The essence of student visual-spatial literacy and higher order thinking skills in undergraduate biology

Science, engineering and mathematics-related disciplines have relied heavily on a researcher's ability to visualize phenomena under study and being able to link and superimpose various abstract and concrete representations including visual, spatial, and temporal. The spatial representations are especially important in all branches of biology (in developmental biology time becomes an important dimension), where 3D and often 4D representations are crucial for understanding the phenomena. By the time biology students get to undergraduate education, they are supposed to have acquired visual-spatial thinking skills, yet it has been documented that very few undergraduates and a small percentage of graduate students have had a chance to develop these skills to a sufficient degree. The current paper discusses the literature that highlights the essence of visual-spatial thinking and the development of visual-spatial literacy, considers the application of the visual-spatial thinking to biology education, and proposes how modern technology can help to promote visual-spatial literacy and higher order thinking among undergraduate students of biology.     

Four decades of teaching developmental biology in Germany

I have taught developmental biology in Essen for 30 years. Since my department is named Zoophysiologie (Zoophysiology), besides Developmental Biology, I also have to teach General Animal Physiology. This explains why the time for teaching developmental biology is restricted to a lecture course, a laboratory course and several seminar courses. However, I also try to demonstrate in the lecture courses on General Physiology the close relationship between developmental biology, physiology, morphology, anatomy, teratology, carcinogenesis, evolution and ecology (importance of environmental factors on embryogenesis). Students are informed that developmental biology is a core discipline of biology. In the last decade, knowledge about molecular mechanisms in different organisms has exponentially increased. The students are trained to understand the close relationship between conserved gene structure, gene function and signaling pathways, in addition to or as an extension of, classical concepts. Public reports about the human genome project and stem cell research (especially therapeutic and reproductive cloning) have shown that developmental biology, both in traditional view and at the molecular level, is essential for the understanding of these complex topics and for serious and non-emotional debate.     

The essence of student visual–spatial literacy and higher order thinking skills in undergraduate biology

Science, engineering and mathematics-related disciplines have relied heavily on a researcher’s ability to visualize phenomena under study and being able to link and superimpose various abstract and concrete representations including visual, spatial, and temporal. The spatial representations are especially important in all branches of biology (in developmental biology time becomes an important dimension), where 3D and often 4D representations are crucial for understanding the phenomena. By the time biology students get to undergraduate education, they are supposed to have acquired visual–spatial thinking skills, yet it has been documented that very few undergraduates and a small percentage of graduate students have had a chance to develop these skills to a sufficient degree. The current paper discusses the literature that highlights the essence of visual–spatial thinking and the development of visual–spatial literacy, considers the application of the visual–spatial thinking to biology education, and proposes how modern technology can help to promote visual–spatial literacy and higher order thinking among undergraduate students of biology.     

Modularity: a new perspective in biology

Several decades of research in biochemistry and molecular biology have been devoted for studies on isolated enzymes and proteins. Recent high throughput technologies in genomics and proteomics have resulted in avalanche of information about several genes, proteins and enzymes in variety of living systems. Though these efforts have greatly contributed to the detailed understanding of a large number of individual genes and proteins, this explosion of information has simultaneously brought out the limitations of reductionism in understanding complex biological processes. The genes or gene products do not function in isolation in vivo. A delicate and dynamic molecular architecture is required for precision of the chemical reactions associated with "life". In future, a paradigm shift is, therefore, envisaged, in biology leading to exploration of molecular organizations in physical and genomic context, a subtle transition from conventional molecular biology to modular biology. A module can be defined as an organization of macromolecules performing a synchronous function in a given metabolic pathway. In modular biology, the biological processes of interest are explored as complex systems of functionally interacting macromolecules. The present article describes the perceptions of the concept of modularity, in terms of associations among genes and proteins, presenting a link between reductionist approach and system biology.     

The phylogeography debate and the epistemology of model-based evolutionary biology

Phylogeography, a relatively new subdicipline of evolutionary biology that attempts to unify the fields of phylogenetics and population biology in an explicit geographical context, has hosted in recent years a highly polarized debate related to the purported benefits and limitations that qualitative versus quantitative methods might contribute or impose on inferential processes in evolutionary biology. Here we present a friendly, non-technical introduction to the conflicting methods underlying the controversy, and exemplify it with a balanced selection of quotes from the primary biological literature, to invite the philosophy of biology community to pay attention to the elements that have played a primary role in its presumed resolution. We also present the basic features of our own metascientific take on the debate, and point out—as a preliminary step in preparation for upcoming, more detailed treatments—the importance that appeals to authority in fields external to phylogeography per se have played in the current status of this highly visible evolutionary biology dispute.     

Biology of primate relaxin: A paracrine signal in early pregnancy?

Relaxin is a peptide hormone that exerts numerous effects in a variety of tissues across a broad range of species. Although first identified more than 75 years ago interest in relaxin biology has waxed and waned over the years consistent with peaks and troughs of new experimental data on its wide-ranging biological effects and advances in relaxin enabling technologies. Recent insights into species-dependent differences in relaxin biology during pregnancy have once again stimulated a relative surge of interest in the study of relaxin's reproductive biology. Identification and pharmacological characterization of orphaned relaxin receptors and exploration of its paracrine effects on pregnancy using genomic and proteomic technologies have succeeded in fueling current interest in relaxin research. Primates and non-primate vertebrates exhibit very disparate profiles of relaxin genomics, proteomics and functional biology. Non-human primates appear to exhibit a very close similarity to humans with respect to relaxin reproductive biology but the similarities and subtle differences are only just beginning to be understood. We, and others, have shown that relaxin produces significant changes to the non-human primate endometrium during the peri-implantation period that are consistent with relaxin's long perceived role as a paracrine modulator of pregnancy. The purpose of this review is to summarize the reproductive biology of relaxin in non-human primates with a specific emphasis on the paracrine role of ovarian and endometrial relaxin during embryo implantation and early pregnancy.     

蛋白质：生物界中又一类信息的储存者和传递者 ——对 prion 生物学相关知识的重新解读

蛋白质在相当一段时间内一直被认为只是 DNA 或 RNA 等遗传物质的表达形式,其单独不具有储存和传递生物信息的功能,而储存和传递生物信息却是遗传物质的两个基本属性 . 随着近年来 prion 生物学的出现和研究的逐步深入,人们已经认识到蛋白质单独就具有储存和传递生物信息的功能,从这个意义上讲,蛋白质也是一类遗传物质 . 所以很有必要站在这个角度对 prion 生物学的相关知识进行重新的梳理和再认识,通过对哺乳动物 prion 生物学和真菌 prion 生物学各自发展历程的简要回顾和最新研究成果的介绍,以及它们之间相同点和不同点的比较,总结出蛋白质储存和传递生物信息的一般规律并指出其表现形式的多样性 .     

Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine

The emergence of systems biology is bringing forth a new set of challenges for advancing science and technology. Defining ways of studying biological systems on a global level, integrating large and disparate data types, and dealing with the infrastructural changes necessary to carry out systems biology, are just a few of the extraordinary tasks of this growing discipline. Despite these challenges, the impact of systems biology will be far-reaching, and significant progress has already been made. Moving forward, the issue of how to use systems biology to improve the health of individuals must be a priority. It is becoming increasingly apparent that the field of systems biology and one of its important disciplines, proteomics, will have a major role in creating a predictive, preventative, and personalized approach to medicine. In this review, we define systems biology, discuss the current capabilities of proteomics and highlight some of the necessary milestones for moving systems biology and proteomics into mainstream health care.     

The evolution of molecular biology into systems biology

Systems analysis has historically been performed in many areas of biology, including ecology, developmental biology and immunology. More recently, the genomics revolution has catapulted molecular biology into the realm of systems biology. In unicellular organisms and well-defined cell lines of higher organisms, systems approaches are making definitive strides toward scientific understanding and biotechnological applications. We argue here that two distinct lines of inquiry in molecular biology have converged to form contemporary systems biology.     

Ontologies for data and knowledge sharing in biology: plant ROS signaling as a case study

Modern technologies have rapidly transformed biology into a data-intensive discipline. In addition to the enormous amounts of existing experimental data in the literature, every new study can produce a large amount of new data, resulting in novel ideas and more publications. In order to understand a biological process as completely as possible, scientists should be able to combine and analyze all such information. Not only molecular biology and bioinformatics, but all the other domains of biology including plant biology, require tools and technologies that enable experts to capture knowledge within distributed and heterogeneous sources of information. Ontologies have proven to be one of the most-useful means of constructing and formalizing expert knowledge. The key feature of an ontology is that it represents a computer-interpretable model of a particular subject area. This article outlines the importance of ontologies for systems biology, data integration and information analyses, as illustrated through the example of reactive oxygen species (ROS) signaling networks in plants.     

Are we doomed to repeat history? A model of the past using tiger beetles (Coleoptera: Cicindelidae) and conservation biology to anticipate the future

Studies of conservation biology involving tiger beetles have become increasingly common in the last 15 years. Governments and NGOs in several countries have considered tiger beetles in making policy decisions of national conservation efforts and have found tiger beetles useful organisms for arguing broad conservation issues. We trace the evolution of the relationship between tiger beetle studies and conservation biology and propose that this history may in itself provide a model for anticipating developments and improvements in the ability of conservation biology to find effective goals, gather appropriate data, and better communicate generalizations to non-scientific decision makers, the public, and other scientists. According to the General Continuum of Scientific Perspectives on Nature model, earliest biological studies begin with natural history and concentrate on observations in the field and specimen collecting, followed by observing and measuring in the field, manipulations in the field, observations and manipulations in the laboratory, and finally enter theoretical science including systems analysis and mathematical models. Using a balance of historical and analytical approaches, we tested the model using scientific studies of tiger beetles (Coleoptera: Cicindelidae) and the field of conservation biology. Conservation biology and tiger beetle studies follow the historical model, but the results for conservation biology also suggest a more complex model of simultaneous parallel developments. We use these results to anticipate ways to better meet goals in conservation biology, such as actively involving amateurs, avoiding exclusion of the public, and improving language and style in scientific communication. CXLV, Studies of Tiger Beetles     

Proteasome modulators: essential chemical genetic tools for understanding human diseases

Primarily used for medicinal purposes in the past, biologically active small molecules have been increasingly employed to explore complex biological processes in the era of "chemical genetics". Since the contributions of this small molecule approach to biology have been extensive, we limit the focus of our review to the use of small-molecule modulators in the exciting field of proteasomal biology, one that has benefited significantly from a chemical genetics approach. Specifically, as the contributions of general inhibitors of proteasomal activity to the fields of cell biology and clinical oncology have been extensively discussed in several excellent reviews, we instead outline recent progress towards the development of novel, specific classes of proteasome modulators for studies of proteasomal biology and the types of proteasome inhibitors emerging as important new treatment options for cancer therapeutics.     

Diffusion of synthetic biology: a challenge to biosafety

One of the main aims of synthetic biology is to make biology easier to engineer. Major efforts in synthetic biology are made to develop a toolbox to design biological systems without having to go through a massive research and technology process. With this “de-skilling” agenda, synthetic biology might finally unleash the full potential of biotechnology and spark a wave of innovation, as more and more people have the necessary skills to engineer biology. But this ultimate domestication of biology could easily lead to unprecedented safety challenges that need to be addressed: more and more people outside the traditional biotechnology community will create self-replicating machines (life) for civil and defence applications, “biohackers” will engineer new life forms at their kitchen table; and illicit substances will be produced synthetically and much cheaper. Such a scenario is a messy and dangerous one, and we need to think about appropriate safety standards now.     

组学技术在核盘菌研究中的应用

核盘菌Sclerotinia sclerotiorum是一种典型的死体营养型植物病原真菌,全球分布且寄主范围广泛,严重危害多种植物,对农业生产造成严重损失。核盘菌研究主要集中在真菌生物学及病理学等方面。近年来,随着高通量分析技术的不断改进,多种组学技术为系统生物学研究提供了平台。文中主要综述利用多种组学研究方法在植物病原真菌核盘菌研究中的应用及研究进展,探讨开展植物病原物及病害发展的系统性研究思路,以期为核盘菌的分子生物学及致病机理等研究提供参考,同时也为其他植物病原物及病害系统研究提供理论依据。     

Interview with Sydney Brenner. The world of genome projects

Dr Sydney Brenner has played a major, and unique, role in biology during the past 40 years. His contributions have ranged from key work on the structure of the genetic code and the existence of mRNA through the development of Caenorhabditis elegans as a key model system in developmental biology to genomic analysis and function in vertebrates. BioEssays went to interview Dr Brenner at his home in the cathedral city of Ely, England, on the significance of the genome projects for human biology, in particular, and for biology, in general.     

合成生物学应用产品开发现状与趋势

目的：从产品开发角度分析全球合成生物学发展现状和趋势。方法：在伍德罗·威尔逊国际学者中心的合成生物学产品和应用清单（synthetic biology products and applications inventory）的数据基础上,对全球合成生物学产品的开发状态、市场应用和发展前景等进行补充检索和分析。结果：至2015年,全球至少已有81家企业（或研究机构）的116种合成生物学产品得到了市场应用开发,主要开发者为美国企业（或研究机构）,产品主要集中于化学和医药领域。结论：合成生物学实现了从生物学分析向生物学合成的范式转移,其产品开发将给一系列的行业带来深刻的变革。     

保护生物学概要

保护生物学的形成是对生物危机的反应和生物科学迅速发展的结果。它是应用科学解决由于人类活动干扰或其它因素引起的物种、群落和生态系统出现的问题的新学科。其”目的是提供保护生物多样性的原理和工具“,其基础科学和应用科学的综合性交叉学科。系统学、生态学、生物地理学和种群生态学的原理和方法是保护生物学重要的理论和实践基础。     

Using evolutionary genomics,transcriptomics, and systems biology to reveal gene networks underlying fungal development

Fungal model species have contributed to many aspects of modern biology, from biochemistry and cell biology to molecular genetics. Nevertheless, only a few genes associated with morphological development in fungi have been functionally characterized in terms of their genetic or molecular interactions. Evolutionary developmental biology in fungi faces challenges from a lack of fossil records and unresolved species phylogeny, to homoplasy associated with simple morphology. Traditionally, reductive approaches use genetic screens to reveal phenotypes from a large number of mutants; the efficiency of these approaches relies on profound prior knowledge of the genetics and biology of the designated development trait—knowledge which is often not available for even well-studied fungal model species. Reductive approaches become less efficient for the study of developmental traits that are regulated quantitatively by more than one gene via networks. Recent advances in genome-wide analysis performed in representative multicellular fungal models and non-models have greatly improved upon the traditional reductive approaches in fungal evo-devo research by providing clues for focused knockout strategies. In particular, genome-wide gene expression data across developmental processes of interest in multiple species can expedite the advancement of integrative synthetic and systems biology strategies to reveal regulatory networks underlying fungal development.     

Phytophthora infestans: the plant (and R gene) destroyer

Phytophthora infestans remains a problem to production agriculture. Historically there have been many controversies concerning its biology and pathogenicity, some of which remain today. Advances in molecular biology and genomics promise to reveal fascinating insight into its pathogenicity and biology. However, the plasticity of its genome as revealed in population diversity and in the abundance of putative effectors means that this oomycete remains a formidable foe.     

Translational synthetic biology

Synthetic biology is a recent scientific approach towards engineering biological systems from both pre-existing and novel parts. The aim is to introduce computational aided design approach in biology leading to rapid delivery of useful applications. Though the term reprogramming has been frequently used in the synthetic biology community, currently the technological sophistication only allows for a probabilistic approach instead of a precise engineering approach. Recently, several human health applications have emerged that suggest increased usage of synthetic biology approach in developing novel drugs. This mini review discusses recent translational developments in the field and tries to identify some of the upcoming future developments.