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41.
42.
Dimitrios Draganidis Athanasios Chatzinikolaou Alexandra Avloniti José C. Barbero-álvarez Magni Mohr Paraskevi Malliou Vassilios Gourgoulis Chariklia K. Deli Ioannis I. Douroudos Konstantinos Margonis Asimenia Gioftsidou Andreas D. Flouris Athanasios Z. Jamurtas Yiannis Koutedakis Ioannis G. Fatouros 《PloS one》2015,10(7)
43.
Genome sequencing has revealed that horizontal gene transfer (HGT) is a major evolutionary process in bacteria. Although it is generally assumed that closely related organisms engage in genetic exchange more frequently than distantly related ones, the frequency of HGT among distantly related organisms and the effect of ecological relatedness on the frequency has not been rigorously assessed. Here, we devised a novel bioinformatic pipeline, which minimized the effect of over-representation of specific taxa in the available databases and other limitations of homology-based approaches by analyzing genomes in standardized triplets, to quantify gene exchange between bacterial genomes representing different phyla. Our analysis revealed the existence of networks of genetic exchange between organisms with overlapping ecological niches, with mesophilic anaerobic organisms showing the highest frequency of exchange and engaging in HGT twice as frequently as their aerobic counterparts. Examination of individual cases suggested that inter-phylum HGT is more pronounced than previously thought, affecting up to ∼16% of the total genes and ∼35% of the metabolic genes in some genomes (conservative estimation). In contrast, ribosomal and other universal protein-coding genes were subjected to HGT at least 150 times less frequently than genes encoding the most promiscuous metabolic functions (for example, various dehydrogenases and ABC transport systems), suggesting that the species tree based on the former genes may be reliable. These results indicated that the metabolic diversity of microbial communities within most habitats has been largely assembled from preexisting genetic diversity through HGT and that HGT accounts for the functional redundancy among phyla. 相似文献
44.
Joan?M.?BernhardEmail authorView authors OrcID profile Colin?R.?Morrison Ellen?Pape David?J.?Beaudoin M.?Antonio?Todaro Maria?G.?Pachiadaki Konstantinos?Ar.?Kormas Virginia?P.?Edgcomb 《BMC biology》2015,13(1):105
Background
The deep-sea hypersaline anoxic basins (DHABs) of the Mediterranean (water depth ~3500 m) are some of the most extreme oceanic habitats known. Brines of DHABs are nearly saturated with salt, leading many to suspect they are uninhabitable for eukaryotes. While diverse bacterial and protistan communities are reported from some DHAB haloclines and brines, loriciferans are the only metazoan reported to inhabit the anoxic DHAB brines. Our goal was to further investigate metazoan communities in DHAB haloclines and brines.Results
We report observations from sediments of three DHAB (Urania, Discovery, L’Atalante) haloclines, comparing these to observations from sediments underlying normoxic waters of typical Mediterranean salinity. Due to technical difficulties, sampling of the brines was not possible. Morphotype analysis indicates nematodes are the most abundant taxon; crustaceans, loriciferans and bryozoans were also noted. Among nematodes, Daptonema was the most abundant genus; three morphotypes were noted with a degree of endemicity. The majority of rRNA sequences were from planktonic taxa, suggesting that at least some individual metazoans were preserved and inactive. Nematode abundance data, in some cases determined from direct counts of sediments incubated in situ with CellTrackerTM Green, was patchy but generally indicates the highest abundances in either normoxic control samples or in upper halocline samples; nematodes were absent or very rare in lower halocline samples. Ultrastructural analysis indicates the nematodes in L’Atalante normoxic control sediments were fit, while specimens from L’Atalante upper halocline were healthy or had only recently died and those from the lower halocline had no identifiable organelles. Loriciferans, which were only rarely encountered, were found in both normoxic control samples as well as in Discovery and L’Atalante haloclines. It is not clear how a metazoan taxon could remain viable under this wide range of conditions.Conclusions
We document a community of living nematodes in normoxic, normal saline deep-sea Mediterranean sediments and in the upper halocline portions of the DHABs. Occurrences of nematodes in mid-halocline and lower halocline samples did not provide compelling evidence of a living community in those zones. The possibility of a viable metazoan community in brines of DHABs is not supported by our data at this time.45.
Thilo Gambichler Iris Plura Monika Schmid‐Wendtner Konstantinos Valavanis Daniela Kulichova Markus Stücker Azem Pljakic Carola Berking Tanja Maier 《Journal of biophotonics》2015,8(8):681-686
High‐definition optical coherence tomography (HD‐OCT) scanners have recently been developed. We assessed micromorphological HD‐OCT correlates of benign naevi (BN) and malignant melanoma (MM). 28 BN and 20 MM were studied using HD‐OCT and histology. Epidermal honeycomb/cobblestone pattern, regular junctional cell nests, and edged papillae are more often observed in BN, whereas fusion of rete ridges, pagetoid cells and junctional and/or dermal nests with atypical cells are more frequently seen in MM. A high overlap of HD‐OCT features in BN and MM was observed and in 20% of MM we did not find evidence for malignancy in OCT images at all. Using HD‐OCT it is possible to visualize architectural and cellular alterations of melanocytic skin lesions. The overlap of HD‐OCT features seen in BN and MM and the absence of suspicious HD‐OCT features in some MM represents an important limitation of HD‐OCT affecting the sensitivity of HD‐OCT in diagnosing MM.
46.
George Pentheroudakis Georgia Raptou Vassiliki Kotoula Ralph M. Wirtz Eleni Vrettou Vasilios Karavasilis Georgia Gourgioti Chryssa Gakou Konstantinos N. Syrigos Evangelos Bournakis Grigorios Rallis Ioannis Varthalitis Eleni Galani Georgios Lazaridis George Papaxoinis Dimitrios Pectasides Gerasimos Aravantinos Thomas Makatsoris Konstantine T. Kalogeras George Fountzilas 《PloS one》2015,10(5)
Background
Although host immune response is an emerging prognostic factor for colorectal cancer, there is no consensus on the optimal methodology, surrogate markers or tissue for study.Patients and Methods
Tumour blocks were prospectively collected from 344 patients with stage II/III colorectal cancer (CRC) treated with adjuvant chemotherapy. Whole section lymphocytic infiltration was studied along with mRNA expression of CD3Z, CD8, CD4, CXCL9, CXCL13, IGHM, FOXP3, SNAI2 and ESR1 by qRT-qPCR in tissue microarray (TMA) cores from the centre of tumour, invasive margin and adjacent normal mucosa.Results
Lymphocytic infiltration, deficient MMR (10.9%), KRAS (40.7%) and BRAF (4.9%) mutations or single mRNA gene expression were not prognostic. Tumour ESR1 gene expression (Hazard Ratio [HR] for relapse 2.33, 95% CI 1.35-4.02; HR for death 1.74, 95% CI 1.02-2.97) and absence of necrosis (HR for relapse 1.71, 95% CI 1.05-2.71; HR for death 1.98, 95% CI 1.14-3.43) were adverse prognostic features. We used CD3Z and CD8 expression in order to devise the mRNA-based Immune Score (mIS) and proceeded to partitioning analysis in 267 patients, with age, stage, tumour site (Right vs Left CRC), KRAS mutation and tumour mIS as input factors. Only in patients with stage III right-sided colon cancer, a low immune response was associated with inferior disease-free survival (mIS-low, HR for relapse 2.28, 95% CI 1.05-8.02). No prognostic significance was seen for tumour mIS in any other stage or site of CRC, or for a similar mIS score derived from adjacent normal mucosa. Independent adverse prognostic significance was retained in multivariable analysis for absence of necrosis, tumour ESR1 expression in all patients and low tumour mIS in stage III right-sided CRC.Conclusions
In localised CRC, mRNA-based CD3Z/CD8 profiling of tumour immune response may have stage, site and tissue-specific prognostic significance, along with ESR1 expression.Trial Registration
ANZCTR.org.au ACTRN12610000509066 相似文献47.
Konstantinos Arapis Jean Baptiste Cavin Laura Gillard Fran?oise Cluzeaud Philippe Lettéron Robert Ducroc Johanne Le Beyec Muriel Hourseau Anne Couvelard Jean-Pierre Marmuse Maude Le Gall André Bado 《PloS one》2015,10(3)
Whereas the remodeling of intestinal mucosa after bariatric surgeries has been the matter of numerous studies to our knowledge, very few reported on the remodeling of the residual gastric mucosa. In this study, we analyzed remodeling of gastric mucosa after Roux-en-Y gastric bypass (RYGB) and vertical sleeve gastrectomy (VSG) in rats. Diet-induced obese rats were subjected to RYGB, VSG or sham surgical procedures. All animals were assessed for food intake, body-weight, fasting blood, metabolites and hormones profiling, as well as insulin and glucose tolerance tests before and up to 5 weeks post-surgery. Remodeling of gastric tissues was analyzed by routine histology and immunohistochemistry studies, and qRT-PCR analyses of ghrelin and gastrin mRNA levels. In obese rats with impaired glucose tolerance, VSG and RYGB caused substantial weight loss and rats greatly improved their oral glucose tolerance. The remaining gastric mucosa after VSG and gastric pouch (GP) after RYGB revealed a hyperplasia of the mucous neck cells that displayed a strong immunoreactivity for parietal cell H+/K+-ATPase. Ghrelin mRNA levels were reduced by 2-fold in remaining fundic mucosa after VSG and 10-fold in GP after RYGB. In the antrum, gastrin mRNA levels were reduced after VSG in line with the reduced number of gastrin positive cells. This study reports novel and important observations dealing with the remaining gastric mucosa after RYGB and VSG. The data demonstrate, for the first time, a hyperplasia of the mucous neck cells, a transit cell population of the stomach bearing differentiating capacities into zymogenic and peptic cells. 相似文献
48.
David S. Lopez Run Wang Konstantinos K. Tsilidis Huirong Zhu Carrie R. Daniel Arup Sinha Steven Canfield 《PloS one》2015,10(4)
Objectives
Caffeine is consumed by more than 85% of adults and little is known about its role on erectile dysfunction (ED) in population-based studies. We investigated the association of caffeine intake and caffeinated beverages with ED, and whether these associations vary among comorbidities for ED.Material and Method
Data were analyzed for 3724 men (≥20 years old) who participated in the National Health and Nutrition Examination Survey (NHANES). ED was assessed by a single question during a self-paced, computer-assisted self-interview. We analyzed 24-h dietary recall data to estimate caffeine intake (mg/day). Multivariable logistic regression analyses using appropriate sampling weights were conducted.Results
We found that men in the 3rd (85-170 mg/day) and 4th (171-303 mg/day) quintiles of caffeine intake were less likely to report ED compared to men in the lowest 1st quintile (0-7 mg/day) [OR: 0.58; 95% CI, 0.37–0.89; and OR: 0.61; 95% CI, 0.38–0.97, respectively], but no evidence for a trend. Similarly, among overweight/obese and hypertensive men, there was an inverse association between higher quintiles of caffeine intake and ED compared to men in the lowest 1st quintile, P≤0.05 for each quintile. However, only among men without diabetes we found a similar inverse association (Ptrend = 0.01).Conclusion
Caffeine intake reduced the odds of prevalent ED, especially an intake equivalent to approximately 2-3 daily cups of coffee (170-375 mg/day). This reduction was also observed among overweight/obese and hypertensive, but not among diabetic men. Yet, these associations are warranted to be investigated in prospective studies. 相似文献49.
50.
Paschalidis A Konstantinos Toumi Imene Moschou N Panagiotis Kalliopi A Roubelakis-Angelakis 《Plant signaling & behavior》2010,5(9):1153-1156
Recently we showed that ABA is at least partly responsible for the induction of the polyamine exodus pathway in Vitis vinifera plants. Both sensitive and tolerant plants employ this pathway to orchestrate stress responses, differing between stress adaptation and programmed cell death. Herein we show that ABA is an upstream signal for the induction of the polyamine catabolic pathway in Vitis vinifera. Thus, amine oxidases are producing H2O2 which signals stomata closure. Moreover, the previously proposed model for the polyamine catabolic pathway is updated and discussed.Key words: plant growth, abscissic acid, polyamines, amine oxidases, signaling, oxidative stress, programmed cell deathWe have shown that tobacco salinity induces an exodus of the polyamine (PA) spermidine (Spd) into the apoplast where it is oxidized by polyamine oxidase (PAO) generating hydrogen peroxide (H2O2). Depending on the size of H2O2, it signals either tolerance-effector genes or the programmed cell death syndrome1 (PCD). PAs are ubiquitous and biologically active molecules. In the recent years remarkable progress has been accomplished regarding the regulation of PAs biosynthesis and catalysis, not only under normal physiological but also under stress conditions.1 The most studied PAs are the diamine Putrescine (Put) and its derivatives the triamine Spd and the tetramine spermine (Spm). They are present in the cells in soluble form (S), or conjugated either to low molecular weight compounds (soluble hydrolyzed form, SH) or to “macro” molecules or cell walls (pellet hydrolyzed form, PH). In higher plants, Put is synthesized either directly from ornithine via ornithine decarboxylase (ODC; EC 4.1.1.17) or indirectly from arginine via arginine decarboxylase (ADC; EC 4.1.1.19). Spd and Spm are synthesized via Spd synthase (EC 2.5.1.16, SPDS) and Spm synthase (EC 2.5.1.22, SPMS), respectively, by sequential addition of aminopropyl groups to Put, catalyzed by S-adenosyl-L-methionine decarboxylase (SAMDC; EC 4.1.1.50).2,3 In plants, PAs are present in the cytoplasm, as well as in cellular organelles.4 Recently it was shown that during stress, they are secreted into the apoplast where they are oxidized by amine oxidases (AOs), such as diamine oxidase for Put (DAO, E.C. 1.4.3.6) and polyamine oxidase (PAO, E.C. 1.4.3.4) for Spd and Spm.1,5,6 Oxidation of PAs generates, amongst other products, H2O21,7,8 which is involved in cell signaling processes coordinated by abscissic acid (ABA),9 but also acts as efficient oxidant and, at high concentration, orchestrates the PCD syndrome.6,10 Two types of PA catabolism by PAO are known in plants: the terminal and the back-conversion pathways. The terminal one takes place in the apoplast, produces except H2O2, 1,3-diaminopropane and an aldehyde depending on the species. On the other hand, the back-conversion pathway is intracellular (cytoplasm and peroxisomes) resulting to the production of H2O2 and the sequential production of Put by Spm via Spd.1,7 Now we have shown that PA exodus also occurs in Vitis vinifera and this phenomenon is at least partially induced by abscissic acid (ABA).11 Thus, exogenous application of ABA results to PA exodus into the apoplast of grapevine. PA is oxidized by an AO resulting to production of H2O2. When the titer of H2O2 is below a threshold, expression of tolerance-effector genes is induced, while when it exceeds this threshold the programmed cell death (PCD) syndrome is induced. 相似文献