Harnessing the Benefits of Open Electronics in Science

Freely and openly shared low-cost electronic applications, known as open electronics, have sparked a new open-source movement, with much un-tapped potential to advance scientific research. Initially designed to appeal to electronic hobbyists, open electronics have formed a global community of "makers" and inventors and are increasingly used in science and industry. Here, we review the current benefits of open electronics for scientific research and guide academics to enter this emerging field. We discuss how electronic applications, from the experimental to the theoretical sciences, can help (I) individual researchers by increasing the customization, efficiency, and scalability of experiments, while improving data quantity and quality; (II) scientific institutions by improving access and maintenance of high-end technologies, visibility and interdisciplinary collaboration potential; and (III) the scientific community by improving transparency and reproducibility, helping decouple research capacity from funding, increasing innovation, and improving collaboration potential among researchers and the public. Open electronics are powerful tools to increase creativity, democratization, and reproducibility of research and thus offer practical solutions to overcome significant barriers in science.Comment: 20 pages, 3 figure, 2 table

Open Hardware in Science: The Benefits of Open Electronics

Openly shared low-cost electronic hardware applications, known as open electronics, have sparked a new open-source movement, with much untapped potential to advance scientific research. Initially designed to appeal to electronic hobbyists, open electronics have formed a global “maker” community and are increasingly used in science and industry. In this perspective article, we review the current costs and benefits of open electronics for use in scientific research ranging from the experimental to the theoretical sciences. We discuss how user-made electronic applications can help (I) individual researchers, by increasing the customization, efficiency, and scalability of experiments, while improving data quantity and quality; (II) scientific institutions, by improving access to customizable high-end technologies, sustainability, visibility, and interdisciplinary collaboration potential; and (III) the scientific community, by improving transparency and reproducibility, helping decouple research capacity from funding, increasing innovation, and improving collaboration potential among researchers and the public. We further discuss how current barriers like poor awareness, knowledge access, and time investments can be resolved by increased documentation and collaboration, and provide guidelines for academics to enter this emerging field. We highlight that open electronics are a promising and powerful tool to help scientific research to become more innovative and reproducible and offer a key practical solution to improve democratic access to science

Genetics of the Actin Gene in the Red Algal Genus Stylonema (Stylonematophyceae)

Diversity within the morphologically simple red algae has been underappreciated until recently.Phylogenetic results, using mostly plastid genes, have shown that several diverse and ancient lineages comprise this morphologically simple group. Many of these groups are believed to lack sex and to be haploid, e.g. Stylonematales. The scope of phylogenetic markers was recently complemented by the ubiquitous actin gene. Its investigation in Stylonema alsidii (Hoef-Emden et al 2005), a world-wide marine species, has shown that it contains a single copy of the actin gene. However, only one isolate was used, and a proper understanding of this gene in Stylonema is still not established. Direct sequencing of the actin gene from various S. alsidii samples often showed a mixed signal with several peaks in third codon positions, suggesting multiple copies of the actin gene in these isolates. This study will: (1) test isolates of S. alsidii to see if multiple copies of the actin gene are found; and (2) enhance general knowledge of the actin gene in Stylonema. Cloned partial actin genes will be analysed to determine if multiple copies of the gene are present in isolates. These results have several implications: either a gene duplication has occurred within S. alsidii between the isolate previously used and our isolates, suggesting a recent duplication event; or our isolates are diploid (two alleles of actin) overturning the belief that all these organisms are haploid and not sexual

Getting to the heart(s) of cuttlefish: thermal sensitivity and mitochondrial function of cuttlefish hearts

Cephalopod molluscs are exceptional athleticinvertebrates that have evolved a high performancecardio-branchial system comprised of three hearts. Ascellular powerhouses, mitochondria have central roles inaerobic heart function. This study tested the acute andchronic impacts of thermal challenges on acclimation andevolution of mitochondria from branchial and systemichearts. Specimens from temperate and subtropicalpopulations of the common cuttlefish Sepia officinaliswere acclimated to 11°C, 16°C and 21°C. Permeabilisedheart fibres were then used to assess mitochondrialfunction using high-resolution respirometry, and asubstrate-inhibitor protocol; followed by measurementsof mitochondrial content and glycolytic enzyme activity.Mitochondria showed varying temperature dependentfuel preferences with proline being a favoured substrateat high temperatures and carbohydrates at lowtemperatures. In addition, apparent contributions of theelectron transport system relative to the phosphorylationsystem diminished with rising temperatures in temperatecuttlefish. This indicates very efficient mitochondrialcoupling at thermal limits, where the effects of thermalacclimation of mitochondrial function were most evident.Smaller hearts with higher oxidative capacities wereapparent in the subtropical specimens, while largerhearts with lower respiratory capacities were favoured intemperate specimens. Apparent fuel preferences for aminoacids and carbohydrates as well as glycolytic enzymeactivities also differed substantially between populations.In conclusion, this study provides evidence that Sepiaofficinalis hearts exhibit various bioenergetic adaptationsin response to acute, seasonal, and evolutionaryexposures to different habitat temperatures. Thisunderlines the high adaptive plasticity of the commoncuttlefish to cope with a broad range of thermalchallenges

Limited by blue blood? Genetic, structural and functional traits driving haemocyanin evolution and thermal adaptation in octopods.

The octopods worldwide colonisation of diverse thermal habitats from -1.8°C to more than 30°C relied on the capacity of their circulatory and ventilatory system to supply sufficie nt oxyg en f or aerob ic metaboli sm at a giv en environmental temperature. The blood pigment haemocyanin transports oxygen in octopods, which however, suffices oxygen supply only within a defined thermal range and thus may limit octopod radiation and distribution. This study aims to determine and link genetic, structural and functional properties of haemocyanin to understand mechanisms of protein evolution relevant to thermal adaptation in octopods. A combinatio n o f oxyge n bindin g experiments , nati ve g el electrophores is a nd gene sequencing was used to compare properties of haemocyanin between cold and warm adapted octopods. orphological and COI barcode identification of octopods collected during cruise ANT XXVII/3 of RV “Polarstern” confirmed high species diversity in sub and high Antarctic waters. Physiological and structural analysis of haemocyanin revealed differential oxygen binding properties and a heterogeneous abundance of two distinct isoforms of the functional unit G (FU-G) among polar species. The haemocyanin of Antarctic Pareledone charcoti displayed fewer acidic amino acids than of the temperate Enteroctopus dofleini. However, comparisons across multiple species from warm and cold habitats showed highly variable isoelectric properties of haemocyanin FU-G. We conclude that differenti al haemocyan in isofo rm patte rns am ong polar species likely explain differences in oxygen binding. The lack of a universal “cool” haemocyanin among Antarctic octopods may reflect independent colonisation and adaptation events to sub-zero temperatures. Further analysis will focus on warm adapted octopods and the search for amino acid residues that account for adaptive changes of haemocyanin

Blue Blood on Ice: Cephalopod haemocyanin function and evolution in a latitudinal cline

The Southern Ocean hosts a rich and diverse fauna that required specialist adaptations to colonize and persist at temperatures close to freezing. While much has been revealed about key adaptations in Antarctic fishes little is known about evolutionary strategies of other Antarctic ectotherms, particularly the abundant benthic incirrate octopods. Their oxygen demand is largely fuelled by the blue oxygen transporter haemocyanin that however, due to its increasing functional failure towards colder temperatures, poses a prime target for cold-adaptive adjustment. While haemocyanin structure has been well understood it remains unclear which molecular features and evolutionary trajectories explain functional properties of octopod haemocyanin. This thesis thus aimed to unravel cold-adaptive features of octopod haemocyanin and the underlying molecular features that evolved to sustain oxygen supply at sub-zero temperatures. Haemocyanin function is best assessed by oxygen binding experiments, which however was challenged due to the minute haemolymph volumes non-model organisms like Antarctic octopods, yield. I thus upgraded an oxygen diffusion chamber with a broad range fibre optic spectrophotometer and a micro-pH optode and tested the setup for Octopus vulgaris, the Antarctic eelpout and a Baikal amphipod. This technical advancement enabled simultaneous recordings of pH and oxygen dependent pigment absorbance in only 15 µl of sample. Results were highly reproducible and accurate and provided detailed insight to the complex and dynamic spectral features of three diverse blood-types. To identify cold-adaptive functional traits of blood oxygen transport this study compared haemocyanin oxygen binding properties, oxygen carrying capacities and haemolymph protein and ion composition between the Antarctic octopod Pareledone charcoti, the temperate Octopus pallidus and the subtropical Eledone moschata. Compared to octopods from warmer climates, Pareledone charcoti showed incomplete but significantly reduced oxygen affinity, which together with increased haemocyanin concentrations and high physically dissolved oxygen levels supported oxygen supply at 0°C. Therefore, unlike many Antarctic fishes Pareledone charcoti continued to rely on an oxygen transporting pigment. High temperature sensitivity of oxygen binding enabled Pareledone charcoti to utilise most of the oxygen bound by haemocyanin at 10°C. The concomitant relief for the circulatory system at warmer temperatures promotes warm tolerance and thus eurythermy in Pareledone charcoti. Underlying molecular mechanisms were studied by comparing 239 partial haemocyanin sequences of the functional unit f and g of 28 octopods species of polar, temperate, subtropical and tropical origin. Despite high conservation of these haemocyanin regions several sites were positively selected for their charge properties at the molecule’s surface. Net surface charges were generally elevated in polar octopods suggesting that charge-charge interactions raise intrinsic pK values to stabilise quaternary structure against higher ambient pH present in cold waters. The presence of at least two haemocyanin isoforms and high allelic variation in polar octopods indicate sustained genetic diversity of haemocyanin and thus the genetic potential to regulate blood oxygen transport in the cold. Further, amino acid variability located within a potential metal binding site suggests regulation of blood oxygen transport in octopods via altered intrinsic sensitivity to allosteric ligands In conclusion, this study revealed significant adaptations of octopod haemocyanin at the functional and molecular level that support oxygen supply at near freezing temperatures. However, ‘imperfect’ functional adaptation and ensuing reliance on high haemocyanin levels in Pareledone charcoti seems to add to the various design constraints of octopods compared to fishes. Hence, at second glance functional oxygen reserves indicate a higher capacity to sustain oxygen transport at warmer temperatures and together with a potential ability to regulate and reverse cold-adaptive molecular traits may be key to determine future winners and losers in an ecosystem facing radical environmental change