Intrinsic post‐ejaculation sperm ageing does not affect offspring fitness in Atlantic salmon

Post‐meiotic sperm ageing, both before ejaculation and after ejaculation, has been shown to negatively affect offspring fitness by lowering the rate of embryonic development, reducing embryonic viability and decreasing offspring condition. These negative effects are thought to be caused by intrinsic factors such as oxidative stress and ATP depletion or extrinsic factors such as temperature and osmosis. Effects of post‐ejaculation sperm ageing on offspring fitness have so far almost exclusively been tested in internal fertilizers. Here, we tested whether intrinsic post‐ejaculation sperm ageing affects offspring performance in an external fertilizer, the Atlantic salmon Salmo salar. We performed in vitro fertilizations with a split‐clutch design where sperm were subjected to four post‐ejaculation ageing treatments. We varied the duration between sperm activation and fertilization while minimizing extrinsic stress factors and tested how this affected offspring fitness. We found no evidence for an effect of our treatments on embryo survival, hatching time, larval standard length, early larval survival or larval growth rate, indicating that intrinsic post‐ejaculation sperm ageing may not occur in Atlantic salmon. One reason may be the short life span of salmon sperm after ejaculation. Whether our findings are true in other external fertilizers with extended sperm activity remains to be tested.     

Maternal genetic legacy of the eastern Adriatic island of Krk--an interplay of evolutionary forces and island's historical events in shaping the genetic structure of contemporary island population

This study presents genetic diversity and structure of contemporary Krk islanders revealed by high-resolution mitochondrial DNA analysis on a sample of 132 unrelated autochthonous adults from seven different settlements and regions of the island. Relatively high level of haplogroup and haplotype diversity in the overall island sample is an indicator of numerous migrations and gene flows throughout the history. Expectedly, the results show the highest frequency of haplogroup H (33.3%), yet this value is much lower compared to different Croatian and other European mainland populations. An interesting finding refers to highly elevated frequencies of some haplogroups, otherwise rare in Croatia and most of the Europe, such as I (11.3%) and W (7.6%) in Krk population, especially pronounced in some settlements. At the level of settlements, many of the major European haplogroups were found to be absent from their mtDNA gene pools, whereas several others show a pronounced deviation from an average. Overall, our results suggest a tangled interplay of different evolutionary forces, such as founder effects and a few strong bottlenecks, presumably due to epidemics, which have occurred in various periods of the island's history. Cultural customs, such as frequent endogamy in some regions of the island during past centuries, have additionally shaped its genetic structure into the observed present-day diversity patterns.     

Swedish population substructure revealed by genome-wide single nucleotide polymorphism data

The use of genome-wide single nucleotide polymorphism (SNP) data has recently proven useful in the study of human population structure. We have studied the internal genetic structure of the Swedish population using more than 350,000 SNPs from 1525 Swedes from all over the country genotyped on the Illumina HumanHap550 array. We have also compared them to 3212 worldwide reference samples, including Finns, northern Germans, British and Russians, based on the more than 29,000 SNPs that overlap between the Illumina and Affymetrix 250K Sty arrays. The Swedes - especially southern Swedes - were genetically close to the Germans and British, while their genetic distance to Finns was substantially longer. The overall structure within Sweden appeared clinal, and the substructure in the southern and middle parts was subtle. In contrast, the northern part of Sweden, Norrland, exhibited pronounced genetic differences both within the area and relative to the rest of the country. These distinctive genetic features of Norrland probably result mainly from isolation by distance and genetic drift caused by low population density. The internal structure within Sweden (F_ST = 0.0005 between provinces) was stronger than that in many Central European populations, although smaller than what has been observed for instance in Finland; importantly, it is of the magnitude that may hamper association studies with a moderate number of markers if cases and controls are not properly matched geographically. Overall, our results underline the potential of genome-wide data in analyzing substructure in populations that might otherwise appear relatively homogeneous, such as the Swedes.     

Rare and common regulatory variation in population-scale sequenced human genomes

Population-scale genome sequencing allows the characterization of functional effects of a broad spectrum of genetic variants underlying human phenotypic variation. Here, we investigate the influence of rare and common genetic variants on gene expression patterns, using variants identified from sequencing data from the 1000 genomes project in an African and European population sample and gene expression data from lymphoblastoid cell lines. We detect comparable numbers of expression quantitative trait loci (eQTLs) when compared to genotypes obtained from HapMap 3, but as many as 80% of the top expression quantitative trait variants (eQTVs) discovered from 1000 genomes data are novel. The properties of the newly discovered variants suggest that mapping common causal regulatory variants is challenging even with full resequencing data; however, we observe significant enrichment of regulatory effects in splice-site and nonsense variants. Using RNA sequencing data, we show that 46.2% of nonsynonymous variants are differentially expressed in at least one individual in our sample, creating widespread potential for interactions between functional protein-coding and regulatory variants. We also use allele-specific expression to identify putative rare causal regulatory variants. Furthermore, we demonstrate that outlier expression values can be due to rare variant effects, and we approximate the number of such effects harboured in an individual by effect size. Our results demonstrate that integration of genomic and RNA sequencing analyses allows for the joint assessment of genome sequence and genome function.     

Reconstructed long-term time series of phytoplankton primary production of a large shallow temperate lake: the basis to assess the carbon balance and its climate sensitivity

Aiming at building the carbon budget for further climate change impact research in the large and shallow northern temperate Lake Võrtsjärv, the present paper focuses on reconstructing the full phytoplankton primary production (PP) data series for the lake for the period of 1982–2009 covered by disconnected measurements, and testing the uncertainties involved both in the PP measurements and bio-optical modelling. During this 28-year period, in situ PP was measured in Võrtsjärv in 18 years with ¹⁴C-assimilation technique. We reconstructed the full time series using a semi-empirical PP simulation model based on continuously measured PAR irradiance and interpolated values of monthly measured chlorophyll a (C _chl). The modelling results, which proved highly reliable during the calibration phase, correlated rather weakly with the annual PP estimates for the 18 years, which were based on 2-h incubations at midday, 1–2 times per month. Being based on continuous irradiance data, the modelled PP can be considered more reliable than the sparse measurements, especially for short to medium term studies. We demonstrate that in the long-term, the bio-optical method can be biased if changes in water colour or water level alter the light climate causing adaptive responses in the cellular chlorophyll content of light-limited phytoplankton.     

Narratives Reflecting the Lived Experiences of People with Brain Disorders: Common Psychosocial Difficulties and Determinants

Background

People with brain disorders - defined as both, mental disorders and neurological disorders experience a wide range of psychosocial difficulties (PSDs) (e.g., concentrating, maintaining energy levels, and maintaining relationships). Research evidence is required to show that these PSDs are common across brain disorders.

Objectives

To explore and gain deeper understanding of the experiences of people with seven brain disorders (alcohol dependency, depression, epilepsy, multiple sclerosis, Parkinson’s disease, schizophrenia, stroke). It examines the common PSDs and their influencing factors.

Methods

Seventy seven qualitative studies identified in a systematic literature review and qualitative data derived from six focus groups are used to generate first-person narratives representing seven brain disorders. A theory-driven thematic analysis of these narratives identifies the PSDs and their influencing factors for comparison between the seven disorders.

Results

First-person narratives illustrate realities for people with brain disorders facilitating a deeper understanding of their every-day life experiences. Thematic analysis serves to highlight the commonalities, both of PSDs, such as loneliness, anger, uncertainty about the future and problems with work activities, and their determinants, such as work opportunities, trusting relationships and access to self-help groups.

Conclusions

The strength of the methodology and the narratives is that they provide the opportunity for the reader to empathise with people with brain disorders and facilitate deeper levels of understanding of the complexity of the relationship of PSDs, determinants and facilitators. The latter reflect positive aspects of the lives of people with brain disorders. The result that many PSDs and their influencing factors are common to people with different brain disorders opens up the door to the possibility of using cross-cutting interventions involving different sectors. This strengthens the message that ‘a great deal can be done’ to improve the lived experience of persons with brain disorders when medical interventions are exhausted.     

Metabolic remodeling in human colorectal cancer and surrounding tissues: alterations in regulation of mitochondrial respiration and metabolic fluxes

The aim of the work was to evaluate whether or not there is glycolytic reprogramming in the neighboring cells of colorectal cancer (CRC). Using postoperative material we have compared the functional capacity of oxidative phosphorylation (OXPHOS) in CRC cells, their glycolytic activity and their inclination to aerobic glycolysis, with those of the surrounding and healthy colon tissue cells. Experiments showed that human CRC cannot be considered a hypoxic tumor, since the malignancy itself and cells surrounding it exhibited even higher rates of OXPHOS than healthy large intestine. The absence of acute hypoxia in colorectal carcinomas was also confirmed by their practically equal glucose-phosphorylating capacity as compared with surrounding non-tumorous tissue and by upregulation of VEGF family and their ligands. Studies indicated that human CRC cells in vivo exert a strong distant effect on the energy metabolism of neighboring cells, so that they acquire the bioenergetic parameters specific to the tumor itself. The growth of colorectal carcinomas was associated with potent downregulation of the creatine kinase system. As compared with healthy colon tissue, the tumor surrounding cells display upregulation of OXPHOS and have high values of basal and ADP activated respiration rates. Strong differences between the normal and CRC cells in the affinity of their mitochondria for ADP were revealed; the corresponding K_m values were measured as 93.6±7.7 µM for CRC cells and 84.9±9.9 µM for nearby tissue; both these apparent K_m (ADP) values were considerably (by almost 3 times) lower in comparison with healthy colon tissue cells (256±34 µM).     

Cardiac metabolism as a driver and therapeutic target of myocardial infarction

Reducing infarct size during a cardiac ischaemic-reperfusion episode is still of paramount importance, because the extension of myocardial necrosis is an important risk factor for developing heart failure. Cardiac ischaemia-reperfusion injury (IRI) is in principle a metabolic pathology as it is caused by abruptly halted metabolism during the ischaemic episode and exacerbated by sudden restart of specific metabolic pathways at reperfusion. It should therefore not come as a surprise that therapy directed at metabolic pathways can modulate IRI. Here, we summarize the current knowledge of important metabolic pathways as therapeutic targets to combat cardiac IRI. Activating metabolic pathways such as glycolysis (eg AMPK activators), glucose oxidation (activating pyruvate dehydrogenase complex), ketone oxidation (increasing ketone plasma levels), hexosamine biosynthesis pathway (O-GlcNAcylation; administration of glucosamine/glutamine) and deacetylation (activating sirtuins 1 or 3; administration of NAD⁺-boosting compounds) all seem to hold promise to reduce acute IRI. In contrast, some metabolic pathways may offer protection through diminished activity. These pathways comprise the malate-aspartate shuttle (in need of novel specific reversible inhibitors), mitochondrial oxygen consumption, fatty acid oxidation (CD36 inhibitors, malonyl-CoA decarboxylase inhibitors) and mitochondrial succinate metabolism (malonate). Additionally, protecting the cristae structure of the mitochondria during IR, by maintaining the association of hexokinase II or creatine kinase with mitochondria, or inhibiting destabilization of F_OF₁-ATPase dimers, prevents mitochondrial damage and thereby reduces cardiac IRI. Currently, the most promising and druggable metabolic therapy against cardiac IRI seems to be the singular or combined targeting of glycolysis, O-GlcNAcylation and metabolism of ketones, fatty acids and succinate.