Unexpected mitochondrial genome diversity revealed by targeted single-cell genomics of heterotrophic flagellated protists

This is the author accepted manuscript. The final version is available from Nature Research via the DOI in this recordData availability: Complete mtDNA sequences assembled from this study are available at GenBank under the accession numbers MK188935 to MK188947, MN082144 and MN082145. Sequencing data are available under NCBI BioProject PRJNA379597. Reads have been deposited at NCBI Sequence Read Archive with accession number SRP102236. Partial mtDNA contigs and other important contigs mentioned in the text are available from Figshare at https://doi.org/10.6084/m9.figshare.7314728. Nuclear SAG assemblies are available from Figshare at https://doi.org/10.6084/m9.figshare.7352966. A protocol is available from protocols.io at: https://doi.org/10.17504/protocols.io.ywpfxdn.Code availability: The bioinformatic workflow is available at https://doi.org/10.5281/zenodo.192677; additional statistical analysis code is available at https://doi.org/10.6084/m9.figshare.9884309.Most eukaryotic microbial diversity is uncultivated, under-studied and lacks nuclear genome data. Mitochondrial genome sampling is more comprehensive, but many phylogenetically important groups remain unsampled. Here, using a single-cell sorting approach combining tubulin-specific labelling with photopigment exclusion, we sorted flagellated heterotrophic unicellular eukaryotes from Pacific Ocean samples. We recovered 206 single amplified genomes, predominantly from underrepresented branches on the tree of life. Seventy single amplified genomes contained unique mitochondrial contigs, including 21 complete or near-complete mitochondrial genomes from formerly under-sampled phylogenetic branches, including telonemids, katablepharids, cercozoans and marine stramenopiles, effectively doubling the number of available samples of heterotrophic flagellate mitochondrial genomes. Collectively, these data identify a dynamic history of mitochondrial genome evolution including intron gain and loss, extensive patterns of genetic code variation and complex patterns of gene loss. Surprisingly, we found that stramenopile mitochondrial content is highly plastic, resembling patterns of variation previously observed only in plants.Gordon and Betty Moore FoundationLeverhulme TrustDavid and Lucile Packard FoundationRoyal SocietyEuropean Molecular Biology OrganizationCONICYT FONDECYTGenome Canad

A global perspective on marine photosynthetic picoeukaryote community structure

A central goal in ecology is to understand the factors affecting the temporal dynamics and spatial distribution of microorganisms and the underlying processes causing differences in community structure and composition. However, little is known in this respect for photosynthetic picoeukaryotes (PPEs), algae that are now recognised as major players in marine CO2 fixation. Here, we analysed dot blot hybridisation and cloning–sequencing data, using the plastid-encoded 16S rRNA gene, from seven research cruises that encompassed all four ocean biomes. We provide insights into global abundance, α- and β-diversity distribution and the environmental factors shaping PPE community structure and composition. At the class level, the most commonly encountered PPEs were Prymnesiophyceae and Chrysophyceae. These taxa displayed complementary distribution patterns, with peak abundances of Prymnesiophyceae and Chrysophyceae in waters of high (25:1) or low (12:1) nitrogen:phosphorus (N:P) ratio, respectively. Significant differences in phylogenetic composition of PPEs were demonstrated for higher taxonomic levels between ocean basins, using Unifrac analyses of clone library sequence data. Differences in composition were generally greater between basins (interbasins) than within a basin (intrabasin). These differences were primarily linked to taxonomic variation in the composition of Prymnesiophyceae and Prasinophyceae whereas Chrysophyceae were phylogenetically similar in all libraries. These data provide better knowledge of PPE community structure across the world ocean and are crucial in assessing their evolution and contribution to CO2 fixation, especially in the context of global climate change

The effects of low and high glycemic index foods on exercise performance and beta-endorphin responses

Τhe aim of this study was to examine the effects of the consumption of foods of various glycemic index values on performance, β-endorphin levels and substrate (fat and carbohydrate) utilization during prolonged exercise. Eight untrained healthy males underwent, in a randomized counterbalanced design, three experimental conditions under which they received carbohydrates (1.5 gr. kg-1 of body weight) of low glycemic index (LGI), high glycemic index (HGI) or placebo. Food was administered 30 min prior to exercise. Subjects cycled for 60 min at an intensity corresponding to 65% of VO2max, which was increased to 90% of VO2max, then they cycled until exhaustion and the time to exhaustion was recorded. Blood was collected prior to food consumption, 15 min prior to exercise, 0, 20, 40, and 60 min into exercise as well as at exhaustion. Blood was analyzed for β-endorphin, glucose, insulin, and lactate. The mean time to exhaustion did not differ between the three conditions (LGI = 3.2 ± 0.9 min; HGI = 2.9 ± 0.9 min; placebo = 2.7 ± 0.7 min). There was a significant interaction in glucose and insulin response (P < 0.05) with HGI exhibiting higher values before exercise. β-endorphin increased significantly (P < 0.05) at the end of exercise without, however, a significant interaction between the three conditions. Rate of perceived exertion, heart rate, ventilation, lactate, respiratory quotient and substrate oxidation rate did not differ between the three conditions. The present study indicates that ingestion of foods of different glycemic index 30 min prior to one hour cycling exercise does not result in significant changes in exercise performance, β-endorphin levels as well as carbohydrate and fat oxidation during exercise

Controlled sampling of ribosomally active protistan diversity in sediment-surface layers identifies putative players in the marine carbon sink

This is the final version. Available on open access from Springer via the DOI in this record. Marine sediments are one of the largest carbon reservoir on Earth, yet the microbial communities, especially the eukaryotes, that drive these ecosystems are poorly characterised. Here, we report implementation of a sampling system that enables injection of reagents into sediments at depth, allowing for preservation of RNA in situ. Using the RNA templates recovered, we investigate the ‘ribosomally active’ eukaryotic diversity present in sediments close to the water/sediment interface. We demonstrate that in situ preservation leads to recovery of a significantly altered community profile. Using SSU rRNA amplicon sequencing, we investigated the community structure in these environments, demonstrating a wide diversity and high relative abundance of stramenopiles and alveolates, specifically: Bacillariophyta (diatoms), labyrinthulomycetes and ciliates. The identification of abundant diatom rRNA molecules is consistent with microscopy-based studies, but demonstrates that these algae can also be exported to the sediment as active cells as opposed to dead forms. We also observe many groups that include, or branch close to, osmotrophic–saprotrophic protists (e.g. labyrinthulomycetes and Pseudofungi), microbes likely to be important for detrital decomposition. The sequence data also included a diversity of abundant amplicon-types that branch close to the Fonticula slime moulds. Taken together, our data identifies additional roles for eukaryotic microbes in the marine carbon cycle; where putative osmotrophic–saprotrophic protists represent a significant active microbial-constituent of the upper sediment layer.Gordon and Betty Moore foundationPhilip Leverhulme AwardDavid and Lucile Packard FoundationCONICYT FONDECYTMBAR

Identification, replication and characterization of epigenetic remodelling in the aging genome:A cross population analysis

Aging is a complex biological process regulated by multiple cellular pathways and molecular mechanisms including epigenetics. Using genome-wide DNA methylation data measured in a large collection of Scottish old individuals, we performed discovery association analysis to identify age-methylated CpGs and replicated them in two independent Danish cohorts. The double-replicated CpGs were characterized by distribution over gene regions and location in relation to CpG islands. The replicated CpGs were further characterized by involvement in biological pathways to study their functional implications in aging. We identified 67,604 age-associated CpG sites reaching genome-wide significance of FWE

Magnetic Resonance Force Microscopy of paramagnetic electron spins at millikelvin temperatures

Magnetic Resonance Force Microscopy (MRFM) is a powerful technique to detect a small number of spins that relies on force-detection by an ultrasoft magnetically tipped cantilever and selective magnetic resonance manipulation of the spins. MRFM would greatly benefit from ultralow temperature operation, because of lower thermomechanical noise and increased thermal spin polarization. Here, we demonstrate MRFM operation at temperatures as low as 30 mK, thanks to a recently developed SQUID-based cantilever detection technique which avoids cantilever overheating. In our experiment, we detect dangling bond paramagnetic centers on a silicon surface down to millikelvin temperatures. Fluctuations of such kind of defects are supposedly linked to 1/f magnetic noise and decoherence in SQUIDs as well as in several superconducting and single spin qubits. We find evidence that spin diffusion plays a key role in the low temperature spin dynamics.Comment: 7 pages, 5 figure

Containment of uranium in the proposed Egyptian geologic repository for radioactive waste using hydroxyapatite.

Currently, the Egyptian Atomic Energy Authority is designing a shallow-land disposal facility for low-level radioactive waste. To insure containment and prevent migration of radionuclides from the site, the use of a reactive backfill material is being considered. One material under consideration is hydroxyapatite, Ca{sub 10}(PO{sub 4}){sub 6}(OH){sub 2}, which has a high affinity for the sorption of many radionuclides. Hydroxyapatite has many properties that make it an ideal material for use as a backfill including low water solubility (K{sub sp}&gt;10{sup -40}), high stability under reducing and oxidizing conditions over a wide temperature range, availability, and low cost. However, there is often considerable variation in the properties of apatites depending on source and method of preparation. In this work, we characterized and compared a synthetic hydroxyapatite with hydroxyapatites prepared from cattle bone calcined at 500 C, 700 C, 900 C and 1100 C. The analysis indicated the synthetic hydroxyapatite was similar in morphology to 500 C prepared cattle hydroxyapatite. With increasing calcination temperature the crystallinity and crystal size of the hydroxyapatites increased and the BET surface area and carbonate concentration decreased. Batch sorption experiments were performed to determine the effectiveness of each material to sorb uranium. Sorption of U was strong regardless of apatite type indicating all apatite materials evaluated. Sixty day desorption experiments indicated desorption of uranium for each hydroxyapatite was negligible

Beneficial effect of the oxygen free radical scavenger amifostine (WR-2721) on spinal cord ischemia/reperfusion injury in rabbits

<p>Abstract</p> <p>Background</p> <p>Paraplegia is the most devastating complication of thoracic or thoraco-abdominal aortic surgery. During these operations, an ischemia-reperfusion process is inevitable and the produced radical oxygen species cause severe oxidative stress for the spinal cord. In this study we examined the influence of Amifostine, a triphosphate free oxygen scavenger, on oxidative stress of spinal cord ischemia-reperfusion in rabbits.</p> <p>Methods</p> <p>Eighteen male, New Zealand white rabbits were anesthetized and spinal cord ischemia was induced by temporary occlusion of the descending thoracic aorta by a coronary artery balloon catheter, advanced through the femoral artery. The animals were randomly divided in 3 groups. Group I functioned as control. In group II the descending aorta was occluded for 30 minutes and then reperfused for 75 min. In group III, 500 mg Amifostine was infused into the distal aorta during the second half-time of ischemia period. At the end of reperfusion all animals were sacrificed and spinal cord specimens were examined for superoxide radicals by an ultra sensitive fluorescent assay.</p> <p>Results</p> <p>Superoxide radical levels ranged, in group I between 1.52 and 1.76 (1.64 ± 0.10), in group II between 1.96 and 2.50 (2.10 ± 0.23), and in group III (amifostine) between 1.21 and 1.60 (1.40 ± 0.19) (p = 0.00), showing a decrease of 43% in the Group of Amifostine. A lipid peroxidation marker measurement ranged, in group I between 0.278 and 0.305 (0.296 ± 0.013), in group II between 0.427 and 0.497 (0.463 ± 0.025), and in group III (amifostine) between 0.343 and 0.357 (0.350 ± 0.007) (p < 0.00), showing a decrease of 38% after Amifostine administration.</p> <p>Conclusion</p> <p>By direct and indirect methods of measuring the oxidative stress of spinal cord after ischemia/reperfusion, it is suggested that intra-aortic Amifostine infusion during spinal cord ischemia phase, significantly attenuated the spinal cord oxidative injury in rabbits.</p

The Effect of Intra-Abdominal Hypertension Incorporating Severe Acute Pancreatitis in a Porcine Model

Introduction: Abdominal compartment syndrome (ACS) and intra abdominal hypertension(IAH) are common clinical findings in patients with severe acute pancreatitis(SAP). It is thought that an increased intra abdominal pressure(IAP) is associated with poor prognosis in SAP patients. But the detailed effect of IAH/ACS on different organ system is not clear. The aim of this study was to assess the effect of SAP combined with IAH on hemodynamics, systemic oxygenation, and organ damage in a 12 h lasting porcine model