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61.
Microbiology in the post-genomic era 总被引:1,自引:0,他引:1
Medini D Serruto D Parkhill J Relman DA Donati C Moxon R Falkow S Rappuoli R 《Nature reviews. Microbiology》2008,6(6):419-430
Genomics has revolutionized every aspect of microbiology. Now, 13 years after the first bacterial genome was sequenced, it is important to pause and consider what has changed in microbiology research as a consequence of genomics. In this article, we review the evolving field of bacterial typing and the genomic technologies that enable comparative analysis of multiple genomes and the metagenomes of complex microbial environments, and address the implications of the genomic era for the future of microbiology. 相似文献
62.
Frascari D Zannoni A Fedi S Pii Y Zannoni D Pinelli D Nocentini M 《Biodegradation》2005,16(2):147-158
The focus of this microcosm study was to monitor the performances of 17 butane-utilizing microcosms during a long-term (100–250 days) aerobic cometabolic depletion of chloroform (CF). The depletion of the contaminant began after a lag-time variable between 0 and 23 days. All microcosms quickly reached a pseudo steady-state condition, in terms of biomass concentration (with an average of 9.3 × 106 CFU ml–1), chloroform depletion rate (5 mol l–1 d–1) and butane utilization rate (730 mol l–1 d–1). After about 100 days of CF depletion, a sudden 5- to 7-fold increase of the chloroform rate was observed in two microcosms, where the highest amount of contaminant had been depleted. In one of these high-performing microcosms, an experiment of chloroform depletion in the absence of butane resulted in the depletion of a surprisingly high amount of contaminant (765 molCF kgdry soil–1 in 2 months) and in a marked selection of a single bacterial strain. Bioaugmentation assays conducted with the biomass selected in this microcosm and with a pure culture of the selected strain immediately resulted in very high chloroform depletion rates. Preliminary results of a study conducted with resting cells of the selected strain indicated that it can degrade chloroform concentrations up to 119 M (14.2 mg l–1) without any sign of substrate toxicity, and that it is able to transform vinyl chloride and 1,1,2-trichloroethane. 相似文献
63.
Soldi M Sarto C Valsecchi C Magni F Proserpio V Ticozzi D Mocarelli P 《Proteomics》2005,5(10):2641-2647
Two-dimensional liquid chromatography separation (2-DL), based on chromatofocusing for first dimension and hydrophobicity for second, can be used as a complementary method to two-dimensional gel electrophoresis (2-DE). A platform now available, ProteomeLab PF 2D provided by Beckman Coulter, (Fullerton, CA, USA), assembles these methods in automation. This system was applied to resolve large numbers of urine proteins. Reproducibility and sensitivity in protein resolution were evaluated in this study using urines collected from male blood donors. About 1000 peaks were detected at a pH range of 4.0-8.5 by applying 1 mg of proteins. Furthermore, the same fractions showing peaks with high absorbance intensities in second dimension were collected and subjected to matrix-assisted laser desorption/ionization-time of flight/mass spectrometry analysis for identification. The results showed that the 2-DL provides high reproducibility of two-dimensional protein map, and lends fractions to subsequent mass spectrometry analysis without the further need for extraction or solubilization of samples as required for spots excised from 2-DE gels. In addition, this system also allows to separate particularly proteins with 40-9 kDa molecular weight. 相似文献
64.
Gian Carlo Manicardi Antonella Tombacco Davide Bizzaro Umberto Bianchi Patrizia Grace Bianchi Denny Sakkas 《The Histochemical journal》1998,30(1):33-39
The nick translation and terminal transferase assays have been compared to test their relative efficiency in detecting DNA breakage in ejaculated human spermatozoa. The results have been correlated with the percentage of chromomycin A3 positive sperm, a fluorochrome that is indicative of the protamination state of sperm. Examination of the ejaculated sperm of 30 subjects revealed that the percentage of positivity to the nick translation and terminal transferase assays did not differ, even when using different fixatives. It is concluded that the inability of the two assays to distinguish the type of DNA damage, as is possible in somatic nuclei, is most probably linked to the unique nature of sperm chromatin. It is proposed that the presence of the damaged DNA may be the remnants of an imperfect spermiogenesis, probably related to an inadequate protamine deposition. This is supported by the strong correlation between the presence of DNA damage and underprotamination as evidenced by chromomycin A3. © Chapman & Hall 相似文献
65.
Hideaki Yuasa Rei Kajitani Yuta Nakamura Kazuki Takahashi Miki Okuno Fumiya Kobayashi Takahiro Shinoda Atsushi Toyoda Yutaka Suzuki Nalinee Thongtham Zac Forsman Omri Bronstein Davide Seveso Enrico Montalbetti Coralie Taquet Gal Eyal Nina Yasuda Takehiko Itoh 《DNA research》2021,28(4)
The crown-of-thorns starfish (COTS) is a coral predator that is widely distributed in Indo-Pacific Oceans. A previous phylogenetic study using partial mitochondrial sequences suggested that COTS had diverged into four distinct species, but a nuclear genome-based analysis to confirm this was not conducted. To address this, COTS species nuclear genome sequences were analysed here, sequencing Northern Indian Ocean (NIO) and Red Sea (RS) species genomes for the first time, followed by a comparative analysis with the Pacific Ocean (PO) species. Phylogenetic analysis and ADMIXTURE analysis revealed clear divergences between the three COTS species. Furthermore, within the PO species, the phylogenetic position of the Hawaiian sample was further away from the other Pacific-derived samples than expected based on the mitochondrial data, suggesting that it may be a PO subspecies. The pairwise sequentially Markovian coalescent model showed that the trajectories of the population size diverged by region during the Mid-Pleistocene transition when the sea-level was dramatically decreased, strongly suggesting that the three COTS species experienced allopatric speciation. Analysis of the orthologues indicated that there were remarkable genes with species-specific positive selection in the genomes of the PO and RS species, which suggested that there may be local adaptations in the COTS species. 相似文献
66.
Letusa Albrecht Davide Angeletti Kirsten Moll Karin Blomqvist Davide Valentini Fabio Luiz D'Alexandri Markus Maurer Mats Wahlgren 《PloS one》2014,9(12)
Plasmodium falciparum is the most lethal of the human malaria parasites. The virulence is associated with the capacity of the infected red blood cell (iRBC) to sequester inside the deep microvasculature where it may cause obstruction of the blood-flow when binding is excessive. Rosetting, the adherence of the iRBC to uninfected erythrocytes, has been found associated with severe malaria and found to be mediated by the NTS-DBL1α-domain of Plasmodium falciparum Erythrocyte Membrane Protein 1 (PfEMP1). Here we show that the reactivity of plasma of Cameroonian children with the surface of the FCR3S1.2-iRBC correlated with the capacity to disrupt rosettes and with the antibody reactivity with a recombinant PfEMP1 (NTS-DBL1α of IT4var60) expressed by parasite FCR3S1.2. The plasma-reactivity in a microarray, consisting of 96 overlapping 15-mer long peptides covering the NTS-DBL1α domain from IT4var60 sequence, was compared with their capacity to disrupt rosettes and we identified five peptides where the reactivity were correlated. Three of the peptides were localized in subdomain-1 and 2. The other two peptide-sequences were localized in the NTS-domain and in subdomain-3. Further, principal component analysis and orthogonal partial least square analysis generated a model that supported these findings. In conclusion, human antibody reactivity with short linear-peptides of NTS-DBL1α of PfEMP1 suggests subdomains 1 and 2 to hold anti-rosetting epitopes recognized by anti-rosetting antibodies. The data suggest rosetting to be mediated by the variable areas of PfEMP1 but also to involve structurally relatively conserved areas of the molecule that may induce biologically active antibodies. 相似文献
67.
Shozo Yokoyama Jinyi Xing Yang Liu Davide Faggionato Ahmet Altun William T. Starmer 《PLoS genetics》2014,10(12)
Establishing genotype-phenotype relationship is the key to understand the molecular mechanism of phenotypic adaptation. This initial step may be untangled by analyzing appropriate ancestral molecules, but it is a daunting task to recapitulate the evolution of non-additive (epistatic) interactions of amino acids and function of a protein separately. To adapt to the ultraviolet (UV)-free retinal environment, the short wavelength-sensitive (SWS1) visual pigment in human (human S1) switched from detecting UV to absorbing blue light during the last 90 million years. Mutagenesis experiments of the UV-sensitive pigment in the Boreoeutherian ancestor show that the blue-sensitivity was achieved by seven mutations. The experimental and quantum chemical analyses show that 4,008 of all 5,040 possible evolutionary trajectories are terminated prematurely by containing a dehydrated nonfunctional pigment. Phylogenetic analysis further suggests that human ancestors achieved the blue-sensitivity gradually and almost exclusively by epistasis. When the final stage of spectral tuning of human S1 was underway 45–30 million years ago, the middle and long wavelength-sensitive (MWS/LWS) pigments appeared and so-called trichromatic color vision was established by interprotein epistasis. The adaptive evolution of human S1 differs dramatically from orthologous pigments with a major mutational effect used in achieving blue-sensitivity in a fish and several mammalian species and in regaining UV vision in birds. These observations imply that the mechanisms of epistatic interactions must be understood by studying various orthologues in different species that have adapted to various ecological and physiological environments. 相似文献
68.
69.
Vicentiu Bogdan Horincar Georgiana Parfene Amit Kumar Tyagi Davide Gottardi Rodica Dinică Maria Elisabetta Guerzoni Gabriela Bahrim 《Journal of applied phycology》2014,26(1):551-559
Three species of macroalgae, Ceramium virgatum (Rhodophyta), Ulva intestinalis, and Cladophora vagabunda (Chlorophyta), harvested from the Romanian Black Sea coast, were studied as sources of valuable compounds that could be used as additives and biopreservatives. Volatile compounds including hexanal (11.2 %), octane (9.8 %), nonanal (7.0 %), octanal (6.7 %), 2,5,5-trimethyl-2-hexene (4.7 %), 3-hexen-2-one (4 %), and o-cymene (3.6 %) were identified as the major components in the biomass extract of C. vagabunda. In C. virgatum, the major volatile components were 3-hexen-2-one (27.9 %), acetone (12.4 %), hexanal (3.4 %), and o-cymene (2.7 %). The major volatile compounds of U. intestinalis were hexanal (14.6 %), trichloromethane (7.3 %), nonanal (5.6 %), 3-hexen-2-one (5.3 %), and octanal (3.1 %). Some of these compounds have industrial applications as additives in the food, pharmaceutical, or cosmetics industries. The U. intestinalis extract had a greater content of mono- and polyunsaturated fatty acids around 46.0 % as compared with 42.0 % for C. vagabunda and 31.9 % for C. virgatum. The most abundant fatty acids were palmitic acid (C16:0), arachidonic acid (C20:4n-6), and oleic acid (C18:1ω-9cis). The antimicrobial effect of fatty acid extracts was tested against four pathogenic bacteria. The minimum inhibitory concentrations of C. vagabunda, C. virgatum, and U. intestinalis fatty acids extracts were 1.8, 3.8, and 3.8 mg mL?1, respectively, for all bacterial strains. This study can help the efforts of finding new, value-added uses for natural marine resources. 相似文献
70.
In a previous work (Kömen et al. 1991) it has been concluded that membrane fragments isolated from autotrophically grown Alcaligenes eutrophus H16 contain several iron-sulphur centres along with haems of a-, b-, c-, and d-type. These redox components have been proposed to be part of a branched respiratory chain leading to multiple membrane bound oxidases. Here, some of the respiratory activities catalyzed by membrane fragments from wild type cells of A. eutrophus (H16) and, for comparison, Paracoccus denitrificans, have been investigated through the use of electron transport inhibitors. Cyanide (CN-) titration curves indicated that in A. eutrophus H16 oxidation of succinate and H2 preferentially proceeds via the cytochrome c oxidase(s) branch (I 50=2 · 10-5 M) whereas the NADH dependent respiration started being inhibited at higher CN- concentrations (I 50=5 · 10-4 M). In membranes isolated from both, cells harvested at late growth-phase (OD 12) and from a mutant deficient in cytochrome c oxidase activity (A. eutrophus RK1), respiration was insensitive to low CN- concentrations (< 10-4 M), and it was sustained by the high catalytic activities of two quinol oxidases. These alternative oxidases of b- (formally o-) and d-type showed different sensitivities to KCN (I 50=10-3 M and 10-2 M, respectively). Interestingly, the cytochrome c oxidase(s) dependent respiration of H16 membranes was insensitive to antimycin A but largely inhibited by myxothiazol (10-6 M). This, and previous work (Kömen et al. 1991), suggest that although the respiratory chain of A. eutrophus is endowed with a putative bc 1 complex, its biochemical nature and role in respiration of this organism are apparently different from those of P. denitrificans. The peculiarity of the respiratory chain of A. eutrophus is confirmed by the rotenone insensitivity of the NADH oxidation in both protoplasts and membrane fragments from wild type and soluble hydrogenase deficient cells (HF14 and HF160). A tentative model of the respiratory chain of autotrophically grown A. eutrophus is presented. 相似文献