Genetic differentiation of brackish water populations of cod Gadus morhua in the southern Baltic, inferred from genotyping using SNP-arrays

The Baltic is a semi-enclosed sea characterised by decreasing salinity in the eastern and northern direction with only the deeper parts of the southern Baltic suitable as spawning grounds for marine species like cod. Baltic cod exhibits various adaptations to brackish water conditions, yet the inflow of salty North Sea water near the bottom remains an influence on the spawning success of the Baltic cod. The eastern Baltic population has been very weakly studied in comparison with the western population. The aim of this study is to demonstrate for the first time genetic differentiation by the use of a large number of SNPs between eastern and western Baltic populations existing in differentiated salinity conditions. Two cod samples were collected from the Bay of Gdańsk, Poland and one from the Kiel Bight, Germany. Samples were genotyped using a cod derived SNP-array (Illumina) with 10 913 SNPs. A selection of diagnostic SNPs was performed. A set of 7944 validated SNPs were analysed to assess the differentiation of three samples of cod. Results indicated a clear distinctness of the Kiel Bight from the populations of the eastern Baltic. FST comparison between both eastern samples was non-significant. Clustering analysis, principal coordinates analysis and assignment test clearly indicated that the eastern samples should be considered as one subpopulation, well differentiated from the western subpopulation. With the SNP approach, no differentiation between groups containing ‘healthy’ and ‘non-healthy’ cod individuals was observed

The Hydrogen–Deuterium Exchange at α-Carbon Atom in N,N,N-Trialkylglycine Residue: ESI-MS Studies

Derivatization of peptides as quaternary ammonium salts (QAS) is a known method for sensitive detection by electrospray ionization tandem mass spectrometry. Hydrogens at α-carbon atom in N,N,N-trialkylglycine residue can be easily exchanged by deuterons. The exchange reaction is base-catalyzed and is dramatically slow at lower pH. Introduced deuterons are stable in acidic aqueous solution and are not back-exchanged during LC-MS analysis. Increased ionization efficiency, provided by the fixed positive charge on QAS group, as well as the deuterium labeling, enables the analysis of trace amounts of peptides

Endosialin-Expressing Pericytes Promote Metastatic Dissemination.

Metastasis is a multistep process that is critically dependent on the interaction of metastasizing tumor cells with cells in the local microenvironment. Within this tumor stroma, vessel-associated pericytes and myofibroblasts share a number of traits, including the upregulated expression of the transmembrane receptor endosialin (CD248). Comparative experiments in wild-type and endosialin-deficient mice revealed that stromal endosialin does not affect primary tumor growth but strongly promotes spontaneous metastasis. Mechanistically, endosialin-expressing pericytes in the primary tumor facilitate distant site metastasis by promoting tumor cell intravasation in a cell contact-dependent manner, resulting in elevated numbers of circulating tumor cells. Corresponding to these preclinical experiments, in independent cohorts of primary human breast cancers, upregulated endosialin expression significantly correlates with increased metastasis and poorer patient survival. Together, the data demonstrate a critical role for endosialin-expressing primary tumor pericytes in mediating metastatic dissemination and identify endosialin as a promising therapeutic target in breast cancer. Cancer Res; 76(18); 5313-25. ©2016 AACR

Identifying Fishes through DNA Barcodes and Microarrays

Background: International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection. Methodology/Principal Findings: This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S), cytochrome b (cyt b), and cytochrome oxidase subunit I (COI) for the identification of 50 European marine fish species by combining techniques of ‘‘DNA barcoding’’ and microarrays. In a DNA barcoding approach, neighbour Joining (NJ) phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the ‘‘position of label’’ effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (.90%) renders the DNA barcoding marker as rather unsuitable for this high-throughput technology. Conclusions/Significance: Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products

A graphical model to determine the influence of surface currents on small objects immersed in water

This paper proposes a model of the interactions between surface currents and small, moving objects. These objects are immersed in water so that the part extending above the water is no larger than a human head. These interactions are defined as the weighted-directed graph. The basis for determining the edge weights are the directions of the surface currents. The speeds of these currents are used to calculate the time of moving objects. According to the modelling method of the surface-current influence on small objects, presented in this paper, it is possible to implement an application supporting search-and-rescue-operation planning. This method can be used to locate small objects, such as survivors, when planning search-and-rescue operations. Thus, the routes of these objects moving together with surface-water masses can be predicted using this method

Route prediction for a person in water drifting in chosen basins using graph theory

In this paper, the route prediction for a person in water was performed on the basis of a developed graph algorithm. This person drifted in water under the influence of surface currents and wind. The total drift route for the person in water was established as the route in a weighted directed graph. Vertices of this graph correspond to given points within a given basin. Additionally, the graph’s edges show possible directions of the overall human drift. The weight of the given edge describes the difference between the gradient of the edge and the total drift direction calculated on the basis of surface current field data and wind field data. An application has been created on the basis of a given algorithm which might be used to support the search for survivors in coastal areas (e.g. port basins, basins adjacent to the port, bays and sea areas) for which hydrodynamic models reliably reflect local phenomena

Modeling vessel passage speed by using passage-time in restricted areas

Vessel passage speed is one of the parameters describing the vessel traffic stream on a selected waterway. Knowing the probability distribution of vessel passage speeds is essential for modeling vessel traffic streams on a waterway. This article undertakes probabilistic modeling for vessel speeds in restricted areas, where the distribution of the vessel passage time of the waterway section is known. The probabilistic procedure of the inverse random variable is used. Four different cases are considered. First, the probabilistic distribution of the vessel passage speed is given, where the vessel passage time is described by the normal distribution in certain restricted areas. The next three cases present the probabilistic distribution of vessel passage speeds on the Szczecin–Świnoujście fairway, where the vessel passage time is described by the extreme value distribution, the Frèchet distribution and the Weibull distribution

Gumbel distribution in analysis of vessel speed on the Świnoujście–Szczecin fairway

The present article concerns a problem of vessel speed modeling in restricted areas, where vessel traffic flow is disturbed. In analysis of vessel speed on the Świnoujście–Szczecin fairway, division into the particular ship types has been made. Probability distributions describing speed of different ship groups have been analysed. Using the chi-square goodness-of-fit test it has been showed that the best distribution describing vessel speed of the most ship groups, is the Gumbel distribution

The wind forecast uncertainty for the Szczecin Lagoon and the Pomeranian Bay as one of error sources for the survivor drift route prediction

W niniejszym artykule naświetlono potrzebę predykcji trasy dryfu rozbitka w wodach Zalewu Szczecińskiego i Zatoki Pomorskiej. Jednakże, aby wyznaczyć tę trasę należy dysponować odpowiednimi parametrami wiatru. Parametry te można pozyskać z numerycznych modeli prognoz pogody. Prognozy tychże parametrów zazwyczaj obarczone są błędami. W artykule, na podstawie przeprowadzonych badań, przeanalizowano przyczyny powstawania błędów prognoz i wskazano możliwe kierunki poprawy jakości prognozowanych parametrów wiatru.In this paper, the need to predict a survivor drift route in the waters of the Szczecin Lagoon and the Pomeranian Bay is highlighted. However, this route will be established when appropriate wind parameters are required to be introduced into a route prediction model. These parameters can be derived from numerical weather forecast models. The forecasts of these parameters have usually errors. In this paper, based on the conducted research, the causes for errors in the wind forecasts have been discussed and possible directions for improving the quality of the forecasted wind parameters have been also indicated