Epigenome-Wide DNA Methylation Profiling in Colorectal Cancer and Normal Adjacent Colon Using Infinium Human Methylation 450K

The aims were to profile the DNA methylation in colorectal cancer (CRC) and to explore cancer-specific methylation biomarkers. Fifty-four pairs of CRCs and the adjacent normal tissues were subjected to Infinium Human Methylation 450K assay and analysed using ChAMP R package. A total of 26,093 differentially methylated probes were identified, which represent 6156 genes; 650 probes were hypermethylated, and 25,443 were hypomethylated. Hypermethylated sites were common in CpG islands, while hypomethylated sites were in open sea. Most of the hypermethylated genes were associated with pathways in cancer, while the hypomethylated genes were involved in the PI3K-AKT signalling pathway. Among the identified differentially methylated probes, we found evidence of four potential probes in CRCs versus adjacent normal; HOXA2 cg06786372, OPLAH cg17301223, cg15638338, and TRIM31 cg02583465 that could serve as a new biomarker in CRC since these probes were aberrantly methylated in CRC as well as involved in the progression of CRC. Furthermore, we revealed the potential of promoter methylation ADHFE1 cg18065361 in differentiating the CRC from normal colonic tissue from the integrated analysis. In conclusion, aberrant DNA methylation is significantly involved in CRC pathogenesis and is associated with gene silencing. This study reports several potential important methylated genes in CRC and, therefore, merit further validation as novel candidate biomarker genes in CRC.

Immense variability in the sea surface temperature near macro tidal flat revealed by high-resolution satellite data (Landsat 8)

Sea surface temperature (SST) is crucial for understanding the physical characteristics and ecosystems of coastal seas. SST varies near the tidal flat, where exposure and flood recur according to the tidal cycle. However, the variability of SST near the tidal flat is poorly understood owing to difficulties in making in-situ observations. The high resolution of Landsat 8 enabled us to determine the variability of SST near the macro tidal flat. The spatial distribution of the SST extracted from Landsat 8 changed drastically. The seasonal SST range was higher near the tidal flat than in the open sea. The maximum seasonal range of coastal SST exceeded 23 °C, whereas the range in the open ocean was approximately 18 °C. The minimum and maximum horizontal SST gradients near the tidal flat were approximately − 0.76 °C/10 km in December and 1.31 °C/10 km in June, respectively. The heating of sea water by tidal flats in spring and summer, and cooling in the fall and winter might result in a large horizontal SST gradient. The estimated heat flux from the tidal flat to the seawater based on the SST distribution shows seasonal change ranging from − 4.85 to 6.72 W/m2.

Trends and Composition—A Sedimentological-Chemical-Mineralogical Approach to Constrain the Origin of Quaternary Deposits and Landforms—From a Review to a Manual

In this study, six basic Quaternary landform series (LFS) and their sedimentary deposits (LFS1 aeolian, LFS 2.1 to 2.2 mass wasting, LFS 3 cryogenic-glacial, LFS 4.1 to 4.6 fluvial, LFS 5.1 to 5.2 coastal-marine, LFS 6.1 to 6.3 lacustrine) are subdivided into subtypes and examined with regard to their sedimentological parameters and their mineralogical and chemical compositions. Emphasis is placed on the textural (related to transport and deposition), compositional (sediment load/weight, Eh and pH) and geodynamic maturity of the sedimentary deposits which are influenced by the parent lithology and bedrock tectonic and by the climate during the last 2 Ma. To constrain the development of the LFS and their sediments, composite trend-line diagrams are designed combining sedimentological (x-axis) and chemical/mineralogical dataset (y-axis): (1) sorting vs. heavy mineral content; (2) sphericity of grains vs. silica/carbonate contents; and (3) median vs. Ti/Fe ratios. In addition, the x-y plots showing the log SiO2/Al2O3 vs. log Na2O/K2O are amended by a dataset of the three most common clay minerals, i.e., kaolinite-, mica-, and smectite-group clay minerals. Such joint sedimentological-chemical-mineralogical investigations focused on the depositional environment of unconsolidated clastic sediments of Quaternary age can be used to describe the economic geology and environmental geology of mineral deposits in the pre-Quaternary sedimentary series according to the phrase: “The Present is the key to the Past”. Both trend diagrams and compositional x-y plots can contribute to constraining the development of the full transect of landform series from the fluvial incision and slope retreat to reef islands fringing the coastal zone towards the open sea as far as they are built up of clastic sedimentary deposits enriched in siliceous and/or carbonate minerals. Climate zonation and crustal maturity are the exogenous and endogenous “drivers”, as can be deduced from the compositional (mineralogy and chemistry) and physical (transport and deposition) variations observed in the Quaternary sediments. The current study bridges the gap between a review only based on literature and a hybrid manual generated by practical field studies devoted to applied geosciences in economic and environmental geology (“E & E issue”).

How Did Seal Lice Turn into the Only Truly Marine Insects?

Insects are the most evolutionarily and ecologically successful group of living animals, being present in almost all possible mainland habitats; however, they are virtually absent in the ocean, which constitutes more than 99% of the Earth’s biosphere. Only a few insect species can be found in the sea but they remain at the surface, in salt marshes, estuaries, or shallow waters. Remarkably, a group of 13 species manages to endure long immersion periods in the open sea, as well as deep dives, i.e., seal lice. Sucking lice (Phthiraptera: Anoplura) are ectoparasites of mammals, living while attached to the hosts’ skin, into their fur, or among their hairs. Among them, the family Echinophthiriidae is peculiar because it infests amphibious hosts, such as pinnipeds and otters, who make deep dives and spend from weeks to months in the open sea. During the evolutionary transition of pinnipeds from land to the ocean, echinophthiriid lice had to manage the gradual change to an amphibian lifestyle along with their hosts, some of which may spend more than 80% of the time submerged and performing extreme dives, some beyond 2000 m under the surface. These obligate and permanent ectoparasites have adapted to cope with hypoxia, high salinity, low temperature, and, in particular, conditions of huge hydrostatic pressures. We will discuss some of these adaptations allowing seal lice to cope with their hosts’ amphibious habits and how they can help us understand why insects are so rare in the ocean.

CONTROL AND METHODOLOGY OF MODELING HYDROLOGICAL PROCESSES IN THE DESIGN OF HYDRAULIC STRUCTURES IN THE ESTUARIES OF RIVERS

The article presents the methodology of hydrological modeling of water flows for constructing flow plans in the design of hydraulic structures. On the basis of these calculations, both the specific costs of bottom and suspended sediments in each flow stream and the deformation of the riverbed at various points in time can be determined. The results of experiments with spatial models of river sections are considered. The developed technique makes it possible to calculate the deformation of the bottom and shores and form a flow organization scheme, which, due to an increase in velocities in some section of the channel, ensures sediment transport to more remote areas of the seashore, up to the open sea.

Swell hindcast statistics for the Baltic Sea

The classic characterisation of swell as regular, almost monochromatic, wave trains does not necessarily accurately describe swell in water bodies shielded from the oceanic wave climate. In such enclosed areas the locally generated swell waves still contribute to processes at the air and seabed interfaces, and their presence can be quantified by partitioning wave components based on their speed relative to the wind. We present swell statistics for the semi-enclosed Baltic Sea using 20 years of swell-partitioned model data. The swell significant wave height was mostly under 2 m, and in the winter (DJF) the mean significant swell height was typically less than 0.4 m; higher swell was found in limited nearshore areas. Swell waves were typically short (under 5 s), with mean periods over 8 s being rare. In open-sea areas the average ratio of swell energy (to total energy) was mostly below 0.4 – significantly less than in the World Ocean. Certain coastal areas were swell dominated over half the time, mostly because of weak winds (U<5 m s−1) rather than high swell heights. Swell-dominated events with a swell height over 1 m typically lasted under 10 h. A cross-correlation analysis indicates that swell in the open sea is mostly generated from local wind sea when wind decays (dominant time lag roughly 15 h). Near the coast, however, the results suggest that the swell is partially detached from the local wind waves, although not necessarily from the weather system that generates them because the highest swell typically arrives with a roughly 10 h delay after the low-pressure system has already passed.

Relationship of Spatial Phytoplankton Variability during Spring with Eutrophic Inshore and Oligotrophic Offshore Waters in the East Sea, Including Dokdo, Korea

The area near the subpolar front of the East Sea has high primary productivity during the spring season. We conducted two surveys, one in early spring and another in late spring, to assess environmental factors that influence phytoplankton community structure during these times. During early spring, vertical mixing supplied abundant nutrients to the surface. Due to the well-mixed water column, there were high nutrient levels, but total phytoplankton abundances and diversity were relatively low and were dominated by the diatom Chaetoceros spp. During late spring, the water column gradually stratified, with relatively high levels of nutrients in the surface layers near the coastal areas. Phytoplankton abundance and diversity at that time were higher, and there were diatoms (Pseudo-nitzschia spp. and Chaetoceros spp.), cryptophytes, and small flagellates. Pseudo-nitzschia spp. were especially abundant in re-sampled areas. The presence of a stratified and stable water mass and sufficient nitrate led to high phytoplankton growth, even in the open sea during late spring. These findings provide a better understanding of how phytoplankton population dynamics in the East Sea depend on water column stability during both early and late spring seasons.

Investigation on Improving Strategies for Navigation Safety in the Offshore Wind Farm in Taiwan Strait

The Taiwan Strait, to the west of Taiwan, is rich in wind energy resources and has the greatest offshore wind power potential in the world. Therefore, Taiwan has been actively expanding its offshore wind power industry in this area in recent years and expects to achieve the total installed capacity to 15.6 GW by 2035. Due to the large vessel traffic flow in Western Taiwan’s sea area, wind farms will inevitably reduce the navigable space and shadow some existing marine aids to navigation, thus worsening navigation safety. An approach using a fault tree analysis was used to carry out analysis of collision risk between ship-to-ship and ship-to-turbine. The vessel density distribution and traffic flow within the open sea of offshore wind farms would further increase to curtail the available navigable space. The shadowing effects along navigation channels would thereafter be worsened to raise the probability of collision risks in the sea. The results of the fault tree analysis revealed that if the ship is out of control, the time allowed to provide assistance is rather short, leading to the increase of collision risk extent between ships and wind turbines. Moreover, the study also found that unfit functions of the Vessel Traffic Service System and navigation aids and frequently and arbitrarily crossing the navigation channel of fishery vessels are the main causes of ship collisions. In order to effectively improve the navigation safety, competitive strategies for navigation safety are investigated and evaluated in this study. These strategies include making a complete plan for utilizing the whole sea, integrating the offshore vessel traffic service and management system, providing remote pilotage services, and building salvage vessels. The above promising strategies would enhance the navigation safety within the open sea. Collision risk might occur once marine accident occurs and no salvage vessel is available.

Metabarcoding Reveals High Diversity of Benthic Foraminifera Driven by Atlantification of Coastal Svalbard

Arctic marine biodiversity is undergoing rapid changes due to global warming and modifications of oceanic water masses circulation. These changes have been demonstrated in the case of mega- and macrofauna, but much less is known about their impact on the biodiversity of smaller size organisms, such as foraminifera that represents a main component of meiofauna in the Arctic. Several studies analysed the distribution and diversity of Arctic foraminifera. However, all these studies are based exclusively on the morphological identification of specimens sorted from sediment samples. Here, we present the first assessment of Arctic foraminifera diversity based on metabarcoding of sediment DNA samples collected in fjords and open sea areas in Svalbard Archipelago. We obtained a total of 5,968,786 reads that represented 1,384 ASVs. More than half of the ASVs (51.7%) could not be assigned to any group in the reference database suggesting a high genetic novelty of Svalbard foraminifera. The sieved and unsieved samples resolved comparable communities, sharing 1023 ASVs, comprising over 97% of reads. Our analyses show that the foraminiferal assemblage differs between the localities, with communities distinctly separated between fjord and open sea stations. Each locality was characterized by a specific assemblage, with only a small overlap in the case of open sea areas. Our study demonstrates a clear pattern of the influence of water masses on the structure of foraminiferal communities. The stations situated on the western coast of Svalbard that is strongly influenced by warm and salty Atlantic Water (AW) are characterized by much higher diversity than stations in the northern and eastern part, where the impact of AW is less pronounced. This high diversity and specificity of Svalbard foraminifera associated with water mass distribution indicate that the foraminiferal metabarcoding data can be a very useful tool for inferring present and past environmental conditions in the Arctic.