New software to detect horizontal gene transfer in microbiomes: from forage to the rumen

检测微生物组水平基因转移的新软件:从饲料到瘤胃

基本信息

  • 批准号:
    2878898
  • 负责人:
  • 金额:
    --
  • 依托单位:
  • 依托单位国家:
    英国
  • 项目类别:
    Studentship
  • 财政年份:
    2023
  • 资助国家:
    英国
  • 起止时间:
    2023 至 无数据
  • 项目状态:
    未结题

项目摘要

HypothesisHorizontal gene transfer (HGT) is the sharing of genetic material between organisms that are not in a vertical relationship of inheritance i.e. between parents and offspring. HGT is widely recognized as a mechanism for evolutionary adaptation. While it is has been studied in bacteria and archaea for some time, it is also being seen of increasing importance for understanding eukaryotic evolution. Recent reviews of HGT emphasise the need to develop better computational methods to detect HGT, especially in eukaryotes. Approaches to detecting HGT events can be divided into two. The first involves the construction of phylogenetic trees using sequence alignment, to detect differences between the evolutionary history of a species and the evolutionary history of individual gene sequences. The second approach involves the analysis of properties intrinsic to genome sequences i.e. the patterns of order and disorder, repeats, codon usage biases, and k-mer content (k-mers are small oligonucleotides). These approaches are collectively known as alignment-free sequence analysis: Dr Swain has recently published a novel machine learning methodology that demonstrates how alignment-free methods can be improved through calibration using training data sets. We hypothesise that our novel process of calibrating alignment-free methods will give significant performance gains over existing approaches. The process of calibration indicates the optimal parameter set to use, and provides a probability score for the likelihood of detecting a true positive. Calibration can be performed in different ways, according to the sequence feature to be detected. These probabilities can then be amalgamated e.g. using Bayesian statistics, and combined with phylogeny analysis. This approach is superior to existing approaches because they estimate appropriate parameters, and cannot allocate probability scores. Our improved approach to HGT detection will generate novel insights into systems where HGT is hypothesised to play an important role. Typically HGTs occur between species that live in biological promiscuity, such as parasites, pathogens (including viruses), symbionts, and their hosts. Objectives1.To develop novel software for detecting horizontal gene transfer that can be applied to existing collections of diverse genome sequences. Demonstrate performance gains through comparison to other current approaches. 2.HGT is hypothesised to generate evolutionary adaptions that allow endophytes (prokaryotes) to enter a symbiotic relationship with their host plants, such as the acquisition of certain metabolic functions. We will apply our software to a unique Aberystwyth collection of approximately 100 endophyte genomes derived from grasses, to detect HGT events in these phenotypes. Endophyte genomes will be compared to their free-living or pathogenic relatives, and those found within the rumen, to better understand the role of HGT in developing their current genetic structure.3.Over fifteen years ago it was shown that ciliates (eukaryotes) in the rumen have acquired, through HGT from bacteria, 46 genes related to carbohydrate degradation. More recent data will enable a much deeper analysis of this important finding, using our software. In addition, we plan to expand our approach to explore horizontal transposable element transfer (HTT) in the ciliates. Ciliates are a model system for the study of the interaction between eukaryotic germlines and somatic lines, especially with regard to the invasion and defence against transposable elements.JustificationHGT and HTT are key processes that help organisms to adapt and generate new phenotypes, it is therefore important to improve our understanding of the roles it plays in ecological systems relating to agriculture. Better understanding of HGT will help monitor the spread of antimicrobial resistance throughout the agricultural system. Moreover, an improved understanding of HGT will provide insights into the development me
假设水平基因转移(HGT)是指在没有垂直遗传关系的生物体之间(即父母和后代之间)共享遗传物质。HGT被广泛认为是一种进化适应机制。虽然它已经在细菌和古细菌中研究了一段时间,但它对于理解真核生物进化也越来越重要。最近的审查HGT强调需要开发更好的计算方法来检测HGT,特别是在真核生物。检测HGT事件的方法可以分为两种。第一个涉及使用序列比对构建系统发育树,以检测物种的进化历史和单个基因序列的进化历史之间的差异。第二种方法涉及分析基因组序列固有的特性,即有序和无序模式、重复序列、密码子使用偏好和k-mer含量(k-mer是小寡核苷酸)。这些方法统称为无干扰序列分析:Swain博士最近发表了一种新的机器学习方法,该方法演示了如何通过使用训练数据集进行校准来改进无干扰方法。我们假设,我们的新的校准过程中,无干扰的方法将提供显着的性能增益超过现有的方法。校准过程指示要使用的最佳参数集,并为检测到真阳性的可能性提供概率得分。可以根据待检测的序列特征以不同的方式执行校准。这些概率然后可以被合并,例如使用贝叶斯统计,并与遗传分析相结合。这种方法是上级现有的方法,因为他们估计适当的参数,不能分配概率得分。我们改进的HGT检测方法将产生新的见解系统HGT假设发挥重要作用。通常HGT发生在生物混杂的物种之间,如寄生虫,病原体(包括病毒),共生体及其宿主。目的1.开发一种新的检测水平基因转移的软件,该软件可以应用于现有的各种基因组序列的收集。通过与其他当前方法的比较,展示性能增益。2. HGT被假设为产生进化适应,允许内生菌(原核生物)与其宿主植物进入共生关系,例如获得某些代谢功能。我们将应用我们的软件到一个独特的阿伯里斯特威斯收集约100内生菌基因组来自草,检测HGT事件在这些表型。将内生菌基因组与其自由生活或致病的亲属以及在瘤胃内发现的基因组进行比较,以更好地理解HGT在发展其当前遗传结构中的作用。最新的数据将使我们能够使用我们的软件对这一重要发现进行更深入的分析。此外,我们计划扩大我们的方法,探索水平转座因子转移(HTT)的纤毛虫。纤毛虫是研究真核生物生殖系和体细胞系之间相互作用的模式系统,特别是在转座因子的入侵和防御方面,HGT和HTT是帮助生物适应和产生新表型的关键过程,因此,提高我们对它在农业生态系统中所起作用的认识是非常重要的。更好地了解HGT将有助于监测抗生素耐药性在整个农业系统中的传播。此外,提高对HGT的理解将为开发我的

项目成果

期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)

数据更新时间:{{ journalArticles.updateTime }}

{{ item.title }}
{{ item.translation_title }}
  • DOI:
    {{ item.doi }}
  • 发表时间:
    {{ item.publish_year }}
  • 期刊:
  • 影响因子:
    {{ item.factor }}
  • 作者:
    {{ item.authors }}
  • 通讯作者:
    {{ item.author }}

数据更新时间:{{ journalArticles.updateTime }}

{{ item.title }}
  • 作者:
    {{ item.author }}

数据更新时间:{{ monograph.updateTime }}

{{ item.title }}
  • 作者:
    {{ item.author }}

数据更新时间:{{ sciAawards.updateTime }}

{{ item.title }}
  • 作者:
    {{ item.author }}

数据更新时间:{{ conferencePapers.updateTime }}

{{ item.title }}
  • 作者:
    {{ item.author }}

数据更新时间:{{ patent.updateTime }}

其他文献

吉治仁志 他: "トランスジェニックマウスによるTIMP-1の線維化促進機序"最新医学. 55. 1781-1787 (2000)
Hitoshi Yoshiji 等:“转基因小鼠中 TIMP-1 的促纤维化机制”现代医学 55. 1781-1787 (2000)。
  • DOI:
  • 发表时间:
  • 期刊:
  • 影响因子:
    0
  • 作者:
  • 通讯作者:
LiDAR Implementations for Autonomous Vehicle Applications
  • DOI:
  • 发表时间:
    2021
  • 期刊:
  • 影响因子:
    0
  • 作者:
  • 通讯作者:
生命分子工学・海洋生命工学研究室
生物分子工程/海洋生物技术实验室
  • DOI:
  • 发表时间:
  • 期刊:
  • 影响因子:
    0
  • 作者:
  • 通讯作者:
吉治仁志 他: "イラスト医学&サイエンスシリーズ血管の分子医学"羊土社(渋谷正史編). 125 (2000)
Hitoshi Yoshiji 等人:“血管医学与科学系列分子医学图解”Yodosha(涉谷正志编辑)125(2000)。
  • DOI:
  • 发表时间:
  • 期刊:
  • 影响因子:
    0
  • 作者:
  • 通讯作者:
Effect of manidipine hydrochloride,a calcium antagonist,on isoproterenol-induced left ventricular hypertrophy: "Yoshiyama,M.,Takeuchi,K.,Kim,S.,Hanatani,A.,Omura,T.,Toda,I.,Akioka,K.,Teragaki,M.,Iwao,H.and Yoshikawa,J." Jpn Circ J. 62(1). 47-52 (1998)
钙拮抗剂盐酸马尼地平对异丙肾上腺素引起的左心室肥厚的影响:“Yoshiyama,M.,Takeuchi,K.,Kim,S.,Hanatani,A.,Omura,T.,Toda,I.,Akioka,
  • DOI:
  • 发表时间:
  • 期刊:
  • 影响因子:
    0
  • 作者:
  • 通讯作者:

的其他文献

{{ item.title }}
{{ item.translation_title }}
  • DOI:
    {{ item.doi }}
  • 发表时间:
    {{ item.publish_year }}
  • 期刊:
  • 影响因子:
    {{ item.factor }}
  • 作者:
    {{ item.authors }}
  • 通讯作者:
    {{ item.author }}

{{ truncateString('', 18)}}的其他基金

An implantable biosensor microsystem for real-time measurement of circulating biomarkers
用于实时测量循环生物标志物的植入式生物传感器微系统
  • 批准号:
    2901954
  • 财政年份:
    2028
  • 资助金额:
    --
  • 项目类别:
    Studentship
Exploiting the polysaccharide breakdown capacity of the human gut microbiome to develop environmentally sustainable dishwashing solutions
利用人类肠道微生物群的多糖分解能力来开发环境可持续的洗碗解决方案
  • 批准号:
    2896097
  • 财政年份:
    2027
  • 资助金额:
    --
  • 项目类别:
    Studentship
A Robot that Swims Through Granular Materials
可以在颗粒材料中游动的机器人
  • 批准号:
    2780268
  • 财政年份:
    2027
  • 资助金额:
    --
  • 项目类别:
    Studentship
Likelihood and impact of severe space weather events on the resilience of nuclear power and safeguards monitoring.
严重空间天气事件对核电和保障监督的恢复力的可能性和影响。
  • 批准号:
    2908918
  • 财政年份:
    2027
  • 资助金额:
    --
  • 项目类别:
    Studentship
Proton, alpha and gamma irradiation assisted stress corrosion cracking: understanding the fuel-stainless steel interface
质子、α 和 γ 辐照辅助应力腐蚀开裂:了解燃料-不锈钢界面
  • 批准号:
    2908693
  • 财政年份:
    2027
  • 资助金额:
    --
  • 项目类别:
    Studentship
Field Assisted Sintering of Nuclear Fuel Simulants
核燃料模拟物的现场辅助烧结
  • 批准号:
    2908917
  • 财政年份:
    2027
  • 资助金额:
    --
  • 项目类别:
    Studentship
Assessment of new fatigue capable titanium alloys for aerospace applications
评估用于航空航天应用的新型抗疲劳钛合金
  • 批准号:
    2879438
  • 财政年份:
    2027
  • 资助金额:
    --
  • 项目类别:
    Studentship
Developing a 3D printed skin model using a Dextran - Collagen hydrogel to analyse the cellular and epigenetic effects of interleukin-17 inhibitors in
使用右旋糖酐-胶原蛋白水凝胶开发 3D 打印皮肤模型,以分析白细胞介素 17 抑制剂的细胞和表观遗传效应
  • 批准号:
    2890513
  • 财政年份:
    2027
  • 资助金额:
    --
  • 项目类别:
    Studentship
CDT year 1 so TBC in Oct 2024
CDT 第 1 年,预计 2024 年 10 月
  • 批准号:
    2879865
  • 财政年份:
    2027
  • 资助金额:
    --
  • 项目类别:
    Studentship
Understanding the interplay between the gut microbiome, behavior and urbanisation in wild birds
了解野生鸟类肠道微生物组、行为和城市化之间的相互作用
  • 批准号:
    2876993
  • 财政年份:
    2027
  • 资助金额:
    --
  • 项目类别:
    Studentship

相似国自然基金

低辐射空间环境下商用多核处理器层次化软件容错技术研究
  • 批准号:
    90818016
  • 批准年份:
    2008
  • 资助金额:
    50.0 万元
  • 项目类别:
    重大研究计划

相似海外基金

A Mobile Health Application to Detect Absence Seizures using Hyperventilation and Eye-Movement Recordings
一款使用过度换气和眼动记录检测失神癫痫发作的移动健康应用程序
  • 批准号:
    10696649
  • 财政年份:
    2023
  • 资助金额:
    --
  • 项目类别:
NSF/FDA: Towards an active surveillance framework to detect AI/ML-enabled Software as a Medical Device (SaMD) data and performance drift in clinical flow
NSF/FDA:建立主动监测框架,以检测支持 AI/ML 的软件即医疗设备 (SaMD) 数据和临床流程中的性能漂移
  • 批准号:
    2326034
  • 财政年份:
    2023
  • 资助金额:
    --
  • 项目类别:
    Standard Grant
A deep learning algorithm to detect signs of cognitive impairment in electronic health records
用于检测电子健康记录中认知障碍迹象的深度学习算法
  • 批准号:
    10900991
  • 财政年份:
    2023
  • 资助金额:
    --
  • 项目类别:
Novel threat detection methodology to detect HIV outbreaks in Washington
用于检测华盛顿艾滋病毒爆发的新型威胁检测方法
  • 批准号:
    10683347
  • 财政年份:
    2022
  • 资助金额:
    --
  • 项目类别:
Novel threat detection methodology to detect HIV outbreaks in Washington
用于检测华盛顿艾滋病毒爆发的新型威胁检测方法
  • 批准号:
    10547381
  • 财政年份:
    2022
  • 资助金额:
    --
  • 项目类别:
Population genetic methods to detect population structure and adaptation using modern and ancient genomic datasets
使用现代和古代基因组数据集检测种群结构和适应的种群遗传学方法
  • 批准号:
    10605315
  • 财政年份:
    2022
  • 资助金额:
    --
  • 项目类别:
Detection of Elder mistreatment Through Emergency Care Technicians - Revised for Primary Care (DETECT-RPC)
通过紧急护理技术人员检测老年人虐待行为 - 初级护理修订版 (DETECT-RPC)
  • 批准号:
    10512948
  • 财政年份:
    2022
  • 资助金额:
    --
  • 项目类别:
Improving an EEG-based neurodiagnostic software platform to detect Alzheimer's Disease in MCI patients
改进基于脑电图的神经诊断软件平台来检测 MCI 患者的阿尔茨海默病
  • 批准号:
    10546255
  • 财政年份:
    2022
  • 资助金额:
    --
  • 项目类别:
Detection of Elder mistreatment Through Emergency Care Technicians - Revised for Primary Care (DETECT-RPC)
通过紧急护理技术人员检测老年人虐待行为 - 初级护理修订版 (DETECT-RPC)
  • 批准号:
    10703453
  • 财政年份:
    2022
  • 资助金额:
    --
  • 项目类别:
smartOCT: a low-cost technology to detect and monitor glaucoma in outpatient and primary care centers
smartOCT:一种在门诊和初级保健中心检测和监测青光眼的低成本技术
  • 批准号:
    10579902
  • 财政年份:
    2021
  • 资助金额:
    --
  • 项目类别:
{{ showInfoDetail.title }}

作者:{{ showInfoDetail.author }}

知道了