1,720,982 research outputs found
Emerging roles of hnRNP's in postranscriptional regulation: what can we learn from flies ?
No full textBiodegradation of oganophosphorus pesticides by soil bacteria
No full textA number of studies in the 1980s and 1990s showed that crop-protection products, applied to drained fields, could
move downwards through the soil profile and to the groundwater. Organophosphorus insecticides (OPs) are used
all over the world for crop protection, for other agricultural practices such as sheep dipping and, in aquaculture, for
the control of sea lice. Ops besides showing a specific neurotoxicity and have also been related to various modern
diseases, including Creutzfeldt–Jakob (CJD) and the Gulf War syndrome. Although OPs are less persistent than
Organoclorine pesticides (OCs), they still constitute an environmental risks thus increasing the social concern
about their levels in soils, surface waters, and ground waters. Degradation of OPs by microorganisms has
been assessed for a few bacterial strains. In the present study the OPs degrading potential of indigenous soil
microorganisms was investigated.
Using enrichment cultures in which parathion was the only C and energy sources many bacterial strains were
isolated from OPs contaminated and pristine agricultural soils characterized by different physico-chemical
properties. More than 40 potential OPs degraders were isolated and grouped in operational taxonomic units (OTU)
using analysis of polymorphism showed by the ribosomal internal transcribed spacer (ITS). Partial sequencing of
16S rRNA gene of representative isolates of each OTU revealed that most of them belong to Proteobacteria and
Actinobacteria. All the analyzed soils showed the presence of putative OPs degraders: the highest diversity was
found in organic cultivated soils, the lowest in chemically cultivated soils.
Degradation of different OPs, characterized by different physical and chemical properties, was obtained by
different selected representative strains using SPME GC-MS analysis on water and soil microcosms. The results
showed that, after the incubation period, the amount of pesticide residues were in the range 20-80%. Some of the
isolates bacterial species are currently unknown as OPs degraders
Differential proteomics highlights metabolic changes associated with n-hexadecane utilization in a Streptomyces coelicolor strain expressing Gordonia sp. SoCg n-alkane monooxigenase.
No full textIntroduction: Alkanes are biodegraded to generate the corresponding primary alcohol trough
alkane hydroxylases (AHs) consisting on an integral membrane alkane monooxygenase (AlkB)
and two soluble proteins, rubredoxin and rubredoxin reductase. Recently, an alkB gene was
reported to be involved in degradation of long chain n-alkanes in the actinobacterium Gordonia
sp. SoCg. This gene was expressed in Streptomyces coelicolor M145 which is unable to
degrade n-alkanes.
Results: The engineered strain, M145-AH, can biotransform n-hexadecane into the
corresponding 1-hexadecanol and it is able to grow on n-hexadecane as sole carbon source.
Changes in global protein expression associated with n-hexadecane metabolism in M145-AH
were studied using a differential proteomic approach. M145-AH was incubated in three different
conditions using a mineral medium supplemented with hexadecane or glucose as the sole
carbon source or without any carbon source, respectively. Total proteins, extracted from
samples collected after 6, 24 and 48 h of incubation in the three conditions, were analyzed by
2D-Differential Gel Electrophoresis (2D-DIGE). Differentially abundant protein spots were
identified by mass spectrometry. The expression profile of proteins involved in central carbon
metabolism, amino acid and protein biosynthesis, fatty acid metabolism and respiration revealed
a gradual metabolic adaptation to n-hexadecane utilization, which is similar to that of specialized
alkane-degraders.
Conclusion: Thus, the addition of the alkB gene confers to Streptomyces coelicolor the ability
to use an insoluble recalcitrant contaminant as an usual carbon source. These data, expanding
the knowledge on n-alkane bioconversion mechanisms in Gram-positive bacteria, provide new
technological platforms for bioremediation studies and strategies
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
Involvement of an alkane hydroxylase system of Gordonia sp. strain SoCg in degradation of solid n-alkanes.
No full textEnzymes involved in oxidation of long-chain n-alkanes are still not well known, especially those in Grampositive
bacteria. This work describes the alkane degradation system of the n-alkane degrader actinobacterium
Gordonia sp. strain SoCg, which is able to grow on n-alkanes from dodecane (C12) to hexatriacontane (C36) as
the sole C source. SoCg harbors in its chromosome a single alk locus carrying six open reading frames (ORFs),
which shows 78 to 79% identity with the alkane hydroxylase (AH)-encoding systems of other alkane-degrading
actinobacteria. Quantitative reverse transcription-PCR showed that the genes encoding AlkB (alkane 1-monooxygenase),
RubA3 (rubredoxin), RubA4 (rubredoxin), and RubB (rubredoxin reductase) were induced by both
n-hexadecane and n-triacontane, which were chosen as representative long-chain liquid and solid n-alkane
molecules, respectively. Biotransformation of n-hexadecane into the corresponding 1-hexadecanol was detected
by solid-phase microextraction coupled with gas chromatography-mass spectrometry (SPME/GC-MS) analysis.
The Gordonia SoCg alkB was heterologously expressed in Escherichia coli BL21 and in Streptomyces coelicolor
M145, and both hosts acquired the ability to transform n-hexadecane into 1-hexadecanol, but the corresponding
long-chain alcohol was never detected on n-triacontane. However, the recombinant S. coelicolor M145-AH,
expressing the Gordonia alkB gene, was able to grow on n-triacontane as the sole C source. A SoCg alkB
disruption mutant that is completely unable to grow on n-triacontane was obtained, demonstrating the role of
an AlkB-type AH system in degradation of solid n-alkanes
Exploring long chain n-alkane metabolism in Gordonia sp. strain SoCg
No full textMany microorganisms are able to degrade aliphatic hydrocarbons and a relationship between n-alkane utilization and storage compound synthesis has been described in bacteria. The Gram positive GC-rich n-alkane degrader Gordonia sp. strain SoCg, isolated from a long-term accidentally contaminated beach in Sicily, is able to grow on long n-alkanes up to. It carries a single copy of the alkane hydroxylase gene alkB on its chromosome and its alk cluster revealed a genomic organization similar to other alk clusters of alkane-degrading Gram positive bacteria. The alk gene expression, analysed by Real-time RT-PCR, is induced by n-hexadecane and n-triacontane and coupled to alkane consumption. Interestingly, SPME GC-MS analysis revealed extracellular production of hexadecyl-hexadecanoic acid (wax ester), during growth on n-triacontane. Degenerated oligonucleotides were used to PCR amplify the Wax Esther Synthase/Acyl-CoA:Diacylglycerol Acyltransferase encoding gene (atfa), responsible for intracellular wax esther synthesis by estherification between palmitoyl-CoA and 1-haxadecanol in the n-alkane degrader Acinetobacter sp. ADP1. The amplicon showed 75% similarity sequence to a putative acyl-CoA transferase gene of Nocardia farcinica. Only one copy of atfa-like gene was detected in Gordonia SoCg chromosome. qRT-PCR analysis showed an up-regulation of atfa gene in the presence of long chain n-alkanes, correlating, for the first time, long chain n-alkane metabolism and wax esthers extracellular production
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Gordonia sp. SoCg alkB gene confers the ability to degrade and use n-alkanes as carbon source in Gram positive bacteria
No full textGordonia sp. SoCg, a Gram positive strain able to grow on long chain n-alkanes1, possess a single copy of
alkB2 gene, whose product is required for n-alkane hydroxylation3. An analysis of alkB flanking regions
revealed five ORFs which were designed as orf1, rubA3, rubA4, rubB and alkU, according to the sequence
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homology with that of known alk clusters3. In G. sp. SoCg the transcription of these genes was induced by
long-chain and solid n-alkanes as revealed by quantitative RT-PCR, and the essential role of alkB in nalkane
degradation was demonstrated by the construction of an alkB disruption mutant strain3. The SoCg
alkB gene was successfully expressed in Streptomyces coelicolor M145 (M145-AH), and the production of
1-hexadecanol from n-hexadecane oxidation was observed3.
A differential study of global gene expression of M145-AH cultures was performed, where n-hexadecane
(C16) glucose (GLU) and none (NC) were provided as only carbon source, respectively. Proteomic analysis,
based on 2D-DIGE and MS procedures, revealed a gradual metabolic adaptation to n-hexadecane
utilization, not dissimilar from that one revealed in specialized alkane-degraders4. In addition, expression
profiles of central carbon metabolism enzymes revealed that the addition of a single gene confers the ability
to use recalcitrant pollutants as simple sugars in Streptomyces.
Altogether these data, expanding the knowledge on n-alkane bioconversion mechanisms in Gram positive
bacteria, could provide new technological platforms for bioremediation studies and strategies.
Quatrini, P., Scaglione, G., De Pasquale, C., Riela, S., & Puglia, A. M. (2008). Isolation of gram-positive n-alkane degraders from a
hydrocarbon- contaminated mediterranean shoreline. Journal of Applied Microbiology, 104(1), 251-259.
Lo Piccolo, L., De Pasquale, C., Fodale, R., Puglia, A. M. & Quatrini, P. . An alkane hydroxylase system of Gordonia sp. Strain SoCg is
involved in degradation of solid n-alkanes. Applied and Environmental Microbiology. In revision.
van Beilen, J. B., & Funhoff, E. G. (2007). Alkane hydroxylases involved in microbial alkane degradation. Applied Microbiology and
Biotechnology, 74(1), 13-21.
Sabirova, J. S., Ferrer, M., Regenhardt, D., Timmis, K. N., & Golyshin, P. N. (2006). Proteomic insights into metabolic adaptations in
Alcanivorax borkumensis induced by alkane utilization. Journal of Bacteriology, 188(11), 3763-3773
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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