3D Modelling of Biological Systems for Biomimetics

1　IntroductionBasedonthereviewofthepreviousworkof 3Dgeometricalmodellingtechniquesandsystemsdevelopedforindustrial,medicalandanimationapplications,thispaperdiscussestheproblemsassociatedwiththeexist ingtechniquesandsystems ,especiallywhenappliedto3Dmodellingof plants ,insectsandanimalsforbiomimeticsresearchanddevelopment .Then ,paperproposessomeareasofresearchinterestsin 3Dmod ellingofplants ,insectsandanimalsforBiomimetics .Toavoidtherepeating ,inthispaper ,biologicalobjectswillbeusedtorep…     

Toward computational systems biology

The development and successful application of high-throughput technologies are transforming biological research. The large quantities of data being generated by these technologies have led to the emergence of systems biology, which emphasizes large-scale, parallel characterization of biological systems and integration of fragmentary information into a coherent whole. Complementing the reductionist approach that has dominated biology for the last century, mathematical modeling is becoming a powerful tool to achieve an integrated understanding of complex biological systems and to guide experimental efforts of engineering biological systems for practical applications. Here I give an overview of current mainstream approaches in modeling biological systems, highlight specific applications of modeling in various settings, and point out future research opportunities and challenges.     

Studying Gene Expression System Regulation at the Program Level

Understanding how gene expression systems influence biological outcomes is an important goal for diverse areas of research. Gene expression profiling allows for the simultaneous measurement of expression levels for thousands of genes and the opportunity to use this information to increase biological understanding. Yet, the best way to relate this immense amount of information to biological outcomes is far from clear. Here, a novel approach to gene expression systems research is presented that focuses on understanding gene expression systems at the level of gene expression program regulation. It is suggested that such an approach has important advantages over current techniques and may provide novel insights into how gene expression systems are regulated to shape biological outcomes such as the development of disease or response to treatment.     

Virtual special issue: Social-ecological systems research in tropical ecosystems

Biodiversity is declining globally, primarily due to anthropogenic threats. Therefore, effective conservation efforts must integrate human and environmental components. Social-ecological systems research is increasingly being adopted as a means of studying complex relationships between people and the environment. I assess how researchers are employing social-ecological systems approaches or frameworks to the study of tropical ecosystems. I reviewed articles published in Biotropica from 2010 through 2022 searching for research on social-ecological systems. A broad keyword search revealed only 2 articles using a variation of social-ecological systems, human-environment systems, or coupled human and natural systems. This contrasts with a growing number of articles published with these search terms in other conservation-related journals, primarily led by environmental scientists. After reviewing titles for all 1298 research articles published during this period, I selected 12 articles for inclusion in the virtual special issue “Social-Ecological Systems Research in Topical Ecosystems”. These articles cover a broad range of geographical locations, ecosystem types, species, and conservation themes. Social-ecological systems frameworks offer an integrated way to study complex relationships between humans and nature, yet this type of research appears under-utilized by authors in Biotropica. I offer seven guidelines for authors interested in pursuing this research such as developing collaborations between social and environmental scientists.     

系统生物学——生命科学的新领域

系统生物学是继基因组学、蛋白质组学之后一门新兴的生物学交叉学科,代表21世纪生物学的未来.最近,系统生物学研究机构纷纷成立.在研究上,了解一个复杂的生物系统需要整合实验和计算方法.基因组学和蛋白质组学中的高通量方法为系统生物学发展提供了大量的数据.计算生物学通过数据处理、模型构建和理论分析,成为系统生物学发展的一个必不可缺、强有力的工具.在应用上,系统生物学代表新一代医药开发和疾病防治的方向.     

Designing research funding schemes to promote global health equity: An exploration of current practice in health systems research

International research is an essential means of reducing health disparities between and within countries and should do so as a matter of global justice. Research funders from high‐income countries have an obligation of justice to support health research in low and middle‐income countries (LMICs) that furthers such objectives. This paper investigates how their current funding schemes are designed to incentivise health systems research in LMICs that promotes health equity. Semi‐structured in‐depth interviews were performed with 16 grants officers working for 11 funders and organisations that support health systems research: the Alliance for Health Policy and Systems Research, Comic Relief, Doris Duke Foundation, European Commission, International Development Research Centre, Norwegian Agency for Development Cooperation, Research Council of Norway, Rockefeller Foundation, UK Department of International Development, UK Medical Research Council, and Wellcome Trust. Thematic analysis of the data demonstrates their funding schemes promote health systems research with (up to) five key features that advance health equity: being conducted with worst‐off populations, focusing on research topics that advance equitable health systems, having LMIC ownership of the research agenda, strengthening LMIC research capacity, and having an impact on health disparities. The different types of incentives that encouraged proposed projects to have these features are identified and classified by their strength (strong, moderate, weak). It is suggested that research funders ought to create and maintain funding schemes with strong incentives for the features identified above in order to more effectively help reduce global health disparities.     

Towards a systematic evaluation of protein mutation extraction systems

The development of text analysis systems targeting the extraction of information about mutations from research publications is an emergent topic in biomedical research. Current systems differ in both scope and approach, thus preventing a meaningful comparison of their performance and therefore possible synergies. To overcome this evaluation bottleneck, we developed a comprehensive framework for the systematic analysis of mutation extraction systems, precisely defining tasks and corresponding evaluation metrics, that will allow a comparison of existing and future applications.     

Osteoimmunology: shared mechanisms and crosstalk between the immune and bone systems

Osteoimmunology is an interdisciplinary research field focused on the molecular understanding of the interplay between the immune and skeletal systems. Although osteoimmunology started with the study of the immune regulation of osteoclasts, its scope has been extended to encompass a wide range of molecular and cellular interactions, including those between osteoblasts and osteoclasts, lymphocytes and osteoclasts, and osteoblasts and haematopoietic cells. Therefore, the two systems should be understood to be integrated and operating in the context of the 'osteoimmune' system, a heuristic concept that provides not only a framework for obtaining new insights by basic research, but also a scientific basis for the discovery of novel treatments for diseases related to both systems.     

以CasX为例简述新型CRISPR-Cas系统的基本属性和研究方法

在细菌与古菌中广泛存在的CRISPR-Cas系统,作为目前发现的原核生物唯一的适应性免疫系统,抵御着病毒和质粒的入侵。自20世纪80年代首次被发现至今,CRISPR-Cas系统的基本情况逐渐清晰,包括名称缩写、分类、进化关系等方面。近年来,由于第二类CRISPR-Cas系统作为一种有潜力的基因编辑工具而逐渐成为应用研究被关注,对CRISPR-Cas系统的基础研究热度也持久不衰。为了使此类基因编辑工具在实际应用领域更加安全便捷,针对已发现的CRISPR-Cas系统在根据基础研究领域的成果进行优化的同时,对新型CRISPR-Cas系统的发掘工作也同等重要。本文以2017年发现的CasX为例,简要概述针对一种新发现的CRISPR-Cas系统需要研究确定的基本属性及相关研究方法。     

Reinterpreting Responsiveness for Health Systems Research in Low and Middle‐Income Countries

The ethical concept of responsiveness has largely been interpreted in the context of international clinical research. In light of the increasing conduct of externally funded health systems research (HSR) in low‐ and middle‐income countries (LMICs), this article examines how responsiveness might be understood for such research and how it can be applied. It contends that four features (amongst others) set HSR in LMICs apart from international clinical research: a focus on systems; being context‐driven; being policy‐driven; and being closely linked to development objectives. These features support reinterpreting responsiveness for HSR in LMICs as responsiveness to systems needs, where health system performance assessments can be relied upon to identify systems needs, and/or responsiveness to systems priorities, which entails aligning research with HSR priorities set through country‐owned processes involving national and sub‐national policymakers from host countries. Both concepts may be difficult to achieve in practice. Country ownership is not an established fact for many countries and alignment to their priorities may be meaningless without it. It is argued that more work is, therefore, needed to identify strategies for how the responsiveness requirement can be ethically fulfilled for HSR in LMICs under non‐ideal conditions such as where host countries have not set HSR priorities via country‐owned processes. Embeddedness is proposed as one approach that could be the focus of further development.     

电阻抗法在植物根系生物学研究中的应用

因受限于检测方法,对埋藏于土壤中植物根系研究的深入程度远低于其地上部分。传统获取根系的方法不仅费时费力,而且对根系原位分布和生存微环境具有明显的扰动破坏,故随着根系研究的不断深入,迫切需要寻求一种非破坏性的根系检测方法。电阻抗法是在一定频率的外加电源下,测量电路中的根系电学特征(电容、电阻和电阻抗图谱),并且电学特征与根系生物量和形态指标之间存在较好的相关性,然而,由于对电阻抗法基于电路中电流流向等的关键机理尚不清楚,有些学者对该方法的大范围应用提出了质疑。本文首先对生物电阻抗法测量根系的原理和模型进行阐述,然后重点综述根系电阻抗法研究的不同理论方法及存在的问题,最后提出电阻抗法研究植物根系应该解决的重要科学问题,并展望电阻抗法更加广泛的研究和应用前景,以期为获取非破坏性的根系研究技术提供参考。     

Multiscale agent-based cancer modeling

Agent-based modeling (ABM) is an in silico technique that is being used in a variety of research areas such as in social sciences, economics and increasingly in biomedicine as an interdisciplinary tool to study the dynamics of complex systems. Here, we describe its applicability to integrative tumor biology research by introducing a multi-scale tumor modeling platform that understands brain cancer as a complex dynamic biosystem. We summarize significant findings of this work, and discuss both challenges and future directions for ABM in the field of cancer research.     

Regulated gene expression from adenovirus vectors: a systematic comparison of various inducible systems

Positively and tightly regulated gene expression is essential for gene function and gene therapy research. The currently-used inducible gene expression systems include tetracycline (Tet-on and T-REx), ecdysone, antiprogestin and dimerizer-based systems. Adenovirus (Ad) vectors play an important role in gene function and gene therapy research for their various advantages over other vector systems. Previously, we reported the inferiority of the Tet-on system as an inducible gene expression system in the context of Ad vectors in comparison with the Tet-off system. In this study, to identify an optimal system for regulated gene expression from Ad vectors, we made a rigorous direct comparison of these five inducible gene expression systems in three cell lines using the luciferase reporter gene. The highest sensitivity to the respective inducer was that of the dimerizer system, followed by the antiprogestin system. The lowest basal expression and the highest induction factor were both characteristic of the dimerizer system. Furthermore, the dimerizer and T-REx systems exhibited much higher induced expression levels than the other three systems. The elucidation of the characteristic features of each system should provide important information for widespread and feasible application of these systems. Overall, these results suggest the most appropriate inducible gene expression system in the context of Ad vectors to be the dimerizer system.     

Network modelling of gene regulation

Gene regulatory network (GRN) modelling has gained increasing attention in the past decade. Many computational modelling techniques have been proposed to facilitate the inference and analysis of GRN. However, there is often confusion about the aim of GRN modelling, and how a gene network model can be fully utilised as a tool for systems biology. The aim of the present article is to provide an overview of this rapidly expanding subject. In particular, we review some fundamental concepts of systems biology and discuss the role of network modelling in understanding complex biological systems. Several commonly used network modelling paradigms are surveyed with emphasis on their practical use in systems biology research.     

Resilience thinking: Interview with Brian Walker

Summary   This interview with Brian Walker, chair of the research-based Resilience Alliance, outlines the main concepts and propositions behind 'resilience thinking' and touches on the importance of this paradigm for individuals and organizations involved in managing complex social-ecological systems. It refers to the origins, work and publications of the Resilience Alliance, listing and elaborating the key case studies used to illustrate the Alliance's main proposition that complex social-ecological systems do not behave in a predictable linear fashion. Rather, research indicates it is normal for complex systems to go through cycles of increasing and decreasing resilience and to have potential to shift, (in a self-organising way) to potentially undesirable states or entirely new systems if certain component variables are severely impacted by management. Such shifts can be novel and 'surprising', and are often not beneficial or desirable for societies. This is particularly the case where small-scale solutions push the problem upwards in a system, causing loss of resilience at a global scale. Predicting thresholds is therefore important to managers and is a key research focus for members of the Resilience Alliance who are currently building an accessible database to support decision-making in global natural resource management.     

Meaning-making in the immune system

Meaning-making is the process by which a system responds to an indeterminate signal. This article focuses on meaning-making in living systems. It proposes several guidelines for studying the process of meaning-making in living systems in general, and in the immune system in particular. Drawing on a general framework for studying meaning-making in living systems, I suggest three basic organizing concepts for studying meaning-making-variability of the signal, context markers, and transgradience. Those concepts present a radical alternative to the information-processing approach that governs biological research and may shed new light on biological processes.     

奥杜威工业石制品分类综述

石制品是旧石器时代考古的主要研究对象,其分类是旧石器生产技术和文化研究的基础与前提,然而,中国旧石器时代考古有关石制品分类目前尚无一致标准,这对开展旧石器时代考古学术研究的国际交流产生了负面影响。鉴于似奥杜威(Oldowan-like)或模式I工业在我国古人类石器工业面貌占有非常特殊的地位,因此,本文对以非洲为代表的奥杜威(Oldowan)工业(模式I)石器技术研究中有关石制品的分类体系进行整合和梳理,同时借鉴Mary Leakey、Glynn Isaac和Nicholas Toth等为代表的不同分类系统,并对中国境内有关石制品分类的现状进行讨论。     

Biological control of arthropod pests using banker plant systems: Past progress and future directions

The goal of banker plant systems is to sustain a reproducing population of natural enemies within a crop that will provide long-term pest suppression. The most common banker plant system consists of cereal plants infested with Rhopalosiphum padi L. as a host for the parasitoid Aphidius colemani L. Aphidius colemani continually reproduce and emerge from the banker plants to suppress aphid pests such as Aphis gossypii Glover and Myzus persicae Sulzer. Banker plant systems have been investigated to support 19 natural enemy species targeting 11 pest species. Research has been conducted in the greenhouse and field on ornamental and food crops. Despite this there is little consensus of an optimal banker plant system for even the most frequently targeted pests. Optimizing banker plant systems requires future research on how banker plants, crop species, and alternative hosts interact to affect natural enemy preference, dispersal, and abundance. In addition, research on the logistics of creating, maintaining, and implementing banker plant systems is essential. An advantage of banker plant systems over augmentative biological control is preventative control without repeated, expensive releases of natural enemies. Further, banker plants conserve a particular natural enemy or potentially the ‘right diversity’ of natural enemies with specific alternative resources. This may be an advantage compared to conserving natural enemy diversity per se with other conservation biological control tactics. Demonstrated grower interest in banker plant systems provides an opportunity for researchers to improve biological control efficacy, economics, and implementation to reduce pesticide use and its associated risks.