Measuring and comparing structural fluctuation patterns in large protein datasets

Motivation: The function of a protein depends not only on its structure but also on its dynamics. This is at the basis of a large body of ex- perimental and theoretical work on protein dynamics. Further insight into the dynamics?function relationship can be gained by studying the evolutionary divergence of protein motions. To investigate this, we need appropriate comparative dynamics methods. The most used dynamical similarity score is the correlation between the root mean square fluctuations (RMSF) of aligned residues. Despite its usefulness, RMSF is in general less evolutionarily conserved than the native struc- ture. A fundamental issue is whether RMSF is not as conserved as structure because dynamics is less conserved or because RMSF is not the best property to use to study its conservation. Results: We performed a systematic assessment of several scores that quantify the (dis)similarity between protein fluctuation patterns. We show that the best scores perform as well as or better than struc- tural dissimilarity, as assessed by their consistency with the SCOP classification. We conclude that to uncover the full extent of the evo- lutionary conservation of protein fluctuation patterns, it is important to measure the directions of fluctuations and their correlations between sites.Fil: Fuglebakk, Edvin. University of Bergen; NoruegaFil: Echave, Julian. Universidad Nacional de San Martín. Escuela de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Reuter, Nathalie. University of Bergen; Norueg

Skreitokt 2021 - Kartlegging av gytebestanden av skrei i 2021

Toktnummer 2021204Skreitokt 2021 - Kartlegging av gytebestanden av skrei i 2021Toktets akustiske dekning av torsk, hyse og sei dekket kystområdet fra 71° nord sørover til og med Røstbanken, samt Vestfjorden, og ga et mengdeanslag på 233 tusen tonn moden skrei (aldersgruppene eldre enn 5 år). Som i 2020 var gyteinnsiget lavere enn ventet ut i fra tidligere bestandsberegninger. Det var også vesentlig lavere enn de to foregående år, og nede på under 2018 nivå. Nær 70% av den gytende skreien så ut til å skrive seg fra 9, 10 og 11 år gammel fisk. Dette var de samme årsklassene som dominerte gyteinnsiget i 2020. I tillegg til at gyteinnsiget var lite, var det vesentlig forskjøvet mot ytre områder i forhold til tidligere år. Gytende torskeforekomster i Vestfjorden var vesentlig mindre enn tidligere år, også sammenlignet med 2018 hvor innsiget totalt sett var av sammenlignbar størrelse. De torskeobservasjonene som ble gjort i Vestfjorden var i hovedsak kysttorsk. Observasjoner av torskeegg var i samsvar med observasjonene av gytefisk; svært lave verdier i Vestfjorden, men mer gjennomsnittlige observasjoner på utsiden. Hydrografiske observasjoner med CTD (salinitet, temperatur og dyp) viste normale forhold i hele toktområdet.publishedVersio

Evaluating assumptions behind design-based estimators for unreported catches

Understanding a fishery’s impact on the marine ecosystem requires a quantification of total catches, which include unreported catches. For recent years in Norwegian waters, unreported catches have been estimated using data collected by the Norwegian Reference Fleet, a fisher self-sampling programme that regularly gathers data on catches of all species (including unwanted bycatches and discards). In this study, we focused on the use of design-based estimators for total catches in offshore fisheries, which have previously been used to estimate discards in the Norwegian coastal gillnet fisheries. After adapting the current methodology to the data available in offshore fisheries, we explored the assumptions behind both unit- and ratio-based estimators, and the effect of ignoring the cluster sampling design. Using a jack-knife resampling method to estimate the true bias in estimates of total catches and associated variability, we found that ignoring the cluster sampling design tended to underestimate the variability, which lead to occurrences where unreported catches were statistically detected when in fact there was too much uncertainty to make such a conclusion. Further validations suggested the cluster unit estimator is not unbiased as theoretically expected due to the sampling design favouring the selection of more active vessels. We therefore concluded that the unit and ratio cluster estimators are applied and compared, as per best practices.publishedVersio

Skreitokt 2023 — Kartlegging av gytebestanden av skrei i 2023

Toktet dekket kystområdet fra 70° nord sørover til og med Røstbanken, samt Vestfjorden, og ga et mengdeanslag på 128 tusen tonn moden skrei (aldersgruppene eldre enn 5 år). Dette er noe lavere enn de siste års resultat, og på størrelse med skreiinnsigene vi så tidlig på 2000-tallet. Ettersom bestanden av Nordøst-arktisk torsk er beregnet å være nedadgående, og ettersom skreinnsigene i 2021 og 2022 også var små, er resultatet i tråd med forventning. Hovedvekten av den gytende skreien var fisk som var mellom 7 og 9 år gamle.Skreitokt 2023 — Kartlegging av gytebestanden av skrei i 2023publishedVersio

Evaluation of sampling strategies for age determination of cod (Gadus morhua) sampled at the North Sea International Bottom Trawl Survey

The North Sea cod stock assessment is based on indices of abundance-at-age from fishery-independent bottom trawl surveys. The age structure of the catch is estimated by sampling fish for otoliths collection in a length-stratified manner from trawl hauls. Since age determination of fish is costly and time consuming, only a fraction of fish is sampled for age from a larger sample of the length distribution and an age–length key (ALK) is then used to obtain the age distribution. In this study, we evaluate ALK estimators for calculating the indices of abundance-at-age, with and without the assumption of constant age–length structures over relatively large areas. We show that the ALK estimators give similar point estimates of abundance-at-age and yield similar performance with respect to precision. We also quantify the uncertainty of indices of abundance and examine the effect of reducing the number of fish sampled for age determination on precision. For various subsampling strategies of otoliths collection, we show that one fish per 5-cm-length group width per trawl haul is sufficient and the total number of fish subsampled for age from trawl surveys could be reduced by at least half (50%) without appreciable loss in precision.publishedVersio

A simulation approach to assessing bias in a fisheries self-sampling programme

The hierarchical structure and non-probabilistic sampling in fisher self-sampling programmes makes it difficult to evaluate biases in total catch estimates. While so, it is possible to evaluate bias in the reported component of catches, which can then be used to infer likely bias in total catches. We assessed bias in the reported component of catches for 18 species in the Barents Sea trawl and longline fisheries by simulating 2000 realizations of the Norwegian Reference Fleet sampling programme using the mandatory catch reporting system, then for each realization we estimated fleet-wide catches using simple design-based estimators and quantified bias. We then inserted variations (e.g. simple random and systematic sampling) at different levels of the sampling design (sampling frame, vessel, and operation) to identify important factors and trends affecting bias in reported catches. We found that whilst current sampling procedures for fishing operations were not biased, non-probabilistic vessel sampling resulted in bias for some species. However, we concluded this was typically within the bounds of expected variation from probabilistic sampling. Our results highlight the risk of applying these simple estimators to all species. We recommend that future estimates of total catches consider alternative estimators and more conservative estimates of uncertainty where necessary.publishedVersio

A novel probabilistic survey method for at sea sampling in pelagic fisheries – the Norwegian catch sampling lottery

Reliable information on the age- and size-structure of the annual harvest of major commercial fish stocks is crucial input to analytical stock assessments. Such information is usually obtained from landing data (census of biomass) combined with biological sampling of selected landings. In this paper we describe a novel catch sampling method that we have developed and implemented for the major Norwegian pelagic fisheries that have annual landings around 1 million tonnes in recent years. The new sampling regime gradually implemented from 2018 is based on three pillars; probabilistic sampling of hauls, use of electronic logbook, and co-sampling. By a minor modification of the electronic logbook the vessels in the pelagic fishery now report the catch quantity at haul level immediately after each catch operation. This electronic report is automatically submitted to the Institute of Marine Research (IMR), where a random draw by computer in real time determines if a small sample of fish should be taken from that haul by the fishermen and be frozen and transported to IMR for analysis. Nearly 100% of the hauls annually goes through this “lottery”, and compliance (fraction of samples received) is currently around 60% and increasing. The sampling regime has been operationalized in cooperation with the fishing industry.publishedVersio

StoX: An open source software for marine survey analyses

Scientists across the globe conduct survey programs to monitor and characterize abundance, population structure, biodiversity and geographical distributions. To assess the state of marine fish and zooplankton, population surveys are often repeated annually using standardized sampling protocols and analysis techniques to establish trustworthy stock status. However, although transparency and repeatability are recognised as important principles of this process, it is often difficult to obtain comprehensive documentation of metadata and data processing steps. This is particularly challenging for workflows that include manual processing steps. StoX was principally built to process research‐vessel survey data, and we have included several standard survey estimation models. The software was developed to be robust and versatile and aimed at the open source community, such that users could easily build their own models. StoX is fully integrated with R to utilize the large number of R‐packages and enable any StoX function and stock estimation model to be controlled using R. There has been a large need for a freely available software for research–vessel survey estimation, and StoX is tested in surveys carried out in four continents and is the official tool for many important fish stock surveys. The basic workflow and transparency principles of StoX, together with a customizable GUI, makes StoX applicable for any geographically coded surveys. Future versions of StoX will include statistical models to estimate the catch composition in commercial fisheries. In fields such as conservation management, there is also a need to document the estimation methods, and additional estimation and analyses models, including biodiversity indices are currently implemented. In parallel, we envision a closer web service integration with existing international and national data centres.publishedVersio

WEBnm@ v2.0: Web server and services for comparing protein flexibility

Background: Normal mode analysis (NMA) using elastic network models is a reliable and cost-effective computational method to characterise protein flexibility and by extension, their dynamics. Further insight into the dynamics–function relationship can be gained by comparing protein motions between protein homologs and functional classifications. This can be achieved by comparing normal modes obtained from sets of evolutionary related proteins. Results: We have developed an automated tool for comparative NMA of a set of pre-aligned protein structures. The user can submit a sequence alignment in the FASTA format and the corresponding coordinate files in the Protein Data Bank (PDB) format. The computed normalised squared atomic fluctuations and atomic deformation energies of the submitted structures can be easily compared on graphs provided by the web user interface. The web server provides pairwise comparison of the dynamics of all proteins included in the submitted set using two measures: the Root Mean Squared Inner Product and the Bhattacharyya Coefficient. The Comparative Analysis has been implemented on our web server for NMA, WEBnm@, which also provides recently upgraded functionality for NMA of single protein structures. This includes new visualisations of protein motion, visualisation of inter-residue correlations and the analysis of conformational change using the overlap analysis. In addition, programmatic access to WEBnm@ is now available through a SOAP-based web service. Webnm@ is available at http://apps.cbu.uib.no/webnma. Conclusion: WEBnm@ v2.0 is an online tool offering unique capability for comparative NMA on multiple protein structures. Along with a convenient web interface, powerful computing resources, and several methods for mode analyses, WEBnm@ facilitates the assessment of protein flexibility within protein families and superfamilies. These analyses can give a good view of how the structures move and how the flexibility is conserved over the different structures.publishedVersio