Limited parallelism in genetic adaptation to brackish water bodies in European sprat and Atlantic herring.

The European sprat is a small plankton-feeding clupeid present in the northeastern Atlantic Ocean, the Mediterranean Sea as well as in the brackish Baltic Sea and Black Sea. This species is the target of a major fishery and therefore an accurate characterization of its genetic population structure is crucial to delineate proper stock assessments that aid ensuring the fishery's sustainability. Here we present (i) a draft genome assembly, (ii) pooled whole genome sequencing of 19 population samples covering most of the species' distribution range, and (iii) the design and test of a SNP-chip resource and use this to validate the population structure inferred from pooled sequencing. These approaches revealed, using the populations sampled here, three major groups of European sprat: Oceanic, Coastal, and Brackish with limited differentiation within groups even over wide geographical stretches. Genetic structure is largely driven by six large putative inversions that differentiate Oceanic and Brackish sprats, while Coastal populations display intermediate frequencies of haplotypes at each locus. Interestingly, populations from the Baltic and the Black Seas share similar frequencies of haplotypes at these putative inversions despite their distant geographic location. The closely related clupeids European sprat and Atlantic herring both show genetic adaptation to the brackish Baltic Sea, providing an opportunity to explore the extent of genetic parallelism. This analysis revealed limited parallelism because out of 125 independent loci detected in the Atlantic herring, three showed sharp signals of selection that overlapped between the two species and contained single genes such as PRLRA, which encodes the receptor for prolactin, a freshwater-adapting hormone in euryhaline species, and THRB, a receptor for thyroid hormones, important both for metabolic regulation and the development of red cone photoreceptors.

Modelling seasonal and geographical n-3 polyunsaturated fatty acid contents in marine fish from the Northeast Atlantic Ocean.

Demand for n-3 polyunsaturated fatty acids (n-3 PUFAs) exceeds supply. Large-scale studies on effects of season and geography of n-3 PUFAs in marine fish from the Northeast Atlantic Ocean (NEAO) may be used to optimize utilization and improve nutrition security. Using a sinusoid model, seasonal cycles of n-3 PUFAs were determined and found to be species-specific and clearly pronounced for the pelagic zooplankton feeding species. The Greenland halibut showed very little seasonal variation. The n-3 PUFA content in North Sea autumn-spawning (NSAS) herring peaked in summer, while Norwegian spring-spawning (NSS) herring and mackerel had their peak in autumn. A time shift of peaks in n-3 PUFAs between the two herring stocks was detected, likely due to different spawning strategies in addition to a delay of n-3 PUFAs flux in the northern regions of the NEAO. This study demonstrates that consideration of nutrient contents, such as n-3 PUFAs, when organizing and structuring fishery approaches may improve overall nutritional yield. Based on total annual Norwegian fish landings and seasonal variation in n-3 PUFA contents, n-3 PUFAs yield could theoretically be increased from 13.79 kilo ton per year from the current fishing tactics, to 15.54 if the pelagic species were only caught during the time of their seasonal n-3 PUFA peaks. Pelagic fish is a good source for dietary n-3 PUFAs, but harvest timing will also influence n-3 PUFAs intake by human consumers. One portion of fatty fish harvested during winter/spring may not meet the weekly intake reference nutritional guidelines for n-3 PUFAs. Marine n-3 PUFAs yields also varied geographically and decreased southwards, with the lowest values in Skagerrak. This study can serve as a model to understand patterns of reproductive cycles and geographical distribution of n-3 PUFAs in fatty fish from the NEAO and the novel approach may be useful to support sustainable, seasonal fishing programmes for optimization of n-3 PUFAs yields.

Diatom-inspired silicification process for development of green flexible silica composite aerogels.

In this study, we have developed novel biomimetic silica composite aerogels and cryogels for the first time, drawing inspiration from the natural diatom's silicification process. Our biomimetic approach involved the modification of tyrosinase-mediated oxidized silk fibroin (SFO) surfaces with polyethyleneimine (PEI). This modification introduced ample amine groups onto the SF polymer, which catalyzed the silicification of the SFO-PEI gel surface with silicic acid. This process emulates the catalytic function of long-chain polyamines and silaffin proteins found in diatoms, resulting in a silica network structure on the primary SFO-PEI network gel's surface. The SFO-PEI gel matrix played a dual role in this process: (1) It provided numerous amine functional groups that directly catalyzed the silicification of silicic acid on the porous structure's exterior surface, without encapsulating the created silica network in the gel. (2) It served as a flexible mechanical support facilitating the creation of the silica network. As a result, the final ceramic composite exhibits a mechanically flexible nature (e.g., cyclic compressibility up to 80% strain), distinguishing it from conventional composite aerogels. By mimicking the diatom's silicification process, we were able to simplify the development of silica-polymer composite aerogels. It eliminates the need for surfactants, multi-step procedures involving solvent exchange, and gel washing. Instead, the reaction occurs under mild conditions, streamlining the composite aerogels fabrication process.

How Fish Population Genomics Can Promote Sustainable Fisheries: A Road Map.

Maintenance of genetic diversity in marine fishes targeted by commercial fishing is a grand challenge for the future. Most of these species are abundant and therefore important for marine ecosystems and food security. Here, we present a road map of how population genomics can promote sustainable fisheries. In these species, the development of reference genomes and whole genome sequencing is key, because genetic differentiation at neutral loci is usually low due to large population sizes and gene flow. First, baseline allele frequencies representing genetically differentiated populations within species must be established. These can then be used to accurately determine the composition of mixed samples, forming the basis for population demographic analysis to inform sustainably set fish quotas. SNP-chip analysis is a cost-effective method for determining baseline allele frequencies and for population identification in mixed samples. Finally, we describe how genetic marker analysis can transform stock identification and management.

Development and first results of a national databank on care and treatment outcome after traumatic brain injury.

PURPOSE: In absence of comprehensive data collection on traumatic brain injury (TBI), the German Society for Neurosurgery (DGNC) and the German Society for Trauma Surgery (DGU) developed a TBI databank for German-speaking countries. METHODS: From 2016 to 2020, the TBI databank DGNC/DGU was implemented as a module of the TraumaRegister (TR) DGU and tested in a 15-month pilot phase. Since its official launch in 2021, patients from the TR-DGU (intermediate or intensive care unit admission via shock room) with TBI (AIS head ≥ 1) can be enrolled. A data set of > 300 clinical, imaging, and laboratory variables, harmonized with other international TBI data collection structures is documented, and the treatment outcome is evaluated after 6- and 12 months. RESULTS: For this analysis, 318 patients in the TBI databank could be included (median age 58 years; 71% men). Falls were the most common cause of injury (55%), and antithrombotic medication was frequent (28%). Severe or moderate TBI were only present in 55% of patients, while 45% suffered a mild injury. Nevertheless, intracranial pathologies were present in 95% of brain imaging with traumatic subarachnoid hemorrhages (76%) being the most common. Intracranial surgeries were performed in 42% of cases. In-hospital mortality after TBI was 21% and surviving patients could be discharged after a median hospital stay of 11 days. At the 6-and 12 months follow-up, a favorable outcome was achieved by 70% and 90% of the participating TBI patients, respectively. Compared to a European cohort of 2138 TBI patients treated in the ICU between 2014 and 2017, patients in the TBI databank were already older, frailer, fell more commonly at home. CONCLUSION: Within five years, the TBI databank DGNC/DGU of the TR-DGU could be established and is since then prospectively enrolling TBI patients in German-speaking countries. With its large and harmonized data set and a 12-month follow-up, the TBI databank is a unique project in Europe, already allowing comparisons to other data collection structures and indicating a demographic change towards older and frailer TBI patients in Germany.

Glutamic acid decarboxylase antibody-associated neurological syndromes: Clinical and antibody characteristics and therapy response.

BACKGROUND: Antibodies against glutamic acid decarboxylase (GAD-abs) at high serum levels are associated with diverse autoimmune neurological syndromes (AINS), including cerebellar ataxia, epilepsy, limbic encephalitis and stiff-person syndrome. The impact of low serum GAD-ab levels in patients with suspected AINS remains controversial. Specific intrathecal GAD-ab synthesis may serve as a marker for GAD-ab-associated nervous system autoimmunity. We present characteristics of a multicentric patient cohort with suspected AINS associated with GAD antibodies (SAINS-GAD+) and explore the relevance of serum GAD-ab levels and intrathecal GAD-ab synthesis. METHODS: All patients with SAINS-GAD+ included in the registry of the German Network for Research on Autoimmune Encephalitis (GENERATE) from 2011 to 2019 were analyzed. High serum GAD-ab levels were defined as RIA>2000 U/mL, ELISA>1000 U/mL, or as a positive staining pattern on cell-based assays. RESULTS: One-hundred-one patients were analyzed. In descending order they presented with epilepsy/limbic encephalitis (39%), cerebellar ataxia (28%), stiff person syndrome (22%), and overlap syndrome (12%). Immunotherapy was administered in 89% of cases with improvements in 46%. 35% of SAINS-GAD+ patients had low GAD-ab serum levels. Notably, unmatched oligoclonal bands in CSF but not in serum were more frequent in patients with low GAD-ab serum levels. GAD-ab-levels (high/low) and intrathecal GAD-ab synthesis (present or not) did not impact clinical characteristics and outcome. CONCLUSIONS: Overall, immunotherapy in SAINS-GAD+ was moderately effective. Serum GAD-ab levels and the absence or presence of intrathecal GAD-ab synthesis did not predict clinical characteristics or outcomes in SAINS-GAD+. The detection of unmatched oligoclonal bands might outweigh low GAD-ab serum levels.

Prospective observational cohort study on epidemiology, treatment and outcome of patients with traumatic brain injury (TBI) in German BG hospitals.

OBJECTIVES: Since 2000/2001, no large-scale prospective studies addressing traumatic brain injury (TBI) epidemiology in Germany have been published. Our aim was to look for a possible shift in TBI epidemiology described in other European countries, to look for possible changes in TBI management and to identify predictors of 1-year outcome especially in patients with mild TBI. DESIGN: Observational cohort study. SETTING: All patients suffering from a TBI of any degree between 1 October 2014 and 30 September 2015, and who arrived in one of the seven participating BG hospitals within 24 hours after trauma, were included. PARTICIPANTS: In total, 3514 patients were included. OUTCOME MEASURES: Initial care, acute hospital care and rehabilitation were documented using standardised documentation forms. A standardised telephone interview was conducted 3 and 12 months after TBI in order to obtain information on outcome. RESULTS: Peaks were identified in males in the early 20s and mid-50s, and in both sexes in the late 70s, with 25% of all patients aged 75 or older. A fall was the most frequent cause of TBI, followed by traffic accidents (especially bicyclists). The number of head CT scans increased, and the number of conventional X-rays of the skull decreased compared with 2000/2001. Besides, more patients were offered rehabilitation than before. Though most TBI were classified as mild, one-third of the patients participating in the telephone interview after 12 months still reported troubles attributed to TBI. Negative predictors in mild TBI were female gender, intracranial bleeding and Glasgow Coma Scale (GCS) 13/14. CONCLUSION: The observed epidemiologic shift in TBI (ie, elderly patients, more falls, more bicyclists) calls for targeted preventive measures. The heterogeneity behind the diagnosis 'mild TBI' emphasises the need for defining subgroups not only based on GCS.

Genetic response to human-induced habitat changes in the marine environment: A century of evolution of European sprat in Landvikvannet, Norway.

Habitat changes represent one of the five most pervasive threats to biodiversity. However, anthropogenic activities also have the capacity to create novel niche spaces to which species respond differently. In 1880, one such habitat alterations occurred in Landvikvannet, a freshwater lake on the Norwegian coast of Skagerrak, which became brackish after being artificially connected to the sea. This lake is now home to the European sprat, a pelagic marine fish that managed to develop a self-recruiting population in barely few decades. Landvikvannet sprat proved to be genetically isolated from the three main populations described for this species; that is, Norwegian fjords, Baltic Sea, and the combination of North Sea, Kattegat, and Skagerrak. This distinctness was depicted by an accuracy self-assignment of 89% and a highly significant F ST between the lake sprat and each of the remaining samples (average of ≈0.105). The correlation between genetic and environmental variation indicated that salinity could be an important environmental driver of selection (3.3% of the 91 SNPs showed strong associations). Likewise, Isolation by Environment was detected for salinity, although not for temperature, in samples not adhering to an Isolation by Distance pattern. Neighbor-joining tree analysis suggested that the source of the lake sprat is in the Norwegian fjords, rather than in the Baltic Sea despite a similar salinity profile. Strongly drifted allele frequencies and lower genetic diversity in Landvikvannet compared with the Norwegian fjords concur with a founder effect potentially associated with local adaptation to low salinity. Genetic differentiation (F ST) between marine and brackish sprat is larger in the comparison Norway-Landvikvannet than in Norway-Baltic, which suggests that the observed divergence was achieved in Landvikvannet in some 65 generations, that is, 132 years, rather than gradually over thousands of years (the age of the Baltic Sea), thus highlighting the pace at which human-driven evolution can happen.

Ecological adaptation in Atlantic herring is associated with large shifts in allele frequencies at hundreds of loci.

Atlantic herring is widespread in North Atlantic and adjacent waters and is one of the most abundant vertebrates on earth. This species is well suited to explore genetic adaptation due to minute genetic differentiation at selectively neutral loci. Here, we report hundreds of loci underlying ecological adaptation to different geographic areas and spawning conditions. Four of these represent megabase inversions confirmed by long read sequencing. The genetic architecture underlying ecological adaptation in herring deviates from expectation under a classical infinitesimal model for complex traits because of large shifts in allele frequencies at hundreds of loci under selection.

Reconstruction of the birth of a male sex chromosome present in Atlantic herring.

The mechanisms underlying sex determination are astonishingly plastic. Particularly the triggers for the molecular machinery, which recalls either the male or female developmental program, are highly variable and have evolved independently and repeatedly. Fish show a huge variety of sex determination systems, including both genetic and environmental triggers. The advent of sex chromosomes is assumed to stabilize genetic sex determination. However, because sex chromosomes are notoriously cluttered with repetitive DNA and pseudogenes, the study of their evolution is hampered. Here we reconstruct the birth of a Y chromosome present in the Atlantic herring. The region is tiny (230 kb) and contains only three intact genes. The candidate male-determining gene BMPR1BBY encodes a truncated form of a BMP1B receptor, which originated by gene duplication and translocation and underwent rapid protein evolution. BMPR1BBY phosphorylates SMADs in the absence of ligand and thus has the potential to induce testis formation. The Y region also contains two genes encoding subunits of the sperm-specific Ca2+ channel CatSper required for male fertility. The herring Y chromosome conforms with a characteristic feature of many sex chromosomes, namely, suppressed recombination between a sex-determining factor and genes that are beneficial for the given sex. However, the herring Y differs from other sex chromosomes in that suppression of recombination is restricted to an ∼500-kb region harboring the male-specific and sex-associated regions. As a consequence, any degeneration on the herring Y chromosome is restricted to those genes located in the small region affected by suppressed recombination.

Genetic factors have a major effect on growth, number of vertebrae and otolith shape in Atlantic herring (Clupea harengus).

Atlantic herring, Clupea harengus, have complex population structures. Mixing of populations is known, but the extent of connectivity is still unclear. Phenotypic plasticity results in divergent phenotypes in response to environmental factors. A marked salinity gradient occurs from Atlantic Ocean (salinity 35) into the Baltic Sea (salinity range 2-12). Herring from both habitats display phenotypic and genetic variability. To explore how genetic factors and salinity influence phenotypic traits like growth, number of vertebrae and otolith shape an experimental population consisting of Atlantic purebreds and Atlantic/Baltic F1 hybrids were incubated and co-reared at two different salinities, 16 and 35, for three years. The F1-generation was repeatedly sampled to evaluate temporal variation. A von Bertalanffy growth model indicated that reared Atlantic purebreds had a higher maximum length (26.2 cm) than Atlantic/Baltic hybrids (24.8 cm) at salinity 35, but not at salinity 16 (25.0 and 24.8 cm, respectively). In contrast, Atlantic/Baltic hybrids achieved larger size-at-age than the wild caught Baltic parental group. Mean vertebral counts and otolith aspect ratios were higher for reared Atlantic purebreds than Atlantic/Baltic hybrids, consistent with the differences between parental groups. There were no significant differences in vertebral counts and otolith aspect ratios between herring with the same genotype but raised in different salinities. A Canonical Analysis of Principal Coordinates was applied to analyze the variation in wavelet coefficients that described otolith shape. The first discriminating axis identified the differences between Atlantic purebreds and Atlantic/Baltic hybrids, while the second axis represented salinity differences. Assigning otoliths based on genetic groups (Atlantic purebreds vs. Atlantic/Baltic hybrids) yielded higher classification success (~90%) than based on salinities (16 vs. 35; ~60%). Our results demonstrate that otolith shape and vertebral counts have a significant genetic component and are therefore useful for studies on population dynamics and connectivity.

Comparative biology and population mixing among local, coastal and offshore Atlantic herring (Clupea harengus) in the North Sea, Skagerrak, Kattegat and western Baltic.

The population structure of Atlantic herring (Clupea harengus) from 13 local, coastal and offshore areas of the North Sea, Skagerrak, Kattegat and western Baltic (northeast Atlantic) was studied using biological and environmental data from 1970-2015. The objective was to identify distinct populations by comparing variability in the temporal and spatial phenotypic characteristics and evaluate the potential for mixing of populations in time and space. The populations varied in biological characteristics such as mean vertebral counts (VS), growth and maturity ogives. Generalized additive models indicated temporally stable VS in the North Sea and western Baltic, whereas intra-annual temporal variation of VS occurred in other areas. High variability of VS within a population was not affected by environmental factors such as temperature and salinity. Consequently, seasonal VS variability can be explained by the presence or absence of herring populations as they migrate between areas. The three main populations identified in this paper correspond to the three managed stocks in this area: Norwegian spring spawners (NSS), western Baltic spring spawners (WBSS) and North Sea autumn spawners (NSAS). In addition, several local populations were identified in fjords or lakes along the coast, but our analyses could not detect direct mixing of local populations with the three main populations. Our results highlight the importance of recognizing herring dynamics and understanding the mixing of populations as a challenge for management of herring.

AFM-based quantification of conformational changes in DNA caused by reactive oxygen species.

Radical induced modification of DNA plays an important role in many pathological pathways like cancer development, aging, etc. In this work, we quantify radical-induced DNA damage that causes transitions from double to single stranded DNA using atomic force microscopy (AFM). The plasmid pBR322 is attacked by free hydroxyl radicals that are produced by Fenton's reaction; the strength of the radical attack is controlled via the ratio of hydroxyl radical molecules to DNA base pairs. The extent of DNA modification is assessed by AFM tapping mode (TM) imaging of the plasmids (after adsorption onto PAH-functionalized mica) in air. As single stranded DNA chains (height ∼2 Å) are much smaller than intact DNA strands (∼5 Å), their fraction can be quantified based on the height distribution, which allows a simplified data analysis in comparison to similar AFM-based approaches. It is found that the amount of damaged DNA strands increases with increasing strength of radical attack, and decreases if ROS scavengers like sodium acetate are added. Competition curves are calculated for the interaction of hydroxyl radicals with DNA and sodium acetate, which finally allows calculation of relative rate constants for the respective reactions.

Effects of reactive oxygen species on single polycation layers.

Positively charged, branched polyethylenimine (PEI) adsorbed onto silicon wafers and silica surfaces are attacked by free hydroxyl radicals. With AFM colloid probe technique, the surface forces between PEI layers are measured. Force profiles show that an electrostatic repulsion dominates the surface forces between freshly deposited PEI layers. After radical attack, both surface potential and surface charge density are reduced by a factor of about 0.5, while the Debye length remains unchanged. Adsorbed gold nanoparticles and force volume measurements show a homogeneous distribution of the surface charge on length scales between 40 nm and 30 µm. For radical attacked PEI layers, we find a 10% decrease of saturation coverage of gold nanoparticles. This is consistent with the decreased surface charge density, if the electrostatic three-body interaction is taken into account. Nevertheless, the NP adsorption kinetics are slowed down suggesting that the PEI layer is inhomogeneous on the nm-scale after radical attack.