Contribution to the Themed Section: Scaling from individual plankton to marine ecosystems HORIZONS Small bugs with a big impact: linking plankton ecology with ecosystem processes

As an introduction to the following Themed Section on the significance of planktonic organisms to the functioning of marine ecosystems and global biogeochemical cycles we discuss the ramifications size imparts on the biology of plankton. We provide examples of how the characteristics of these microscopic organisms shape plankton population dynamics, distributions, and ecosystem functions. Key features of the marine environment place constraints on the ecology and evolution of plankton. Understanding these constraints is critical in developing a mechanistic understanding and predictive capacity of how planktonic ecosystems function, render their capacities in terms of biogeochemical cycling and trophic transfer, and how planktonic communities might respond to changing climate conditions

Current knowledge and recent advances in understanding metabolism of the model cyanobacterium Synechocystis sp. PCC 6803

Cyanobacteria are key organisms in the global ecosystem, useful models for studying metabolic and physiological processes conserved in photosynthetic organisms, and potential renewable platforms for production of chemicals. Characterising cyanobacterial metabolism and physiology is key to understanding their role in the environment and unlocking their potential for biotechnology applications. Many aspects of cyanobacterial biology differ from heterotrophic bacteria. For example, most cyanobacteria incorporate a series of internal thylakoid membranes where both oxygenic photosynthesis and respiration occur, while CO2 fixation takes place in specialised compartments termed carboxysomes. In this review, we provide a comprehensive summary of our knowledge on cyanobacterial physiology and the pathways in Synechocystis sp. PCC 6803 (Synechocystis) involved in biosynthesis of sugar-based metabolites, amino acids, nucleotides, lipids, cofactors, vitamins, isoprenoids, pigments and cell wall components, in addition to the proteins involved in metabolite transport. While some pathways are conserved between model cyanobacteria, such as Synechocystis, and model heterotrophic bacteria like Escherichia coli, many enzymes and/or pathways involved in the biosynthesis of key metabolites in cyanobacteria have not been completely characterised. These include pathways required for biosynthesis of chorismate and membrane lipids, nucleotides, several amino acids, vitamins and cofactors, and isoprenoids such as plastoquinone, carotenoids, and tocopherols. Moreover, our understanding of photorespiration, lipopolysaccharide assembly and transport, and degradation of lipids, sucrose, most vitamins and amino acids, and heme, is incomplete. We discuss tools that may aid characterisation of cyanobacterial metabolism, notably CyanoSource, a barcoded library of targeted Synechocystis mutants, which will significantly accelerate characterisation of individual proteins

GWU Student Selected for National Field Trip & Internship Experiences

Wendy Harmon grew up with the mountains, rivers, lakes, and streams of western North Carolina at her back door. Born and raised in Rutherfordton, N.C., some of her fondest memories are of outdoor exploratory excursions with her parents, Tommy and Darlene Harmon, where she literally first got her feet wet in ecology—the study of how organisms interact with their environments. When Harmon began looking at colleges, she wanted to find a place where she could further develop her love for science, biology, and ecology.https://digitalcommons.gardner-webb.edu/gardner-webb-newscenter-archive/2393/thumbnail.jp

Systems developmental biology: the use of ontologies in annotating models and in identifying gene function within and across species

Systems developmental biology is an approach to the study of embryogenesis that attempts to analyze complex developmental processes through integrating the roles of their molecular, cellular, and tissue participants within a computational framework. This article discusses ways of annotating these participants using standard terms and IDs now available in public ontologies (these are areas of hierarchical knowledge formalized to be computationally accessible) for tissues, cells, and processes. Such annotations bring two types of benefit. The first comes from using standard terms: This allows linkage to other resources that use them (e.g., GXD, the gene-expression [G-E] database for mouse development). The second comes from the annotation procedure itself: This can lead to the identification of common processes that are used in very different and apparently unrelated events, even in other organisms. One implication of this is the potential for identifying the genes underpinning common developmental processes in different tissues through Boolean analysis of their G-E profiles. While it is easiest to do this for single organisms, the approach is extendable to analyzing similar processes in different organisms. Although the full computational infrastructure for such an analysis has yet to be put in place, two examples are briefly considered as illustration. First, the early development of the mouse urogenital system shows how a line of development can be graphically formalized using ontologies. Second, Boolean analysis of the G-E profiles of the mesenchyme-to-epithelium transitions that take place during mouse development suggest Lhx1, Foxc1, and Meox1 as candidate transcription factors for mediating this process

Regulation of gene expression and control of protein synthesis in different biotechnological process: Theory and Reality

The impressive biodiversity of microorganisms on the Earth represents an endless source of genetic elements that can be rationally combined by synthetic biology to solve different biotechnological issues.In our laboratory, we have contributed to the development of a protein expression system, which responds to permissive concentrations of different inducers such as salicylate, acetyl salicylic acid or 3-methyl benzoate. The system involves two transcriptional regulators working in cascade, whereas the first one controls the expression of the second that finally activates the expression of heterologous genes cloned under the control of an inducible promoter. In addition to conventional processes of bioproduction developed in bioreactors, this cascade system has been adapted to its use in bacteria inside higher organisms.The study of the interactions between micro-organisms and their hosts presents certain limitations during the infection process as bacterial tracking inside higher organisms. The restricted number of tools that allow the control of genes involved in bacteria-host interactions hampers the ability to activate or inactivate these genes at the time or place desired during the course of the infection. These elements come from different bacteria, and have shown their effectiveness in the production of heterologous proteins in various organisms pathogenic for animals (Salmonella) or plant symbionts (Sinorhizobium). One of the interesting features of this system is that inducers freely diffuse between the different tissues of the host without toxicity at tested concentrations. This feature in combination with a good system to monitoring the infection process in vivo, allows to switch on the expression of genes of interest at the desired “time and place”, what could help in the understanding of its role during the infection process

A global community effort to decipher the unique biology of annual killifish

Over the past 50 years, annual killifishes arose as alternative model organisms for studies of vertebrate biology. The annual fish offers exceptional advantages for studies of genetics, genomics, developmental biology, population dynamics, ecology, biogeography, and evolution. They inhabit extremely variable freshwater environments in Africa and South America, have a short lifespan and a set of unique and fascinating developmental characteristics. Embryos survive within the dry substrate during the dry season, whereas the adult population dies. Thus, the survival of the populations is entirely dependent on the buried embryos that hatch the next rainy season. Although Old and New World species share similarities in their life cycle, they also have different adaptive responses associated with climate-related selective pressures. Therefore, contrasting different species from these areas is essential to understand unique adaptations to heterogeneous environment. A network of laboratories (United States, Czech Republic, Italy, Brazil, Chile, and Uruguay) is working and collaborating on many aspects of the biology of annual fishes. Participating researchers share projects and cross-training undergraduate and graduate students. These efforts resulted in two International Symposia (2010 and 2015) that took place in Montevideo and an international book. Herein, we summarize the progress made by this global community of scientists

Overcoming the Newtonian Paradigm: The Unfinished Project of Theoretical Biology from a Schellingian Perspective

Defending Robert Rosen’s claim that in every confrontation between physics and biology it is physics that has always had to give ground, it is shown that many of the most important advances in mathematics and physics over the last two centuries have followed from Schelling’s demand for a new physics that could make the emergence of life intelligible. Consequently, while reductionism prevails in biology, many biophysicists are resolutely anti-reductionist. This history is used to identify and defend a fragmented but progressive tradition of anti-reductionist biomathematics. It is shown that the mathematicoephysico echemical morphology research program, the biosemiotics movement, and the relational biology of Rosen, although they have developed independently of each other, are built on and advance this antireductionist tradition of thought. It is suggested that understanding this history and its relationship to the broader history of post-Newtonian science could provide guidance for and justify both the integration of these strands and radically new work in post-reductionist biomathematics

Ask Not "What is an Individual?"

Philosophers of biology typically pose questions about individuation by asking “what is an individual?” For example, we ask, “what is an individual species”, “what is an individual organism”, and “what is an individual gene?” In the first part of this chapter, I present my account of the gene concept and how it is used in investigative practices in order to motivate a more pragmatic approach. Instead of asking “what is a gene?”, I ask: “how do biologists individuate genes?”, “for what purposes?”, and “do their practices of individuating genes serve these purposes?" In the second part of this chapter, I propose that we use this approach when analyzing concepts of organisms and biological individuals. Following philosophical pragmatism, I argue that we should abstain from attempts to situate individuation of Darwinian individuals or of holobionts in a philosophy of nature. Instead, we should analyze practices of individuating organisms in terms of three-place relations between the world, ideas, and human purposes and actions. I conclude with three lessons: an ontological, an epistemological, and a meta-philosophical lesson, which I suggest, apply to philosophy of science generally and to philosophy and metaphysics at large

What sorts of worlds do we live in nowadays? Teaching biology in a post-modern age.

Most historians of science, sociologists of science, philosophers of science and science educators now accept that there is no such thing as 'the scientific method'. We explore the implications of this view of the nature of science for biology education in particular. Accepting that there is no single way of investigating and describing the world scientifically presents both challenges and opportunities, especially when teaching biology. We illustrate these opportunities by suggesting fresh approaches to the teaching of drawing in biology, the teaching of classification and the teaching of human biology