The Pleiomorphic Plant MTOC： An Evolutionary Perspective

γ-Tubulin is an essential component of the microtubule organizing center （MTOC） responsible for nucleating microtubules in both plants and animals. Whereas γ-tubulin is tightly associated with centrosomes that are inheritable organelles in cells of animals and most algae, it appears at different times and places to organize the myriad specialized microtubule systems that characterize plant cells. We have traced the distribution of γ-tubulin through the cell cycle in representative land plants （embryophytes） and herein present data that have led to a concept of the pleiomorphic and migratory MTOC. The many forms of the plant MTOC at spindle organization constitute pleiomorphism, and stage-specific “migration” is suggested by the consistent pattern of redistribution of γ-tubulin during mitosis. Mitotic spindles may be organized at centriolar centrosomes （only in final divisions of spermatogenesis）, polar organizers （POs）, plastid MTOCs, or nuclear envelope MTOCs （NE-MTOCs）. In all cases, with the possible exception of centrosomes in spermatogenesis, the γ-tubulin migrates to broad polar regions and along the spindle fibers, even when it is initially a discrete polar entity. At anaphase it moves poleward, and subsequently migrates from polar regions （distal nuclear surfaces） into the interzone （proximal nuclear surfaces） where interzonal microtubule arrays and phragmoplasts are organized. Following cytokinesis, γ-tubulin becomes associated with nuclear envelopes and organizes radial microtubule systems （RMSs）. These may exist only briefly, before establishment of hoop-like cortical arrays in vegetative tissues, or they may be characteristic of interphase in syncytial systems where they serve to organize the common cytoplasm into nuclear cytoplasmic domains （NCDs）.     

An Evolutionary Perspective on Sedentary Behavior

Most people are aware of the health benefits of being physically active. The question arises then why people so easily fall into sedentary habits. The idea developed here is that sedentary behavior is part of a suite of behaviors to reduce levels of physical activity that were strongly selected in the evolutionary past, likely because high levels of physical activity had direct negative consequences for survival. However, hunter-gatherer populations could not reduce activity indefinitely because of the need to be active to hunt for, and gather food. Hence they never experienced low levels of activity that are damaging to health, and no corresponding mechanism avoiding low activity evolved. Consequently, gene variants promoting efficiency of activity and increased sedentariness were never selected against. Modern society facilitates reduced activity by providing many options to become less active and divorcing food intake from the need to be active. Choosing the less active option is hard wired in the genes; this explains why being sedentary is so common, and why reversing it is so difficult. Incentivizing activity may be enabled using modern technology, but ultimately may only end up replacing one set of health issues with others. Also see the video abstract here https://youtu.be/ekHbUwPw-v4 .     

Evolutionary Developmental Biology: the Interaction of Developmental Biology,Evolutionary Biology,Paleontology, and Genomics

Paleontological Journal - Evolutionary developmental biology (evo-devo) formed due to the interactions of evolutionary biology, paleontology, and comparative genomics, analyzes the interrelations...     

The Cell Biology of the Endocytic System from an Evolutionary Perspective

Evolutionary cell biology can afford an interdisciplinary comparative view that gives insights into both the functioning of modern cells and the origins of cellular systems, including the endocytic organelles. Here, we explore several recent evolutionary cell biology studies, highlighting investigations into the origin and diversity of endocytic systems in eukaryotes. Beginning with a brief overview of the eukaryote tree of life, we show how understanding the endocytic machinery in a select, but diverse, array of organisms provides insights into endocytic system origins and predicts the likely configuration in the last eukaryotic common ancestor (LECA). Next, we consider three examples in which a comparative approach yielded insight into the function of modern cellular systems. First, using ESCRT-0 as an example, we show how comparative cell biology can discover both lineage-specific novelties (ESCRT-0) as well as previously ignored ancient proteins (Tom1), likely of both evolutionary and functional importance. Second, we highlight the power of comparative cell biology for discovery of previously ignored but potentially ancient complexes (AP5). Finally, using examples from ciliates and trypanosomes, we show that not all organisms possess canonical endocytic pathways, but instead likely evolved lineage-specific mechanisms. Drawing from these case studies, we conclude that a comparative approach is a powerful strategy for advancing knowledge about the general mechanisms and functions of endocytic systems.The endomembrane system mediates transport of lipids, proteins, and other molecules to the various locations in the eukaryotic cell. It also underlies the interactions with the extracellular environment, presenting material at the cell surface as well as secreting and internalizing material. In modern cells, these latter aspects are important for signal transduction, surface remodeling, and nutrient acquisition. Just as these abilities are crucial to modern cells, they were likely equally important for the very first eukaryotes as they underwent speciation from prokaryotic-like ancestors via niche competition in the ancient world (Cavalier-Smith 2002). Understanding the events and biological processes involved in the evolution of the membrane-trafficking system in general, and the endocytic system in particular, gives us insights into landmark events in our cellular past.Evolutionary insight about cellular phenomenon is derived from two basic types of comparative study: from molecular cell biological analyses of increasingly tractable model organisms across the diversity of eukaryotes, and by computational analyses of genomic information (i.e., the genes encoding the membrane-trafficking machinery). Whereas the information gathered from taking this comparative, or evolutionary cell biology, approach (Brodsky et al. 2012) is valuable for evolutionary content, these same analyses are potentially highly valuable in understanding basic cell biology, a benefit that is perhaps less obvious and hence less appreciated. In this article, we frame what has been learned about the evolution of the endocytic system, in the dual context of what it tells us about ancient cells together with what it can tell us about modern ones. We begin with a brief introduction to eukaryotic diversity and the evolution of the membrane-trafficking system. We then delve into the evolution of specific endocytic factors to illustrate the ways in which cell biologists of all stripes can benefit from the emerging field of evolutionary cell biology.     

Restoration Biology: A Population Biology Perspective

A major goal of population biologists involved in restoration work is to restore populations to a level that will allow them to persist over the long term within a dynamic landscape and include the ability to undergo adaptive evolutionary change. We discuss five research areas of particular importance to restoration biology that offer potentially unique opportunities to couple basic research with the practical needs of restorationists. The five research areas are: (1) the influence of numbers of individuals and genetic variation in the initial population on population colonization, establishment, growth, and evolutionary potential; (2) the role of local adaptation and life history traits in the success of restored populations; (3) the influence of the spatial arrangement of landscape elements on metapopulation dynamics and population processes such as migration; (4) the effects of genetic drift, gene flow, and selection on population persistence within an often accelerated, successional time frame; and (5) the influence of interspecific interactions on population dynamics and community development. We also provide a sample of practical problems faced by practitioners, each of which encompasses one or more of the research areas discussed, and that may be solved by addressing fundamental research questions.     

Chaste: An Open Source C++ Library for Computational Physiology and Biology

Chaste — Cancer, Heart And Soft Tissue Environment — is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high-performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to ‘re-invent the wheel’ with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials.

This is a PLOS Computational Biology Software Article