comparative biology

比较生物学
  • 文章类型: Journal Article
    高度迁移的研究和重要性引起了动物学家的兴趣。海拔移民在分类上分布广泛,并作为部分或完全移民跨越海拔梯度,让他们接受广泛的环境和生态相互作用。这里,我们简要介绍了该领域的最新发展,并提出了未来的方向,以建立更具分类学包容性的比较框架来研究海拔迁移。我们的框架以高度迁移的工作定义为中心,该定义取决于其生物学相关性,这是尺度依赖性的,与健身结果有关。我们讨论了海拔运动的语言细微差别,并提供了具体步骤来比较传统上不同的研究系统中的海拔迁移现象。一起,我们的比较框架概述了一个“表型空间”,它将来自不同血统和生物群落的高原移民所遇到的生物和非生物相互作用进行了背景化。我们还总结了新的机会,方法,以及正在进行的海拔迁移研究面临的挑战。一个执着的,主要挑战是表征物种内部和物种之间海拔迁移的分类学范围。幸运的是,已经开发了许多新方法来帮助研究人员评估海拔迁移的分类患病率-每种方法都有自己的优缺点。改进的比较框架将使研究不同学科和分类组的研究人员能够更好地交流和测试有关种群和物种之间海拔迁移变化的进化和生态驱动因素的假设。
    The study and importance of altitudinal migration has attracted increasing interest among zoologists. Altitudinal migrants are taxonomically widespread and move across altitudinal gradients as partial or complete migrants, subjecting them to a wide array of environments and ecological interactions. Here, we present a brief synthesis of recent developments in the field and suggest future directions toward a more taxonomically inclusive comparative framework for the study of altitudinal migration. Our framework centers on a working definition of altitudinal migration that hinges on its biological relevance, which is scale-dependent and related to fitness outcomes. We discuss linguistic nuances of altitudinal movements and provide concrete steps to compare altitudinal migration phenomena across traditionally disparate study systems. Together, our comparative framework outlines a \"phenotypic space\" that contextualizes the biotic and abiotic interactions encountered by altitudinal migrants from divergent lineages and biomes. We also summarize new opportunities, methods, and challenges for the ongoing study of altitudinal migration. A persistent, primary challenge is characterizing the taxonomic extent of altitudinal migration within and among species. Fortunately, a host of new methods have been developed to help researchers assess the taxonomic prevalence of altitudinal migration-each with their own advantages and disadvantages. An improved comparative framework will allow researchers that study disparate disciplines and taxonomic groups to better communicate and to test hypotheses regarding the evolutionary and ecological drivers underlying variation in altitudinal migration among populations and species.
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  • 文章类型: Journal Article
    各种感觉方式的相对重要性可以随着进化转变而变化,导致编码其接收系统的潜在基因家族发生变化。作为大型嗅觉受体(OR)基因家族进化基础的快速出生和死亡过程尤其加速了嗅觉的基因组水平变化。海洋哺乳动物从陆地到海洋的过渡是一个有吸引力的模型,可以理解栖息地变化对感觉系统的影响,保留的或保留的须鲸种类与其在齿鲸中的损失形成鲜明对比。在这项研究中,我们研究了从陆地环境到海洋环境的过渡在多大程度上影响了须鲸或鱼种的演变。我们开发了基因采矿管道(GMPipe)(https://github.com/AprilJauhal/GMPipe),可以准确识别大量的候选OR基因。GMPipe从八个须鲸物种中鉴定出707个OR序列。与陆地哺乳动物相比,这些库表现出明显的家族数量分布,包括OR10、OR11和OR13家族相对扩张的迹象。虽然许多受体在须鲸中丢失或显示出随机漂移的迹象,其他人表现出在净化或正选择下进化的迹象。超过85%的OR基因可以被分选到含有至少四个同源序列的直系同源序列组中。这些团体中的许多人,特别是来自OR10家族,呈现出相对扩张和净化选择压力的迹象。总的来说,我们的结果表明,相对较小的须鲸或剧目是由于专业化到新颖的嗅觉景观,而不是随机漂移。
    The relative importance of various sensory modalities can shift in response to evolutionary transitions, resulting in changes to underlying gene families encoding their reception systems. The rapid birth-and-death process underlying the evolution of the large olfactory receptor (OR) gene family has accelerated genomic-level change for the sense of smell in particular. The transition from the land to sea in marine mammals is an attractive model for understanding the influence of habitat shifts on sensory systems, with the retained OR repertoire of baleen whales contrasting with its loss in toothed whales. In this study, we examine to what extent the transition from a terrestrial to a marine environment has influenced the evolution of baleen whale OR repertoires. We developed Gene Mining Pipeline (GMPipe) (https://github.com/AprilJauhal/GMPipe), which can accurately identify large numbers of candidate OR genes. GMPipe identified 707 OR sequences from eight baleen whale species. These repertoires exhibited distinct family count distributions compared to terrestrial mammals, including signs of relative expansion in families OR10, OR11 and OR13. While many receptors have been lost or show signs of random drift in baleen whales, others exhibit signs of evolving under purifying or positive selection. Over 85% of OR genes could be sorted into orthologous groups of sequences containing at least four homologous sequences. Many of these groups, particularly from family OR10, presented signs of relative expansion and purifying selective pressure. Overall, our results suggest that the relatively small size of baleen whale OR repertoires result from specialisation to novel olfactory landscapes, as opposed to random drift.
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  • 文章类型: Journal Article
    结构和功能的不对称在每一种生命形式中都可以追溯到,和一些侧缘是同源的。从功能上讲,大脑两半之间的分工是神经系统的基本特征,甚至在脊椎动物出现之前就出现了。这种专业化在人类中最著名的表达是手支配,也被称为惯用手。即使手/肢/爪优势与神经系统的存在更常见,它也以其自身的形式在非生物体中观察到,比如植物。迄今为止,关于这种优势在植物中可能的功能意义知之甚少,许多问题仍然悬而未决(其中,它是否反映了广义的行为不对称)。这里,我们提出了一种比较方法来研究惯用手法,包括植物,通过利用已经用于研究人类和各种动物物种的侧向性的实验模型和范例。通过这种方法,我们的目标是丰富我们对自然王国中惯用手的概念的了解。
    Structural and functional asymmetries are traceable in every form of life, and some lateralities are homologous. Functionally speaking, the division of labour between the two halves of the brain is a basic characteristic of the nervous system that arose even before the appearance of vertebrates. The most well-known expression of this specialisation in humans is hand dominance, also known as handedness. Even if hand/limb/paw dominance is far more commonly associated with the presence of a nervous system, it is also observed in its own form in aneural organisms, such as plants. To date, little is known regarding the possible functional significance of this dominance in plants, and many questions remain open (among them, whether it reflects a generalised behavioural asymmetry). Here, we propose a comparative approach to the study of handedness, including plants, by taking advantage of the experimental models and paradigms already used to study laterality in humans and various animal species. By taking this approach, we aim to enrich our knowledge of the concept of handedness across natural kingdoms.
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  • 文章类型: Journal Article
    寻找变幻莫测的衰老解决方案,历史上,通过利用少数现有的和完善的动物模型系统,类似于夜间在路灯下的明亮光线下进行搜索。在我作为比较生物学家的整个职业生涯中,我冒险进入四大洲的黑暗,研究了150多种不同的动物,其中许多已经进化出了非凡的适应性,可以在实验室环境之外的严酷和崎岖的健身环境中生存。在这个研究员论坛上,我将讨论我过去25年研究的主要重点,并深入挖掘超自然长寿裸痣鼠的生物学,使其成为表征成功的抗衰老策略的理想模型系统。
    The search for solutions to the vagaries of aging has, historically, been akin to searching at night in the bright light under street lamps by utilizing the few preexisting and well-established animal model systems. Throughout my career as a comparative biologist, I have ventured into the darkness across 4 continents and studied over 150 different animal species, many of which have evolved remarkable adaptations to survive on the harsh and rugged fitness landscape that exists outside of the laboratory setting. In this Fellows Forum, I will discuss the main focus of my research for the last 25 years and dig deeply into the biology of the preternaturally long-lived naked mole-rat that makes it an ideal model system for the characterization of successful strategies to combat aging.
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  • 文章类型: Journal Article
    基于静息状态功能磁共振成像(fMRI)的功能性脑连接已被证明与人类的个性和行为相关。在这项研究中,我们试图知道狗的能力和特征是否可以从它们的静息状态连通性来预测,就像人类一样。我们训练清醒的狗在获取静息状态fMRI数据时,将它们的头部保持在3TMRI扫描仪中。犬的行为特征是捕捉它们狩猎的综合行为得分,检索,和环境健全。在检测器狗训练的三个不同时间点获取功能扫描和行为测量。第一时间点(TP1)是在狗进入正式的工作检测器狗训练之前。第二个时间点(TP2)是在正式的探测器犬训练后不久。第三个时间点(TP3)是在对检测犬进行训练后的三个月,而狗则参与了检测工作的维护训练计划。我们假设,狗大脑中的静息状态FC与行为测量之间的相关性将在其检测训练过程中(从TP1到TP2)发生显着变化,并且在随后的几个月的检测工作(从TP2到TP3)中保持不变。为了进一步研究可以预测训练成功的静息状态FC特征,在TP1的狗被分为成功组和不成功组。我们观察到一个核心大脑网络,该网络显示出相对稳定(相对于时间)的相互作用模式,与失败相比,成功的检测犬明显更强,并且其连接强度在第一个时间点预测了给定的狗是否最终成功成为检测犬。观察到第二个基于本体的灵活外围网络,其连接强度随检测训练的变化跟踪了训练程序上行为的相应变化。比较狗和人类的大脑,狗的脑干和额叶皮层之间的功能连接与人类的蓝斑和左中额回之间的功能连接相对应,暗示了一种共享的气味学习和检索机制。总的来说,研究结果指出了系统发育和个体发育对产生两个可分离的功能性神经网络的狗的影响。
    Functional brain connectivity based on resting-state functional magnetic resonance imaging (fMRI) has been shown to be correlated with human personality and behavior. In this study, we sought to know whether capabilities and traits in dogs can be predicted from their resting-state connectivity, as in humans. We trained awake dogs to keep their head still inside a 3T MRI scanner while resting-state fMRI data was acquired. Canine behavior was characterized by an integrated behavioral score capturing their hunting, retrieving, and environmental soundness. Functional scans and behavioral measures were acquired at three different time points across detector dog training. The first time point (TP1) was prior to the dogs entering formal working detector dog training. The second time point (TP2) was soon after formal detector dog training. The third time point (TP3) was three months\' post detector dog training while the dogs were engaged in a program of maintenance training for detection work. We hypothesized that the correlation between resting-state FC in the dog brain and behavior measures would significantly change during their detection training process (from TP1 to TP2) and would maintain for the subsequent several months of detection work (from TP2 to TP3). To further study the resting-state FC features that can predict the success of training, dogs at TP1 were divided into a successful group and a non-successful group. We observed a core brain network which showed relatively stable (with respect to time) patterns of interaction that were significantly stronger in successful detector dogs compared to failures and whose connectivity strength at the first time point predicted whether a given dog was eventually successful in becoming a detector dog. A second ontologically based flexible peripheral network was observed whose changes in connectivity strength with detection training tracked corresponding changes in behavior over the training program. Comparing dog and human brains, the functional connectivity between the brain stem and the frontal cortex in dogs corresponded to that between the locus coeruleus and left middle frontal gyrus in humans, suggestive of a shared mechanism for learning and retrieval of odors. Overall, the findings point toward the influence of phylogeny and ontogeny in dogs producing two dissociable functional neural networks.
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  • 文章类型: Journal Article
    目的:腺毛与植物的直接和间接防御有关。然而,由于草食性,腺毛和非腺毛的进化程度尚不清楚,因为他们的遗传能力,它们与食草动物抗性的联系,他们之间的取舍,它们与其他功能的关联很少被量化。
    方法:我们对毛虫和食草动物对通才毛虫的抗性进行了系统发育比较,Heliothisviresces,在tarweed物种(Asteraceae:Madiinae)之间进行遗传相关性研究,比较了三种tarweed物种的母体半同胞之间的相同性状。
    结果:在一种tarweet物种中,我们没有发现草食动物的生长速率在有更多腺体或更密集的毛状体的tarweet个体或母体同胞组上下降的证据。然而,具有更多腺体和更少的非腺体毛状体的tarweet物种导致生长较慢的草食动物。同样,在tarweet物种中,腺毛和非腺毛之间的权衡很明显,但不是在一个物种内的个体或同胞群体之间。
    结论:我们的结果表明,这种关键的草食动物没有选择毛状体作为tarweet物种的直接防御。然而,毛状体在物种之间差异很大,可能会影响食草动物对这些物种的压力。我们的结果表明,植物性状之间的权衡,以及对这些特征功能的推断,可以取决于规模。
    Glandular trichomes are implicated in direct and indirect defense of plants. However, the degree to which glandular and non-glandular trichomes have evolved as a consequence of herbivory remains unclear, because their heritability, their association with herbivore resistance, their trade-offs with one another, and their association with other functions are rarely quantified.
    We conducted a phylogenetic comparison of trichomes and herbivore resistance against the generalist caterpillar, Heliothis virescens, among tarweed species (Asteraceae: Madiinae) and a genetic correlation study comparing those same traits among maternal half-sibs of three tarweed species.
    Within a tarweed species, we found no evidence that herbivore growth rate decreased on tarweed individuals or maternal sib groups with more glandularity or denser trichomes. However, tarweed species with more glandularity and fewer non-glandular trichomes resulted in slower-growing herbivores. Likewise, a trade-off between glandular and non-glandular trichomes was apparent among tarweed species, but not among individuals or sib groups within a species.
    Our results suggest that this key herbivore does not select for trichomes as a direct defense in tarweed species. However, trichomes differed substantially among species and likely affect herbivore pressure on those species. Our results demonstrate that trade-offs among plant traits, as well as inference on the function of those traits, can depend on scale.
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  • 文章类型: Journal Article
    识别结构-功能对应关系是生物学家的主要目标,认知神经科学家,和大脑映射器。最近的研究已经确定了认知任务的表现与是否存在小的,浅压痕,或沟,人类的大脑。在先前发现的基础上,左前外侧前额叶皮层(aLPFC)中腹侧中间额叶沟(pimfs-v)的存在与儿童和青少年的推理任务表现有关,我们测试了这种关系是否扩展到不同的样本,年龄组,和推理任务。正如预测的那样,在年轻人(22~36岁)中,该aLPFC沟的存在也与较高的推理评分相关.这些发现不仅直接发展,但也是进化的相关性-最近的工作表明,pimfs-v在黑猩猩中极为罕见。因此,pimfs-v是一个关键的发展,认知,和进化相关的特征,应该在未来的研究中考虑,研究大脑多尺度解剖和功能特征之间的复杂关系如何引起抽象思维。
    Identifying structure-function correspondences is a major goal among biologists, cognitive neuroscientists, and brain mappers. Recent studies have identified relationships between performance on cognitive tasks and the presence or absence of small, shallow indentations, or sulci, of the human brain. Building on the previous finding that the presence of the ventral para-intermediate frontal sulcus (pimfs-v) in the left anterior lateral prefrontal cortex (aLPFC) was related to reasoning task performance in children and adolescents, we tested whether this relationship extended to a different sample, age group, and reasoning task. As predicted, the presence of this aLPFC sulcus was also associated with higher reasoning scores in young adults (ages 22-36). These findings have not only direct developmental, but also evolutionary relevance-as recent work shows that the pimfs-v is exceedingly rare in chimpanzees. Thus, the pimfs-v is a key developmental, cognitive, and evolutionarily relevant feature that should be considered in future studies examining how the complex relationships among multiscale anatomical and functional features of the brain give rise to abstract thought.
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  • 文章类型: Journal Article
    老化的比较研究是确定导致老化的一般性质和过程的有前途的方法。到目前为止,许多动物衰老的比较研究都集中在相对狭窄的物种群体上,方法创新现在允许研究,包括进化遥远的物种。然而,在具有不同生活史的各种物种中进行衰老的比较研究,给实验设计带来了额外的挑战。这里,我们讨论这些挑战,突出需要解决的最紧迫问题,并根据目前的方法提供建议,以成功地在整个动物界进行比较衰老研究。
    Comparative studies of aging are a promising approach to identifying general properties of and processes leading to aging. While to date, many comparative studies of aging in animals have focused on relatively narrow species groups, methodological innovations now allow for studies that include evolutionary distant species. However, comparative studies of aging across a wide range of species that have distinct life histories introduce additional challenges in experimental design. Here, we discuss these challenges, highlight the most pressing problems that need to be solved, and provide suggestions based on current approaches to successfully carry out comparative aging studies across the animal kingdom.
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  • 文章类型: Journal Article
    背景:实验模型是神经退行性疾病研究中必不可少的工具。然而,在模型系统中发现的见解和药物的翻译已被证明具有极大的挑战性,在人体临床试验中受到高失败率的损害。
    方法:在这里,我们回顾了人工智能(AI)和机器学习(ML)在痴呆症研究的实验医学中的应用。
    结果:考虑到临床前痴呆研究中其他物种或模型系统与人类生物学之间的可重复性和翻译的特定挑战,我们重点介绍了可用于量化和评估可译性的最佳实践和资源。然后,我们评估了如何应用AI和ML方法来增强跨模型的可重复性和对人类生物学的翻译。同时保持生物学的可解释性。
    结论:实验医学中的AI和ML方法仍处于起步阶段。然而,如果有足够的基础,它们有很大的潜力来加强临床前研究和翻译,健壮,和可重复的实验数据。
    结论:AI在实验医学中的应用越来越多。我们发现了再现性方面的问题,跨物种翻译,以及该领域的数据管理。我们的审查重点介绍了数据资源和AI方法作为解决方案。使用AI进行的多组分析为药物发现提供了令人兴奋的未来可能性。
    Experimental models are essential tools in neurodegenerative disease research. However, the translation of insights and drugs discovered in model systems has proven immensely challenging, marred by high failure rates in human clinical trials.
    Here we review the application of artificial intelligence (AI) and machine learning (ML) in experimental medicine for dementia research.
    Considering the specific challenges of reproducibility and translation between other species or model systems and human biology in preclinical dementia research, we highlight best practices and resources that can be leveraged to quantify and evaluate translatability. We then evaluate how AI and ML approaches could be applied to enhance both cross-model reproducibility and translation to human biology, while sustaining biological interpretability.
    AI and ML approaches in experimental medicine remain in their infancy. However, they have great potential to strengthen preclinical research and translation if based upon adequate, robust, and reproducible experimental data.
    There are increasing applications of AI in experimental medicine. We identified issues in reproducibility, cross-species translation, and data curation in the field. Our review highlights data resources and AI approaches as solutions. Multi-omics analysis with AI offers exciting future possibilities in drug discovery.
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  • 文章类型: Journal Article
    在设计实验研究时,了解所问问题的生物学背景很重要。例如,许多生物穿刺实验根据工具总长度的百分比将穿刺工具嵌入到标准化的深度,比较工具之间的性能。然而,这可能并不总是与被问到的问题在生物学上相关。为了解渗透深度的定义如何影响比较结果,我们使用毒液孔位置作为功能相关的深度标准,对一系列毒蛇毒牙进行了穿刺实验。在探索了蛇系统发育过程中孔隙位置的变化之后,我们使用各种深度标准比较了在一组蛇尖牙穿刺实验期间花费的工作:穿刺开始,穿透到由毒液孔定义的一系列深度,并穿透到方长的15%。与我们的假设相反,我们在进化枝之间的孔隙位置几乎没有发现任何模式,饮食组或毒液毒性。我们的实验能量学结果的等级相关统计数据显示,当使用不同的穿刺深度标准时,尖牙的广泛比较没有差异。然而,尖牙之间的成对比较表明,所使用的不同深度标准之间的显著性模式发生了重大变化。这些结果表明,对实验穿刺数据的解释将在很大程度上取决于实验期间使用的深度标准。我们的结果说明了在设计比较实验时理解所要解决的问题的生物学背景的重要性。
    When designing experimental studies, it is important to understand the biological context of the question being asked. For example, many biological puncture experiments embed the puncture tool to a standardized depth based on a percentage of the total tool length, to compare the performance between tools. However, this may not always be biologically relevant to the question being asked. To understand how definitions of penetration depth may influence comparative results, we performed puncture experiments on a series of venomous snake fangs using the venom pore location as a functionally relevant depth standard. After exploring variation in pore placement across snake phylogeny, we compared the work expended during puncture experiments across a set of snake fangs using various depth standards: puncture initiation, penetration to a series of depths defined by the venom pore and penetration to 15% of fang length. Contrary to our hypothesis, we found almost no pattern in pore placement between clades, dietary groups or venom toxicity. Rank correlation statistics of our experimental energetics results showed no difference in the broad comparison of fangs when different puncture depth standards were used. However, pairwise comparisons between fangs showed major shifts in significance patterns between the different depth standards used. These results imply that the interpretation of experimental puncture data will heavily depend upon which depth standard is used during the experiments. Our results illustrate the importance of understanding the biological context of the question being addressed when designing comparative experiments.
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