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Abstract Ocean oxygen content is decreasing with global change. A major challenge for modelling future declines in oxygen concentration is our lack of knowledge of the natural variability associated with marine oxygen inventory on interannual and multidecadal timescales. Here, we present 10 annually resolved 200 year-long records of denitrification, a marker of deoxygenation, from a varved sedimentary archive in the North Pacific oxygen minimum zone covering key periods over the last glacial–interglacial cycle. Spectral analyses on these records reveal strong signals at periodicities typical of today’s Atlantic multidecadal oscillation. Modern subsurface circulation reanalyses regressed on the positive Atlantic and Pacific Climatic Oscillation indices further confirm that North Atlantic temperature patterns are the main control on the subsurface zonal circulation and therefore the most likely dominant driver of oxygen variability in the tropical Pacific. With currently increasing temperatures in the Northern Hemisphere high latitudes and North Atlantic, we suggest deoxygenation will intensify in the region.

Abstract Marine sedimentary rocks deposited across the Neoproterozoic Cryogenian Snowball interval, ~720-635 million years ago, suggest that post-Snowball fertilization of shallow continental margin seawater with phosphorus accelerated marine primary productivity, ocean-atmosphere oxygenation, and ultimately the rise of animals. However, the mechanisms that sourced and delivered bioavailable phosphate from land to the ocean are not fully understood. Here we demonstrate a causal relationship between clay mineral production by the melting Sturtian Snowball ice sheets and a short-lived increase in seawater phosphate bioavailability by at least 20-fold and oxygenation of an immediate post-Sturtian Snowball ocean margin. Bulk primary sediment inputs and inferred dissolved seawater phosphate dynamics point to a relatively low marine phosphate inventory that limited marine primary productivity and seawater oxygenation before the Sturtian glaciation, and again in the later stages of the succeeding interglacial greenhouse interval.

Abstract Repetitive DNA make up a considerable fraction of most eukaryotic genomes. In fish, transposable element (TE) activity has coincided with rapid species diversification. Here, we annotated the repetitive content in 100 genome assemblies, covering the major branches of the diverse lineage of teleost fish. We investigated if TE content correlates with family level net diversification rates and found support for a weak negative correlation. Further, we demonstrated that TE proportion correlates with genome size, but not to the proportion of short tandem repeats (STRs), which implies independent evolutionary paths. Marine and freshwater fish had large differences in STR content, with the most extreme propagation detected in the genomes of codfish species and Atlantic herring. Such a high density of STRs is likely to increase the mutational load, which we propose could be counterbalanced by high fecundity as seen in codfishes and herring.

The volume of human carbon (δ13C) and nitrogen (δ15N) isotope data produced in archaeological research has increased markedly in recent years. However, knowledge of bone remodelling, its impact on isotope variation, and the temporal resolution of isotope data remains poorly understood. Varied remodelling rates mean different elements (e.g., femur and rib) produce different temporal signals but little research has examined intra-element variability. This study investigates human bone remodelling using osteon population density and the relationship with carbon and nitrogen isotope data at a high resolution, focusing on variation through femoral cross-sections, from periosteal to endosteal surfaces. Results demonstrate considerable differences in isotope values between cross-sectional segments of a single fragment, by up to 1.3‰ for carbon and 1.8‰ for nitrogen, illustrating the need for standardised sampling strategies. Remodelling also varies between bone sections, occurring predominantly within the endosteal portion, followed by the midcortical and periosteal. Therefore, the endosteal portion likely reflects a shorter period of life closer to the time of death, consistent with expectations. By contrast, the periosteal surface provides a longer average, though there were exceptions to this. Results revealed a weak negative correlation between osteon population density and δ15N or δ13C, confirming that remodelling has an effect on isotope values but is not the principal driver. However, a consistent elevation of δ15N and δ13C (0.5‰ average) was found between the endosteal and periosteal regions, which requires further investigation. These findings suggest that, with further research, there is potential for single bone fragments to reconstruct in-life dietary change and mobility, thus reducing destructive sampling.

Abstract Background Interstitial Cystitis (IC) is a chronic inflammatory condition of the bladder with unknown etiology. The aim of this study was to characterize the microbial community present in the urine from IC female patients by 454 high throughput sequencing of the 16S variable regions V1V2 and V6. The taxonomical composition, richness and diversity of the IC microbiota were determined and compared to the microbial profile of asymptomatic healthy female (HF) urine. Results The composition and distribution of bacterial sequences differed between the urine microbiota of IC patients and HFs. Reduced sequence richness and diversity were found in IC patient urine, and a significant difference in the community structure of IC urine in relation to HF urine was observed. More than 90% of the IC sequence reads were identified as belonging to the bacterial genus Lactobacillus, a marked increase compared to 60% in HF urine. Conclusion The 16S rDNA sequence data demonstrates a shift in the composition of the bacterial community in IC urine. The reduced microbial diversity and richness is accompanied by a higher abundance of the bacterial genus Lactobacillus, compared to HF urine. This study demonstrates that high throughput sequencing analysis of urine microbiota in IC patients is a powerful tool towards a better understanding of this enigmatic disease.

Abstract Background Urine within the urinary tract is commonly regarded as "sterile" in cultivation terms. Here, we present a comprehensive in-depth study of bacterial 16S rDNA sequences associated with urine from healthy females by means of culture-independent high-throughput sequencing techniques. Results Sequencing of the V1V2 and V6 regions of the 16S ribosomal RNA gene using the 454 GS FLX system was performed to characterize the possible bacterial composition in 8 culture-negative (Lactobacillus, Prevotella and Gardnerella. The bacterial profiles in the female urine samples studied were complex; considerable variation between individuals was observed and a common microbial signature was not evident. Notably, a significant amount of sequences belonging to bacteria with a known pathogenic potential was observed. The number of operational taxonomic units (OTUs) for individual samples varied substantially and was in the range of 20 - 500. Conclusions Normal female urine displays a noticeable and variable bacterial 16S rDNA sequence richness, which includes fastidious and anaerobic bacteria previously shown to be associated with female urogenital pathology.

Abstract Background Cardiomyopathy syndrome (CMS) is a severe disease affecting large farmed Atlantic salmon. Mortality often appears without prior clinical signs, typically shortly prior to slaughter. We recently reported the finding and the complete genomic sequence of a novel piscine reovirus (PRV), which is associated with another cardiac disease in Atlantic salmon; heart and skeletal muscle inflammation (HSMI). In the present work we have studied whether PRV or other infectious agents may be involved in the etiology of CMS. Results Using high throughput sequencing on heart samples from natural outbreaks of CMS and from fish experimentally challenged with material from fish diagnosed with CMS a high number of sequence reads identical to the PRV genome were identified. In addition, a sequence contig from a novel totivirus could also be constructed. Using RT-qPCR, levels of PRV in tissue samples were quantified and the totivirus was detected in all samples tested from CMS fish but not in controls. In situ hybridization supported this pattern indicating a possible association between CMS and the novel piscine totivirus. Conclusions Although causality for CMS in Atlantic salmon could not be proven for either of the two viruses, our results are compatible with a hypothesis where, in the experimental challenge studied, PRV behaves as an opportunist whereas the totivirus might be more directly linked with the development of CMS.

Abstract Background The vertebrate globin genes encoding the α- and β-subunits of the tetrameric hemoglobins are clustered at two unlinked loci. The highly conserved linear order of the genes flanking the hemoglobins provides a strong anchor for inferring common ancestry of the globin clusters. In fish, the number of α-β-linked globin genes varies considerably between different sublineages and seems to be related to prevailing physico-chemical conditions. Draft sequences of the Atlantic cod genome enabled us to determine the genomic organization of the globin repertoire in this marine species that copes with fluctuating environments of the temperate and Arctic regions. Results The Atlantic cod genome was shown to contain 14 globin genes, including nine hemoglobin genes organized in two unlinked clusters designated β5-α1-β1-α4 and β3-β4-α2-α3-β2. The diverged cod hemoglobin genes displayed different expression levels in adult fish, and tetrameric hemoglobins with or without a Root effect were predicted. The novel finding of maternally inherited hemoglobin mRNAs is consistent with a potential role played by fish hemoglobins in the non-specific immune response. In silico analysis of the six teleost genomes available showed that the two α-β globin clusters are flanked by paralogs of five duplicated genes, in agreement with the proposed teleost-specific duplication of the ancestral vertebrate globin cluster. Screening the genome of extant urochordate and cephalochordate species for conserved globin-flanking genes revealed linkage of RHBDF1, MPG and ARHGAP17 to globin genes in the tunicate Ciona intestinalis, while these genes together with LCMT are closely positioned in amphioxus (Branchiostoma floridae), but seem to be unlinked to the multiple globin genes identified in this species. Conclusion The plasticity of Atlantic cod to variable environmental conditions probably involves the expression of multiple globins with potentially different properties. The interspecific difference in number of fish hemoglobin genes contrasts with the highly conserved synteny of the flanking genes. The proximity of globin-flanking genes in the tunicate and amphioxus genomes resembles the RHBDF1-MPG-α-globin-ARHGAP17-LCMT linked genes in man and chicken. We hypothesize that the fusion of the three chordate linkage groups 3, 15 and 17 more than 800 MYA led to the ancestral vertebrate globin cluster during a geological period of increased atmospheric oxygen content.

Abstract Background Cyanobacteria often produce several different oligopeptides, with unknown biological functions, by nonribosomal peptide synthetases (NRPS). Although some cyanobacterial NRPS gene cluster types are well described, the entire NRPS genomic content within a single cyanobacterial strain has never been investigated. Here we have combined a genome-wide analysis using massive parallel pyrosequencing ("454") and mass spectrometry screening of oligopeptides produced in the strain Planktothrix rubescens NIVA CYA 98 in order to identify all putative gene clusters for oligopeptides. Results Thirteen types of oligopeptides were uncovered by mass spectrometry (MS) analyses. Microcystin, cyanopeptolin and aeruginosin synthetases, highly similar to already characterized NRPS, were present in the genome. Two novel NRPS gene clusters were associated with production of anabaenopeptins and microginins, respectively. Sequence-depth of the genome and real-time PCR data revealed three copies of the microginin gene cluster. Since NRPS gene cluster candidates for microviridin and oscillatorin synthesis could not be found, putative (gene encoded) precursor peptide sequences to microviridin and oscillatorin were found in the genes mdnA and oscA, respectively. The genes flanking the microviridin and oscillatorin precursor genes encode putative modifying enzymes of the precursor oligopeptides. We therefore propose ribosomal pathways involving modifications and cyclisation for microviridin and oscillatorin. The microviridin, anabaenopeptin and cyanopeptolin gene clusters are situated in close proximity to each other, constituting an oligopeptide island. Conclusion Altogether seven nonribosomal peptide synthetase (NRPS) gene clusters and two gene clusters putatively encoding ribosomal oligopeptide biosynthetic pathways were revealed. Our results demonstrate that whole genome shotgun sequencing combined with MS-directed determination of oligopeptides successfully can identify NRPS gene clusters and the corresponding oligopeptides. The analyses suggest independent evolution of all NRPS gene clusters as functional units. Our data indicate that the Planktothrix genome displays evolution of dual pathways (NRPS and ribosomal) for production of oligopeptides in order to maximize the diversity of oligopeptides with similar but functional discrete bioactivities.

Programmering og modellering har i de senere år blitt innført i høyere utdanning og ble innført i skolen med fagfornyelsen fra høsten 2020. Det har skapt behov for mer kunnskap om motivasjon og læring i emner som integrerer programmering som et nytt element i ellers veletablerte fagdisipliner. Denne studien undersøkte motivasjon for beregningsorientering (programmering og modellering) ved studieprogrammet biovitenskap ved Universitetet i Oslo. Spørreundersøkelser basert på Eccles’ forventning-verdi-modell ble gjennomført ved semesterstart og -slutt i to påfølgende år (2018 og 2019), før og etter innføring av krav om matematikk R2 (R2-kravet). Motivasjonsvariabler ble validert ved faktoranalyse og undersøkelse av indre konsistens. Resultatene viste at studentene hadde mye lavere mestringsforventning og mye større interesse for et emne som integrerer programmering i biologi enn for studieprogrammet generelt. Nytteverdien var den sterkeste motiverende faktoren for emnet. Studenter med matematikk R2 hadde litt større mestringsforventning til emnet enn de som ikke hadde denne fordypningen. Studentene med R2 opplevde likevel bare litt mindre utfordring med matematikk i emnet, og ingen forskjell i utfordringer knyttet til programmering i emnet, sammenlignet med studenter uten R2. Samtidig opplevde studenter med R2 litt større utfordring med biologien i emnet, og det viste seg at studenter med full fordypning i R2 hadde mindre biologi fra videregående opplæring enn studenter uten R2. Resultatene drøftes i lys av motivasjonsteori med tanke på implikasjoner for undervisning, inntakskrav og videre forskning.

The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/.

The volume of human carbon (δ13C) and nitrogen (δ15N) isotope data produced in archaeological research has increased markedly in recent years. However, knowledge of bone remodelling, its impact on isotope variation, and the temporal resolution of isotope data remains poorly understood. Varied remodelling rates mean different elements (e.g., femur and rib) produce different temporal signals but little research has examined intra-element variability. This study investigates human bone remodelling using osteon population density and the relationship with carbon and nitrogen isotope data at a high resolution, focusing on variation through femoral cross-sections, from periosteal to endosteal surfaces. Results demonstrate considerable differences in isotope values between cross-sectional segments of a single fragment, by up to 1.3‰ for carbon and 1.8‰ for nitrogen, illustrating the need for standardised sampling strategies. Remodelling also varies between bone sections, occurring predominantly within the endosteal portion, followed by the midcortical and periosteal. Therefore, the endosteal portion likely reflects a shorter period of life closer to the time of death, consistent with expectations. By contrast, the periosteal surface provides a longer average, though there were exceptions to this. Results revealed a weak negative correlation between osteon population density and δ15N or δ13C, confirming that remodelling has an effect on isotope values but is not the principal driver. However, a consistent elevation of δ15N and δ13C (0.5‰ average) was found between the endosteal and periosteal regions, which requires further investigation. These findings suggest that, with further research, there is potential for single bone fragments to reconstruct in-life dietary change and mobility, thus reducing destructive sampling. [ABSTRACT FROM AUTHOR]

Programmering og modellering har i de senere år blitt innført i høyere utdanning og be innført i skolen med fagfornyelsen fra høsten 2020. Det har skapt behov for mer kunnskap om motivasjon og læring i emner som integrerer programmering som et nytt element i ellers veletablerte fagdisipliner. Denne studien undersøkte motivasjon for beregningsorientering (programmering og modellering) ved studieprogrammet biovitenskap ved Universitetet i Oslo. Spørreundersøkelser basert på Eccles’ forventning-verdi-modell ble gjennomført ved semesterstart og -slutt i to påfølgende år, før og etter innføring av krav om matematikk R2 (R2-kravet). Motivasjonsvariabler ble validert ved faktoranalyse og undersøkelse av indre konsistens. Resultatene viste at studentene hadde lavere mestringsforventning og interesse for et emne som integrerer programmering i biologi enn for studieprogrammet generelt. Nytteverdien var den sterkeste motiverende faktoren for emnet. Studenter med matematikk R2 hadde større mestringsforventning til emnet enn de som ikke hadde denne fordypningen, og opplevde mindre utfordring med matematikk og programmering i emnet. Samtidig opplevde disse studentene større utfordring med biologien i emnet, og det viste seg at studenter med full fordypning i matematikk R2 i mindre grad enn studenter uten R2 hadde full fordypning i biologi fra videregående opplæring. Resultatene drøftes i lys av motivasjonsteori med tanke på implikasjoner for undervisning, inntakskrav og videre forskning.

The δ13C composition of Cibicidoides wuellerstorfi and other Cibicidoides spp is an important tool to reconstruct past changes in the deep ocean carbon cycle. The species are expected to match the δ13C of ambient dissolved inorganic carbon (DIC), although it has been recognized that substantial offsets can occur. Here, I present a compilation of modern δ13C and δ18O data for named Cibicidoides species in combination with fully resolved carbonate chemistry at each core location. The data show for C. wuellerstorfi that the offset from the expected value in both carbon (∆13C) and oxygen (∆18O) is correlated with seawater carbonate chemistry. The result is comparable to, but not identical with, published culture experiments in which marine organisms were grown under variable pH‐conditions. Overall, ∆13C in C. wuellerstorfi correlates positively with carbonate saturation, [DIC], and temperature. The three variables together explain 47.1% of the variation in ∆13C. The trend for ∆18O is similar, except that the effect of temperature has been removed through correction with a published δ18O‐temperature equation. Up to 35% of the remaining variation in ∆18O can be explained by ambient carbonate chemistry. Data for other named Cibicidoides species are broadly similar, but are too sparse for a detailed analysis. The results indicate that strongly negative ∆13C occurs predominantly in the deep Atlantic in response to a combination of low [DIC], low temperature, and undersaturation within the lysocline. Implications for paleoceanographic reconstructions are discussed. Key Points: The offset between the measured and expected δ13C and δ18O of Cibicidoides wuellerstorfi correlates with seawater carbonate chemistryNegative ∆13C occurs mainly in the deep Atlantic due to a combination of low temperature, under‐saturation, and low to intermediate dissolved inorganic carbon [ABSTRACT FROM AUTHOR]