Variability of environmental factors of an eastern Mediterranean Sea river influenced coastal system

Spercheios River discharge rates of nutrients, suspended particulate matter (SPM) and particulate organic carbon (POC) and seawater concentrations of these parameters as well as chlorophyll a(chl a) were measured in the Maliakos Gulf, Greece, on a monthly basis between 1992-1993. From all the nutrients measured, silicate showed the highest discharge rates followed by nitrate, phosphate and nitrite. The river introduced significant amounts of SPM (8.5 – 35.5 Kg d -1 ) with very low POC content (<3%). Most of the variables measured showed no gradient from the river to the outer gulf, which could be attributed to fast mixing of the incoming water. However, chl a had higher concentrations in the inner (0.3 – 4.9 Μg l -1 ) and lower in the outer gulf (0.05 – 2.5 Μg l -1 ). It is suggested that the nutrients introduced by the river are consumed faster in the inner gulf and that a number of temporal streams and non-point sources at the periphery of the gulf prevent the formation of a gradient

Development of an optimized method for the detection of airborne viruses with real-time PCR analysis

<p>Abstract</p> <p>Background</p> <p>Airborne viruses remain one of the major public health issues worldwide. Detection and quantification of airborne viruses is essential in order to provide information regarding public health risk assessment.</p> <p>Findings</p> <p>In this study, an optimized new, simple, low cost method for sampling of airborne viruses using Low Melting Agarose (LMA) plates and a conventional microbial air sampling device has been developed. The use of LMA plates permits the direct nucleic acids extraction of the captured viruses without the need of any preliminary elution step. Molecular detection and quantification of airborne viruses is performed using real-time quantitative (RT-)PCR (Q(RT-)PCR) technique. The method has been tested using Adenoviruses (AdVs) and Noroviruses (NoVs) GII, as representative DNA and RNA viruses, respectively. Moreover, the method has been tested successfully in outdoor experiments, by detecting and quantifying human adenoviruses (HAdVs) in the airborne environment of a wastewater treatment plant.</p> <p>Conclusions</p> <p>The great advantage of LMA is that nucleic acids extraction is performed directly on the LMA plates, while the eluted nucleic acids are totally free of inhibitory substances. Coupled with QPCR the whole procedure can be completed in less than three (3) hours.</p

Value, but high costs in post-deposition data curation

Discoverability of sequence data in primary data archives is proportional to the richness of contextual information associated with the data. Here, we describe an exercise in the improvement of contextual information surrounding sample records associated with metagenomics sequence reads available in the European Nucleotide Archive. We outline the annotation process and summarize findings of this effort aimed at increasing usability of publicly available environmental data. Furthermore, we emphasize the benefits of such an exercise and detail its costs. We conclude that such a third party annotation approach is expensive and has value as an element of curation, but should form only part of a more sustainable submitter-driven approach

Value, but high costs in post-deposition data Curation

© The Author(s) 2016. Published by Oxford University Press. Discoverability of sequence data in primary data archives is proportional to the richness of contextual information associated with the data. Here, we describe an exercise in the improvement of contextual information surrounding sample records associated with metagenomics sequence reads available in the European Nucleotide Archive. We outline the annotation process and summarize findings of this effort aimed at increasing usability of publicly available environmental data. Furthermore, we emphasize the benefits of such an exercise and detail its costs. We conclude that such a third party annotation approach is expensive and has value as an element of curation, but should form only part of a more sustainable submitter-driven approach

Novel genetic risk variants for pediatric celiac disease

Background: Celiac disease is a complex chronic immune-mediated disorder of the small intestine. Today, the pathobiology of the disease is unclear, perplexing differential diagnosis, patient stratification, and decision-making in the clinic. Methods: Herein, we adopted a next-generation sequencing approach in a celiac disease trio of Greek descent to identify all genomic variants with the potential of celiac disease predisposition. Results: Analysis revealed six genomic variants of prime interest: SLC9A4 c.1919G gt A, KIAA1109 c.2933T gt C and c. 4268_4269delCCinsTA, HoxB6 c.668C gt A, HoxD12 c.418G gt A, and NCK2 c.745_746delAAinsG, from which NCK2 c.745_746delAAinsG is novel. Data validation in pediatric celiac disease patients of Greek (n=109) and Serbian (n=73) descent and their healthy counterparts (n=111 and n=32, respectively) indicated that HoxD12 c.418G gt A is more prevalent in celiac disease patients in the Serbian population (P lt 0.01), while NCK2 c.745_746delAAinsG is less prevalent in celiac disease patients rather than healthy individuals of Greek descent (P = 0. 03). SLC9A4 c.1919G gt A and KIAA1109 c.2933T gt C and c.4268_4269delCCinsTA were more abundant in patients; nevertheless, they failed to show statistical significance. Conclusions: The next-generation sequencing-based family genomics approach described herein may serve as a paradigm towards the identification of novel functional variants with the aim of understanding complex disease pathobiology

Metastasis to the breast from an adenocarcinoma of the lung with extensive micropapillary component: a case report and review of the literature

Breast metastasis from extra-mammary malignancy is rare. Based on the literature an incidence of 0.4-1.3% is reported. The primary malignancies most commonly metastasizing to the breast are leukemia-lymphoma, and malignant melanoma. We present a case of metastasis to the breast from a pulmonary adenocarcinoma, with extensive micropapillary component, diagnosed concomitantly with the primary tumor. A 73-year-old female presented with dyspnea and dry cough of 4 weeks duration and a massive pleural effusion was found on a chest radiograph. Additionally, on physical examination a poorly defined mass was noted in the upper outer quadrant of the left breast. The patient underwent bronchoscopy, excisional breast biopsy and medical thoracoscopy. By cytology, histology and immunohistochemistry primary lung adenocarcinoma with metastasis to the breast and parietal pleura was diagnosed. Both the primary and metastatic anatomic sites demonstrated histologically extensive micropapillary component, which is recently recognized as an important prognostic factor. The patient received chemotherapy but passed away within 7 months. Accurate differentiation of metastatic from primary carcinoma is of crucial importance because the treatment and prognosis differ significantly

New Mediterranean biodiversity records (October, 2014)

The Collective Article 'New Mediterranean Biodiversity Records' of the Mediterranean Marine Science journal offers the means to publish biodiversity records in the Mediterranean Sea. The current article is divided in two parts, for records of alien and native species respectively. The new records of alien species include: the red alga Asparagopsis taxiformis (Crete and Lakonikos Gulf, Greece); the red alga Grateloupia turuturu (along the Israeli Mediterranean shore); the mantis shrimp Clorida albolitura (Gulf of Antalya, Turkey); the mud crab Dyspanopeus sayi (Mar Piccolo of Taranto, Ionian Sea); the blue crab Callinectes sapidus (Chios Island, Greece); the isopod Paracerceis sculpta (northern Aegean Sea, Greece); the sea urchin Diadema setosum (Gökova Bay, Turkey); the molluscs Smaragdia souverbiana, Murex forskoehlii, Fusinus verrucosus, Circenita callipyga, and Aplysia dactylomela (Syria); the cephalaspidean mollusc Haminoea cyanomarginata (Baia di Puolo, Massa Lubrense, Campania, southern Italy); the topmouth gudgeon Pseudorasbora parva (Civitavecchia, Tyrrhenian Sea); the fangtooth moray Enchelycore anatina (Plemmirio marine reserve, Sicily); the silver-cheeked toadfish Lagocephalus sceleratus (Saros Bay, Turkey; and Ibiza channel, Spain); the Indo-Pacific ascidian Herdmania momus in Kastelorizo Island (Greece); and the foraminiferal Clavulina multicamerata (Saronikos Gulf, Greece). The record of L. sceleratus in Spain consists the deepest (350-400m depth) record of the species in the Mediterranean Sea. The new records of native species include: first record of the ctenophore Cestum veneris in Turkish marine waters; the presence of Holothuria tubulosa and Holothuria polii in the Bay of Igoumenitsa (Greece); the first recorded sighting of the bull ray Pteromylaeus bovinus in Maltese waters; and a new record of the fish Lobotes surinamensis from Maliakos Gulf.peer-reviewe

First record of the Red Sea immigrant Chrysallida fischeri (Hornung and Mermod, 1925) (Gastropoda: Pyramidellidae) from Greek waters

The Red Sea mollusc Chrysallida fischeri (Hornung and Mermod, 1925) was collected in 2005 off Makri, Rhodes, Greece. This is the first record of the species in the Aegean Sea. The presence of both live specimens and shells suggest that C. fischeri is well established in the area. © 2007 The Author(s)