Cell biology, chemogenomics and chemoproteomics

The scientific techniques used in molecular biological research and drug discovery have changed dramatically over the past 10 years due to the influence of genomics, proteomics and bioinformatics. Furthermore, genomics and functional genomics are now merging into a new scientific approach called chemogenomics. Advancements in the study of molecular cell biology are dependent upon "omics" researchers realizing the importance of and using the experimental tools currently available to cell biologists. For example, novel microscopic techniques utilizing advanced computer imaging allow for the examination of live specimens in a fourth dimension, viz., time. Yet, molecular biologists have not taken full advantage of these and other traditional and novel cell biology techniques for the further advancement of genomic and proteomic-oriented research. The application of traditional and novel cellular biological techniques will enhance the science of genomics. The authors hypothesize that a stronger interdisciplinary approach must be taken between cell biology (and its closely related fields) and genomics, proteomics and bio-chemoinformatics. Since there is a lot of confusion regarding many of the "omics" definitions, this article also clarifies some of the basic terminology used in genomics, and related fields. It also reviews the current status and future potential of chemogenomics and its relationship to cell biology. The authors also discuss and expand upon the differences between chemogenomics and the relatively new term--chemoproteomics. We conclude that the advances in cell biology methods and approaches and their adoption by "omics" researchers will allow scientists to maximize our knowledge about life.     

MACBenAbim: A Multi-platform Mobile Application for searching keyterms in Computational Biology and Bioinformatics

Computational biology and bioinformatics are gradually gaining grounds in Africa and other developing nations of the world. However, in these countries, some of the challenges of computational biology and bioinformatics education are inadequate infrastructures, and lack of readily-available complementary and motivational tools to support learning as well as research. This has lowered the morale of many promising undergraduates, postgraduates and researchers from aspiring to undertake future study in these fields. In this paper, we developed and described MACBenAbim (Multi-platform Mobile Application for Computational Biology and Bioinformatics), a flexible user-friendly tool to search for, define and describe the meanings of keyterms in computational biology and bioinformatics, thus expanding the frontiers of knowledge of the users. This tool also has the capability of achieving visualization of results on a mobile multi-platform context.

Availability

MACBenAbim is available from the authors for non-commercial purposes.     

复杂疾病靶基因识别与网络重建的计算系统生物研究

复杂疾病相关靶基因的识别、构建疾病驱使相关基因网络及进行疾病机制研究,是功能基因组学研究中非常重要的科学问题。文章以计算系统生物学的观点和三维的角度,综述了基于生物谱（SNP遗传谱、芯片表达谱和2D-PAGE蛋白质谱等）的复杂疾病靶基因识别、多水平（SNPs虚拟网络、基因调控网络、蛋白质互作网络等）遗传网络逆向重构方法,及不同水平的网络之间在生物学和拓扑学上的纵向映射关系,并给出复杂疾病靶基因识别与网络关系的计算系统生物方法研究的未来展望。     

How Are Academic Age,Productivity and Collaboration Related to Citing Behavior of Researchers?

References are an essential component of research articles and therefore of scientific communication. In this study we investigate referencing (citing) behavior in five diverse fields (astronomy, mathematics, robotics, ecology and economics) based on 213,756 core journal articles. At the macro level we find: (a) a steady increase in the number of references per article over the period studied (50 years), which in some fields is due to a higher rate of usage, while in others reflects longer articles and (b) an increase in all fields in the fraction of older, foundational references since the 1980s, with no obvious change in citing patterns associated with the introduction of the Internet. At the meso level we explore current (2006–2010) referencing behavior of different categories of authors (21,562 total) within each field, based on their academic age, productivity and collaborative practices. Contrary to some previous findings and expectations we find that senior researchers use references at the same rate as their junior colleagues, with similar rates of re-citation (use of same references in multiple papers). High Modified Price Index (MPI, which measures the speed of the research front more accurately than the traditional Price Index) of senior authors indicates that their research has the similar cutting-edge aspect as that of their younger colleagues. In all fields both the productive researchers and especially those who collaborate more use a significantly lower fraction of foundational references and have much higher MPI and lower re-citation rates, i.e., they are the ones pushing the research front regardless of researcher age. This paper introduces improved bibliometric methods to measure the speed of the research front, disambiguate lead authors in co-authored papers and decouple measures of productivity and collaboration.     

Data Sharing in Medical Research: An Empirical Investigation

Background:
Scientific research entails systematic investigation. Publishing the findings of research in peer reviewed journals implies a high level of confidence by the authors in the veracity of their interpretation. Therefore it stands to reason that researchers should be prepared to share their raw data with other researchers, so that others may enjoy the same level of confidence in the findings.
Method:
In a prospective study, 29 corresponding authors of original research articles in a medical journal (the British Medical Journal ) were contacted to ascertain their preparedness to share the data from their research. The email contact was in one of two forms, a general request and a specific request. The type of request a researcher received was randomly allocated.
Findings:
Researchers receiving specific requests for data were less likely, and slower, to respond than researchers receiving general requests. Only one researcher released data. Most researchers were reluctant to release their data. Some required further information, clarification, or authorship.
Interpretation:
The general reluctance of researchers to consider requests for their data is of concern. It raises questions about the level of confidence that should be placed on their interpretations of the data. It also highlights an unfortunate situation where researchers are more concerned with losing an advantage than advancing science.     

Commentaries on field‐laboratory collaborations in primatology: Introduction to a special section of the American Journal of Primatology

Finding better approaches to bridge field and laboratory primate research was identified as an important goal in a recent (2017) member survey of the American Society of Primatologists. Collaborative field‐captive research was identified by >60% of respondents as somewhat or very underrepresented in the Society. In this introductory essay for a special section of American Journal of Primatology, I review commonalities and differences in the papers that were requested from field‐captive primate collaborative teams. Each team approached important primate biology or welfare problems from different perspectives. The five commentaries in this section addressed how the collaborations began, scientific benefits that accrued, and insights or challenges that researchers faced in the collaboration. Despite the fact that the specific fields of inquiry were different (conservation genetics, chimpanzee captive welfare, environmental physiology, feeding biology, and reproductive physiology), the commentaries converged on the concept that an intentional, interdisciplinary approach, that included field observations and experiments informed by laboratory expertise, were essential to achieving innovative results.     

Construction,visualization, and analysis of biological network models in Dynetica

Mathematical modeling has become an increasingly important aspect of biological research. Computer simulations help to improve our understanding of complex systems by testing the validity of proposed mechanisms and generating experimentally testable hypotheses. However, significant overhead is generated by the creation, debugging, and perturbation of these computational models and their parameters, especially for researchers who are unfamiliar with programming or numerical methods. Dynetica 2.0 is a user-friendly dynamic network simulator designed to expedite this process. Models are created and visualized in an easy-to-use graphical interface, which displays all of the species and reactions involved in a graph layout. System inputs and outputs, indicators, and intermediate expressions may be incorporated into the model via the versatile “expression variable” entity. Models can also be modular, allowing for the quick construction of complex systems from simpler components. Dynetica 2.0 supports a number of deterministic and stochastic algorithms for performing time-course simulations. Additionally, Dynetica 2.0 provides built-in tools for performing sensitivity or dose response analysis for a number of different metrics. Its parameter searching tools can optimize specific objectives of the time course or dose response of the system. Systems can be translated from Dynetica 2.0 into MATLAB code or the Systems Biology Markup Language (SBML) format for further analysis or publication. Finally, since it is written in Java, Dynetica 2.0 is platform independent, allowing for easy sharing and collaboration between researchers.     

Organic fluorescent compounds based on phenanthroimidazole: A review of highlight studies

Organic compounds containing phenanthroimidazole, and its optical, thermal, chemical, and high fluorescence, have drawn the interest of numerous researchers. Phenanthroimidazole derivatives are appealing for various applications due to these characteristics. This research provides a summary of the general information contained in studies on the synthesis, characterization, photophysical characteristics, and possible applications of phenanthroimidazole derivative compounds. The focus of this study revolves around the topic of utilization in technological fields such as sensors, solar cells, optical brighteners, and organic light-emitting diodes, and covers significant studies on mentioned topics. We anticipate that this study will provide an outline for researchers aiming to further examine fluorescent organic compounds for technological innovations. Furthermore, we anticipate that this research will be crucial in developing long-term high-organic compounds for optoelectronic devices.     

黏菌学的发展

黏菌是一类在陆地生态系统中广泛分布的真核生物,在其生活史的不同阶段,既有体现原生动物运动性的营养体,也具有高度特异化的繁殖体,其形态结构与生理特征,兼具了“菌物”与“动物”的特性,独特的进化地位以及与环境、人类健康的密切关系,使得以黏菌为模式生物的研究在生物学、遗传学、生理学、生态学、信息科学等学科均具有广泛的科学意义和重要的应用价值。自17世纪以来,黏菌研究者们从早期的经典分类学,逐步拓展到从生物学各分支学科领域系统全面地认识黏菌类群。在近几十年中,黏菌研究在系统学、生物学、生态学等方向取得了长足的进步。本文扼要介绍了黏菌学在各领域内的代表性研究进展和前沿性科学问题,同时对相关领域未来的发展进行了展望。     

From low to high gear: there has been a paradigm shift in our understanding of evolution

Experimental studies of evolution performed in nature and the associated demonstration of rapid evolution, observable on a time scale of months to years, were an acclaimed novelty in the 1980–1990s. Contemporary evolution is now considered ordinary and is an integrated feature of many areas of research. This shift from extraordinary to ordinary reflects a change in the perception of evolution. It was formerly thought of as a historical process, perceived through the footprints left in the fossil record or living organisms. It is now seen as a contemporary process that acts in real time. Here we review how this shift occurred and its consequences for fields as diverse as wildlife management, conservation biology, and ecosystems ecology. Incorporating contemporary evolution in these fields has caused old questions to be recast, changed the answers, caused new and previously inconceivable questions to be addressed, and inspired the development of new subdisciplines. We argue further that the potential of contemporary evolution has yet to be fulfilled. Incorporating evolutionary dynamics in any research program can provide a better assessment of how and why organisms and communities came to be as they are than is attainable without an explicit treatment of these dynamics.     

植病生防菌盾壳霉的分子生物学研究进展

盾壳霉是一种重要的核盘菌寄生茵.近年来,该菌在分子水平的研究取得了一定的进展.本文概述了盾壳霉在产孢调控、与核盘菌互作、遗传转化以及动态检测和遗传多样性等方面的研究现状,并对研究中存在的问题进行了讨论.希望在此基础上能够促进该茵分子生物学研究的不断深入,更好地开发利用该菌的基因资源.     

钙在有花植物受精过程中的作用

钙作为第二信使在植物信号转导中的作用一直是植物生理学、细胞生物学和发育生物学研究的热点。近年已有不少综述和专著从不同角度对此作了详细评论［1～5］。虽然这些文章中只有部分内容涉及本文的主题———钙在植物受精中的作用,但是它们所论述的关于钙信使系统在植物...     

Eye development at the Houston "Fly Meeting"

The 47th Annual Drosophila Research Conference or "Fly Meeting" took place at Houston, Texas, USA from March 29th- April 2nd, 2006, under the aegis of the Genetics Society of America. The Fly Meeting provides an excellent opportunity for fly researchers to present their work and to get a snapshot of recent developments and upcoming trends in their research field. The fruit fly, Drosophila melanogaster is a very versatile model to study growth, patterning, neural development, evolution, systemetics and various other facets of biomedical science. The topics presented in the meeting covered a very broad spectrum of fly research. In this commentary, I have focused mainly on the presentations related to two fields: 1) research in various fields that use the Drosophila eye as a model system, and 2) the community resources available to all fly researchers.     

The Role of Calcium in the Fertilization Process in Flowering Plants

The fertilization process in flowering plants in a broad sense includes a progamic phase preceding the phase of double fertilization. To our present knowledge, calcium as a second messenger in the signal transduction plays important roles in all the links of this process. The present review attempts to highlight the recent advances in this research field, including: calcium in relation to in vitro pollen tube growth (distribution of calcium in pollen tube tip; regulation of pollen tube growth by calcium; calcium oscillation in pollen tube); distribution of calcium in pistil and its relation to in vivo pollen tube growth (calcium in relation to pollen-pistil recognition; pollen tube growth in pistil; pollen tube entry into embryo sac and the discharge and transportation of sperms); and calcium in relation to sperm-egg fusion and egg cell activation. In conclusion the author summarizes into several main view points, and gives recommendation for further researches on this topic.     

Two sides of the same coin? The (techno)epistemic cultures of systems and synthetic biology

Systems and synthetic biology both emerged around the turn of this century as labels for new research approaches. Although their disciplinary status as well as their relation to each other is rarely discussed in depth, now and again the idea is invoked that both approaches represent ‘two sides of the same coin’. The following paper focuses on this general notion and compares it with empirical findings concerning the epistemic cultures prevalent in the two contexts. Drawing on interviews with researchers from both fields, on participatory observation in conferences and courses and on documentary analysis, this paper delineates differences and similarities, incompatibilities and blurred boundaries. By reconstructing systems and synthetic biology’s epistemic cultures, this paper argues that they represent two ‘communities of vision’, encompassing heterogeneous practices. Understanding the relation of the respective visions of understanding nature and engineering life is seen as indispensible for the characterisation of (techno)science in more general terms. Depending on the conceptualisation of understanding and construction (or: science and engineering), related practices such as in silico modelling for enhancing understanding or enabling engineering can either be seen as incommensurable or ‘two sides of one coin’.     

Left Atrial Size and Function in a Canine Model of Chronic Atrial Fibrillation and Heart Failure

Background

Our aim was to assess how atrial fibrillation (AF) induction, chronicity, and RR interval irregularity affect left atrial (LA) function and size in the setting of underlying heart failure (HF), and to determine whether AF effects can be mitigated by vagal nerve stimulation (VNS).

Methods

HF was induced by 4-weeks of rapid ventricular pacing in 24 dogs. Subsequently, AF was induced and maintained by atrial pacing at 600 bpm. Dogs were randomized into control (n = 9) and VNS (n = 15) groups. In the VNS group, atrioventricular node fat pad stimulation (310 μs, 20 Hz, 3–7 mA) was delivered continuously for 6 months. LA volume and LA strain data were calculated from bi-weekly echocardiograms.

Results

RR intervals decreased with HF in both groups (p = 0.001), and decreased further during AF in control group (p = 0.014), with a non-significant increase in the VNS group during AF. LA size increased with HF (p<0.0001), with no additional increase during AF. LA strain decreased with HF (p = 0.025) and further decreased after induction of AF (p = 0.0001). LA strain decreased less (p = 0.001) in the VNS than in the control group. Beat-by-beat analysis showed a curvilinear increase of LA strain with longer preceding RR interval, (r = 0.45, p <0.0001) with LA strain 1.1% higher (p = 0.02) in the VNS-treated animals, independent of preceding RR interval duration. The curvilinear relationship between ratio of preceding and pre-preceding RR intervals, and subsequent LA strain was weaker, (r = 0.28, p = 0.001). However, VNS-treated animals again had higher LA strain (by 2.2%, p = 0.002) independently of the ratio of preceding and pre-preceding RR intervals.

Conclusions

In the underlying presence of pacing-induced HF, AF decreased LA strain, with little impact on LA size. LA strain depends on the preceding RR interval duration.     

Survey of Argentine Health Researchers on the Use of Evidence in Policymaking

Objective

In this study, Argentine health researchers were surveyed regarding their perceptions of facilitators and barriers to evidence-based policymaking in Argentina, as well as their publication activities, and research environment satisfaction.

Methods

A self-administered online survey was sent to health researchers in Argentina. The survey questions were based on a preceding qualitative study of Argentine health researchers, as well as the scientific literature.

Results

Of the 647 researchers that were reached, 226 accessed the survey, for a response rate of 34.9%. Over 80% of researchers surveyed had never been involved in or contributed to decision-making, while over 90% of researchers indicated they would like to be involved in the decision-making process. Decision-maker self-interest was perceived to be the driving factor in the development of health and healthcare policies. Research conducted by a research leader was seen to be the most influential factor in influencing health policy, followed by policy relevance of the research. With respect to their occupational environment, researchers rated highest and most favourably the opportunities available to present, discuss and publish research results and their ability to further their education and training. Argentine researchers surveyed demonstrated a strong interest and willingness to contribute their work and expertise to inform Argentine health policy development.

Conclusion

Despite Argentina’s long scientific tradition, there are relatively few institutionalized linkages between health research results and health policymaking. Based on the results of this study, the disconnect between political decision-making and the health research system, coupled with fewer opportunities for formalized or informal researcher/decision-maker interaction, contribute to the challenges in evidence informing health policymaking in Argentina. Improving personal contact and the building of relationships between researchers and policymakers in Argentina will require taking into account researcher perceptions of policymakers, as highlighted in this study.     

基于古菌酪氨酰tRNA合成酶非天然氨基酸插入的研究进展

构筑蛋白质的编码信息存在于高度保守的密码子表中,而生物体仅利用20种天然氨基酸,就能排列组合出不同的蛋白质来行使多种生物学功能。通过合成生物学的飞速发展,使得在蛋白质合成中可控地引入非天然氨基酸成为可能。这极大地拓展了蛋白质的结构和功能,并为生物学工具的开发和生物生理过程的研究提供了便利。具有活性基团的非天然氨基酸可以广泛地应用于蛋白质结构研究、蛋白质功能调控以及新型生物材料构建和医药研发等诸多领域。基因密码子拓展技术利用正交翻译系统,通过重新分配密码子改造中心法则,可以在蛋白质的指定位点引入非天然氨基酸。系统地介绍了目前提升密码子拓展技术插入非天然氨基酸效率的方法,包括tRNA以及氨酰tRNA合成酶的各种突变方法和翻译辅助因子的改造。汇总了利用古细菌酪氨酰tRNA合成酶插入的非天然氨基酸和突变位点并总结了密码子拓展技术在生物医药领域的前沿进展。最后讨论了该项技术目前所面临的挑战,如可利用的密码子数量不多、正交翻译系统的种类有限和非天然氨基酸多插效率低下。希望能够帮助研究者建立适合的非天然氨基酸插入方法并推动密码子拓展技术进一步发展。     

How cells process information: quantification of spatiotemporal signaling dynamics

Arguably, one of the foremost distinctions between life and non-living matter is the ability to sense environmental changes and respond appropriately—an ability that is invested in every living cell. Within a single cell, this function is largely carried out by networks of signaling molecules. However, the details of how signaling networks help cells make complicated decisions are still not clear. For instance, how do cells read graded, analog stress signals but convert them into digital live-or-die responses? The answer to such questions may originate from the fact that signaling molecules are not static but dynamic entities, changing in numbers and activity over time and space. In the past two decades, researchers have been able to experimentally monitor signaling dynamics and use mathematical techniques to quantify and abstract general principles of how cells process information. In this review, the authors first introduce and discuss various experimental and computational methodologies that have been used to study signaling dynamics. The authors then discuss the different types of temporal dynamics such as oscillations and bistability that can be exhibited by signaling systems and highlight studies that have investigated such dynamics in physiological settings. Finally, the authors illustrate the role of spatial compartmentalization in regulating cellular responses with examples of second-messenger signaling in cardiac myocytes.     

Laser Capture Microdissection in the Tissue Biorepository

An important need of many cancer research projects is the availability of high-quality, appropriately selected tissue. Tissue biorepositories are organized to collect, process, store, and distribute samples of tumor and normal tissue for further use in fundamental and translational cancer research. This, in turn, provides investigators with an invaluable resource of appropriately examined and characterized tissue specimens and linked patient information. Human tissues, in particular, tumor tissues, are complex structures composed of heterogeneous mixtures of morphologically and functionally distinct cell types. It is essential to analyze specific cell types to identify and define accurately the biologically important processes in pathologic lesions. Laser capture microdissection (LCM) is state-of-the-art technology that provides the scientific community with a rapid and reliable method to isolate a homogeneous population of cells from heterogeneous tissue specimens, thus providing investigators with the ability to analyze DNA, RNA, and protein accurately from pure populations of cells. This is particularly well-suited for tumor cell isolation, which can be captured from complex tissue samples. The combination of LCM and a tissue biorepository offers a comprehensive means by which researchers can use valuable human biospecimens and cutting-edge technology to facilitate basic, translational, and clinical research. This review provides an overview of LCM technology with an emphasis on the applications of LCM in the setting of a tissue biorepository, based on the author''s extensive experience in LCM procedures acquired at Fox Chase Cancer Center and Hollings Cancer Center.