Ticket to spawn: Combining economic and genetic data to evaluate the effect of climate and demographic structure on spawning distribution in Atlantic cod

Climate warming and harvesting affect the dynamics of species across the globe through a multitude of mechanisms, including distribution changes. In fish, migrations to and distribution on spawning grounds are likely influenced by both climate warming and harvesting. The Northeast Arctic (NEA) cod (Gadus morhua) performs seasonal migrations from its feeding grounds in the Barents Sea to spawning grounds along the Norwegian coast. The distribution of cod between the spawning grounds has historically changed at decadal scales, mainly due to variable use of the northern and southern margins of the spawning area. Based on historical landing records, two major hypotheses have been put forward to explain these changes: climate and harvesting. Climate could affect the distribution through, for example, spatial habitat shifts. Harvesting could affect the distribution through impacting the demographic structure. If demographic structure is important, theory predicts increasing spawner size with migration distance. Here, we evaluate these hypotheses with modern data from a period (2000–2016) of increasing temperature and recovering stock structure. We first analyze economic data from the Norwegian fisheries to investigate geographical differences in size of spawning fish among spawning grounds, as well as interannual differences in mean latitude of spawning in relation to changes in temperature and demographic parameters. Second, we analyze genetically determined fish sampled at the spawning grounds to unambiguously separate between migratory NEA cod and potentially smaller sized coastal cod of local origin. Our results indicate smaller spawners farther away from the feeding grounds, hence not supporting the hypothesis that harvesting is a main driver for the contemporary spawning ground distribution. We find a positive correlation between annual mean spawning latitude and temperature. In conclusion, based on contemporary data, there is more support for climate compared to harvesting in shaping spawning ground distribution in this major fish stock in the North Atlantic Ocean.     

Consolidation of proteomics data in the Cancer Proteomics database

Cancer is a class of diseases characterized by abnormal cell growth and one of the major reasons for human deaths. Proteins are involved in the molecular mechanisms leading to cancer, furthermore they are affected by anti‐cancer drugs, and protein biomarkers can be used to diagnose certain cancer types. Therefore, it is important to explore the proteomics background of cancer. In this report, we developed the Cancer Proteomics database to re‐interrogate published proteome studies investigating cancer. The database is divided in three sections related to cancer processes, cancer types, and anti‐cancer drugs. Currently, the Cancer Proteomics database contains 9778 entries of 4118 proteins extracted from 143 scientific articles covering all three sections: cell death (cancer process), prostate cancer (cancer type) and platinum‐based anti‐cancer drugs including carboplatin, cisplatin, and oxaliplatin (anti‐cancer drugs). The detailed information extracted from the literature includes basic information about the articles (e.g., PubMed ID, authors, journal name, publication year), information about the samples (type, study/reference, prognosis factor), and the proteomics workflow (Subcellular fractionation, protein, and peptide separation, mass spectrometry, quantification). Useful annotations such as hyperlinks to UniProt and PubMed were included. In addition, many filtering options were established as well as export functions. The database is freely available at http://cancerproteomics.uio.no .     

Horseradish peroxidase in plasma studied by gel filtration

Summary The problem whether the molecular size of horseradish peroxidase is significantly altered when the enzyme is injected into the blood stream in tracer studies, has been studied by molecular sieve chromatography (gel filtration). The results obtained rule out the possibility that the horseradish peroxidase molecule (containing about 20% carbohydrates) is significantly degraded by carbohydrate-splitting enzymes or by proteases in the circulation into a smaller active unit. Furthermore, significant binding of peroxidase to plasma proteins or polymerization of the enzyme, has not been detected. It is concluded, therefore, that conclusions about the size of functional pores based on the known molecular weight (40000 daltons) are permitted, when the enzyme is used in permeability studies.     

The origin of variability in cell cycle durations of NHIK 3025 cells

The origin of cell cycle variability was investigated in NHIK 3025 cells synchronized by mitotic selection from an exponentially growing population. The variability in G1 durations was measured by flow cytometric analysis of the fraction of cells in G1 as a function of time after mitotic selection. Immediately before the first cells entered S, medium containing 2.0 mM thymidine was added to the cells, and removed when all the cells had reached S. Since the cells had approximately the same DNA content upon removal of the thymidine, the variability in the durations of S+G2+M was measured by counting the fraction of undivided cells as a function of time after removing the thymidine. Such a thymidine treatment did not affect the naturally occurring variability in cell cycle durations generated after the start of S. The results indicate that the cell cycle variability of NHIK 3025 cells can be adequately described by a cell cycle model consisting of at least two compartments, which the cells leave according to first order kinetics. The model accounts for the initial shoulder of the curve representing the fraction of undivided cells as a function of time after mitotic selection. Furthermore, it accounts for the reduction in the rate of entry into the subsequent cell cycle compared to the rate of entry into S. Both rate constants were equally reduced after serum stepdown.     

Plasma Testosterone in Cows Related to Day of Gestation and Sex of the Foetus,and Plasma Testosterone Levels Around Parturition

No significant differences in plasma testosterone level were observed between cows carrying a male foetus and cows carrying a female foetus at any ten-day interval from day 35 of gestation until parturition. Reported higher abortion rates for male than for female foetuses would thus appear not to be due to effects of foetal testosterone on the maternal endocrine balance. In spite of a great individual variation in plasma testosterone values at similar stages of gestation, certain trends are evident. From the 35th to the 80th day of gestation the average concentration was 90–100 pg/ml. Later it rose and reached 200 pg/ml on the 180th day, remaining at this level until after partus. During the first day after parturition plasma testosterone fell significantly and stabilized around 120 pg/ml.     

Regional trends for bud burst and flowering of woody plants in Norway as related to climate change

Data series for bud burst, beginning of flowering and petal fall for 20 species of deciduous trees and conifers at four sites in different regions of southern Norway have been analysed and related to temperature series. On average, the spring phenophases occurred 7 days earlier during the period 1971-2005. The most significant linear trends were observed for the earliest phases. The trends in this period were compared with trends in other periods, the longest one starting in 1927. Those starting in cold decades and ending in 2005 were in most instances statistically significant, whereas hardly any significant trend appeared for series starting in warm decades. This fact showed that the results of trend studies are very sensitive to the choice of starting year. There were significant decadal variations in 40% of the series. The dates of occurrence of the phenophases, varying from the first days of May to the first days of June, correlated with seasonal temperature series, in most cases strongest to mean temperatures for the seasons March-May and April-May. The North Atlantic Oscillation Index (NAOI) for January and February appeared to have some predictive power for the date of occurrence of the recorded phases. The basis for this may be that the oscillations described by the index are of importance for the fulfilment of physiological chilling requirements needed to break bud dormancy. The same genotypes of the trees were grown in region West Norway and in Central Norwegian region; during the period 1965-2005 the trends towards earlier bud burst were more pronounced and steeper at the western site.     

Effects of aluminum,iron, oxygen and nitrate additions on phosphorus release from the sediment of a Danish softwater lake

The effects of oxygen, aluminum, iron and nitrate additions on phosphate release from the sediment were evaluated in the softwater Lake Vedsted, Denmark, by a 34-day experiment with undisturbed sediment cores. Six treatments were applied: (1) Control - O₂ (0–20% saturation), (2) O₂ (100% saturation) (3) Al³⁺ – O₂, (4) Fe³⁺ + O₂, (5) Fe³⁺ – O₂, and (6) NO₃ ^– – O₂. Al₂(SO₄)₃*18 H₂O and FeCl₃*4H₂O were added in amounts that theoretically should immobilize the exchangeable P-pool in the top 5 cm of the sediment, while sodium nitrate concentrations were increased to 5 mg N l^–1. The four treatments with metals or NO₃ ^– reduced the P efflux from the sediment significantly as compared to the suboxic control treatment. Mean accumulated P-release rates for suboxic treatments with Al³⁺, Fe³⁺, and NO₃ ^– were: –0.27 mmol m^–2 (st. dev = 0.02 mmol m^–2, N = 5), 0.58 mmol m^–2 (st. dev = 0.30 mmol m^–2, N = 5) and 1.40 mmol m^–2 (st. dev = 0.14 mmol m^–2, N = 5), respectively. The oxic treatment with Fe³⁺ had a P efflux of 0.36 mmol m^–2 (st. dev = 0.08 mmol m^–2, N = 5). The two highest P-release rates were observed in the control treatment and the treatment with O₂ (14.50 mmol m^–2 (st. dev = 3.90 mmol m^–2, N = 5) and 2.31 mmol m^–2 (st. dev = 0.80 mmol m^–2, N = 5), respectively). In order to identify changes in the P and Fe binding sites in the sediment as caused by the treatments, a sequential P extraction procedure was applied on the sediment before and after the efflux experiment. Addition of O₂, Fe³⁺ and NO₃ ^– to the sediment increased the amounts of oxidized Fe³⁺ and P_BD. Al³⁺ addition resulted in a lower fraction of P_BD but a correspondingly higher fraction of Al-bound P. Addition of Al³⁺ decreased the Fe-efflux from the suboxic sediment as well as the amount of oxidized Fe³⁺ in the sediment. This questions the use of Al compounds that contain sulfate because of the possible formation of FeS, which will restrict upward migration of Fe²⁺ and the formation of new Fe-oxides in the surface sediment. Instead, we suggest the use of AlCl₃ for lake restoration purposes.     

Oospore Wall Ornamentation in the Genus Tolypella (Charales,Charophyceae)

The ultrastructural features of oospore wall ornamentation in the genus Tolypella were examined using scanning electron microscopy (SEM). The taxonomic relationships among several species were discussed on the basis of oospore ultrastructure and measurements. In the case of T. glomerata and T. nidifica, our results support the status of separate species. Close relationships and transitional forms may exist between T. nidifica and T. normaniana, and not only in oospore wall ornamentation. Oospores of T. hispanica exhibited the same distinct type of reticulate oospore wall as previously reported, but our results do not support the recognition of T. hispanica as a separate species. Ultrastructure of the oospore walls of T. prolifera and T. intricata was almost identical, suggesting that these species are closely related. We therefore reject previous suggestions that morphological characteristics of oospores as observed in SEM are sufficient for identification of individual species. Although significant differences were found among oospores in individual species of Tolypella, large variation among populations, and among individuals belonging to the same population, caused substantial overlap among species.     

Systematizing the generation of missing metabolic knowledge

Genome‐scale metabolic network reconstructions are built from all of the known metabolic reactions and genes in a target organism. However, since our knowledge of any organism is incomplete, these network reconstructions contain gaps. Reactions may be missing, resulting in dead‐ends in pathways, while unknown gene products may catalyze known reactions. New computational methods that analyze data, such as growth phenotypes or gene essentiality, in the context of genome‐scale metabolic networks, have been developed to predict these missing reactions or genes likely to fill these knowledge gaps. A growing number of experimental studies are appearing that address these computational predictions, leading to discovery of new metabolic capabilities in the target organism. Gap‐filling methods can thus be used to improve metabolic network models while simultaneously leading to discovery of new metabolic gene functions. Biotechnol. Bioeng. 2010;107: 403–412. © 2010 Wiley Periodicals, Inc.