1,721,234 research outputs found
The Philosophy of Computer Science
No full textThe philosophy of computer science is concerned with those ontological, methodological, and ethical issues that arise from within the academic discipline of computer science as well as from the practice of software development. Thus, the philosophy of computer science shares the same philosophical goals as the philosophy of mathematics and the many subfields of the philosophy of science, such as the philosophy of biology or the philosophy of the social sciences. The philosophy of computer science also considers the analysis of computational artifacts, that is, human-made computing systems, and it focuses on methods involved in the design, specification, programming, verification, implementation, and testing of those systems. The abstract nature of computer programs and the resulting complexity of implemented artifacts, coupled with the technological ambitions of computer science, ensures that many of the conceptual questions of the philosophy of computer science have analogues in the philosophy of mathematics, the philosophy of empirical sciences, and the philosophy of technology. Other issues characterize the philosophy of computer science only. We shall concentrate on three tightly related groups of topics that form the spine of the subject. First we discuss topics related to the ontological analysis of computational artifacts, in Sections 1-5 below. Second, we discuss topics involved in the methodology and epistemology of software development, in Sections 6-9 below. Third, we discuss ethical issues arising from computer science practice, in Section 10 below. Applications of computer science are briefly considered in section 11
Interaction of Rhodococcus with Metals and Biotechnological Applications
No full textIn studies of environmental stresses caused by metals, Rhodococcus species are routinely identified as part of a beneficial microbial rhizosphere community. These bacterial strains, inhabiting diverse ecological niches, possess a variety of enzymatic activities to carry out relevant biodegradation reactions, such as degradation of organic pollutants in some cases using them for both carbon and energy. In this context, most Rhodococcus strains have been found to have very high levels of metal resistance. Thus, these microorganisms are not only capable of metabolizing various organic pollutants in the presence of co-contaminating heavy metals, but they can also bioadsorb and/or bioconvert various metals and metalloids [metal(loid)s]. Indeed, some Rhodococcus exploit these metal(loid) compounds to generate biogenic nanoscale materials of intriguing physical-chemical properties, which can find applications in biotechnology.
This book chapter has the focus in overviewing the biotechnological relevance of the Rhodococcus genus relationship with metal(loid)s, the bioprocesses elicited by these microorganisms in handling metal(loid)s’ toxicity, and the importance of these actinomycetes in the context of the bioremediation and bionanotechnology fields
From 0D-complex to 3D-MOF: changing the antimicrobial activity of zinc(II) via reaction with aminocinnamic acids
Full text linkCombining zinc nitrate with 3- and/or 4- aminocinnamic acid (3-ACA and 4-ACA, respectively) leads to the formation of the 0D complex [Zn(4-AC)2(H2O)2], the 1D coordination polymer [Zn(3-AC)(4-AC)], and the 2D and 3D MOFs [Zn(3-AC)2]∙2H2O and [Zn(4-AC)2]∙H2O, respectively. These compounds result from the deprotonation of the acid molecules, with the resulting 3- and 4-aminocinnamate anions serving as bidentate terminal or bridging ligands. All solids were fully characterized via single crystal and powder X-ray diffraction and thermal techniques. Given the mild antimicrobial properties of cinnamic acid derivatives and the antibacterial nature of the metal cation, these compounds were assessed and demonstrated very good planktonic cell killing as well as inhibition of biofilm growth against Pseudomonas aeruginosa, Escherichia coli, and Staphylococcus aureus
Tunable photoluminescence properties of selenium nanoparticles: biogenic versus chemogenic synthesis
Full text linkVarious technological and biomedical applications
rely on the ability of materials to emit light (photoluminescence
[PL]), and, among them, metal nanoparticles
(NPs) and semi-conductor Quantum Dots (QDs) represent
ideal candidates as sensing probes and imaging tools, portraying
better PL features than conventional organic dyes.
However,theknowledgeofPLbehaviorofsemiconductorNPs
– i.e., selenium; SeNPs – is still in its infancy, especially for
those synthesized by microorganisms. Considering the
essential role played by biogenic SeNPs as antimicrobial,
anticancer, and antioxidant agents, or food supplements,
their PL properties must be explored to take full advantage of
them as eco-friendly and versatile tools. Here, PL features of
SeNPs produced by the Se-tolerant Stenotrophomonasmaltophilia
SeITE02 strain, compared with chemogenic ones, are
investigated, highlighting the PL dependency on the NP size.
Indeed, PL emission shifted from indigo-blue (emission
wavelength λem 400–450 nm) to green-yellow (λem 480–
570 nm) and orange-red (λem 580–700 nm) for small (ca.
50 nm) and big (ca. 100 nm) SeNPs respectively, revealing the
versatility of an environmental bacterial isolate to synthesize
diverse PL probes. Besides, biogenic SeNPs show PL lifetime
comparable to those of the most used fluorophores, supporting
their potential application as markers for (bio)imaging
Some facts about the respiratory enzymes of Pseudomonas pseudoalcaligenes KF707 recently renamed as Pseudomonas furukawaii sp. nov., type strain KF707
No full textRecently proposed renaming the obligate aerobe Pseudomonas pseudoalcaligenes KF707 as Pseudomonas furukawiisp. nov. type strain KF707. Since the first quasi-complete genome sequence of KF707 was reported in 2012 (accession number: PRJNA83639) numerous reports on chemotaxis and function/composition of the respiratory redox chain of KF707 have been published, demonstrating that KF707 contains three cheA genes for aerobic motility, four cytochrome oxidases of c(c)aa3- and cbb3-type and one bd-type quinol oxidase. With this background in mind, it has been quite a surprise to read within Table 1 of the paper by Kimura et al. that strain KF707 is phenotypically characterized as cytochrome oxidase-negative. Further, Table 1 also reports that KF707 is b-galactosidase-positive, an affirmation that is not consistent with results documented in the current literature. In this present ‘Letter to the Editor’ we show that Kimura et al. have contradicted themselves and provided inaccurate information in respect to the respiratory phenotypic features of P. furukawii
A comparison of the response of two Burkholderia fungorum strains grown as planktonic cells versus biofilm to dibenzothiophene and select polycyclic aromatic hydrocarbons
Full text linkIn natural environments, bacteria often exist in close association with surfaces and interfaces by establishing biofilms. Here, we report on the ability of Burkholderia fungorum strains DBT1 and 95 to survive in high concentrations of hydrocarbons, and we compare their growth as a biofilm vs. planktonic cells. The 2 compounds tested were dibenzothiophene (DBT) and a mixture of naphthalene, phenanthrene, and pyrene (5:2:1) as representative compounds of thiophenes and polycyclic aromatic hydrocarbons (PAHs), respectively. The results showed that both strains were able to degrade DBT and to survive in the presence of up to a 2000 mg·L−1 concentration of this compound both as a biofilm and as free-living cells. Moreover, B. fungorum DBT1 showed reduced tolerance towards the mixed PAHs (2000 mg·L−1 naphthalene, 800 mg·L−1 phenanthrene, and 400 mg·L−1 pyrene) both as a biofilm and as free-living cells. Conversely, biofilms of B. fungorum 95 enhanced resistance against these toxic compounds compared with planktonic cells (P < 0.05). Visual observation through confocal laser scanning microscopy showed that exposure of biofilms to DBT and PAHs altered their structure: high concentrations of DBT triggered an aggregation of biofilm cells. These findings provide new perspectives on the effectiveness of using DBT-degrading bacterial strains in bioremediation of hydrocarbon-contaminated sites
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
The Role of cheA Genes in Swarming and Swimming Motility of Pseudomonas pseudoalcaligenes KF707
Full text linkA genome analysis of Pseudomonas pseudoalcaligenes KF707, a PCBs degrader and metal-resistant soil microorganism, revealed the presence of two novel gene clusters named che2 and che3, which were predicted to be involved in chemotaxis-like pathways, in addition to a che1 gene cluster. We herein report that the histidine kinase coding genes, cheA2 and cheA3, have no role in swimming or chemotaxis in P. pseudoalcaligenes KF707, in contrast to cheA1. However, the cheA1 and cheA2 genes were both necessary for cell swarming, whereas the cheA3 gene product had a negative effect on the optimal swarming phenotype of KF707 cells
Biphenyl Modulates the Expression and Function of Respiratory Oxidases in the Polychlorinated-Biphenyls Degrader Pseudomonas pseudoalcaligenes KF707
Full text linkPseudomonas pseudoalcaligenes KF707 is a soil bacterium which is known for its capacity to aerobically degrade harmful organic compounds such as polychlorinated biphenyls (PCBs) using biphenyl as co-metabolite. Here we provide the first genetic and functional analysis of the KF707 respiratory terminal oxidases in cells grown with two different carbon sources: glucose and biphenyl. We identified five terminal oxidases in KF707: two c(c)aa3 type oxidases (Caa3 and Ccaa3), two cbb3 type oxidases (Cbb31 and Cbb32), and one bd type cyanide-insensitive quinol oxidase (CIO). While the activity and expression of both Cbb31 and Cbb32 oxidases was prevalent in glucose grown cells as compared to the other oxidases, the activity and expression of the Caa3 oxidase increased considerably only when biphenyl was used as carbon source in contrast to the Cbb32 oxidase which was repressed. Further, the respiratory activity and expression of CIO was up-regulated in a Cbb31 deletion strain as compared to W.T. whereas the CIO up-regulation was not present in Cbb32 and C(c)aa3 deletion mutants. These results, together, reveal that both function and expression of cbb3 and caa3 type oxidases in KF707 are modulated by biphenyl which is the co-metabolite needed for the activation of the PCBs-degradation pathway
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