Browsing by Author "Wang J"

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    A Genetic Locus within the FMN1/GREM1 Gene Region Interacts with Body Mass Index in Colorectal Cancer Risk.
    (American Association for Cancer Research, 2023-08-01) Aglago EK; Kim A; Lin Y; Qu C; Evangelou M; Ren Y; Morrison J; Albanes D; Arndt V; Barry EL; Baurley JW; Berndt SI; Bien SA; Bishop DT; Bouras E; Brenner H; Buchanan DD; Budiarto A; Carreras-Torres R; Casey G; Cenggoro TW; Chan AT; Chang-Claude J; Chen X; Conti DV; Devall M; Diez-Obrero V; Dimou N; Drew D; Figueiredo JC; Gallinger S; Giles GG; Gruber SB; Gsur A; Gunter MJ; Hampel H; Harlid S; Hidaka A; Harrison TA; Hoffmeister M; Huyghe JR; Jenkins MA; Jordahl K; Joshi AD; Kawaguchi ES; Keku TO; Kundaje A; Larsson SC; Marchand LL; Lewinger JP; Li L; Lynch BM; Mahesworo B; Mandic M; Obón-Santacana M; Moreno V; Murphy N; Nan H; Nassir R; Newcomb PA; Ogino S; Ose J; Pai RK; Palmer JR; Papadimitriou N; Pardamean B; Peoples AR; Platz EA; Potter JD; Prentice RL; Rennert G; Ruiz-Narvaez E; Sakoda LC; Scacheri PC; Schmit SL; Schoen RE; Shcherbina A; Slattery ML; Stern MC; Su Y-R; Tangen CM; Thibodeau SN; Thomas DC; Tian Y; Ulrich CM; van Duijnhoven FJ; Van Guelpen B; Visvanathan K; Vodicka P; Wang J; White E; Wolk A; Woods MO; Wu AH; Zemlianskaia N; Hsu L; Gauderman WJ; Peters U; Tsilidis KK; Campbell PT
    Colorectal cancer risk can be impacted by genetic, environmental, and lifestyle factors, including diet and obesity. Gene-environment interactions (G × E) can provide biological insights into the effects of obesity on colorectal cancer risk. Here, we assessed potential genome-wide G × E interactions between body mass index (BMI) and common SNPs for colorectal cancer risk using data from 36,415 colorectal cancer cases and 48,451 controls from three international colorectal cancer consortia (CCFR, CORECT, and GECCO). The G × E tests included the conventional logistic regression using multiplicative terms (one degree of freedom, 1DF test), the two-step EDGE method, and the joint 3DF test, each of which is powerful for detecting G × E interactions under specific conditions. BMI was associated with higher colorectal cancer risk. The two-step approach revealed a statistically significant G×BMI interaction located within the Formin 1/Gremlin 1 (FMN1/GREM1) gene region (rs58349661). This SNP was also identified by the 3DF test, with a suggestive statistical significance in the 1DF test. Among participants with the CC genotype of rs58349661, overweight and obesity categories were associated with higher colorectal cancer risk, whereas null associations were observed across BMI categories in those with the TT genotype. Using data from three large international consortia, this study discovered a locus in the FMN1/GREM1 gene region that interacts with BMI on the association with colorectal cancer risk. Further studies should examine the potential mechanisms through which this locus modifies the etiologic link between obesity and colorectal cancer. Significance: This gene-environment interaction analysis revealed a genetic locus in FMN1/GREM1 that interacts with body mass index in colorectal cancer risk, suggesting potential implications for precision prevention strategies.
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    Achieving Carbon Neutrality – The Role of Heterogeneous Environmental Regulations on Urban Green Innovation
    (Frontiers Media S.A., 2022-06-09) Liu B; Wang J; Li RYM; Peng L; Mi L; Kirikkaleli D
    This article examines the impact of heterogeneous environmental regulations on urban green innovation using panel data from 285 prefecture-level cities in mainland China from 2008 to 2019. From the perspective of green patents, this article utilizes a two-way fixed-effect model and the mediation effect model to examine the mechanism of the impact of heterogeneous environmental regulations on urban green innovation in China. Results show that the urban green innovation development in China is relatively slow and can be easily influenced by national policies. More specifically, the relationship between the command-based environmental regulation and urban green innovation presents an inverted non-linear U-shaped model, whereas the relationship between the market-based and voluntary environmental regulation presents a positive U-shaped model. Further investigation of this mechanism concludes that the progression of regional green innovation is primarily accelerated by technological development, effective energy allocation, and industrial structural upgrading. However, the implementation of relevant environmental regulations varies, resulting in various green innovation progression rates. Therefore, in order to achieve the carbon neutrality goal that China proposes, the effectiveness of environmental regulation implementation should be improved. Moreover, the development of various environmental regulation tools should be better coordinated.
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    Age Differences in Ileum Microbiota Density: VFAs and Their Transport-Related Gene Interactions in Tibetan Sheep
    (MDPI (Basel, Switzerland), 2024-10-03) Wang F; Sha Y; He Y; Liu X; Chen X; Yang W; Chen Q; Gao M; Huang W; Wang J; Hao Z; Wang L; Yang F
    Microbiota density plays an important role in maintaining host metabolism, immune function, and health, and age has a specific effect on the composition of intestinal microbiota. Therefore, the age-specific effects of age differences on the structure and function of the ileum microbiota in Tibetan sheep were investigated by determining the density of the ileum microbiota, the content of VFAs, and the expression levels of their transporter-related genes at different ages. The results showed that the contents of acetic acid and propionic acid in the ileum of Tibetan sheep in the 1.5-year-old group were significantly higher (p < 0.05) than those in other age groups, and that the contents of total VFAs were also significantly higher (p < 0.05) than those in other age groups. The relative densities of ileum Rf, Ra, and Fs were significantly higher in the 1.5-year-old group than in the other age groups (p < 0.05). The ileum epithelial VFAs transport-related genes AE2, MCT-4, and NHE1 had the highest expression in the 1.5-year-old group, and the expression of DRA was significantly lower in the 1.5-year-old group than in the 6-year-old group (p < 0.05). Correlation analysis showed that Cb, Sr, and Tb were significantly positively correlated with butyric acid concentration (p < 0.05) and negatively correlated with acetic acid, but the difference was not significant (p > 0.05); MCT-1, MCT-4, and AE2 were significantly positively correlated (p < 0.05) with acetic, propionic, and isobutyric acid concentrations; NHE1, NHE2, and MCT-4 were highly significantly positively correlated (p < 0.01) with Romboutsia and unclassified_Peptostreptococcaceae, while acetic acid was significantly positively correlated (p < 0.05) with NK4A214_group; Romboutsia, and unclassified_Peptostreptococcaceae were significantly positively correlated (p < 0.05). Therefore, compared with other ages, the 1.5-year-old Tibetan sheep had a stronger fermentation and metabolic capacity in the ileum under traditional grazing conditions on the plateau, which could provide more energy for Tibetan sheep during plateau acclimatization.
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    An improved method for monitoring multiscale plant species diversity of alpine grassland using UAVs: A case study in the source region of the Yellow River, China
    (Frontiers Media, 9/06/2022) Sun Y; Yuan Y; Luo Y; Ji W; Bian Q; Zhu Z; Wang J; Qin Y; He XZ; Li M; Yi S
    Plant species diversity (PSD) is essential in evaluating the function and developing the management and conservation strategies of grassland. However, over a large region, an efficient and high precision method to monitor multiscale PSD (α-, β-, and γ-diversity) is lacking. In this study, we proposed and improved an unmanned aerial vehicle (UAV)-based PSD monitoring method (UAVB) and tested the feasibility, and meanwhile, explored the potential relationship between multiscale PSD and precipitation on the alpine grassland of the source region of the Yellow River (SRYR), China. Our findings showed that: (1) UAVB was more representative (larger monitoring areas and more species identified with higher α- and γ-diversity) than the traditional ground-based monitoring method, though a few specific species (small in size) were difficult to identify; (2) UAVB is suitable for monitoring the multiscale PSD over a large region (the SRYR in this study), and the improvement by weighing the dominance of species improved the precision of α-diversity (higher R 2 and lower P values of the linear regressions); and (3) the species diversity indices (α- and β-diversity) increased first and then they tended to be stable with the increase of precipitation in SRYR. These findings conclude that UAVB is suitable for monitoring multiscale PSD of an alpine grassland community over a large region, which will be useful for revealing the relationship of diversity-function, and helpful for conservation and sustainable management of the alpine grassland.
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    Author Correction: Dense sampling of bird diversity increases power of comparative genomics.
    (2021-04) Feng S; Stiller J; Deng Y; Armstrong J; Fang Q; Reeve AH; Xie D; Chen G; Guo C; Faircloth BC; Petersen B; Wang Z; Zhou Q; Diekhans M; Chen W; Andreu-Sánchez S; Margaryan A; Howard JT; Parent C; Pacheco G; Sinding M-HS; Puetz L; Cavill E; Ribeiro ÂM; Eckhart L; Fjeldså J; Hosner PA; Brumfield RT; Christidis L; Bertelsen MF; Sicheritz-Ponten T; Tietze DT; Robertson BC; Song G; Borgia G; Claramunt S; Lovette IJ; Cowen SJ; Njoroge P; Dumbacher JP; Ryder OA; Fuchs J; Bunce M; Burt DW; Cracraft J; Meng G; Hackett SJ; Ryan PG; Jønsson KA; Jamieson IG; da Fonseca RR; Braun EL; Houde P; Mirarab S; Suh A; Hansson B; Ponnikas S; Sigeman H; Stervander M; Frandsen PB; van der Zwan H; van der Sluis R; Visser C; Balakrishnan CN; Clark AG; Fitzpatrick JW; Bowman R; Chen N; Cloutier A; Sackton TB; Edwards SV; Foote DJ; Shakya SB; Sheldon FH; Vignal A; Soares AER; Shapiro B; González-Solís J; Ferrer-Obiol J; Rozas J; Riutort M; Tigano A; Friesen V; Dalén L; Urrutia AO; Székely T; Liu Y; Campana MG; Corvelo A; Fleischer RC; Rutherford KM; Gemmell NJ; Dussex N; Mouritsen H; Thiele N; Delmore K; Liedvogel M; Franke A; Hoeppner MP; Krone O; Fudickar AM; Milá B; Ketterson ED; Fidler AE; Friis G; Parody-Merino ÁM; Battley PF; Cox MP; Lima NCB; Prosdocimi F; Parchman TL; Schlinger BA; Loiselle BA; Blake JG; Lim HC; Day LB; Fuxjager MJ; Baldwin MW; Braun MJ; Wirthlin M; Dikow RB; Ryder TB; Camenisch G; Keller LF; DaCosta JM; Hauber ME; Louder MIM; Witt CC; McGuire JA; Mudge J; Megna LC; Carling MD; Wang B; Taylor SA; Del-Rio G; Aleixo A; Vasconcelos ATR; Mello CV; Weir JT; Haussler D; Li Q; Yang H; Wang J; Lei F; Rahbek C; Gilbert MTP; Graves GR; Jarvis ED; Paten B; Zhang G
    In Supplementary Table 1 of this Article, 23 samples (B10K-DU-029-32, B10K-DU-029-33, B10K-DU-029-36 to B10K-DU-029-44, B10K-DU- 029-46, B10K-DU-029-47, B10K-DU-029-49 to B10K-DU-029-53, B10K-DU- 029-75 to B10K-DU-029-77, B10K-DU-029-80, and B10K-DU-030-03; styled in boldface in the revised table) were assigned to the incorrect institution. Supplementary Table 1 has been amended to reflect the correct source institution for these samples, and associated data (tissue, museum ID/source specimen ID, site, state/province, latitude, longitude, date collected and sex) have been updated accordingly. The original table is provided as Supplementary Information to this Amendment, and the original Article has been corrected online.
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    Characterizing the dynamics of the rumen microbiota, its metabolites, and blood metabolites across reproductive stages in Small-tailed Han sheep.
    (American Society for Microbiology, 2023-11-10) Sha Y; Liu X; Pu X; He Y; Wang J; Zhao S; Shao P; Wang F; Xie Z; Chen X; Yang W
    Different reproductive stages of mammals involve complex biological processes, and the intestinal microbiota, as an endocrine organ or an “invisible organ,” is involved in the regulation of hormone levels, immune function, and metabolism. However, the effects of the rumen microbiota, its metabolites, and blood metabolites on the reproductive performance of ruminants remain unclear. This study revealed that the Prevotella abundance increased significantly during pregnancy (P < 0.01); the Fibrobacter abundance increased significantly during lactation (P < 0.05); and rumen microbial carbohydrate metabolism, glucose biosynthesis, and metabolic functions were significantly enriched during pregnancy (P < 0.05). Microbial metabolic profile analysis showed that the differentially abundant microbial metabolites during pregnancy and lactation were mainly enriched in the biosynthesis of ubiquinone and other terpenoid quinones, and there was a certain correlation with the microbiota. Among them, sapindoside A was increased during pregnancy, nicotinamide riboside and β-cryptoxanthin were reduced during pregnancy, and L-tryptophan was significantly increased during lactation. In addition, the volatile fatty acid levels in lactation were significantly higher than those in non-pregnancy and pregnancy (P < 0.05), and the NH3-N content during pregnancy was significantly higher than that during lactation and non-pregnancy (P < 0.05). Moreover, there were differences in the serum metabolite levels at different reproductive stages, and similar metabolites existed when comparing the rumen metabolites, which were mainly enriched in arachidonic acid metabolism, vitamin B6 metabolism, and ABC transporter protein, resulting in significantly higher serum IgA and IgM levels during lactation than during non-pregnancy and pregnancy (P < 0.05).
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    Clustering Analysis on Sustainable Development Goal Indicators for Forty-Five Asian Countries
    (28/03/2023) Mathrani A; Wang J; Li D; Zhang X; Sacco, PL
    This paper draws upon the United Nations 2022 data report on the achievement of Sustainable Development Goals (SDGs) across the following four dimensions: economic, social, environmental and institutional. Ward’s method was applied to obtain clustering results for forty-five Asian countries to understand their level of progress and overall trends in achieving SDGs. We identified varying degrees of correlation between the four dimensions. The results show that East Asian countries performed poorly in the economic dimension, while some countries in Southeast Asia and Central and West Asia performed relatively well. Regarding social and institutional dimensions, the results indicate that East and Central Asian countries performed relatively better than others. Finally, in the environmental dimension, West and South Asian countries showed better performance than other Asian countries. The insights gathered from this study can inform policymakers of these countries about their own country’s position in achieving SDGs in relation to other Asian countries, as they work towards establishing strategies for improving their sustainable development targets.
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    DiffusionDCI: A Novel Diffusion-Based Unified Framework for Dynamic Full-Field OCT Image Generation and Segmentation
    (IEEE Access, 2024) Yang B; Li J; Wang J; Li R; Gu K; Liu B; Militello C
    Rapid and accurate identification of cancerous areas during surgery is crucial for guiding surgical procedures and reducing postoperative recurrence rates. Dynamic Cell Imaging (DCI) has emerged as a promising alternative to traditional frozen section pathology, offering high-resolution displays of tissue structures and cellular characteristics. However, challenges persist in segmenting DCI images using deep learning methods, such as color variation and artifacts between patches in whole slide DCI images, and the difficulty in obtaining precise annotated data. In this paper, we introduce a novel two-stage framework for DCI image generation and segmentation. Initially, the Dual Semantic Diffusion Model (DSDM) is specifically designed to generate high-quality and semantically relevant DCI images. These images not only serve as an effective means of data augmentation to assist downstream segmentation tasks but also help in reducing the reliance on expensive and hard-to-obtain large annotated medical image datasets. Furthermore, we reuse the pretrained DSDM to extract diffusion features, which are then infused into the segmentation network via a cross-attention alignment module. This approach enables our network to capture and utilize the characteristics of DCI images more effectively, thereby significantly enhancing segmentation results. Our method was validated on the DCI dataset and compared with other methods for image generation and segmentation. Experimental results demonstrate that our method achieves superior performance in both tasks, proving the effectiveness of the proposed model.
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    Forecasting the publication and citation outcomes of COVID-19 preprints
    (The Royal Society, 2022-09) Gordon M; Bishop M; Chen Y; Dreber A; Goldfedder B; Holzmeister F; Johannesson M; Liu Y; Tran L; Twardy C; Wang J; Pfeiffer T
    Many publications on COVID-19 were released on preprint servers such as medRxiv and bioRxiv. It is unknown how reliable these preprints are, and which ones will eventually be published in scientific journals. In this study, we use crowdsourced human forecasts to predict publication outcomes and future citation counts for a sample of 400 preprints with high Altmetric score. Most of these preprints were published within 1 year of upload on a preprint server (70%), with a considerable fraction (45%) appearing in a high-impact journal with a journal impact factor of at least 10. On average, the preprints received 162 citations within the first year. We found that forecasters can predict if preprints will be published after 1 year and if the publishing journal has high impact. Forecasts are also informative with respect to Google Scholar citations within 1 year of upload on a preprint server. For both types of assessment, we found statistically significant positive correlations between forecasts and observed outcomes. While the forecasts can help to provide a preliminary assessment of preprints at a faster pace than traditional peer-review, it remains to be investigated if such an assessment is suited to identify methodological problems in preprints.
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    Fungi regulate the response of the N2O production process to warming and grazing in a Tibetan grassland
    (Copernicus Publications on behalf of the European Geosciences Union, 2018-07-20) Zhong L; Wang S; Xu X; Wang Y; Rui Y; Zhou X; Shen Q; Wang J; Jiang L; Luo C; Gu T; Ma W; Chen G; Kuzyakov Y
    Lack of understanding of the effects of warming and winter grazing on soil fungal contribution to the nitrous oxide (N2O) production process has limited our ability to predict N2O fluxes under changes in climate and land use management, because soil fungi play an important role in driving terrestrial N cycling. A controlled warming and winter grazing experiment that included control (C), winter grazing (G), warming (W) and warming with winter grazing (WG) was conducted to investigate the effects of warming and winter grazing on soil N2O production potential in an alpine meadow on the Tibetan Plateau. Our results showed that soil bacteria and fungi contributed 46 ± 2% and 54 ± 2% to nitrification, and 37 ± 3% and 63 ± 3% to denitrification in the control treatment, respectively. We conclude that soil fungi could be the main source of N2O production potential for the Tibetan alpine grasslands. In our results, neither warming nor winter grazing affected the activity of enzymes responsible for overall nitrification and denitrification. However, warming significantly increased the enzyme activity of bacterial nitrification and potential of N2O production from denitrification to 53 ± 2% and 55 ± 3%, respectively, but decreased them to 47 ± 2% and 45 ± 3%, respectively. Winter grazing had no such effects. Warming and winter grazing may not affect the soil N2O production potential, but climate warming can alter biotic pathways responsible for N2O production process. These findings confirm the importance of soil fungi in the soil N2O production process and how they respond to environmental and land use changes in alpine meadow ecosystems. Therefore, our results provide some new insights into ecological controls on the N2O production process and contribute to the development of an ecosystem nitrogen cycle model.
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    Genome-Wide Analysis of BBX Gene Family in Three Medicago Species Provides Insights into Expression Patterns under Hormonal and Salt Stresses.
    (MDPI (Basel, Switzerland), 2024-05-26) Wang J; Meng Z; He H; Du P; Dijkwel PP; Shi S; Li H; Xie Q; Igamberdiev AU
    BBX protein is a class of zinc finger transcription factors that have B-box domains at the N-terminus, and some of these proteins contain a CCT domain at the C-terminus. It plays an important role in plant growth, development, and metabolism. However, the expression pattern of BBX genes in alfalfa under hormonal and salt stresses is still unclear. In this study, we identified a total of 125 BBX gene family members by the available Medicago reference genome in diploid alfalfa (Medicago sativa spp. Caerulea), a model plant (M. truncatula), and tetraploid alfalfa (M. sativa), and divided these members into five subfamilies. We found that the conserved motifs of BBXs of the same subfamily reveal similarities. We analyzed the collinearity relationship and duplication mode of these BBX genes and found that the expression pattern of BBX genes is specific in different tissues. Analysis of the available transcriptome data suggests that some members of the BBX gene family are involved in multiple abiotic stress responses, and the highly expressed genes are often clustered together. Furthermore, we identified different expression patterns of some BBX genes under salt, ethylene, salt and ethylene, salicylic acid, and salt and salicylic acid treatments, verified by qRT-PCR, and analyzed the subcellular localization of MsBBX2, MsBBX17, and MsBBX32 using transient expression in tobacco. The results showed that BBX genes were localized in the nucleus. This study systematically analyzed the BBX gene family in Medicago plants, which provides a basis for the study of BBX gene family tolerance to abiotic stresses.
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    Genome-Wide Analysis of the SRPP/REF Gene Family in Taraxacum kok-saghyz Provides Insights into Its Expression Patterns in Response to Ethylene and Methyl Jasmonate Treatments.
    (MDPI (Basel, Switzerland), 2024-07-07) He H; Wang J; Meng Z; Dijkwel PP; Du P; Shi S; Dong Y; Li H; Xie Q; Pollmann S
    Taraxacum kok-saghyz (TKS) is a model plant and a potential rubber-producing crop for the study of natural rubber (NR) biosynthesis. The precise analysis of the NR biosynthesis mechanism is an important theoretical basis for improving rubber yield. The small rubber particle protein (SRPP) and rubber elongation factor (REF) are located in the membrane of rubber particles and play crucial roles in rubber biosynthesis. However, the specific functions of the SRPP/REF gene family in the rubber biosynthesis mechanism have not been fully resolved. In this study, we performed a genome-wide identification of the 10 TkSRPP and 2 TkREF genes' family members of Russian dandelion and a comprehensive investigation on the evolution of the ethylene/methyl jasmonate-induced expression of the SRPP/REF gene family in TKS. Based on phylogenetic analysis, 12 TkSRPP/REFs proteins were divided into five subclades. Our study revealed one functional domain and 10 motifs in these proteins. The SRPP/REF protein sequences all contain typical REF structural domains and belong to the same superfamily. Members of this family are most closely related to the orthologous species T. mongolicum and share the same distribution pattern of SRPP/REF genes in T. mongolicum and L. sativa, both of which belong to the family Asteraceae. Collinearity analysis showed that segmental duplication events played a key role in the expansion of the TkSRPP/REFs gene family. The expression levels of most TkSRPP/REF members were significantly increased in different tissues of T. kok-saghyz after induction with ethylene and methyl jasmonate. These results will provide a theoretical basis for the selection of candidate genes for the molecular breeding of T. kok-saghyz and the precise resolution of the mechanism of natural rubber production.
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    Genome-wide interaction analysis of folate for colorectal cancer risk.
    (Elsevier B.V., 2023-11) Bouras E; Kim AE; Lin Y; Morrison J; Du M; Albanes D; Barry EL; Baurley JW; Berndt SI; Bien SA; Bishop TD; Brenner H; Budiarto A; Burnett-Hartman A; Campbell PT; Carreras-Torres R; Casey G; Cenggoro TW; Chan AT; Chang-Claude J; Conti DV; Cotterchio M; Devall M; Diez-Obrero V; Dimou N; Drew DA; Figueiredo JC; Giles GG; Gruber SB; Gunter MJ; Harrison TA; Hidaka A; Hoffmeister M; Huyghe JR; Joshi AD; Kawaguchi ES; Keku TO; Kundaje A; Le Marchand L; Lewinger JP; Li L; Lynch BM; Mahesworo B; Männistö S; Moreno V; Murphy N; Newcomb PA; Obón-Santacana M; Ose J; Palmer JR; Papadimitriou N; Pardamean B; Pellatt AJ; Peoples AR; Platz EA; Potter JD; Qi L; Qu C; Rennert G; Ruiz-Narvaez E; Sakoda LC; Schmit SL; Shcherbina A; Stern MC; Su Y-R; Tangen CM; Thomas DC; Tian Y; Um CY; van Duijnhoven FJ; Van Guelpen B; Visvanathan K; Wang J; White E; Wolk A; Woods MO; Ulrich CM; Hsu L; Gauderman WJ; Peters U; Tsilidis KK
    Background Epidemiological and experimental evidence suggests that higher folate intake is associated with decreased colorectal cancer (CRC) risk; however, the mechanisms underlying this relationship are not fully understood. Genetic variation that may have a direct or indirect impact on folate metabolism can provide insights into folate’s role in CRC. Objectives Our aim was to perform a genome-wide interaction analysis to identify genetic variants that may modify the association of folate on CRC risk. Methods We applied traditional case-control logistic regression, joint 3-degree of freedom, and a 2-step weighted hypothesis approach to test the interactions of common variants (allele frequency >1%) across the genome and dietary folate, folic acid supplement use, and total folate in relation to risk of CRC in 30,550 cases and 42,336 controls from 51 studies from 3 genetic consortia (CCFR, CORECT, GECCO). Results Inverse associations of dietary, total folate, and folic acid supplement with CRC were found (odds ratio [OR]: 0.93; 95% confidence interval [CI]: 0.90, 0.96; and 0.91; 95% CI: 0.89, 0.94 per quartile higher intake, and 0.82 (95% CI: 0.78, 0.88) for users compared with nonusers, respectively). Interactions (P-interaction < 5×10-8) of folic acid supplement and variants in the 3p25.2 locus (in the region of Synapsin II [SYN2]/tissue inhibitor of metalloproteinase 4 [TIMP4]) were found using traditional interaction analysis, with variant rs150924902 (located upstream to SYN2) showing the strongest interaction. In stratified analyses by rs150924902 genotypes, folate supplementation was associated with decreased CRC risk among those carrying the TT genotype (OR: 0.82; 95% CI: 0.79, 0.86) but increased CRC risk among those carrying the TA genotype (OR: 1.63; 95% CI: 1.29, 2.05), suggesting a qualitative interaction (P-interaction = 1.4×10-8). No interactions were observed for dietary and total folate. Conclusions Variation in 3p25.2 locus may modify the association of folate supplement with CRC risk. Experimental studies and studies incorporating other relevant omics data are warranted to validate this finding.
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    Interaction between Rumen Epithelial miRNAs-Microbiota-Metabolites in Response to Cold-Season Nutritional Stress in Tibetan Sheep.
    (MDPI (Basel, Switzerland), 2023-09-23) Lv W; Sha Y; Liu X; He Y; Hu J; Wang J; Li S; Guo X; Shao P; Zhao F; Li M; Freking B
    Tibetan sheep are already well adapted to cold season nutrient stress on the Tibetan Plateau. Rumen, an important nutrient for metabolism and as an absorption organ in ruminants, plays a vital role in the cold stress adaptations of Tibetan sheep. Ruminal microbiota also plays an indispensable role in rumen function. In this study, combined multiomics data were utilized to comprehensively analyze the interaction mechanism between rumen epithelial miRNAs and microbiota and their metabolites in Tibetan sheep under nutrient stress in the cold season. A total of 949 miRNAs were identified in the rumen epithelium of both cold and warm seasons. A total of 62 differentially expressed (DE) miRNAs were screened using FC > 1.5 and p value < 0.01, and a total of 20,206 targeted genes were predicted by DE miRNAs. KEGG enrichment analysis revealed that DE miRNA-targeted genes were mainly enriched in axon guidance(ko04360), tight junction(ko04530), inflammatory mediator regulation of TRP channels(ko04750) and metabolism-related pathways. Correlation analysis revealed that rumen microbiota, rumen VFAs and DE miRNAs were all correlated. Further study revealed that the targeted genes of cold and warm season rumen epithelial DE miRNAs were coenriched with differential metabolites of microbiota in glycerophospholipid metabolism (ko00564), apoptosis (ko04210), inflammatory mediator regulation of TRP channels (ko04750), small cell lung cancer (ko05222), and choline metabolism in cancer (ko05231) pathways. There are several interactions between Tibetan sheep rumen epithelial miRNAs, rumen microbiota, and microbial metabolites, mainly through maintaining rumen epithelial barrier function and host homeostasis of choline and cholesterol, improving host immunity, and promoting energy metabolism pathways, thus enabling Tibetan sheep to effectively respond to cold season nutrient stress. The results also suggest that rumen microbiota have coevolved with their hosts to improve the adaptive capacity of Tibetan sheep to cold season nutrient stress, providing a new perspective for the study of cold season nutritional stress adaptation in Tibetan sheep.
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    Multi-omics revealed rumen microbiota metabolism and host immune regulation in Tibetan sheep of different ages
    (Frontiers Media S.A., 2024-02-13) Sha Y; Liu X; He Y; Zhao S; Hu J; Wang J; Li W; Shao P; Wang F; Chen X; Yang W; Xie Z; Chen Z
    The rumen microbiota and metabolites play an important role in energy metabolism and immune regulation of the host. However, the regulatory mechanism of rumen microbiota and metabolite interactions with host on Tibetan sheep's plateau adaptability is still unclear. We analyzed the ruminal microbiome and metabolome, host transcriptome and serum metabolome characteristics of Tibetan sheep at different ages. Biomarkers Butyrivibrio, Lachnospiraceae_XPB1014_group, Prevotella, and Rikenellaceae_RC9_gut_group were found in 4 months, 1.5 years, 3.5 years, and 6 years Tibetan sheep, respectively. The rumen microbial metabolites were mainly enriched in galactose metabolism, unsaturated fatty acid biosynthesis and fatty acid degradation pathways, and had significant correlation with microbiota. These metabolites further interact with mRNA, and are co-enriched in arginine and proline metabolism, metabolism of xenobiotics by cytochrome P450, propanoate metabolism, starch and sucrose metabolism, gap junction pathway. Meanwhile, serum metabolites also have a similar function, such as chemical carcinogenesis - reactive oxygen species, limonene and pinene degradation, and cutin, suberine and wax biosynthesis, thus participating in the regulation of the body's immune and energy-related metabolic processes. This study systematically revealed that rumen microbiota, metabolites, mRNA and serum metabolites of Tibetan sheep were involved in the regulation of fermentation metabolic function and immune level of Tibetan sheep at different ages, which provided a new perspective for plateau adaptability research of Tibetan sheep at different ages.
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    Obligate mutualism within a host drives the extreme specialization of a fig wasp genome
    (BioMed Central Ltd, 20/12/2013) Xiao J-H; Yue Z; Jia L-Y; Yang X-H; Niu L-H; Wang Z; Zhang P; Sun B-F; He S-M; Li Z; Xiong T-L; Xin W; Gu H-F; Wang B; Werren JH; Murphy RW; Wheeler D; Niu L-M; Ma G-C; Tang T; Bian S-N; Wang N-X; Yang C-Y; Wang N; Fu Y-G; Li W-Z; Yi SV; Yang X-Y; Zhou Q; Lu C-X; Xu C-Y; He L-J; Yu L-L; Chen M; Zheng Y; Wang S-W; Zhao S; Li Y-H; Yu Y-Y; Qian X-J; Cai Y; Bian L-L; Zhang S; Wang J-Y; Yin Y; Xiao H; Wang G-H; Yu H; Wu W-S; Cook JM; Wang J; Huang D-W
    Background: Fig pollinating wasps form obligate symbioses with their fig hosts. This mutualism arose approximately 75 million years ago. Unlike many other intimate symbioses, which involve vertical transmission of symbionts to host offspring, female fig wasps fly great distances to transfer horizontally between hosts. In contrast, male wasps are wingless and cannot disperse. Symbionts that keep intimate contact with their hosts often show genome reduction, but it is not clear if the wide dispersal of female fig wasps will counteract this general tendency. We sequenced the genome of the fig wasp Ceratosolen solmsi to address this question. Results: The genome size of the fig wasp C. solmsi is typical of insects, but has undergone dramatic reductions of gene families involved in environmental sensing and detoxification. The streamlined chemosensory ability reflects the overwhelming importance of females finding trees of their only host species, Ficus hispida, during their fleeting adult lives. Despite long-distance dispersal, little need exists for detoxification or environmental protection because fig wasps spend nearly all of their lives inside a largely benign host. Analyses of transcriptomes in females and males at four key life stages reveal that the extreme anatomical sexual dimorphism of fig wasps may result from a strong bias in sex-differential gene expression. Conclusions: Our comparison of the C. solmsi genome with other insects provides new insights into the evolution of obligate mutualism. The draft genome of the fig wasp, and transcriptomic comparisons between both sexes at four different life stages, provide insights into the molecular basis for the extreme anatomical sexual dimorphism of this species. © 2013 Xiao et al.; licensee BioMed Central Ltd.
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    Recurrent horizontal transfer identifies mitochondrial positive selection in a transmissible cancer.
    (Springer Nature Limited, 2020-06-16) Strakova A; Nicholls TJ; Baez-Ortega A; Ní Leathlobhair M; Sampson AT; Hughes K; Bolton IAG; Gori K; Wang J; Airikkala-Otter I; Allen JL; Allum KM; Arnold CL; Bansse-Issa L; Bhutia TN; Bisson JL; Blank K; Briceño C; Castillo Domracheva A; Corrigan AM; Cran HR; Crawford JT; Cutter SM; Davis E; de Castro KF; De Nardi AB; de Vos AP; Delgadillo Keenan L; Donelan EM; Espinoza Huerta AR; Faramade IA; Fazil M; Fotopoulou E; Fruean SN; Gallardo-Arrieta F; Glebova O; Gouletsou PG; Häfelin Manrique RF; Henriques JJGP; Horta RS; Ignatenko N; Kane Y; King C; Koenig D; Krupa A; Kruzeniski SJ; Lanza-Perea M; Lazyan M; Lopez Quintana AM; Losfelt T; Marino G; Martínez Castañeda S; Martínez-López MF; Masuruli BM; Meyer M; Migneco EJ; Nakanwagi B; Neal KB; Neunzig W; Nixon SJ; Ortega-Pacheco A; Pedraza-Ordoñez F; Peleteiro MC; Polak K; Pye RJ; Ramirez-Ante JC; Reece JF; Rojas Gutierrez J; Sadia H; Schmeling SK; Shamanova O; Sherlock AG; Steenland-Smit AE; Svitich A; Tapia Martínez LJ; Thoya Ngoka I; Torres CG; Tudor EM; van der Wel MG; Vițălaru BA; Vural SA; Walkinton O; Wehrle-Martinez AS; Widdowson SAE; Zvarich I; Chinnery PF; Falkenberg M; Gustafsson CM; Murchison EP
    Autonomous replication and segregation of mitochondrial DNA (mtDNA) creates the potential for evolutionary conflict driven by emergence of haplotypes under positive selection for 'selfish' traits, such as replicative advantage. However, few cases of this phenomenon arising within natural populations have been described. Here, we survey the frequency of mtDNA horizontal transfer within the canine transmissible venereal tumour (CTVT), a contagious cancer clone that occasionally acquires mtDNA from its hosts. Remarkably, one canine mtDNA haplotype, A1d1a, has repeatedly and recently colonised CTVT cells, recurrently replacing incumbent CTVT haplotypes. An A1d1a control region polymorphism predicted to influence transcription is fixed in the products of an A1d1a recombination event and occurs somatically on other CTVT mtDNA backgrounds. We present a model whereby 'selfish' positive selection acting on a regulatory variant drives repeated fixation of A1d1a within CTVT cells.
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    Response of Ruminal Microbiota-Host Gene Interaction to High-Altitude Environments in Tibetan Sheep.
    (MDPI (Basel, Switzerland), 2022-10-17) Sha Y; Ren Y; Zhao S; He Y; Guo X; Pu X; Li W; Liu X; Wang J; Li S; Wahli W
    Altitude is the main external environmental pressure affecting the production performance of Tibetan sheep, and the adaptive evolution of many years has formed a certain response mechanism. However, there are few reports on the response of ruminal microbiota and host genomes of Tibetan sheep to high-altitude environments. Here, we conducted an integrated analysis of volatile fatty acids (VFAs), microbial diversity (16S rRNA), epithelial morphology, and epithelial transcriptome in the rumen of Tibetan sheep at different altitudes to understand the changes in ruminal microbiota−host interaction in response to high altitude. The differences in the nutritional quality of forage at different altitudes, especially the differences in fiber content (ADF/NDF), led to changes in rumen VFAs of Tibetan sheep, in which the A/P value (acetic acid/propionic acid) was significantly decreased (p < 0.05). In addition, the concentrations of IgA and IgG in Middle-altitude (MA) and High-altitude Tibetan sheep (HA) were significantly increased (p < 0.05), while the concentrations of IgM were significantly increased in MA (p < 0.05). Morphological results showed that the width of the rumen papilla and the thickness of the basal layer increased significantly in HA Tibetan sheep (p < 0.05). The 16S rRNA analysis found that the rumen microbial diversity of Tibetan sheep gradually decreased with increasing altitude, and there were some differences in phylum- and genus-level microbes at the three altitudes. RDA analysis found that the abundance of the Rikenellaceae RC9 gut group and the Ruminococcaceae NK4A214 group increased with altitudes. Furthermore, a functional analysis of the KEGG microbial database found the “lipid metabolism” function of HA Tibetan sheep to be significantly enriched. WGCNA revealed that five gene modules were enriched in “energy production and conversion”, “lipid transport and metabolism”, and “defense mechanisms”, and cooperated with microbiota to regulate rumen fermentation and epithelial immune barrier function, so as to improve the metabolism and immune level of Tibetan sheep at high altitude.
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    Rumen Epithelial Development- and Metabolism-Related Genes Regulate Their Micromorphology and VFAs Mediating Plateau Adaptability at Different Ages in Tibetan Sheep.
    (MDPI (Basel, Switzerland), 2022-12-16) Sha Y; He Y; Liu X; Zhao S; Hu J; Wang J; Li S; Li W; Shi B; Hao Z; Martinez-Pastor F
    The rumen is an important hallmark organ of ruminants and plays an important role in the metabolism and immune barrier of Tibetan sheep on the Plateau. However, there are few studies on rumen development and metabolism regulation in Tibetan sheep at different ages. Here, we comprehensively analyzed the immune function, fermentation function, rumen epithelial micromorphology and transcriptome profile of Tibetan sheep at different ages. The results showed that the concentration of IgG decreased and the concentration of IgM increased with age (p < 0.05), and the highest concentration of IgA was observed at 1.5 and 3.5 years of age. In terms of rumen fermentation characteristics, VFAs of 4-month-old lambs were the highest, followed by VFAs and NH3-N of Tibetan sheep at 3.5 years of age. Hematoxylin-eosin staining and transmission electron microscopy section examination of rumen epithelial tissue showed that the rumen papilla width increased with age (p < 0.001), the thickness of the stratum corneum decreased, the cells in the stratum corneum showed accelerated migration and the thickness of the rumen muscle layer increased (p < 0.001). Desmosomal junctions between the layers of rumen epithelium increased at 1.5 and 3.5 years old, forming a compact barrier structure, and the basal layer had more mitochondria involved in the regulation of energy metabolism. RNA-seq analysis revealed that a total of 1006 differentially expressed genes (DEGs) were identified at four ages. The DEGs of Tibetan sheep aged 4 months and 6 years were mainly enriched in the oxidation−reduction process and ISG15-protein conjugation pathway. The 1.5 and 3.5-year-olds were mainly enriched in skeletal muscle thin filament assembly, mesenchyme migration and the tight junction pathway. WGCNA showed that DEGs related to rumen microbiota metabolite VFAs and epithelial morphology were enriched in “Metabolism of xenobiotics by cytochrome P450, PPAR signaling pathway, Butanoate metabolism pathways” and participated in the regulation of rumen epithelial immune and fermentation metabolism functions of Tibetan sheep at different ages. This study systematically revealed the regulatory mechanism of rumen epithelial development and metabolism in the plateau adaptation of Tibetan sheep, providing a new approach for the study of plateau adaptation.
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    Sensitivity reliability and neutral tendency of hedonic ratings as affected by scale types and lengths and overall product impression
    (26/06/2012) Jirangrat W; Wang J; Corredor JAH; Sriwattana S; Prinyawiwatkul W
    Several scales are available for measuring degrees of liking/disliking. Information on characteristics of hedonic ratings as affected by scale types/lengths and overall product impression is limited. Therefore, we compared discriminatory power, sensitivity, reliablity, and neutral tendency of hedonic ratings collected from 9-point categorical (CAT), line (LIN), and labeled affective magnitude (LAM) scales (100-mm compared 300-mm length). Three grape juices (classified as A=liked, B=moderate, C=disliked) were arranged in 4 sets (AB-AC, BA-CA, AC-AB, or CA-BA; the left sample served first). Each panelist (N=60) evaluated color (OC), taste (OT), and overall-liking (OL) of 1 set (of 4 possible random serving sets) in all 6 independent sessions (3 scale types x 2 lengths). For OL determined on a 100-mm scale, the order of discriminatory power (determined by the MIXED procedure) was CAT>LAM>LIN. The 300-mm LAM scale was consistently more discriminatory than the 100-mm LAM scale for all attributes. For sensitivity (the number of significantly different pairs), CAT exhibited the highest sensitivity, considering simultaneously all products (A, B, C) categories. Regardless of attributes, product categories, and scale types, ratings tended to be lower with the 300-mm scale. For reliability (consistency of responses towards OC/OT/OL) of different scale/length types, Cronbach’s alpha values were 0.78-0.92, with slightly higher (0.89-0.92) values toward the disliked sample. Another reliability index (consistency of responses between 2 identical test samples) across different scale/length types was exhibited by Pearson’s correlation coefficients (r=0.32-0.75), with higher values toward the LAM scale; OC (a less complicated attribute) was less affected (higher r values). Product categories and scale types affected neutral tendency of responses, with moderate and disliked products being more affected when evaluated on LAM scales. This study demonstrated characteristics of hedonic scales as affected by scale lengths and overall product impression. Using proper scales to assess liking/disliking would help increase power of the experiment.