基于深度学习的作物基因组学和遗传改良

随着世界人口的不断增长、食物需求量的不断增加,以及气候的不断变化,如何提高农作物产量已成为人类面临的一个巨大挑战。传统设计育种耗时长、效率低,已经不能满足新时代的育种需求。随着基因型和表型数据成本的不断降低,以及各种组学数据的爆炸式增长,人工智能技术作为能够在大数据中高效率挖掘信息的工具,在生物学领域受到了广泛关注。人工智能指导的设计育种将大大加快育种的效率,给育种带来革命性的变化。介绍了人工智能特别是深度学习在作物基因组学和遗传改良中的应用,并进行了总结与展望,以期为智能设计育种提供新的思路。     

Plastic,inquisitive roots and intelligent plants in the light of some new vistas in plant biology

Abstract

Metaphors, such as those used in the title of this article, are often useful for the comprehension of specialised topics in plant biology. A brief attempt is made to elucidate one of these metaphors, plant “intelligence”, as it relates to the plastic responses of roots and root systems to their environment. Tropisms and nastic movements of root apices are two expressions of an inherent plasticity of form exhibited by roots. In soil, roots are exposed to multiple stimuli, many of which can potentially elicit such movements. Hence, a key question is how roots respond to and process the different stimuli which simultaneously reach their surfaces. Assuming that roots always use the same site along their length to express their movement responses, and that they also use an auxin‐based information‐transduction pathway, the most evident choices for the processing of stimuli are that roots either prioritise the various incoming stimuli and respond only to the strongest or they amalgamate stimuli and mount an averaged compromise response to all of them. The proposal that plants may be “intelligent”, especially in respect to their plastic growth responses, is one that draws upon knowledge of this faculty from animal biology. Also implied is that plants and animals are sufficiently similar to share usage of this term “intelligence”. But an alternative view is that plants and animals are sufficiently different and so intelligence is an unfitting term. Following the line of enquiry into creative evolution initiated by Henri Bergson, plants can be viewed differently to animals. The tendency of plants is towards instinctive behaviour rather than intelligent behaviour.     

Enzymes and theoretical biology: sketch of an informational perspective of the cell.

In the theoretical scenarios of biology, new insights can be gained by the introduction of information-processing and artificial intelligence concepts, helping to organize the explanation of the many intra- and inter-cellular phenomena that molecular biology is accumulating. Enzymes contain some of the immediate clues; the whole informational processing of prokaryotic cells is another central subject of search. Additionally, prolonging the informational perspective of the cell, a significant parallel can be drawn between informational processes in biological, social and artificial intelligence systems. A more tangible definition of biological complexity and biological intelligence emerges.     

活细胞单分子实时视见研究

我们对细胞生物学与分子生物学中有关分子事件和相互作用的认识,大部分都是集团平均水平研究的结果,并且基于所有的分子在给定时间内以完全相同的方式运动这样一种不真实的假设。现在,激光技术和全内反射显微镜的应用,以及绿色荧光蛋白(green fluorescent proteins,GFPs)等新的分子荧光探针的出现,使得显示活细胞单个生物分子的运动行为和轨迹成为可能。单分子水平的研究将会加深人们对分子和细胞生物学的基本概念的认识。     

高等植物开花时程的基因调控(Ⅱ)

主要探讨如下几个问题:转基因植物中的拟南芥开花时程基因;拟南芥中的甲基化与实验胚胎学研究;高等植物开花时程控制的可能机制.目前本领域已成为植物发育分子生物学的前沿热点研究领域之一.结合有关工作,对这一世界性热门领域进行了系统的评述,希望能为国内同行提供有关参考,赶超世界的植物分子生物学先进水平,对分子水平与生物技术角度改良黄土高原生态环境有指导意义.     

Time estimation predicts mathematical intelligence

Background

Performing mental subtractions affects time (duration) estimates, and making time estimates disrupts mental subtractions. This interaction has been attributed to the concurrent involvement of time estimation and arithmetic with general intelligence and working memory. Given the extant evidence of a relationship between time and number, here we test the stronger hypothesis that time estimation correlates specifically with mathematical intelligence, and not with general intelligence or working-memory capacity.

Methodology/Principal Findings

Participants performed a (prospective) time estimation experiment, completed several subtests of the WAIS intelligence test, and self-rated their mathematical skill. For five different durations, we found that time estimation correlated with both arithmetic ability and self-rated mathematical skill. Controlling for non-mathematical intelligence (including working memory capacity) did not change the results. Conversely, correlations between time estimation and non-mathematical intelligence either were nonsignificant, or disappeared after controlling for mathematical intelligence.

Conclusions/Significance

We conclude that time estimation specifically predicts mathematical intelligence. On the basis of the relevant literature, we furthermore conclude that the relationship between time estimation and mathematical intelligence is likely due to a common reliance on spatial ability.     

Tempo and mode of evolutionary radiation in Diabroticina beetles (genera Acalymma,Cerotoma, and Diabrotica)

Adaptive radiation is an aspect of evolutionary biology encompassing microevolution and macroevolution, for explaining the principles of lineage divergence. There are intrinsic as well as extrinsic factors that can be postulated to explain that adaptive radiation has taken place in specific lineages. The Diabroticina beetles are a prominent example of differential diversity that could be examined in detail to explain the diverse paradigms of adaptive radiation. Macroevolutionary analyses must present the differential diversity patterns in a chronological framework. The current study reviews the processes that shaped the differential diversity of some Diabroticina lineages (i.e. genera Acalymma, Cerotoma, and Diabrotica). These diversity patterns and the putative processes that produced them are discussed within a statistically reliable estimate of time. This was achieved by performing phylogenetic and coalescent analyses for 44 species of chrysomelid beetles. The data set encompassed a total of 2,718 nucleotide positions from three mitochondrial and two nuclear loci. Pharmacophagy, host plant coevolution, competitive exclusion, and geomorphological complexity are discussed as putative factors that might have influenced the observed diversity patterns. The coalescent analysis concluded that the main radiation within Diabroticina beetles occurred between middle Oligocene and middle Miocene. Therefore, the radiation observed in these beetles is not recent (i.e. post-Panamanian uplift, 4 Mya). Only a few speciation events in the genus Diabrotica might be the result of the Pleistocene climatic oscillations.     

A transformer architecture for retention time prediction in liquid chromatography mass spectrometry-based proteomics

Accurate retention time (RT) prediction is important for spectral library-based analysis in data-independent acquisition mass spectrometry-based proteomics. The deep learning approach has demonstrated superior performance over traditional machine learning methods for this purpose. The transformer architecture is a recent development in deep learning that delivers state-of-the-art performance in many fields such as natural language processing, computer vision, and biology. We assess the performance of the transformer architecture for RT prediction using datasets from five deep learning models Prosit, DeepDIA, AutoRT, DeepPhospho, and AlphaPeptDeep. The experimental results on holdout datasets and independent datasets exhibit state-of-the-art performance of the transformer architecture. The software and evaluation datasets are publicly available for future development in the field.     

CHANCE,PURPOSE, AND PROGRESS IN EVOLUTION AND CHRISTIANITY

Evolutionary biology has a complex relationship with ideas of chance, purpose, and progress. Probability plays a subtle role; strikingly, founding figures in statistics were motivated by evolutionary questions. The findings of evolutionary biology have been used both in support of narratives of progress, and in their deconstruction. Likewise, professional biologists bring to their scientific work a set of preconceptions about chance and progress, grounded in their philosophical, religious, and/or political views. From the religious side, questions of purpose are ever‐present. We explore this interplay in five broad categories: chance, progress, intelligence, eugenics, and the evolution of religious practices, each the subject of a semester long symposium. The intellectual influence of evolutionary biology has had a broad societal impact in these areas. Based on our experience, we draw attention to a number of relevant facts that, while accepted by experts in their respective fields, may be unfamiliar outside them. We list common areas of miscommunication, including specific examples and discussing causes: sometimes semantics and sometimes more substantive knowledge barriers. We also make recommendations for those attempting similar dialogue.     

Ability and achievement

Abstract

In the model used in this study, father's occupation and education, the number of siblings, and the early intelligence level of the respondent are taken to be “predetermined” variables, with no assumption made as to causal order, with respect to later achieved status and to intelligence measured at maturity. Four successive dependent variables are educational attainment, intelligence at maturity, occupational achievement, and monetary earning. Results indicate that the ideal of equal educational opportunity is realized in the white population studied to the extent that progress through the school system is influenced at least as much by how bright you are as by “who” you are. However, the fact that the latter, indexed by measures of family size and status, does make a substantial difference in educational outcome, apart from its correlation with intelligence, is an indication that the ideal is far from being completely realized at this time.     

Synthetic biology of minimal systems

“Synthetic biology” is a concept that has developed together with, or slightly after, “systems biology”. But while systems biology aims at the full understanding of large systems by integrating more and more details into their models, synthetic biology phrases different questions, namely: what particular biological function could be obtained with a certain known subsystem of reduced complexity; can this function be manipulated or engineered in artificial environments or genetically modified organisms; and if so, how? The most prominent representation of synthetic biology has so far been microbial engineering by recombinant DNA technology, employing modular concepts known from information technology. However, there are an increasing number of biophysical groups who follow similar strategies of dissecting cellular processes and networks, trying to identify functional minimal modules that could then be combined in a bottom-up approach towards biology. These modules are so far not as particularly defined by their impact on DNA processing, but rather influenced by core fields of biophysics, such as cell mechanics and membrane dynamics. This review will give an overview of some classical and some quite new biophysical strategies for constructing minimal systems of certain cellular modules. We will show that with recent advances in understanding of cytoskeletal and membrane elements, the time might have come to experimentally challenge the concept of a minimal cell.     

Residence time and potential range: crucial considerations in modelling plant invasions

A prime aim of invasion biology is to predict which species will become invasive, but retrospective analyses have so far failed to develop robust generalizations. This is because many biological, environmental, and anthropogenic factors interact to determine the distribution of invasive species. However, in this paper we also argue that many analyses of invasiveness have been flawed by not considering several fundamental issues: (1) the range size of an invasive species depends on how much time it has had to spread (its residence time); (2) the range size and spread rate are mediated by the total extent of suitable (i.e. potentially invasible) habitat; and (3) the range size and spread rate depend on the frequency and intensity of introductions (propagule pressure), the position of founder populations in relation to the potential range, and the spatial distribution of the potential range. We explored these considerations using a large set of invasive alien plant species in South Africa for which accurate distribution data and other relevant information were available. Species introduced earlier and those with larger potential ranges had larger current range sizes, but we found no significant effect of the spatial distribution of potential ranges on current range sizes, and data on propagule pressure were largely unavailable. However, crucially, we showed that: (1) including residence time and potential range always significantly increases the explanatory power of the models; and (2) residence time and potential range can affect which factors emerge as significant determinants of invasiveness. Therefore, analyses not including potential range and residence time can come to misleading conclusions. When these factors were taken into account, we found that nitrogen‐fixing plants and plants invading arid regions have spread faster than other species, but these results were phylogenetically constrained. We also show that, when analysed in the context of residence time and potential range, variation in range size among invasive species is implicitly due to variation in spread rates, and, that by explicitly assuming a particular model of spread, it is possible to estimate changes in the rates of plant invasions through time. We believe that invasion biology can develop generalizations that are useful for management, but only in the context of a suitable null model.     

Molecular and cellular key players in human islet transplantation

Human islet transplantation could represent an attractive alternative to insulin injections for the treatment of diabetes type 1. However, such an approach requires a better understanding of the molecular and cellular switches controlling β-cell function in general as well as after transplantation into the liver. Although much research has been done into the suitability of stem or progenitor cells to generate a limitless supply of human β-cells, a reproducible and efficient protocol for the differentiation of such cells into stably insulin-secreting β-cells suitable for transplantation has yet to be reported. Fueled by recent findings showing that mature β-cells are able to regenerate, many efforts have been undertaken to expand this cell pool. Unfortunately, also these approaches had problems to yield sufficiently differentiated human islet cells. The aim of this review is to summarize recent findings describing some of the molecular and cellular key players of islet biology. A more complete understanding of their orchestration and the use of new methods such as real time confocal imaging for the assessment of islet quality may yield the necessary advancements for more successful human islet transplantation.     

Data assimilation and multisource decision-making in systems biology based on unobtrusive Internet-of-Things devices

Biological and medical diagnoses depend on high-quality measurements. A wearable device based on Internet of Things (IoT) must be unobtrusive to the human body to encourage users to accept continuous monitoring. However, unobtrusive IoT devices are usually of low quality and unreliable because of the limitation of technology progress that has slowed down at high peak. Therefore, advanced inference techniques must be developed to address the limitations of IoT devices. This review proposes that IoT technology in biological and medical applications should be based on a new data assimilation process that fuses multiple data scales from several sources to provide diagnoses. Moreover, the required technologies are ready to support the desired disease diagnosis levels, such as hypothesis test, multiple evidence fusion, machine learning, data assimilation, and systems biology. Furthermore, cross-disciplinary integration has emerged with advancements in IoT. For example, the multiscale modeling of systems biology from proteins and cells to organs integrates current developments in biology, medicine, mathematics, engineering, artificial intelligence, and semiconductor technologies. Based on the monitoring objectives of IoT devices, researchers have gradually developed ambulant, wearable, noninvasive, unobtrusive, low-cost, and pervasive monitoring devices with data assimilation methods that can overcome the limitations of devices in terms of quality measurement. In the future, the novel features of data assimilation in systems biology and ubiquitous sensory development can describe patients’ physical conditions based on few but long-term measurements.     

Intelligence can be detected but is not found attractive in videos and live interactions

Self-reported mate preferences suggest intelligence is valued across cultures, consistent with the idea that human intelligence evolved as a sexually selected trait. The validity of self-reports has been questioned though, so it remains unclear whether objectively assessed intelligence is indeed attractive. In Study 1, 88 target men had their intelligence measured and based on short video clips were rated on intelligence, funniness, physical attractiveness and mate appeal by 179 women. In Study 2 (N = 763), participants took part in 2 to 5 speed-dating sessions in which their intelligence was measured and they rated each other's intelligence, funniness, and mate appeal. Measured intelligence did not predict increased mate appeal in either study, whereas perceived intelligence and funniness did. More intelligent people were perceived as more intelligent, but not as funnier. Results suggest that intelligence is not important for initial attraction, which raises doubts concerning the sexual selection theory of intelligence.     

Federico Delpino and the foundation of plant biology

In 1867, Federico Delpino, with his seminal work Pensieri sulla Biologia Vegetale (Thoughts on Plant Biology) established plant biology by defining it not in the broad general sense, namely as the science of living beings, but as a branch of natural science dedicated to the study of plant life in relation to the environment. Today, the figure and achievements of this outstanding plant scientist is almost unknown. In the following pages, I will concisely describe the main realizations of Federico Delpino and outline the significance of his work for modern plant science.Key words: Charles Darwin, evolution, history of botany, myrmecophily, plant biology, plant intelligence, plant-insect     

The evolution of brain size and intelligence in man

The brain size of hominids has increased approximately threefold during the evolution of the hominids fromAustralopithecus toHomo sapiens. It is proposed that the principal reason for this increase is that larger brains conferred greater intelligence, and greater intelligence conferred a selection advantage. A number of anthropologists have difficulty accepting this thesis because they believe that brain size is not associated with intelligence in man. Evidence is reviewed, and new evidence from two studies is presented, to show that brain size as measured by head size is positively correlated with intelligence as measured by intelligence tests. On two recent samples statistically significant correlations of .21 and .30 were obtained between estimates of brain size and IQ. It is considered that brain size is positively associated with intelligence in man and that this is the major reason for the increase in brain size of the hominids during the last 3.2 million years.     

Future medicine: from molecular pathways to the collective intelligence of the body

The remarkable anatomical homeostasis exhibited by complex living organisms suggests that they are inherently reprogrammable information-processing systems that offer numerous interfaces to their physiological and anatomical problem-solving capacities. We briefly review data suggesting that the multiscale competency of living forms affords a new path for biomedicine that exploits the innate collective intelligence of tissues and organs. The concept of tissue-level allostatic goal-directedness is already bearing fruit in clinical practice. We sketch a roadmap towards 'somatic psychiatry' by using advances in bioelectricity and behavioral neuroscience to design methods that induce self-repair of structure and function. Relaxing the assumption that cellular control mechanisms are static, exploiting powerful concepts from cybernetics, behavioral science, and developmental biology may spark definitive solutions to current biomedical challenges.     

Seeing the forest for the trees: the limitations of phylogenies in comparative biology. (American Society of Naturalists Address)

The past 30 years have seen a revolution in comparative biology. Before that time, systematics was not at the forefront of the biological sciences, and few scientists considered phylogenetic relationships when investigating evolutionary questions. By contrast, systematic biology is now one of the most vigorous disciplines in biology, and the use of phylogenies not only is requisite in macroevolutionary studies but also has been applied to a wide range of topics and fields that no one could possibly have envisioned 30 years ago. My message is simple: phylogenies are fundamental to comparative biology, but they are not the be-all and end-all. Phylogenies are powerful tools for understanding the past, but like any tool, they have their limitations. In addition, phylogenies are much more informative about pattern than they are about process. The best way to fully understand the past-both pattern and process-is to integrate phylogenies with other types of historical data as well as with direct studies of evolutionary process.