No abstract

Deep-sea sediment is one of the most important microbial-driven ecosystems, yet it is not well characterized. Genome sequence analyses of deep-sea sedimentary bacteria would shed light on the understanding of this ecosystem. In this study, the complete genome of deep-sea sedimentary bacterium Pseudoalteromonas sp. SM9913 (SM9913) is described and compared with that of the closely related Antarctic surface sea-water ecotype Pseudoalteromonas haloplanktis TAC125 (TAC125). SM9913 has fewer dioxygenase genes than TAC125, indicating a possible sensitivity to reactive oxygen species. Accordingly, experimental results showed that SM9913 was less tolerant of H 2 O 2 than TAC125. SM9913 has gene clusters related to both polar and lateral flagella biosynthesis. Lateral flagella, which are usually present in deep-sea bacteria and absent in the related surface bacteria, are important for the survival of SM9913 in deep-sea environments. With these two flagellar systems, SM9913 can swim in sea water and swarm on the sediment particle surface, favoring the acquisition of nutrients from particulate organic matter and reflecting the particle-associated alternative lifestyle of SM9913 in the deep sea. A total of 12 genomic islands were identified in the genome of SM9913 that may confer specific features unique to SM9913 and absent from TAC125, such as drug and heavy metal resistance. Many signal transduction genes and a glycogen production operon were also present in the SM9913 genome, which may help SM9913 respond to food pulses and store carbon and energy in a deep-sea environment.

To what extent the genomes of different species belonging to one genus can be diverse and the relationship between genomic differentiation and environmental factor remain unclear for oceanic bacteria. With many new bacterial genera and species being isolated from marine environments, this question warrants attention. In this study, we sequenced all the type strains of the published species of Glaciecola, a recently defined cold-adapted genus with species from diverse marine locations, to study the genomic diversity and cold-adaptation strategy in this genus.The genome size diverged widely from 3.08 to 5.96 Mb, which can be explained by massive gene gain and loss events. Horizontal gene transfer and new gene emergence contributed substantially to the genome size expansion. The genus Glaciecola had an open pan-genome. Comparative genomic research indicated that species of the genus Glaciecola had high diversity in genome size, gene content and genetic relatedness. This may be prevalent in marine bacterial genera considering the dynamic and complex environments of the ocean. Species of Glaciecola had some common genomic features related to cold adaptation, which enable them to thrive and play a role in biogeochemical cycle in the cold marine environments.

A Gram-negative, nonmotile, aerobic and oxidase- and catalase-positive bacterium, designated D25T, was isolated from the deep-sea sediments of the southern Okinawa Trough area. Phylogenetic analyses of 16S rRNA gene sequences showed that strain D25T fell within the genus Myroides, with 99.2%, 96.0% and 93.4% sequence similarities to the only three recognized species of Myroides. However, the DNA-DNA similarity value between strain D25T and its nearest neighbour Myroides odoratimimus JCM 7460T was only 49.9% (<70%). Several phenotypic properties could be used to distinguish strain D25T from other Myroides species. The main cellular fatty acids of strain D25T were iso-C15:0, iso-C17:1omega9c, iso-C17:03-OH and Summed Feature 3 (comprising C16:1omega7c and/or iso-C15:02-OH). The major respiratory quinone was MK-6. The DNA G+C content was 33.0 mol%. The results of the polyphasic taxonomy analysis suggested that strain D25T represents a novel species of the genus Myroides, for which the name Myroides profundi sp. nov. is proposed. The type strain is D25T (=CCTCC M 208030T=DSM 19823T).

The ability of combining serum surface-enhanced Raman spectroscopy (SERS) with support vector machine (SVM) for improving classification esophageal cancer patients from normal volunteers is investigated. Two groups of serum SERS spectra based on silver nanoparticles (AgNPs) are obtained: one group from patients with pathologically confirmed esophageal cancer (n=30) and the other group from healthy volunteers (n=31). Principal components analysis (PCA), conventional SVM (C-SVM) and conventional SVM combination with PCA (PCA-SVM) methods are implemented to classify the same spectral dataset. Results show that a diagnostic accuracy of 77.0% is acquired for PCA technique, while diagnostic accuracies of 83.6% and 85.2% are obtained for C-SVM and PCA-SVM methods based on radial basis functions (RBF) models. The results prove that RBF SVM models are superior to PCA algorithm in classification serum SERS spectra. The study demonstrates that serum SERS in combination with SVM technique has great potential to provide an effective and accurate diagnostic schema for noninvasive detection of esophageal cancer.

Clopidogrel has significantly reduced the incidence of recurrent atherothrombotic events in patients with acute coronary syndrome (ACS) and in those undergoing percutaneous coronary intervention (PCI). However, recurrence events still remain, which may be partly due to inadequate platelet inhibition by standard clopidogrel therapy. Genetic polymorphisms involved in clopidogrel’s absorption, metabolism, and the P2Y12 receptor may interfere with its antiplatelet activity. Recent evidence indicated that epigenetic modification may also affect clopidogrel response. In addition, non-genetic factors such as demographics, disease complications, and drug-drug interactions can impair the antiplatelet effect of clopidogrel. The identification of factors contributing to the variation in clopidogrel response is needed to improve platelet inhibition and to reduce risk for cardiovascular events. This review encompasses the most recent updates on factors influencing pharmacokinetic and pharmacodynamic responses to clopidogrel.

A 12‐week feeding trial was conducted to investigate the potential protective effects of citric acid against soybean meal‐induced intestinal oxidative damage and micro‐ecological imbalance in juvenile turbot (S. maximus L.). Four isonitrogenous and isolipidic experimental diets, that is fish meal‐based diet (FM), FM with 40% fish meal protein replaced with soybean meal protein diet (SBM), supplemented with 1.5% citric acid (1.5% CA) or 3% citric acid (3% CA). Results showed that both citric acid diets significantly enhanced the total antioxidative capacity and the gene expression of superoxide dismutase, glutathione peroxidase and heme oxygenase 1, while also decreasing the malondialdehyde content in the distal intestine. Compared to diet SBM, the genes expression of p53, protein kinase C and Caspase‐3 were remarkably declined by dietary citric acid supplementation, while the genes expression of proliferating cell nuclear antigen and mucins showed an opposite trend. The structural integrity of the distal intestine in fish fed citric acid was showed in the histological results. Sequencing of bacterial 16s rRNA V4 region showed that the profile of intestinal bacteria was altered by dietary citric acid supplementation, which was supported by the diet‐cluster of PCoA and phylogenetic tree. MetaStat analysis indicated that dietary citric acid dramatically reduced the relative abundance of the Vibrio genus. In conclusion, dietary citric acid mitigated soybean meal‐induced intestinal oxidative damage, beneficially alleviated the micro‐ecological imbalance and specifically reduced the relative abundance of the Vibrio genus in the distal intestine of juvenile turbot.

A 10‐week feeding experiment was conducted to investigate the effects of dietary DHA/EPA ratio on juvenile Japanese seabass reared in sea floating cages. Six practical diets were formulated differing only in DHA/EPA ratio: 0.55 (Diet D/E0.55), 1.04 (D/E1.04), 1.53 (D/E1.53), 2.08 (D/E2.08), 2.44 (D/E2.44) and 2.93 (D/E2.93). All diets had the same contents of total n‐3 long‐chain polyunsaturated fatty acid (LC‐PUFA) and arachidonic acid (ARA). The results showed that the final weight and specific growth rate significantly increased with increasing dietary DHA/EPA ratio from 0.55 to 2.08 and thereafter declined. Activities of lysozyme and superoxide dismutase in serum in groups with DHA/EPA of 1.53–2.93 was significantly higher compared to group D/E0.55 while the activity of serum alternative complement pathway in group D/E2.93 was significantly lower compared with group D/E1.53. However, no difference was observed in activities of both respiratory burst of head kidney macrophage and serum catalase among dietary treatments. The per cent survival after air exposure in group D/E1.53, D/E2.08 and D/E2.93 was significantly higher compared with group D/E0.55. The fatty acid composition of whole body and tissues reflected closely those of diets, while fish accumulated more DHA than EPA in fish tissues, especially in muscle. These results suggested that at the same dietary contents of n‐3 LC‐PUFA (appr. 18% of TFA) and ARA (appr. 0.7% of TFA), moderate dietary DHA/EPA ratios of 1.53–2.08 significantly enhanced growth performances, certain innate immune responses, and the stress tolerance of Japanese seabass, in accordance with the preferential incorporation of DHA into fish tissues.