DNA Fingerprinting: Identification of Organisms Using the Polymerase Chain Reaction and Various Primers

The study undertaken involved small scale DNA isolation from eight different fruits using a modified technique written for leaf material. Genetic analysis of this extracted DNA was performed by PCR. Four primers known to target specific DNA sequences were utilized: Analu, Bactoribo, HHFl, and Mitocox. PCR with the Analu, HHFl, and Mitocox primers resulted in a unique pattern of bands that enabled each fruit to be differentiated. Since one major band was observed with the Bactoribo primers and the size of that amplified DNA fragment was either the same or very similar for each fruit, they could not be distinguished based on this primer. Furthermore, the amplification products yielded by the fruits were different from the positive control thus allowing them to be distinguished also. In most cases, 10 μl of fruit DNA extract in the PCR resulted in the best banding pattern, although informative bands were detected with 1 and 5 μl of DNA also. Interestingly, 5 μl of fruit DNA extract in the PCR reaction yielded variable results whereby in some cases, such as with the analu primers, either fewer bands were seen compared to 1 and 10 μl of DNA, or no bands were visible at all, thus providing less meaningful data. Like RFLP and RAPD analysis, this study demonstrated that the entire genome does not have to be sequenced to detect DNA polymorphisms between different organisms

The SST multidecadal variability in the Atlantic-Mediterranean region and its relation to AMO

Abstract Two sea surface temperature (SST) time series, the Extended Reconstructed SST version 3 (ERSST.v3) and the Hadley Centre Sea Ice and Sea Surface Temperature dataset (HadISST), are used to investigate SST multidecadal variability in the Mediterranean Sea and to explore possible connections with other regions of the global ocean. The consistency between these two time series and the original International Comprehensive Ocean–Atmosphere Dataset version 2.5 (ICOADS 2.5) over the Mediterranean Sea is investigated, evaluating differences from monthly to multidecadal scales. From annual to longer time scales, the two time series consistently describe the same trends and multidecadal oscillations and agree with Mediterranean ICOADS SSTs. At monthly time scales the two time series are less consistent with each other because of the evident annual cycle that characterizes their difference. The subsequent analysis of the Mediterranean annual SST time series, based on lagged-correlation analysis, multitaper method (MTM), and singular spectral analysis (SSA), revealed the presence of a significant oscillation with a period of about 70 yr, very close to that of the Atlantic multidecadal oscillation (AMO). An extension of the analysis to other World Ocean regions confirmed that the predominance of this multidecadal signal with respect to longer period trends is a unique feature of the Mediterranean and North Atlantic Ocean, where it reaches its maximum at subpolar latitudes. Signatures of multidecadal oscillations are also found in the global SST time series after removing centennial and longer-term components. The analysis also reveals that Mediterranean SST and North Atlantic indices are significantly correlated and coherent for periods longer than about 40 yr. For time scales in the range 40–55 yr the coherence between the Mediterranean and subpolar gyre temperatures is higher than the coherence between the Mediterranean SST and North Atlantic Oscillation (NAO) or AMO. Finally, the results of the analysis are discussed in the light of possible climate mechanisms that can couple the Mediterranean Sea with the North Atlantic and the Global Ocean

The role of Internal Solitary Waves on deep-water sedimentary processes. The case of up-slope migrating sediment waves off the Messina Strait

Subaqueous, asymmetric sand waves are typically observed in marine channel/canyon systems, tidal environments, and continental slopes exposed to strong currents, where they are formed by current shear resulting from a dominant unidirectional flow. However, sand-wave fields may be readily observed in marine environments where no such current exists; the physical processes driving their formation are enigmatic or not well understood. We propose that internal solitary waves (ISWs) induced by tides can produce an effective, unidirectional boundary “current” that forms asymmetric sand waves. We test this idea by examining a sand-wave field off the Messina Strait, where we hypothesize that ISWs formed at the interface between intermediate and surface waters are refracted by topography. Hence, we argue that the deflected pattern (i.e., the depth-dependent orientation) of the sand-wave field is due to refraction of such ISWs. Combining field observations and numerical modelling, we show that ISWs can account for three key features: ISWs produce fluid velocities capable of mobilizing bottom sediments; the predicted refraction pattern resulting from the interaction of ISWs with bottom topography matches the observed deflection of the sand waves; and predicted migration rates of sand waves match empirical estimates. This work shows how ISWs may contribute to sculpting the structure of continental margins and it represents a promising link between the geological and oceanographic communities

Komponenta projekta ADRICOSM – sustav promatranja na velikoj skali – satelitski sustav

In the framework of the ADRICOSM project, the Satellite Oceanography Group (GOS) of Rome developed a Fast Delivery System (FDS) for providing the partner modeling centres with remotelysensed ocean colour and sea surface temperature (SST) data. Data are processed, mapped and binned on the Adriatic Sea area in order to be assimilated into both ecosystem models and circulation models for ocean forecasting. Further technological improvements permitted the building and optimization of a system suitable for meeting the increasing demand for near-real-time ocean colour and SST products for applications in operational oceanography. Real-Time Images of SeaWiFS chlorophyll concentration, clouds/case I/case II water flags and true colour images are obtained by processing the satellite passes using climatological ancillary data. These images are provided daily through an ad hoc automatic system that processes the raw satellite data and makes it available on the web within an hour of satellite overpass acquisition. All of the images are stored in a gallery web archive organized in a calendar chart. Accurate chlorophyll maps for assimilation are produced in near real time (typically after 4 days) as soon as daily meteorological ancillary data are made available on the NASA website. Each chlorophyll map is flagged for clouds or other contamination factors using the corresponding 24 quality flag maps. This implies that case-2 waters and spurious atmospheric effects have been removed from the pigment data set. This final product is binned on the Adriatic model grid and made available for the ADRICOSM project on the GOS web site. NOAA/AVHRR data are also acquired by the GOS ground station in Rome and managed by the FDS from their reception up to their distribution. Daily SST maps of the Adriatic Sea binned over the AREG model grid at 1/16° resolution are distributed weekly in Near-Real-Time along with the daily SST maps of the eastern Mediterranean Sea delivered at 1/8° resolution to the MFSTEP project. Real-Time SST maps of the Adriatic Sea at 1km resolution are posted daily in GIF format on the GOS website.U okviru projekta ADRISOSM, GOS (Grupa za satelitsku oceanografiju) iz Rima razvila je Sustav za brzu isporuku FDS, snabdijevanje partnerskih centara za modeliranje satelitskim snimcima boje mora i tem-peraturnim podacima površine mora (SST). Podaci za Jadran su obrađeni, pretvoreni u grafičke produkte i digitalizirani kako bi se mogli asimilirati u model strujanja i model ekosistema, te koristiti oceanografskoj prognozi. Daljnja tehnološka poboljšanja su omogućila izgradnju i optimalizaciju sustava, zbog rastućih potreba za produktima boje mora i površinske temperature za različite primjene u operativnoj oceanografiji. Slike koncentracije klorofila od senzora SeaWiFS, slike oblaka te Case1 i Case2 oznake, kao i slike prave boje dobivaju se procesiranjem satelitskih scena uz popratne klimatološke podatke. Slike se procesiraju dnevno kroz ad-hoc automatski sustav koji obrađuje sirove satelitske podatke i omogućuje njihovu isporuku na mrežu, sat vremena nakon prikupljanja satelitskih podataka tj. nakon prolaska satelita. Sve se slike spremaju u arihvu na mreži koja je organizirana prema datumima. Korigirane slike koncentracije klorofila za asimilaciju u model proizvode se u skoro realnom vremenu (tipično 4 dana kasnije) čim se dobiju popratni meteorološki podaci s mreže NASA-e. Na svakoj slici klorofila su označeni oblaci ili drugi kontaminirajući faktori, prema 24 kategorije kvalitete slika. To znači da su Case 2 slučajevi piksela uklonjeni iz snimaka kao i atmosferske sme-tnje. Konačni produkt se usklađuje s koordinatnom mrežom Jadrana i stavlja na raspolaganje na stranicama ADRICOSM-a preko GOS-ove Internet stranice. GOS zemaljska stanica u Rimu prikuplja i podatke NOAA/ AVHRR koji se procesiraju kroz FDS sustav, od prijema do konačne distribucije podataka. Dnevne se slike površinske temperature mora (SST), usklađene preko koordinatne mreže AREG-a pri prostornom razlučivanju od 1/16 stupnja, distribuiraju tjedno u skoro realnom vremenu, zajedno sa slikama istočnog Sredozemlja koje imaju razlučivanje od 1/8 stupnja prema MFSTEP projektu. Dnevno, u skoro realnom vremenu, isporučuju se slike SST za Jadran uz prostorno razlučivanje od 1 km u GIF formatu na Internet stranici GOS-a

An Artificial Neural Network to Infer the Mediterranean 3D Chlorophyll-a and Temperature Fields from Remote Sensing Observations

Remote sensing data provide a huge number of sea surface observations, but cannot give direct information on deeper ocean layers, which can only be provided by sparse in situ data. The combination of measurements collected by satellite and in situ sensors represents one of the most effective strategies to improve our knowledge of the interior structure of the ocean ecosystems. In this work, we describe a Multi-Layer-Perceptron (MLP) network designed to reconstruct the 3D fields of ocean temperature and chlorophyll-a concentration, two variables of primary importance for many upper-ocean bio-physical processes. Artificial neural networks can efficiently model eventual non-linear relationships among input variables, and the choice of the predictors is thus crucial to build an accurate model. Here, concurrent temperature and chlorophyll-a in situ profiles and several different combinations of satellite-derived surface predictors are used to identify the optimal model configuration, focusing on the Mediterranean Sea. The lowest errors are obtained when taking in input surface chlorophyll-a, temperature, and altimeter-derived absolute dynamic topography and surface geostrophic velocity components. Network training and test validations give comparable results, significantly improving with respect to Mediterranean climatological data (MEDATLAS). 3D fields are then also reconstructed from full basin 2D satellite monthly climatologies (1998–2015) and resulting 3D seasonal patterns are analyzed. The method accurately infers the vertical shape of temperature and chlorophyll-a profiles and their spatial and temporal variability. It thus represents an effective tool to overcome the in-situ data sparseness and the limits of satellite observations, also potentially suitable for the initialization and validation of bio-geophysical models

Observing The Mediterranean Sea from space: 21 years of Pathfinder-AVHRR Sea Surface Temperatures (1985 to 2005). Re-analysis and validation

International audienceThe time series of satellite infrared AVHRR data from 1985 to 2005 has been used to produce a daily series of optimally interpolated SST maps over the regular grid of the operational MFSTEP OGCM model of the Mediterranean basin. A complete validation of this OISST (Optimally Interpolated Sea Surface Temperature) product with in situ measurements has been performed in order to exclude any possibility of spurious trends due to instrumental calibration errors/shifts or algorithms malfunctioning related to local geophysical factors. The validation showed that satellite OISST is able to reproduce in situ measurements with a mean bias of less than 0.1°C and RMSE of about 0.5°C and that errors do not drift with time or with the percent interpolation error

Spatio-temporal variability of micro-, nano- and pico-phytoplankton in the Mediterranean Sea from satellite ocean colour data of SeaWiFS

Abstract. The seasonal and year-to-year variability of the phytoplankton size class (PSC) spatial distribution has been examined in the Mediterranean Sea by using the entire time series of Sea-viewing Wide Field-of-view Sensor (SeaWiFS) space observations (1998–2010). Daily maps of PSCs have been determined using an empirical model based on a synoptic relationship between surface chlorophyll a and diagnostic pigments referred to different taxonomic groups. The analysis of micro-, nano- and pico-phytoplankton satellite time series (1998–2010) describes, quantitatively, the algal assemblage structure over the basin and reveals that the main contribution to chlorophyll a in most of the Mediterranean Sea comes from the pico-phytoplankton component, especially in nutrient-poor environments. Regions with different and peculiar features are the Northwestern Mediterranean Sea, the Alborán Sea and several coastal areas, such as the North Adriatic Sea. In these areas, local interactions between physical and biological components modulate the composition of the three phytoplankton size classes. It results that, during the spring bloom season, micro-phytoplankton dominates in areas of intense vertical winter mixing and deep/intermediate water formation, while in coastal areas micro-phytoplankton dominates in all seasons because of the nutrient supply from the terrestrial inputs. In the Alborán Sea, where the Atlantic inflow modulates the nutrient availability, any predominance of one class over the other two has been observed. The nano-phytoplankton component instead remains widespread over the entire basin along the year, and its contribution to chlorophyll a is of the order of 30–40 %. The largest inter-annual signal occurs in the Northwestern Mediterranean Sea, driven by the year-to-year variation in intensity and extension of the spring bloom, followed by the Alborán Sea, in which the inter-annual variability is strongly modulated by the Atlantic inflow. In absence of sufficient in situ data of community composition, the satellite-based analysis demonstrated that pico-, nano- and micro-phytoplankton classes often coexist. The predominance of one group over the other ones is strongly dependent on the physical and biological processes occurring at the mesoscale. These processes directly influence the nutrient and light availability, which are the principal forcing for the algae growth