Space Station Freedom: a unique laboratory for gravitational biology research

The advent of Space Station Freedom (SSF) will provide a permanent laboratory in space with unparalleled opportunities to perform biological research. As with any spacecraft there will also be limitations. It is our intent to describe this space laboratory and present a picture of how scientists will conduct research in this unique environment we call space. SSF is an international venture which will continue to serve as a model for other peaceful international efforts. It is hoped that as the human race moves out from this planet back to the moon and then on to Mars that SSF can serve as a successful example of how things can and should be done.     

Structure and Function of the Water-Soluble Carotenoid-Binding Proteins of Cyanobacteria

The orange carotenoid protein (OCP) and its derivative, the red carotenoid protein (RCP), appear to play important photoprotective roles in cyanobacteria. Structural and functional characterization is gradually elucidating the specific details of how carotenoid-protein interactions, including the role of six methionine residues oriented toward the pigment, contribute to the spectral and functional properties of these proteins.     

Characterization of structure and properties of bone by spectral measure method

Novel mathematical method called spectral measure method (SMM) is developed for characterization of bone structure and indirect estimation of bone properties. The spectral measure method is based on an inverse homogenization technique which allows to derive information about the structure of composite material from measured effective electric or viscoelastic properties. The mechanical properties and ability to withstand fracture depend on the structural organization of bone as a hierarchical composite. Information about the bone structural parameters is contained in the spectral measure in the Stieltjes integral representation of the effective properties. The method is based on constructing the spectral measure either by calculating it directly from micro-CT images or using measurements of electric or viscoelastic properties over a frequency range. In the present paper, we generalize the Stieltjes representation to the viscoelastic case and show how bone microstructure, in particular, bone volume or porosity, can be characterized by the spectral function calculated using measurements of complex permittivity or viscoelastic modulus. For validation purposes, we numerically simulated measured data using micro-CT images of cancellous bone. Recovered values of bone porosity are in excellent agreement with true porosity estimated from the micro-CT images. We also discuss another application of this method, which allows to estimate properties difficult to measure directly. The spectral measure method based on the derived Stieltjes representation for viscoelastic composites, has a potential for non-invasive characterization of bone structure using electric or mechanical measurements. The method is applicable to sea ice, porous rock, and other composite materials.     

The second warning to humanity—Why ethology matters?

In 2017, more than 15,000 scientists signed a second warning to humanity to halt human-made destruction of our planet. The authors of that study encouraged further contributions highlighting specific subjects. With this perspectives article, we follow their call and explore why and how behavioural studies can matter for a better stewardship of the planet. The second warning article suggested 13 effective steps humanity needs to take to transition to a sustainable life. Here, we first provide some examples of how concepts and tools of behavioural biology can aid understanding and solving real-world conservation problems relating to some of the effective sustainability steps suggested by Ripple et al., (Bioscience, 67, 2017, 1026). Then, we outline how ethological research can contribute to sustainability beyond its contributions to conserving species. Finally, we turn to the second warning and the behaviour of scientists themselves. Science has provided unequivocal evidence that we are destroying the very basis of the existence of millions of species including ourselves. To convince humanity about the urgent necessity to halt and change our behaviour, science organizations, funding bodies and scientists themselves need to become role models for sustainability.     

Use of antibodies to the lipopolysaccharide core region in the treatment of gram-negative sepsis and shock

In this paper we review evidence in favor of a protective role for antibodies directed at the lipopolysaccharide (LPS) core region of Gram-negative bacilli. It will be shown that, given the right animal model, polyclonal antisera raised against O-antigen lacking, rough mutant strains, can be shown to protect animals against lethal sepsis due to a variety a bacterial species. Evidence for a protective role obtained from clinical studies will also be discussed. It will be stressed how difficult it is to prove that the antibodies directed against the LPS-core, and not other proteins present in the polyclonal anti-rough strain antisera, were responsible for the observed protective effects. The solution to some of these problems is the production of monoclonal antibodies (Mabs). We will discuss the findings that purified anti-core Mabs may give false-positive outcomes of protection studies, due to the induction of tolerance by small amounts of contaminating endotoxin, present in the antibody preparation. The need to administer the Mab therapeutically instead of prophylactically to the test animals, will be stressed. It will be shown how we succeeded in determining the epitope-specificities of several anti-core antibodies. It will be shown also that use of Elisa alone for characterization of anti-core Mabs may lead to false conclusions concerning epitope specificities. We will prove that synthetic KDO-(=ketodeoxycctanate) and lipid A-containing antigens are indispensable tools for thorough characterization of Mabs. Using this methodology we were able to discriminate between specific antigen-antibody interactions, and the ability of some Mabs to bind “non-specifically” to hydrophobic surfaces. The relationship between epitope specificity and protective effects of anti-core Mabs will be described. Finally, we will demonstrate that a KDO-specific Mabs is capable of protecting mice against lethal sepsis; in other words, it will be shown conclusively that Mabs to defined epitopes in LPS core region are cross-protective.     

The early atmosphere: a new picture

Over the last several years, many of the fundamental ideas concerning the composition and chemical evolution of the Earth's early atmosphere have changed. While many aspects of this subject are clouded--either uncertain or unknown, a new picture is emerging. We are just beginning to understand how astronomical, geochemical, and atmospheric processes each contributed to the development of the gaseous envelope around the third planet from the sun some 4.6 billion years ago and how that envelope chemically evolved over the history of our planet. Simple compounds in that gaseous envelope, energized by atmospheric lightning and/or solar ultraviolet radiation, formed molecules of increasing complexity that eventually evolved into the first living systems on our planet. This process is called "chemical evolution" and immediately preceded biological evolution; once life developed and evolved, it began to alter the chemical composition of the atmosphere that provided the very essence of its creation. Photosynthetic organisms which have the ability to biochemically transform carbon dioxide and water to carbohydrates, which they use for food, produce large amounts of molecular oxygen (O2) as a by-product of the reaction. Atmospheric oxygen photochemically formed ozone, which absorbs ultraviolet radiation from the sun and shields the Earth's surface from this biologically lethal radiation. Once atmospheric ozone levels increased sufficiently, life could leave the safety of the oceans and go ashore for the first time. Throughout the history of our planet, there has been strong interaction between life and the atmosphere. Understanding our cosmic roots is particularly relevant as we embark on a search for life outside the Earth. At this very moment, several radio telescopes around the world are searching for extraterrestrial intelligence (SETI).     

Viral information

Viruses are major drivers of global biogeochemistry and the etiological agents of many diseases. They are also the winners in the game of life: there are more viruses on the planet than cellular organisms and they encode most of the genetic diversity on the planet. In fact, it is reasonable to view life as a viral incubator. Nevertheless, most ecological and evolutionary theories were developed, and continue to be developed, without considering the virosphere. This means these theories need to be to reinterpreted in light of viral knowledge or we need to develop new theory from the viral point-of-view. Here we briefly introduce our viral planet and then address a major outstanding question in biology: why is most of life viral? A key insight is that during an infection cycle the original virus is completely broken down and only the associated information is passed on to the next generation. This is different for cellular organisms, which must pass on some physical part of themselves from generation to generation. Based on this premise, it is proposed that the thermodynamic consequences of physical information (e.g., Landauer’s principle) are observed in natural viral populations. This link between physical and genetic information is then used to develop the Viral Information Hypothesis, which states that genetic information replicates itself to the detriment of system energy efficiency (i.e., is viral in nature). Finally, we show how viral information can be tested, and illustrate how this novel view can explain existing ecological and evolutionary theories from more fundamental principles.     

Putting Your Money Where Your Mouth Is: Why Sustainability Reporting Based on the Triple Bottom Line Can Be Misleading

In the packaged food industry, Corporate Social Responsibility (CSR) is an informal requirement for which firms account through sustainability reporting. CSR behaviors are often reported and analyzed using the Triple Bottom Line (3BL) framework, which categorizes them as affecting people, planet, or profit. 3BL is useful in determining which of these categories is most elaborated upon by the firm, but has a limited scope and many documented criticisms. This paper aims to address the aforementioned insufficiencies by augmenting the 3BL framework with two important attributes of CSR practices: (1) the presence of change in core firm behavior of the firm itself or of others in the supply chain, and (2) whether the behavior qualifies as being outside of the firm’s normal business practice or is something that they might have done anyway. We qualitatively analyze CSR behaviors described in sustainability reports and interviews from major players in the packaged food industry and categorize them using these attributes as a supplement to 3BL. This enables us to separate the behaviors from their framing and analyze them more critically. Our results demonstrate how the visible CSR efforts of a firm can be misleading at first glance. Using only 3BL, we find that the CSR focus of firms in this industry is people. We then discover that the codes focusing on people (as opposed to planet or profit) require the least amount of real structural change from a firm or its supply chain partners, and thus arguably, the least amount of effort. We also find that behaviors that focus on planet require the most effort within the firm itself, but for behaviors involving supply chain partners, effort is required for behaviors in all three categories. Finally, we find that CSR behavior that is related to planet tends to go beyond normal business practice.     

The International Year of Biodiversity: A Celebration and Cogitation

To both celebrate and reflect upon this International Year of Biodiversity, Biotropica has invited opinion articles from a number of scientists across the globe. As lightly edited personal opinions, the commentaries reflect the diversity of passionate and often controversial views expressed across the scientific community. Thus, these commentaries should provide much food for thought, and hopefully some inspiration, on how we perceive biodiversity on our currently human-dominated planet and how we should respond to its loss.     

Just How Emergent is the Emergence of Semiosis?

Studying the origin of semiosis is a task obscured by terminological and metaphysical issues which create an ambiguous set of definitions for biosemiotics when referring to the concept of emergence. The question is, how emergent can semiosis be? And what are the conditions for semiosis to be an emergent of a certain type? This paper will attempt to briefly deal with the general terminology of emergence from a philosophical point of view and will discuss the characterization of semiosis as an emergent phenomenon based on the distinctions made by Bedau, Kim and Chalmers. Accordingly, we will consider the possibility of strong and weak emergence in an attempt to bring some clarity to what it means for something in biosemiotics to be an emergent and how the philosophical concepts play out when applied to biosemiotic research. In inquiring into the metaphysical status of semiosis, we change our semiotic theories to correspond to the assumptions contained in the elementary objects of our theories. This being the case, the way semiosis–the constitutive element that it is for semiotics–is taken to be with regards to its possible ontology, will conduct to different research objects for the long-term investigation of its origins and necessary conditions.     

A Scientometric Prediction of the Discovery of the First Potentially Habitable Planet with a Mass Similar to Earth

Background

The search for a habitable extrasolar planet has long interested scientists, but only recently have the tools become available to search for such planets. In the past decades, the number of known extrasolar planets has ballooned into the hundreds, and with it, the expectation that the discovery of the first Earth-like extrasolar planet is not far off.

Methodology/Principal Findings

Here, we develop a novel metric of habitability for discovered planets and use this to arrive at a prediction for when the first habitable planet will be discovered. Using a bootstrap analysis of currently discovered exoplanets, we predict the discovery of the first Earth-like planet to be announced in the first half of 2011, with the likeliest date being early May 2011.

Conclusions/Significance

Our predictions, using only the properties of previously discovered exoplanets, accord well with external estimates for the discovery of the first potentially habitable extrasolar planet and highlight the the usefulness of predictive scientometric techniques to understand the pace of scientific discovery in many fields.     

Is there a connection between biodiversity and the greenhouse effect

It was discussed the role of biodiversity in ecosystems capacity to control CO2 in atmosphere as the main reason not only of "greenhouse effect" but "greenhouse catastrophe". The necessity to perfect the preventive measures has been defined by time factor. This time may be so little for completing the evolution theory and models of biosphere management. The temps of contemporaneous species extinction exceed two orders as minimum ones how it has been known from planet history. It doesn't permit to discharge that evolutional process will be successful to create organisms which have been capable to stabilize biosphere in conditions of its changing status. It's possible that such change may be provocated with the crisis in civilization-biosphere interrelations.     

The genes underlying the process of speciation

The long-standing goal of finding genes causing reproductive isolation is being achieved. To better link the genetics with the process of speciation, we propose that 'speciation gene' be defined as any gene contributing to the evolution of reproductive isolation. Characterizing a speciation gene involves establishing that the gene affects a component of reproductive isolation; demonstrating that divergence at the locus occurred before completion of speciation; and quantifying the effect size of the gene (i.e. the increase in total reproductive isolation caused by its divergence). Review of a sample of candidate speciation genes found that few meet these criteria. Improved characterization of speciation genes will clarify how numerous they are, their properties and how they affect genome-wide patterns of divergence.     

Synthesis and Characterization of a Fluorescent Analogue of Cyclic di-GMP

Cyclic di-GMP (c-di-GMP), a ubiquitous bacterial second messenger, has emerged as a key controller of several biological processes. Numbers of reports that deal with the mechanistic aspects of this second messenger have appeared in the literature. However, the lack of a reporter tag attached to the c-di-GMP at times limits the understanding of further details. In this study, we have chemically coupled N-methylisatoic anhydride (MANT) with c-di-GMP, giving rise to Mant-(c-di-GMP) or MANT-CDG. We have characterized the chemical and physical properties and spectral behavior of MANT-CDG. The fluorescence of MANT-CDG is sensitive to changes in the microenvironment, which helped us study its interaction with three different c-di-GMP binding proteins (a diguanylate cyclase, a phosphodiesterase, and a PilZ domain-containing protein). In addition, we have shown here that MANT-CDG can inhibit diguanylate cyclase activity; however, it is hydrolyzed by c-di-GMP specific phosphodiesterase. Taken together, our data suggest that MANT-CDG behaves like native c-di-GMP, and this study raises the possibility that MANT-CDG will be a valuable research tool for the in vitro characterization of c-di-GMP signaling factors.     

Pathways to Earth-Like Atmospheres

We discuss the evolution of the atmosphere of early Earth and of terrestrial exoplanets which may be capable of sustaining liquid water oceans and continents where life may originate. The formation age of a terrestrial planet, its mass and size, as well as the lifetime in the EUV-saturated early phase of its host star play a significant role in its atmosphere evolution. We show that planets even in orbits within the habitable zone of their host stars might not lose nebular- or catastrophically outgassed initial protoatmospheres completely and could end up as water worlds with CO₂ and hydrogen- or oxygen-rich upper atmospheres. If an atmosphere of a terrestrial planet evolves to an N₂-rich atmosphere too early in its lifetime, the atmosphere may be lost. We show that the initial conditions set up by the formation of a terrestrial planet and by the evolution of the host star’s EUV and plasma environment are very important factors owing to which a planet may evolve to a habitable world. Finally we present a method for studying the discussed atmosphere evolution hypotheses by future UV transit observations of terrestrial exoplanets.     

Photoreceptor spectral sensitivities in terrestrial animals: adaptations for luminance and colour vision

This review outlines how eyes of terrestrial vertebrates and insects meet the competing requirements of coding both spatial and spectral information. There is no unique solution to this problem. Thus, mammals and honeybees use their long-wavelength receptors for both achromatic (luminance) and colour vision, whereas flies and birds probably use separate sets of photoreceptors for the two purposes. In particular, we look at spectral tuning and diversification among 'long-wavelength' receptors (sensitivity maxima at greater than 500 nm), which play a primary role in luminance vision. Data on spectral sensitivities and phylogeny of visual photopigments can be incorporated into theoretical models to suggest how eyes are adapted to coding natural stimuli. Models indicate, for example, that animal colour vision--involving five or fewer broadly tuned receptors--is well matched to most natural spectra. We can also predict that the particular objects of interest and signal-to-noise ratios will affect the optimal eye design. Nonetheless, it remains difficult to account for the adaptive significance of features such as co-expression of photopigments in single receptors, variation in spectral sensitivities of mammalian L-cone pigments and the diversification of long-wavelength receptors that has occurred in several terrestrial lineages.     

Climate change and marine plankton

Understanding how climate change will affect the planet is a key issue worldwide. Questions concerning the pace and impacts of climate change are thus central to many ecological and biogeochemical studies, and addressing the consequences of climate change is now high on the list of priorities for funding agencies. Here, we review the interactions between climate change and plankton communities, focusing on systematic changes in plankton community structure, abundance, distribution and phenology over recent decades. We examine the potential socioeconomic impacts of these plankton changes, such as the effects of bottom-up forcing on commercially exploited fish stocks (i.e. plankton as food for fish). We also consider the crucial roles that plankton might have in dictating the future pace of climate change via feedback mechanisms responding to elevated atmospheric CO(2) levels. An important message emerges from this review: ongoing plankton monitoring programmes worldwide will act as sentinels to identify future changes in marine ecosystems.     

Electron transfer dissociation mass spectrometry in proteomics

Mass spectrometry has rapidly evolved to become the platform of choice for proteomic analysis. While CID remains the major fragmentation method for peptide sequencing, electron transfer dissociation (ETD) is emerging as a complementary method for the characterization of peptides and post-translational modifications (PTMs). Here, we review the evolution of ETD and some of its newer applications including characterization of PTMs, non-tryptic peptides and intact proteins. We will also discuss some of the unique features of ETD such as its complementarity with CID and the use of alternating CID/ETD along with issues pertaining to analysis of ETD data. The potential of ETD for applications such as multiple reaction monitoring and proteogenomics in the future will also be discussed.     

Born‐digital biodiversity data: Millions and billions

Given the dramatic pace of change of our planet, we need rapid collection of environmental data to document how species are coping and to evaluate the impact of our conservation interventions. To address this need, new classes of “born digital” biodiversity records are now being collected and curated many orders of magnitude faster than traditional data. In addition to the millions of citizen science observations of species that have been accumulating over the last decade, the last few years have seen a surge of sensor data, with eMammal's camera trap archive passing 1 million photo‐vouchered specimens and Movebank's animal tracking database recently passing 1.5 billion animal locations. Data from digital sensors have other advantages over visual citizen science observation in that the level of survey effort is intrinsically documented and they can preserve digital vouchers that can be used to verify species identity. These novel digital specimens are leading spatial ecology into the era of Big Data and will require a big tent of collaborating organizations to make these databases sustainable and durable. We urge institutions to recognize the future of born‐digital records and invest in proper curation and standards so we can make the most of these records to inform management, inspire conservation action and tell natural history stories about life on the planet.     

Mind the Gap: Molecular Architecture of the Axon Initial Segment – From Fold Prediction to a Mechanistic Model of Function?

The axon initial segment (AIS) is a distinct neuronal domain, which is responsible for initiating action potentials, and therefore of key importance to neuronal signaling. To determine how it functions, it is necessary to establish which proteins reside there, how they are organized, and what the dynamic features are. Great strides have been made in recent years, and it is now clear that several AIS cytoskeletal and membrane proteins interact to form a higher-order periodic structure. Here we briefly describe AIS function, protein composition and molecular architecture, and discuss perspectives for future structural characterization, and if structure predictions will be able to model complex higher-order assemblies.