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  • Author: Artur Nowicki x
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The Use of Satellite Data in the Operational 3D Coupled Ecosystem Model of the Baltic Sea (3D Cembs)

Abstract

The objective of this paper is to present an automatic monitoring system for the 3D CEMBS model in the operational version. This predictive, eco hydrodynamic model is used as a tool to control the conditions and bio productivity of the Baltic sea environment and to forecast physical and ecological changes in the studied basin. Satellite-measured data assimilation is used to constrain the model and achieve higher accuracy of its results.

3D CEMBS is a version of the Community Earth System Model, adapted for the Baltic Sea. It consists of coupled ocean and ice models, working in active mode together with the ecosystem module. Atmospheric forecast from the UM model (Interdisciplinary Centre for Mathematical and Computational Modelling of the Warsaw University) are used as a forcing fields feed through atmospheric data model. In addition, river inflow of freshwater and nutrient deposition from 71 main rivers is processed by land model. At present, satellite data from AQUA MODIS, processed by the SatBałtyk project Operational System are used for the assimilation of sea surface temperature and chlorophyll a concentration. In the operational mode, 48-hour forecasts are produced at six-hour intervals, providing a wide range of hydrodynamic and biochemical parameters.

Open access
Structure of the FindFish Knowledge Transfer Platform

Abstract

As consumer awareness increases in Poland, fish consumption is on an upward trend. While new technologies permit meeting increasing demand, they significantly increase the pressure on fish supplies. As a result, many fish stocks are over-exploited, which threatens marine ecosystems. Declining fisheries, increasing fishing operating costs, and the necessity of making longer fishing expeditions at greater distances that often end with catches of fewer or less valuable fish mean that in some fisheries sectors are currently running at the margins of profit or at a loss. At the same time, the European Union’s fisheries policy aims to create more selective and sustainable fisheries, to implement limitations through fishing quotas, and to ban the recognition of discards. The aim is to ensure that individual fish species are protected while providing the European Union with stable, secure supplies of fresh fish. The FindFish Knowledge Transfer Platform project was launched to provide solutions for challenges facing commercial fisheries. Its purpose is to provide fishers with a knowledge transfer platform and a numerical forecasting system for the marine environment of the Gulf of Gdansk. By combining in-situ research, environmental data, fish catch data, and numerical calculations, this tool will improve the accuracy of targeted fishing while reducing by-catch. The system will provide more reliable data on fish stocks and facilitate more efficient resource management.

Open access
Expression Changes in Fatty acid Metabolic Processrelated Genes in Porcine Oocytes During in Vitro Maturation

Abstract

Mammalian oocytes undergo compound processes of nuclear and cytoplasmic maturation that allow them to reach MII stage. Only fully mature, oocyte can be successfully fertilized by a single spermatozoon. Fatty acids, apart from their role in cellular metabolism, inflammation and tissue development, have positive and detrimental effects on oocyte maturation, fertilization, blastocyst cleavage rate and embryo development in mammals. Using microarrays, we have analyzed the expression changes in fatty acids- -related genes during in vitro maturation of porcine oocytes. The oocytes were recovered from ovaries of 45 pubertal crossbred Landrace gilts and subsequently subjected to BCB test. For further analyses, only granulosa cell-free BCB+ oocytes were used and divided into two groups. The first one, described as “before IVM”, was directly exposed to molecular assays, the second one, described as “after IVM”, was first in vitro matured and then subjected to a second BCB test. Oocytes, if classified as BCB+, were then passed to corresponding molecular analyses. We found significant down-regulation of genes involved in fatty acid metabolic process, such as: ACSL6, EPHX2, FADS2, PTGES, TPI1, TBXAS1, NDUFAB1, MIF, ACADSB and DECR1 in porcine oocytes analyzed after IVM, in comparison to those analyzed before IVM. In conclusion, apart from poor data available concerning analyzed genes in relation to reproductive events, significant changes in their expression point to their potential role as an oocyte developmental competence markers in pigs. Introducing molecular diagnostics of oocytes could be the prospective tool for selection of best gametes, leading to improved outcomes of in vitro fertilization.

Open access
Numerical Simulations of Sea Ice Conditions in the Baltic Sea for 2010–2016 Winters Using the 3D CEMBS Model

Abstract

Sea ice conditions in the Baltic Sea during six latest winters – 2010/2011 to 2015/2016 are analysed using coupled ice–ocean numerical model 3D CEMBS (3D Coupled Ecosystem Model of the Baltic Sea). Simulation results are compared with observations from monitoring stations, ice charts and satellite data. High correlation between model results and observations has been confirmed both in terms of spatial and temporal approach. The analysed period has a high interannual variability of ice extent, the number of ice days and ice thickness. Increasing number of relatively mild winters in the Northern Europe directly associated with climate change results in reduced ice concentration in the Baltic Sea. In this perspective, the implementation and development of the sea ice modelling approach (in addition to standard monitoring techniques) is critical to assess current state of the Baltic Sea environment and predict possible climate related changes in the ecosystem and their influence for human marine–related activities, such as fishery or transportation.

Open access
Ontology groups representing angiogenesis and blood vessels development are highly up-regulated during porcine oviductal epithelial cells long-term real-time proliferation – a primary cell culture approach

Abstract

The morphological and biochemical modification of oviductal epithelial cells (OECs) belongs to the group of compound processes responsible for proper oocyte transport and successful fertilization. The cellular interactions between cumulus-oocyte complexes (COCs) and oviductal epithelial cells (OECs) are crucial for this unique mechanism. In the present study we have analyzed angiogenesis and blood vessel development processes at transcript levels. By employing microarrays, four ontological groups associated with these mechanisms have been described. Differentially expressed genes belonging to the “angiogenesis”, “blood circulation”, “blood vessel development” and “blood vessel morphogenesis” GO BP terms were investigated as a potential markers for the creation of new blood vessels in cells under in vitro primary culture conditions.

Open access
Analysis of fructose and mannose – regulatory peptides signaling pathway in porcine epithelial oviductal cells (OECs) primary cultured long-term in vitro

Abstract

The morphological and biochemical modification of oviductal epithelial cells (OECs) belongs to the compound process responsible for proper oocytes transport and successful fertilization. However, the main mechanisms which regulated this process are still not entirely known. Moreover, the OECs metabolism, which may be identified as the “cellular activity” marker, is poorly recognized. In this study we investigated the fructose and mannose metabolic pathway in porcine OECs primary long-term cultured in vitro.

In our study, we employ a primary long term in vitro culture (IVC) and microarray approach (the Affymetrix microarray were used for analysis of transcriptomic profile of OECs) for expression levels analysis.

We found that from the whole analyzed transcriptome, 1537 genes were upregulated and 995 were down regulated after 7 days of culture, 1471 genes were upregulated and 1061 were downregulated after 15 days of culture and 1329 genes were upregulated and 1203 were downregulated after 30 days of culture. Moreover, the differential expression of SORD, FPGT, PFKFB4, TPI1, MPI, ALDOC, HK2 and PFKFB3 at 24 hours, 7 day, 15 day and 30 day, was also observed.

We suggested that fructose and mannose metabolism may be important molecular bio-marker of porcine OECs capability in in vitro model. The metabolic profile is significantly accompanied by cells proliferation in vitro. The transcriptomic profile of SORD, FPGT, PFKFB4, TPI1, MPI, ALDOC, HK2 and PFKFB3 expression may be identified as “fingerprint” of fructose and mannose metabolism in OECs as well as involved in cellular in vitro developmental capacity in pigs.

Open access
Ion homeostasis and transport are regulated by genes differentially expressed in porcine buccal pouch mucosal cells during long-term culture in vitro – a microarray approach

Abstract

The oral mucosa is a compound tissue composed of several cells types, including fibroblasts and keratinocytes, that are characterized by different morphology, as well as biochemical and metabolomic properties. The oral mucosal cells are the most important factors mediated between transport and drugs delivery. The changes in cellular ion homeostasis may significantly affect the bioavailability of administrated drugs and their transport across the mucous membrane. Therefore we investigated the expression profile of genes involved in ion transport and homeostasis in porcine buccal pouch mucosal cells.

The oral mucosa was separated surgically and isolated enzymatically. The cells were examined during long-term in vitro culture (IVC). The cultured cells were collected at 7, 15 and 30 days of IVC and subsequently transferred to RNA isolation and next, the gene expression profile was measured using Affymetrix microarray assays.

In the results, we can extract genes belonging to four ontology groups: “ion homeostasis”, “ion transport”, “metal ion transport”, and “inorganic ion homeostasis”. For TGFB1 and CCL2, we observed up-regulation after 7 days of IVC, down-regulation after 15 days of IVC and upregulation again after 30 days of IVC. The ATP13A3, ATP1B1, CCL8, LYN, STEAP1, PDPN, PTGS2, and SLC5A3genes showed high activity after day 7 of IVC, and in the days 15 and 30 of IVC showed low activity.

We showed an expression profile of genes associated with the effects of ion influence on the porcine normal oral mucosal cell development in IVC. These studies may be the starting point for further research into oral diseases and will allow for the comparison of the gene expression profile of normal and disease altered cells.

Open access
The differentiation and transdifferentiation of epithelial cells in vitro – is it a new strategy in regenerative biomedicine?

Abstract

In modern medical research, stem cells are one of the main focuses, believed to be able to provide the solution to many currently unsolvable medical cases. However, their extraordinary potential for differentiation creates much obstacles in their potential application in clinical environment, without understanding the whole array of molecular mechanisms that drive the processes associated with their development and maturation. Because of that, there is a large need for studies that concern the most basic levels of those processes. Progenitor stem cells are a favorable target, as they are relatively lineage committed, making the amount of signaling required to reach the final form much lower. Their presence in the adult organism is also an advantage in their potential use, as they can be extracted without the need for storage from the moment of pre-natal development or birth. Epithelial tissues, because of their usual location or function, exhibit extraordinary level of plasticity and proliferative potential. That fact makes them one of the top candidates for use in applications such as tissue engineering, cell based therapies, regenerative and reconstructive medicine. The potential clinical application, however, need to be based on well developed methods, in order to provide an effective treatment without causing major side effects. To achieve that goal, a large amount of research, aiming to analyze the molecular basics of proliferation and differentiation of epithelial stem cells, and stem cells in general, needs to be conducted.

Open access
Cation homeostasis and transport related gene markers are differentially expressed in porcine buccal pouch mucosal cells during long-term cells primary culture in vitro

Abstract

The mucous membrane is composed of two layers. The layer of stratified squamous epithelium and the underlying layer of the connective tissue. The epithelium is composed of keratinocytes that are in different stages of differentiation, depending on their localization. In our research, after isolation of primary in vitro cultured buccal pouch mucosal cells, we observed keratinocytes in various stages of differentiation and fibroblasts. These cells, depending on the ionic dynamics, may be subject to different morphological and biochemical transformations. Understanding the expression profile of the normal oral mucosal tissue is important for further research into the effects of biomaterials on the mucosal cells, their growth, proliferation, and differentiation.

The porcine buccal pouch mucosal cells were used in this study. The oral mucosa was separated surgically and isolated enzymatically. The cells were in vitro cultured for 30 days, and after each step of in vitro culture (7 days, 15 days, 30 days), samples were collected for isolation of total RNA. The gene expression profile was measured using Affymetrix microarray assays.

In results, we observed genes belonging to two ontology groups: cation homeostasis and cation transport. These genes were up-regulated after 7 days of in vitro culture as compared to down-regulation after 15 and 30 days of in vitro culture. These results suggested that dynamic growth, proliferation and cell adhesion are more intense in the first 7 days of in vitro culture. We also observed, for the first time, the expression of ATP13A3 in porcine oral mucosal cells.

Open access
Does Porcine Oocytes Maturation in Vitro is Regulated by Genes Involved in Transforming Growth Factor Beta Receptor Signaling Pathway?

Summary

The oocyte growth and development in follicular environment are substantially accompanied by surrounding somatic cumulus (CCs) and granulosa cells (GCs). During these processes, the mammalian gametes reach full maturational stage and may be further successfully fertilized by single spermatozoon. These unique mechanisms are regulated by expression of clusters of genes and their biochemical signaling pathways.

In this article we described differential expression pattern of transforming growth factor beta (TGFB) gene superfamily in porcine oocytes before and after in vitro maturation (IVM).

We performed Affymetrix® microarray assays to investigate the TGFB-related genes expression profile in porcine immature oocytes and gametes cultured for 44h in vitro.

In results we found 419 different genes, 379 genes with lower expression, and 40 genes characterized by increased RNA profile. Moreover, significant up-regulation of 6 genes belonging to TGFB signaling pathway such as: TGFBR3, SMAD4, FOS, KLF10, ID1, MAP3K1 in immature porcine oocytes (before IVM), was also observed.

It may be suggested that genes involved in TGFB-related signaling pathway are substantially regulated before IVM. Furthermore, these genes may play a significant role during early stages of nuclear and/or cytoplasmic porcine oocytes maturation. The investigated transcripts may be also recommended as the markers of oocytes maturational capability in pigs.

Open access