

    Abstract RNA sequencing (RNA-seq) is a high-throughput technology that provides in-depth information on transcriptome. The advancement and dropping costs of RNA sequencing, accompanied by more available reference genomes for different species, make transcriptome analysis in non-model organisms possible. Current obstacles in analyzing RNA-seq data include a lack of functional annotation, which may complicate the process of linking genes to corresponding functions. Here, we provide a one-stop RNA-seq analysis pipeline, PipeOne-NM, for transcriptome functional annotation, non-coding RNA identification, and transcripts alternative splicing analysis of non-model organisms, intended for use with Illumina platform-based RNA-seq data. We performed PipeOne-NM on 237 Schmidtea mediterranea RNA-seq runs and assembled a transcriptome with 84,827 sequences from 49,320 genes, identifying 64,582 mRNA from 35,485 genes, 20,217 lncRNA from 17,084 genes, and 3481 circRNAs from 1103 genes. In addition, we performed a co-expression analysis of lncRNA and mRNA and identified that 1319 lncRNA co-express with at least one mRNA. Further analysis of samples from S. mediterranea sexual and asexual strains revealed the role of sexual reproduction in gene expression profiles. Samples from different parts of asexual S. mediterranea revealed that differential expression profiles of different body parts correlated with the function of conduction of nerve impulses. In conclusion, PipeOne-NM has the potential to provide comprehensive transcriptome information for non-model organisms on a single platform.
    Keywords Schmidtea mediterranea ; gene expression ; gene expression regulation ; genome ; nerve tissue ; non-coding RNA ; sequence analysis ; sexual reproduction ; transcriptome ; transcriptomics
    Language English
    Dates of publication 2023-0427
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article ; Online
    ZDB-ID 2527218-4
    ISSN 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes14050989
    Database NAL-Catalogue (AGRICOLA)

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