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Functional genetics

Section edited by Federico Canzian

This section incorporates all aspects of the functional analysis of genes and genomes including but not limited to: sequence analysis and genotyping approaches to finding functional variation in genes and gene families, experimental studies of gene function, transcriptional regulation and gene expression.

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  1. In order to study the relations of hepatocellular functions, weight gain and metabolic imbalance caused by low-dose antibiotics (LDA) via epigenetic regulation of gene transcription, 32 weaned piglets were emp...

    Authors: Yue Hu, Yihe Zhang, Cong Liu, Rui Qin, Desheng Gong, Ru Wang, Du Zhang, Lianqiang Che, Daiwen Chen, Guizhong Xin, Fei Gao and Qi Hu

    Citation: BMC Genetics 2020 21:112

    Content type: Research article

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  2. Reference genes are usually stably expressed in various cells and tissues. However, it was reported that the expression of some reference genes may be distinct in different species. In this study, we intend to...

    Authors: Wenbin Liu, Xiudan Yuan, Shuli Yuan, Liuye Dai, Shenghua Dong, Jinhui Liu, Liangyue Peng, Minmeng Wang, Yi Tang and Yamei Xiao

    Citation: BMC Genetics 2020 21:107

    Content type: Research article

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  3. Plant calmodulin-binding transcription activator (CAMTA) proteins play important roles in hormone signal transduction, developmental regulation, and environmental stress tolerance. However, in wheat, the CAMTA ge...

    Authors: Fan Yang, Fu-shuang Dong, Fang-hui Hu, Yong-wei Liu, Jian-fang Chai, He Zhao, Meng-yu Lv and Shuo Zhou

    Citation: BMC Genetics 2020 21:105

    Content type: Research article

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  4. WRKY transcription factors (TFs) have been suggested to play crucial roles in the response to biotic and abiotic stresses. This study is the first to report the alkaline salt regulation of the WRKY gene.

    Authors: Xin Wang, Zainab Ajab, Chenxi Liu, Songmiao Hu, Jiali Liu and Qingjie Guan

    Citation: BMC Genetics 2020 21:103

    Content type: Research article

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  5. The complement cascade is increasingly implicated in development of a variety of diseases with strong immune contributions such as Alzheimer’s disease and Systemic Lupus Erythematosus. Mouse models have been u...

    Authors: Harriet M. Jackson, Kate E. Foley, Rita O’Rourke, Timothy M. Stearns, Dina Fathalla, B. Paul Morgan and Gareth R. Howell

    Citation: BMC Genetics 2020 21:101

    Content type: Research article

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  6. The Human Leukocyte Antigen G (HLA-G) protein is an immune tolerogenic molecule with 7 isoforms. The change of expression level and some polymorphisms of the HLA-G gene are involved in various pathologies. The...

    Authors: Elaheh Emadi, Fatemeh Akhoundi, Seyed Mehdi Kalantar and Modjtaba Emadi-Baygi

    Citation: BMC Genetics 2020 21:94

    Content type: Research article

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  7. Although the molecular function of wolframin remains unclear, the lack of this protein is known to cause stress in the endoplasmic reticulum. Some variants in the Wolfram Syndrome 1 gene (WFS1) were associated wi...

    Authors: Dora Koller, Eniko Kubinyi, Zsuzsanna Elek, Helga Nemeth, Adam Miklosi, Maria Sasvari-Szekely and Zsolt Ronai

    Citation: BMC Genetics 2020 21:82

    Content type: Research article

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  8. The HTR1B gene encodes the 5-hydroxytryptamine (5-HT1B) receptor, which is involved in a variety of brain activities and mental disorders. The regulatory effects of non-coding regions on genomic DNA are one of ma...

    Authors: Xi Xia, Mei Ding, Jin-feng Xuan, Jia-xin Xing, Hao Pang, Jun Yao, Xue Wu and Bao-jie Wang

    Citation: BMC Genetics 2020 21:79

    Content type: Research article

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  9. RNA-sequencing was performed to explore the bovine liver transcriptomes of Holstein cows to detect potential functional genes related to lactation and milk composition traits in dairy cattle. The bovine transc...

    Authors: Qian Li, Ruobing Liang, Yan Li, Yanxia Gao, Qiufeng Li, Dongxiao Sun and Jianguo Li

    Citation: BMC Genetics 2020 21:72

    Content type: Research article

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  10. Activated charcoal (AC) is highly adsorbent and is often used to promote seedling growth in plant tissue culture; however, the underlying molecular mechanism remains unclear. In this study, root and leaf tissu...

    Authors: Fu-shuang Dong, Meng-yu lv, Jin-ping Wang, Xue-ping Shi, Xin-xia Liang, Yong-wei Liu, Fan Yang, He Zhao, Jian-Fang Chai and Shuo Zhou

    Citation: BMC Genetics 2020 21:69

    Content type: Research article

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  11. Antimicrobial peptides play important roles in both plant and animal defense systems. Moreover, over-expression of CaAMP1 (Capsicum annuum antimicrobial protein 1), an antimicrobial protein gene isolated from C. ...

    Authors: Lu Niu, Xiaofang Zhong, Yuanyu Zhang, Jing Yang, Guojie Xing, Haiyun Li, Dongbo Liu, Rui Ma, Yingshan Dong and Xiangdong Yang

    Citation: BMC Genetics 2020 21:68

    Content type: Research article

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  12. The exploitation of novel alleles from wild rice that were lost during rice cultivation could be very important for rice breeding and evolutionary studies. Plant height (PH) was a target of artificial selectio...

    Authors: Lizhen Zhang, Jingfen Huang, Yanyan Wang, Rui Xu, Ziyi Yang, Zhigang Zhao, Shijia Liu, Yunlu Tian, Xiaoming Zheng, Fei Li, Junrui Wang, Yue Song, Jiaqi Li, Yongxia Cui, Li-Fang Zhang, Yunlian Cheng…

    Citation: BMC Genetics 2020 21:62

    Content type: Research article

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  13. Bacterial chondronecrosis with osteomyelitis (BCO) develops in the growth plate (GP) of the proximal femur and tibia and is initiated by damage to the less mineralized chondrocytes followed by colonization of ...

    Authors: Haniel Cedraz de Oliveira, Adriana Mércia Guaratini Ibelli, Simone Eliza Facioni Guimarães, Mauricio Egídio Cantão, Jane de Oliveira Peixoto, Luiz Lehmann Coutinho and Mônica Corrêa Ledur

    Citation: BMC Genetics 2020 21:58

    Content type: Research article

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  14. TERMINAL FLOWER 1 (TFL1) is a member of phosphatidylethanolamine-binding protein (PEBP) family, which plays an important role in the determination of floral meristem identity and regulates flowering time in highe...

    Authors: Sukarkarn Sriboon, Haitao Li, Chaocheng Guo, Thaveep Senkhamwong, Cheng Dai and Kede Liu

    Citation: BMC Genetics 2020 21:52

    Content type: Research article

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  15. Development of wheat cultivars with multiple disease resistance and high quality are major objectives in modern wheat breeding programs. Gene stacking is an efficient approach to achieve this target. In this s...

    Authors: Weijun Zheng, Song Li, ZiHui Liu, Qi Zhou, Yanru Feng and Shoucheng Chai

    Citation: BMC Genetics 2020 21:45

    Content type: Research article

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  16. While sodium is attractive at low and aversive at high concentrations in most studied species, including Caenorhabditis elegans, the molecular mechanisms behind transduction remain poorly understood. Additionally...

    Authors: Joseph Dao, Aileen Lee, Dana K. Drecksel, Nicole M. Bittlingmaier and Theodore M. Nelson

    Citation: BMC Genetics 2020 21:37

    Content type: Research article

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  17. Intramuscular fat (IMF) content is an important factor in porcine meat quality. Previously, we showed that miR-34a was less abundant in liver tissue from pigs with higher backfat thickness, compared to pigs wi...

    Authors: Wenwen Wang, Xiuxiu Li, Ning Ding, Jun Teng, Shen Zhang, Qin Zhang and Hui Tang

    Citation: BMC Genetics 2020 21:33

    Content type: Research article

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  18. Hox transcription factors are master regulators of animal development. Although highly conserved, they can contribute to the formation of novel biological characteristics when modified, such as during the generat...

    Authors: Rurong Zhao, Yude Wang, Li Zou, Yaxin Luo, Huifang Tan, Jiajun Yao, Minghe Zhang and Shaojun Liu

    Citation: BMC Genetics 2020 21:24

    Content type: Research article

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  19. Buffalo milk is considered as a highly nutritious food owing to its higher contents of fatty acids (FA) and rich nutrient profile. Higher fat contents of buffalo milk make it suitable for processing to develop...

    Authors: Zhipeng Li, Suyu Lu, Kuiqing Cui, Laiba Shafique, Saif ur Rehman, Chan Luo, Zhiqiang Wang, Jue Ruan, Qian Qian and Qingyou Liu

    Citation: BMC Genetics 2020 21:23

    Content type: Research article

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  20. Solute carrier family 35 (SLC35) is one of a large number of membrane transporter protein families. Member D3 of this family is thought to be involved in adipose deposition and metabolic control.

    Authors: Wentong Li, Keliang Wu, Ying Liu, Yalan Yang, Wenwen Wang, Xiuxiu Li, Yanmin Zhang, Qin Zhang, Rong Zhou and Hui Tang

    Citation: BMC Genetics 2020 21:20

    Content type: Research article

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  21. Red deer with very pale coat colour are observed sporadically. In the red deer (Cervus elaphus) population of Reinhardswald in Germany, about 5% of animals have a white coat colour that is not associated with alb...

    Authors: Gerald Reiner, Kirsten Tramberend, Florian Nietfeld, Klaus Volmer, Christine Wurmser, Ruedi Fries and Hermann Willems

    Citation: BMC Genetics 2020 21:14

    Content type: Research article

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  22. Cage-rearing in laying ducks, as a novel rearing system, not only fundamentally solves the pollution problem of the duck industry and improve bio-safety and product quality but also exhibits more benefits by i...

    Authors: Yang Zhang, Tiantian Gu, Yong Tian, Li Chen, Guoqin Li, Wei Zhou, Guofa Liu, Xinsheng Wu, Tao Zeng, Qi Xu, Guohong Chen and Lizhi Lu

    Citation: BMC Genetics 2019 20:103

    Content type: Research article

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  23. Grain weight is an important yield component. Selection of advanced lines with heavy grains show high grain sink potentials and strong sink activity, which is an increasingly important objective in wheat breed...

    Authors: Jian Yang, Yanjie Zhou, Yu’e Zhang, Weiguo Hu, Qiuhong Wu, Yongxing Chen, Xicheng Wang, Guanghao Guo, Zhiyong Liu, Tingjie Cao and Hong Zhao

    Citation: BMC Genetics 2019 20:98

    Content type: Research article

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  24. Fish immunity is not only affected by the innate immune pathways but is also triggered by stress. Transport and loading stress can induce oxidative stress and further activate the immune inflammatory response,...

    Authors: Fukuan Du, Yan Li, Jing Shen, Yueshui Zhao, Parham Jabbarzadeh Kaboli, Shixin Xiang, Xu Wu, Mingxing Li, Jiangyao Zhou, Yuan Zheng, Tao Yi, Xiang Li, Jing Li, Zhangang Xiao and Qinglian Wen

    Citation: BMC Genetics 2019 20:95

    Content type: Research article

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  25. Tea-oil tree (Camellia oleifera) is a unique edible-oil tree in China, and anthracnose occurs in wherever it is cultivated, causing great economic losses each year. We have previously identified the Ascomycete fu...

    Authors: Shengpei Zhang, Yuan Guo, Sizheng Li, Guoying Zhou, Junang Liu, Jianping Xu and He Li

    Citation: BMC Genetics 2019 20:94

    Content type: Research article

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  26. WRKY DNA-binding protein (WRKY) is a large gene family involved in plant responses and adaptation to salt, drought, cold and heat stresses. Sweet potato from the genus Ipomoea is a staple food crop, but the WRKY ...

    Authors: Yuxia Li, Lei Zhang, Panpan Zhu, Qinghe Cao, Jian Sun, Zongyun Li and Tao Xu

    Citation: BMC Genetics 2019 20:90

    Content type: Research article

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  27. Over the relatively short history of Genome Wide Association Studies (GWASs), hundreds of GWASs have been published and thousands of disease risk-associated SNPs have been identified. Summary statistics from t...

    Authors: Ivan Gorlov, Xiangjun Xiao, Maureen Mayes, Olga Gorlova and Christopher Amos

    Citation: BMC Genetics 2019 20:85

    Content type: Research article

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  28. Crossover localization during meiotic recombination is mediated by the fast-evolving zinc-finger (ZnF) domain of gene PRDM9. To study its impact on dairy cattle performance, we compared its genetic variation betw...

    Authors: Eyal Seroussi, Andrey Shirak, Moran Gershoni, Ephraim Ezra, Daniel Jordan de Abreu Santos, Li Ma and George E. Liu

    Citation: BMC Genetics 2019 20:71

    Content type: Research article

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  29. The tryptophan-arginine-lysine-tyrosine (WRKY) transcription factors play important roles in plants, allowing them to adapt to environmental conditions that are not normally conducive to plant growth; in parti...

    Authors: Yuan Guo, Wenjing Ping, Jingtang Chen, Liying Zhu, Yongfeng Zhao, Jinjie Guo and Yaqun Huang

    Citation: BMC Genetics 2019 20:63

    Content type: Research article

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  30. Auxins play an important role in plant growth and development; the auxins responsive gene; auxin/indole-3-acetic acid (Aux/IAA), small auxin-up RNAs (SAUR) and Gretchen Hagen3 (GH3) control their mechanisms. The

    Authors: Joy Nyangasi Kirungu, Richard Odongo Magwanga, Pu Lu, Xiaoyan Cai, Zhongli Zhou, Xingxing Wang, Renhai Peng, Kunbo Wang and Fang Liu

    Citation: BMC Genetics 2019 20:62

    Content type: Research article

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  31. Overgrazing is a major factor that causes steppe degradation in Inner Mongolian, resulting in extensive ecosystem damage. Scarcity of grass means sheep are smaller and therefore mutton and cashmere production ...

    Authors: Weibo Ren, Warwick Badgery, Yong Ding, Huiqin Guo, Yang Gao and Jize Zhang

    Citation: BMC Genetics 2019 20:54

    Content type: Research article

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  32. We have previously identified 11 promising candidate genes for milk composition traits by resequencing the whole genomes of 8 Holstein bulls with extremely high and low estimated breeding values for milk prote...

    Authors: Jianping Jiang, Lin Liu, Yahui Gao, Lijun Shi, Yanhua Li, Weijun Liang and Dongxiao Sun

    Citation: BMC Genetics 2019 20:48

    Content type: Research article

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  33. Sesame (Sesamum indicum) can accumulate over 60% oil in its seed. However, low oil content genotypes with an oil content of less than 50% are also observed. To gain insights into how genes shape this variation, w...

    Authors: Linhai Wang, Yanxin Zhang, Donghua Li, Komivi Dossa, Ming Li Wang, Rong Zhou, Jingyin Yu and Xiurong Zhang

    Citation: BMC Genetics 2019 20:45

    Content type: Research article

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  34. High isoelectric point α-amylase genes (Amy1) play major roles during cereal seed germination, and are associated with unacceptable high residual α-amylase activities in ripe wheat grains. However, in wheat and b...

    Authors: Liangliang Ju, Guangbing Deng, Junjun Liang, Haili Zhang, Qiao Li, Zhifen Pan, Maoqun Yu and Hai Long

    Citation: BMC Genetics 2019 20:25

    Content type: Research article

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  35. Whey acidic protein (WAP) is a major protein identified in the milk of several mammalian species with cysteine-rich domains known as four-disulfide cores (4-DSC). The organization of the eutherian WAP genes is...

    Authors: Alma Ryskaliyeva, Céline Henry, Guy Miranda, Bernard Faye, Gaukhar Konuspayeva and Patrice Martin

    Citation: BMC Genetics 2019 20:14

    Content type: Research article

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  36. Brachydactyly type A1 (BDA1, OMIM 112500) is a rare inherited malformation characterized primarily by shortness or absence of middle bones of fingers and toes. It is the first recorded disorder of the autosoma...

    Authors: Lu Shen, Gang Ma, Ye Shi, Yunfeng Ruan, Xuhan Yang, Xi Wu, Yuyu Xiong, Chunling Wan, Chao Yang, Lei Cai, Likuan Xiong, Xueli Gong, Lin He and Shengying Qin

    Citation: BMC Genetics 2019 20:10

    Content type: Research article

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  37. Selenium (Se), an essential micronutrient in both animals and humans, has various biological functions, and its deficiency can lead to various diseases. The most common method for increasing Se uptake is the c...

    Authors: Lijun Wu, Tao Liu, Yongsheng Xu, Wenjie Chen, Baolong Liu, Lianquan Zhang, Dengcai Liu, Huaigang Zhang and Bo Zhang

    Citation: BMC Genetics 2019 20:9

    Content type: Research article

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  38. The serotonin neurotransmitter (5-HT) and its receptors have important roles in neuropsychiatric disorders such as schizophrenia. The aim of this study was to investigate the functional sequences of the 5′ reg...

    Authors: Xue Wu, Feng-ling Xu, Mei Ding, Jing-jing Zhang, Jun Yao and Bao-jie Wang

    Citation: BMC Genetics 2018 19:115

    Content type: Research article

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  39. Fungal fruiting bodies are complex three-dimensional structures that are formed to protect and disperse the sexual spores. Their morphogenesis requires the concerted action of numerous genes; however, at the m...

    Authors: David Immanuel Schumacher, Ramona Lütkenhaus, Florian Altegoer, Ines Teichert, Ulrich Kück and Minou Nowrousian

    Citation: BMC Genetics 2018 19:112

    Content type: Research article

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  40. The expression of genes involved in regulating adipogenesis and lipid metabolism may affect economically important fatness traits in pigs. Allele-specific expression (ASE) reflects imbalance between allelic tr...

    Authors: Monika Stachowiak, Izabela Szczerbal and Krzysztof Flisikowski

    Citation: BMC Genetics 2018 19:107

    Content type: Research article

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  41. Bud mutation is a vital method of citrus. ‘Wuzi Ougan’ (mutant type, MT) as a bud variant of ‘Ougan’ (wild type, WT) was first found in 1996 and has become popular because of its male sterility and seedless ch...

    Authors: Chi Zhang, Dihu Yu, Fuzhi Ke, Mimi Zhu, Jianguo Xu and Min Zhang

    Citation: BMC Genetics 2018 19:106

    Content type: Research article

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  42. Previous studies have identified genetic variants associated with bronchopulmonary dysplasia (BPD) in extremely preterm infants. However, findings with genome-wide significance have been rare, and not replicat...

    Authors: Aaron Hamvas, Rui Feng, Yingtao Bi, Fan Wang, Soumyaroop Bhattacharya, Jared Mereness, Madhurima Kaushal, C Michael Cotten, Philip L Ballard and Thomas J Mariani

    Citation: BMC Genetics 2018 19:94

    Content type: Research article

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  43. Long non-coding RNAs (lncRNAs) have crucial roles in various biological regulatory processes. However, the study of lncRNAs is limited in woody plants. Catalpa bungei is a valuable ornamental tree with a long cul...

    Authors: Zhi Wang, Tianqing Zhu, Wenjun Ma, Nan Wang, Guanzheng Qu, Shougong Zhang and Junhui Wang

    Citation: BMC Genetics 2018 19:86

    Content type: Research article

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  44. One of the most popular ornamental plants worldwide, roses (Rosa sp.), are very susceptible to Botrytis gray mold disease. The necrotrophic infection of rose petals by B. cinerea causes the collapse and death of ...

    Authors: Xintong Liu, Xiaoqian Cao, Shaochuan Shi, Na Zhao, Dandan Li, Peihong Fang, Xi Chen, Weicong Qi and Zhao Zhang

    Citation: BMC Genetics 2018 19:62

    Content type: Research article

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  45. NOD-like receptors (NLRs) are a family of cytoplasmic pattern recognition receptors (PRRs), of which NOD1 and NOD2, are the main representative members. Many investigations have focused on the role of NOD1 and NO...

    Authors: Tiantian Gu, Lu Lu, Jingwen Wang, Lili Tian, Wenzhi Wei, Xinsheng Wu, Qi Xu and Guohong Chen

    Citation: BMC Genetics 2018 19:61

    Content type: Research article

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  46. Aging leads to decreased skeletal muscle function in mammals and is associated with a progressive loss of muscle mass, quality and strength. Age-related muscle loss (sarcopenia) is an important health problem ...

    Authors: I-Hsuan Lin, Junn-Liang Chang, Kate Hua, Wan-Chen Huang, Ming-Ta Hsu and Yi-Fan Chen

    Citation: BMC Genetics 2018 19:55

    Content type: Research article

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  47. WRKY transcription factors (TFs) participate in various physiological processes of plants. Although WRKY genes have been well studied in model plants, knowledge of the functional roles of these genes is still ...

    Authors: Lijiao Gu, Hengling Wei, Hantao Wang, Junji Su and Shuxun Yu

    Citation: BMC Genetics 2018 19:48

    Content type: Research article

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  48. This study aimed to explore the molecular mechanism of estrogen-mediated neuroprotection in the relief of cerebral ischemic injury. The gene expression profiles were downloaded from Gene Expression Omnibus dat...

    Authors: Jiaxuan He, Ya Gao, Gang Wu, Xiaoming Lei, Yong Zhang, Weikang Pan and Hui Yu

    Citation: BMC Genetics 2018 19:46

    Content type: Research article

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  49. Glutathione S-transferases (GSTs) have been reported to regulate the plant tolerance to environmental stresses. Many plant GSTs exhibited the roles on promoting tolerance to drought stress, oxidative stress an...

    Authors: Wenbin Liao, Shuxia Li, Cheng Lu and Ming Peng

    Citation: BMC Genetics 2018 19:45

    Content type: Research article

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