In situ primary production in young Antarctic sea ice

An in situ incubation technique used successfully to measure the photosynthetic carbon assimilation of internal algal assemblages within thick multiyear Arctic sea ice was developed and improved to measure the photosynthetic carbon assimilation within young sea ice only 50 cm thick (Eastern Weddell Sea, Antarctica). The new device enabled some of the first precise measurements of in situ photosynthetic carbon assimilation in newly formed Antarctic sea ice

A novel cost effective and high-throughput isolation and identification method for marine microalgae

Background: Marine microalgae are of major ecologic and emerging economic importance. Biotechnological screening schemes of microalgae for specific traits and laboratory experiments to advance our knowledge on algal biology and evolution strongly benefit from culture collections reflecting a maximum of the natural inter- and intraspecific diversity. However, standard procedures for strain isolation and identification, namely DNA extraction, purification, amplification, sequencing and taxonomic identification still include considerable constraints increasing the time required to establish new cultures. Results: In this study, we report a cost effective and high-throughput isolation and identification method for marine microalgae. The throughput was increased by applying strain isolation on plates and taxonomic identification by direct PCR (dPCR) of phylogenetic marker genes in combination with a novel sequencing electropherogram based screening method to assess the taxonomic diversity and identity of the isolated cultures. For validation of the effectiveness of this approach, we isolated and identified a range of unialgal cultures from natural phytoplankton communities sampled in the Arctic Ocean. These cultures include the isolate of a novel marine Chlorophyceae strain among several different diatoms. Conclusions: We provide an efficient and effective approach leading from natural phytoplankton communities to isolated and taxonomically identified algal strains in only a few weeks. Validated with sensitive Arctic phytoplankton, this approach overcomes the constraints of standard molecular characterisation and establishment of unialgal cultures

Metatranscriptomes from diverse microbial communities: assessment of data reduction techniques for rigorous annotation

Background Metatranscriptome sequence data can contain highly redundant sequences from diverse populations of microbes and so data reduction techniques are often applied before taxonomic and functional annotation. For metagenomic data, it has been observed that the variable coverage and presence of closely related organisms can lead to fragmented assemblies containing chimeric contigs that may reduce the accuracy of downstream analyses and some advocate the use of alternate data reduction techniques. However, it is unclear how such data reduction techniques impact the annotation of metatranscriptome data and thus affect the interpretation of the results. Results To investigate the effect of such techniques on the annotation of metatranscriptome data we assess two commonly employed methods: clustering and de-novo assembly. To do this, we also developed an approach to simulate 454 and Illumina metatranscriptome data sets with varying degrees of taxonomic diversity. For the Illumina simulations, we found that a two-step approach of assembly followed by clustering of contigs and unassembled sequences produced the most accurate reflection of the real protein domain content of the sample. For the 454 simulations, the combined annotation of contigs and unassembled reads produced the most accurate protein domain annotations. Conclusions Based on these data we recommend that assembly be attempted, and that unassembled reads be included in the final annotation for metatranscriptome data, even from highly diverse environments as the resulting annotations should lead to a more accurate reflection of the transcriptional behaviour of the microbial population under investigation

The response of diatom central carbon metabolism to nitrogen starvation is different from that of green algae and higher plants

The availability of nitrogen varies greatly in the ocean and limits primary productivity over large areas. Diatoms, a group of phytoplankton that are responsible for about 20% of global carbon fixation, respond rapidly to influxes of nitrate and are highly successful in upwelling regions. Although recent diatom genome projects have highlighted clues to the success of this group, very little is known about their adaptive response to changing environmental conditions. Here, we compare the proteome of the marine diatom Thalassiosira pseudonana (CCMP 1335) at the onset of nitrogen starvation with that of nitrogen-replete cells using two-dimensional gel electrophoresis. In total, 3,310 protein spots were distinguishable, and we identified 42 proteins increasing and 23 decreasing in abundance (greater than 1.5-fold change; P < 0.005). Proteins involved in the metabolism of nitrogen, amino acids, proteins, and carbohydrates, photosynthesis, and chlorophyll biosynthesis were represented. Comparison of our proteomics data with the transcriptome response of this species under similar growth conditions showed good correlation and provided insight into different levels of response. The T. pseudonana response to nitrogen starvation was also compared with that of the higher plant Arabidopsis (Arabidopsis thaliana), the green alga Chlamydomonas reinhardtii, and the cyanobacterium Prochlorococcus marinus. We have found that the response of diatom carbon metabolism to nitrogen starvation is different from that of other photosynthetic eukaryotes and bears closer resemblance to the response of cyanobacteria

A Model of Genome Size Evolution for Prokaryotes in Stable and Fluctuating Environments

Temporal variability in ecosystems significantly impacts species diversity and ecosystem productivity and therefore the evolution of organisms. Different levels of environmental perturbations such as seasonal fluctuations, natural disasters, and global change have different impacts on organisms and therefore their ability to acclimatize and adapt. Thus, to understand howorganisms evolve under different perturbations is a key for predicting how environmental change will impact species diversity and ecosystem productivity. Here, we developed a computer simulation utilizing the individual-based model approach to investigate genome size evolution of a haploid, clonal and free-living prokaryotic population across different levels of environmental perturbations. Our results showthat a greater variability of the environment resulted in genomes with a larger number of genes. Environmental perturbations were more effectively buffered by populations of individuals with relatively large genomes. Unpredictable changes of the environment led to a series of population bottlenecks followed by adaptive radiations. Our model shows that the evolution of genome size is indirectly driven by the temporal variability of the environment. This complements the effects of natural selection directly acting on genome optimization. Furthermore, species that have evolved in relatively stable environments may face the greatest risk of extinction under global change as genome streamlining genetically constrains their ability to acclimatize to the new environmental conditions, unless mechanisms of genetic diversification such as horizontal gene transfer will enrich their gene pool and therefore their potential to adapt

Rmagine: 3D Range Sensor Simulation in Polygonal Maps via Raytracing for Embedded Hardware on Mobile Robots

Sensor simulation has emerged as a promising and powerful technique to find solutions to many real-world robotic tasks like localization and pose tracking.However, commonly used simulators have high hardware requirements and are therefore used mostly on high-end computers. In this paper, we present an approach to simulate range sensors directly on embedded hardware of mobile robots that use triangle meshes as environment map. This library called Rmagine allows a robot to simulate sensor data for arbitrary range sensors directly on board via raytracing. Since robots typically only have limited computational resources, the Rmagine aims at being flexible and lightweight, while scaling well even to large environment maps. It runs on several platforms like Laptops or embedded computing boards like Nvidia Jetson by putting an unified API over the specific proprietary libraries provided by the hardware manufacturers. This work is designed to support the future development of robotic applications depending on simulation of range data that could previously not be computed in reasonable time on mobile systems

Omega-3 fatty acids in Atlantic salmon: dietary and environmental effects

This research into the effect of lipid source in aquafeed provides quantifiable information on many aspects of Atlantic salmon nutrition and product quality, specifically, in the area of fatty acid metabolism with particular reference to fillet levels of health beneficial omega-3 fatty acids. It is intended that this body of work will assist in the development of the aquaculture industry in a manner that is both environmentally and economically sound

Silicon drives the evolution of complex crystal morphology in calcifying algae

This article is a Commentary on Langer et al. (2021), doi: 10.1111/nph.17230

Identification and Characterisation of Protein Phosphatase 1, Catalytic Subunit Alpha (PP1alpha) as a Regulator of NF-kappaB in T Lymphocytes

Der Transkriptionsfaktor nuclear factor-kappa B (NF-kappaB) ist für die Aktivierung und das Überleben von T-Lymphozyten essentiell. NF-κB reguliert die Expression von Zytokinen, Wachstumsfaktoren und anti-apoptotischen Genen. Entsprechend ist die physiologische NF-kappaB-Aktivierung von zentraler Bedeutung für eine effiziente Immunantwort. Verschiedenste Neoplasien weisen Genmutationen auf, die zu einer aberranten, meist konstitutiven NF-kappaB-Aktivität führen. Diese erlaubt es Tumorzellen, den Zell-intrinsischen Kontrollmechanismen zu entgehen und unkontrolliert zu proliferieren. Die T-Zell Rezeptor (TZR)-induzierte Signalleitung, die zur Aktivierung von NF-kappaB führt, basiert größtenteils auf Phosphorylierungsreaktionen, die zu Veränderungen in der Funktion und Aktivität der phosphorylierten Proteine führen. Diese Phosphorylierung von Proteinen ist aber meist transient. Während viele Kinasen und ihre Substrate charakterisiert wurden, ist die Rolle von Phosphatasen in der Modulierung der NF-kappaB Signalkaskade bisher wenig untersucht. Um Phosphatasen zu identifizieren, die eine Rolle bei der TZR-induzierten NF-kappaB-Aktivierung spielen, wurde ein RNA Interferenz (RNAi) Screen in Jurkat T Zellen durchgeführt. Mit Hilfe dieser Methode konnten verschiedene Phosphatasen und Phosphatase-assoziierte Proteine identifiziert werden, welche die NF-kappaB-Aktivität positiv oder negativ regulieren. Entsprechend wurde die protein phosphatase 1, calalytic subunit alpha (PP1alpha) als Positivregulator identifiziert. RNAi-vermittelte Verminderung der PP1alpha-Expression führte zu einer verringerten NF-kappaB-Aktivität. Umgekehrt führte die Überexpression von PP1alpha zu einer erhöhten NF-κB-Aktivität. Es konnte jedoch kein deutlicher Einfluss von PP1alpha im Hinblick auf zytoplasmatische Phosphorylierungsreaktionen im NF-κB-Signalweg detektiert werden. Allerdings wurde festgestellt, dass PP1alpha, vermutlich Promotor-spezifisch, die Expression einzelner bona fide NF-kappaB-regulierter Gene beeinflusst. Entsprechend führte eine verringerte PP1alpha-Expression zu einer verminderten DNA-Bindeaktivität von NF-kappaB. Zudem wurde gezeigt, dass PP1alpha für die Proliferation von primären humanen CD4+ T-Lymphozyten benötigt wird. Darüber hinaus, induzierte eine verringerte PP1alpha Expression oder Inhibition der enzymatischen Aktivität der Phosphatase Apoptose in NF-kappaB-abhängigen kutanen T Zell Lymphom (engl.: cutaneous T cell lymphoma, CTCL) Zellen. In dieser Arbeit konnte ein neuer Regulator der TZR-induzierten NF-kappaB-Aktivität identifiziert werden. Diese Ergebnisse tragen zu einem genaueren Verständnis der NF-kappaB-Regulation in T Lymphozyten bei und sind möglicherweise für die zukünftige therapeutische Behandlung von NF-kappaB-assoziierten Erkrankungen von Bedeutung