Potential uptake of dissolved organic matter by seagrasses and macroalgae

Dissolved organic nitrogen (DON) acts as a large reservoir of fixed nitrogen. Whereas DON utilization is common in the microbial community, little is known about utilization by macrophytes. We investigated the ability of the coexisting temperate marine macrophytes Zostera noltii, Cymodocea nodosa, and Caulerpa prolifera to take up nitrogen and carbon from small organic substrates of different molecular complexities (urea, glycine, L-leucine, and L-phenylalanine) and from dissolved organic matter (DOM) derived from algal and bacterial cultures (substrates with a complex composition). In addition to inorganic nitrogen, nitrogen from small organic substrates could be taken up in significant amounts by all macrophytes. Substrate uptake by the aboveground tissue differed from that of the belowground tissue. No relationships between carbon and nitrogen uptake of small organics were found. The preference for individual organic substrates was related to their structural complexity and C:N ratio. Uptake of algae-derived organic nitrogen was of similar magnitude as inorganic nitrogen, and was preferred over bacteria-derived nitrogen. These results add to the growing evidence that direct or quick indirect DON utilization may be more widespread among aquatic macrophytes than traditionally thought.This research was supported by the regional government of Andalusia project FUNDIV (P07-RNM-2516), the Spanish Project CTM2008-00012/MAR, a European Reintegration Grant (MERG-CT-2007-205675), a travel grant from Schure-Beijerinck-Popping Fund (SBP/JK/2007-32) and the Netherlands Organization for Scientific Research. Thanks to Fidel Echevarrìa Navas (Director of CACYTMAR) for granting us access to facilities, and to Bas Koutstaal for helping with sample processing. We also thank the anonymous reviewers for their valuable comments which significantly improved this manuscript

Computer vision enables short- and long-term analysis of Lophelia pertusa polyp behaviour and colour from an underwater observatory.

Osterloff J, Nilssen I, Jarnegren J, Van Engeland T, Buhl-Mortensen P, Nattkemper TW. Computer vision enables short- and long-term analysis of Lophelia pertusa polyp behaviour and colour from an underwater observatory. Scientific reports. 2019;9(1): 6578.An array of sensors, including an HD camera mounted on a Fixed Underwater Observatory (FUO) were used to monitor a cold-water coral (Lophelia pertusa) reef in the Lofoten-Vesteralen area from April to November 2015. Image processing and deep learning enabled extraction of time series describing changes in coral colour and polyp activity (feeding). The image data was analysed together with data from the other sensors from the same period, to provide new insights into the short- and long-term dynamics in polyp features. The results indicate that diurnal variations and tidal current influenced polyp activity, by controlling the food supply. On a longer time-scale, the coral's tissue colour changed from white in the spring to slightly red during the summer months, which can be explained by a seasonal change in food supply. Our work shows, that using an effective integrative computational approach, the image time series is a new and rich source of information to understand and monitor the dynamics in underwater environments due to the high temporal resolution and coverage enabled with FUOs

Diversity and seasonal development of large zooplankton along physical gradients in the Arctic Barents Sea

Due to ongoing climate change, a new Arctic Ocean ecosystem is emerging. Within the framework of the Nansen Legacy project, we investigated the community composition of the large zooplankton and its seasonal development along a latitudinal gradient in the northern Barents Sea. Total biomass was maximal in summer and early winter, and minimal in spring, with copepods contributing considerably in all seasons. Euphausiids represented a minor fraction of the biomass, whereas chaetognaths and other gelatinous zooplankton contributed substantially to the sampled zooplankton at all stations, particularly in winter. Amphipod biomass was high in early winter, but otherwise low. Temperature in the water column interior and bottom-depth had the highest explanatory power for the community composition of the large zooplankton, both revealing the same distinct Atlantic and Arctic domains along the studied section. The continental shelf of the northern Barents Sea had an Arctic signature and was in terms of biomass characterized by a dominance of cold-water species, such as Themisto libellula, and Calanus glacialis. The copepod Calanus hyperboreus was the dominant over the continental slope. Locations at the southern and northern end of the studied section were influenced by Atlantic Water (at intermediate depth at the northern stations), and contained a mixture of temperate species, deep-water species, and sympagic amphipods in northern ice-covered waters. In the northern Barents Sea, a seasonal change was observed in the biomass fractions of different zooplankton feeding guilds, with dominance of herbivores in summer and carnivores in winter. This suggests switching between bottom-up and top-down control through the year. On the continental slope, species that are typically considered omnivores seemed to increase in importance. The role of seasonally changing food preferences to bridge periods outside of the main primary production season is discussed in light of ecosystem resilience to the expected changes in the Arctic Ocean.publishedVersio

Fiskeriakustikk og akustisk målklassifisering - Rapport frå COGMAR/CRIMAC arbeidsmøte om maskinlæring og fiskeriakustikk

Source at https://www.hi.no/hi/nettrapporter/rapport-fra-havforskningen-en-2021-25This report documents a workshop organised by the COGMAR and CRIMAC projects. The objective of the workshop was twofold. The first objective was to give an overview of ongoing work using machine learning for Acoustic Target Classification (ATC). Machine learning methods, and in particular deep learning models, are currently being used across a range of different fields, including ATC. The objective was to give an overview of the status of the work. The second objective was to familiarise participants with machine learning background to fisheries acoustics and to discuss a way forward towards a standard framework for sharing data and code. This includes data standards, standard processing steps and algorithms for efficient access to data for machine learning frameworks. The results from the discussion contributes to the process in ICES for developing a community standard for fisheries acoustics data

Early onset MSI-H colon cancer with MLH1 promoter methylation, is there a genetic predisposition?

<p>Abstract</p> <p>Background</p> <p>To investigate the etiology of <it>MLH1 </it>promoter methylation in mismatch repair (MMR) mutation-negative early onset MSI-H colon cancer. As this type of colon cancer is associated with high ages, young patients bearing this type of malignancy are rare and could provide additional insight into the etiology of sporadic MSI-H colon cancer.</p> <p>Methods</p> <p>We studied a set of 46 MSI-H colon tumors cases with <it>MLH1 </it>promoter methylation which was enriched for patients with an age of onset below 50 years (n = 13). Tumors were tested for CIMP marker methylation and mutations linked to methylation: <it>BRAF, KRAS</it>, <it>GADD45A </it>and the <it>MLH1 </it>-93G>A polymorphism. When available, normal colon and leukocyte DNA was tested for <it>GADD45A </it>mutations and germline <it>MLH1 </it>methylation. SNP array analysis was performed on a subset of tumors.</p> <p>Results</p> <p>We identified two cases (33 and 60 years) with <it>MLH1 </it>germline promoter methylation. <it>BRAF </it>mutations were less frequent in colon cancer patients below 50 years relative to patients above 50 years (p-value: 0.044). CIMP-high was infrequent and related to <it>BRAF </it>mutations in patients below 50 years. In comparison with published controls the G>A polymorphism was associated with our cohort. Although similar distribution of the pathogenic A allele was observed in the patients with an age of onset above and below 50 years, the significance for the association was lost for the group under 50 years. <it>GADD45A </it>sequencing yielded an unclassified variant. Tumors from both age groups showed infrequent copy number changes and loss-of-heterozygosity.</p> <p>Conclusion</p> <p>Somatic or germline <it>GADD45A </it>mutations did not explain sporadic MSI-H colon cancer. Although germline <it>MLH1 </it>methylation was found in two individuals, locus-specific somatic <it>MLH1 </it>hypermethylation explained the majority of sporadic early onset MSI-H colon cancer cases. Our data do not suggest an intrinsic tendency for CpG island hypermethylation in these early onset MSI-H tumors other than through somatic mutation of <it>BRAF</it>.</p

A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorder

Autism spectrum disorder (ASD) is a highly heritable disorder of complex and heterogeneous aetiology. It is primarily characterized by altered cognitive ability including impaired language and communication skills and fundamental deficits in social reciprocity. Despite some notable successes in neuropsychiatric genetics, overall, the high heritability of ASD (~90%) remains poorly explained by common genetic risk variants. However, recent studies suggest that rare genomic variation, in particular copy number variation, may account for a significant proportion of the genetic basis of ASD. We present a large scale analysis to identify candidate genes which may contain low-frequency recessive variation contributing to ASD while taking into account the potential contribution of population differences to the genetic heterogeneity of ASD. Our strategy, homozygous haplotype (HH) mapping, aims to detect homozygous segments of identical haplotype structure that are shared at a higher frequency amongst ASD patients compared to parental controls. The analysis was performed on 1,402 Autism Genome Project trios genotyped for 1 million single nucleotide polymorphisms (SNPs). We identified 25 known and 1,218 novel ASD candidate genes in the discovery analysis including CADM2, ABHD14A, CHRFAM7A, GRIK2, GRM3, EPHA3, FGF10, KCND2, PDZK1, IMMP2L and FOXP2. Furthermore, 10 of the previously reported ASD genes and 300 of the novel candidates identified in the discovery analysis were replicated in an independent sample of 1,182 trios. Our results demonstrate that regions of HH are significantly enriched for previously reported ASD candidate genes and the observed association is independent of gene size (odds ratio 2.10). Our findings highlight the applicability of HH mapping in complex disorders such as ASD and offer an alternative approach to the analysis of genome-wide association data

Dissolved organic matter uptake in a temperate seagrass ecosystem

Engeland, Tom Van et al.We assessed the utilization of inorganic and organic nitrogen compounds of different complexity by primary producers and bacteria in a seagrass ecosystem. Using double-labeled (13C and 15N) substrates, the net transfers from the dissolved nitrogen and carbon pools to phytoplankton, planktonic bacteria, epiphytes, seagrasses (Zostera noltii and Cymodocea nodosa), and a macroalga (Caulerpa prolifera) were quantified in field incubations. Phytoplankton was the largest nitrogen sink, followed by the epiphytic community. In contrast, carbon fixation was dominated by the macrophytes. Although compartment-specific variations existed, NH4 + was generally preferred over NO3 - and urea. Specific uptake rates of individual amino acids were inversely related to their C:N ratio and their structural complexity (glycine > L-leucine > L-phenylalanine). In addition, biomarker-specific measurements (polar lipid-derived fatty acids and D-alanine) indicated increasing bacterial contributions to carbon uptake with increasing amino acid structural complexity. All primary producers acquired nitrogen from a complex pool of algae-derived dissolved organic matter (DOM), but algae-derived dissolved organic carbon (DOC) was almost exclusively used by the planktonic compartment. In contrast, a similar complex pool of bacteriaderived DOM was not taken up in significant quantities by any of the primary producers. Our results illustrate that dissolved organic nitrogen (DON) can provide bioavailable nitrogen to primary producers and bacteria in seagrass ecosystems on very short time-scales, and DON and DOC dynamics are largely uncoupled and must be investigated as 2 separate interacting pools. © Inter-Research 2013.Peer Reviewe