1,721,314 research outputs found
Extended multilocus sequence typing system for Campylobacter coli, C lari, C-upsaliensis, and C-helveticus
No full textA multilocus sequence typing (MLST) system has been reported previously for Campylobacter jejuni to both differentiate strains and identify clonal lineages. However, sequence variation at the MLST loci prevents its use for closely related Campylobacter species. We describe herein an expanded MLST method to include three clinically relevant Campylobacter species, C. coli, C. lari, and C. upsaliensis, and a fourth Campylobacter species, C. helveticus. The C. coli and C. helveticus methods use the same seven C. jejuni loci (aspA, atpA, glnA, gltA, glyA, pgm, and tkt); however, adk and pgi were substituted for aspA and gltA in C. lari and for gltA and pgm in C. upsaliensis. Multiple C. coli (n = 57), C. lari (n = 20), C. upsaliensis (n = 78), and C. helveticus (n = 9) isolates, representing both clinical and environmental sources, were typed. All four species were genetically diverse: the majority (> 80%) of the isolates had unique sequence types (STs). Using this method, mixed C. lari, C. upsaliensis, and C. helveticus isolates were identified; upon separation, each isolate was shown to contain two strains of the same species with distinct STs. Additionally, the expanded MLST method was able to detect potential lateral transfer events between C. jejuni and either C. coli or C. lari and between C. upsaliensis and C. helveticus. Thus, the expanded MLST method will prove useful in differentiating strains of five Campylobacter species, identifying mixed Campylobacter cultures, and detecting genetic exchange within the genus
Gene expression profiling during stress response of selected Campylobacter (C.) jejuni, C. coli and C. lari strains
No full textZiel dieser Arbeit war es, die Stressantwort von C. jejuni, C. coli und C.
lari auf erhöhte Temperaturen zu charakterisieren. C. coli und C. lari zeigen
gegenüber C. jejuni eine verringerte Fähigkeit, bei 46 °C zu überleben.
Untersuchungen zur Expression der Hitzeschockgene mittels Real-Time qPCR
konnten diese phänotypischen Unterschiede nicht vollständig erklären. Deshalb
wurden in dieser Arbeit erstmalig die Veränderungen der Genexpression durch
Sequenzierung der Transkriptome (RNA-Seq) bei 46 °C gegenüber 37 °C bei C.
jejuni, C. coli und C. lari untersucht. Diese Form der Analyse bestätigt und
erweitert das über andere Methoden wie Microarray- und RT-qPCR-Studien
generierte Wissen über die Hitzeschockantwort bei C. jejuni. Darüber hinaus
liefert diese Arbeit erstmalig Erkenntnisse über die Hitzeschockantwort auf
transkriptioneller Ebene bei C. coli und C. lari. Die RNA-Seq-Daten zeigen
erhebliche Unterschiede in der temperaturabhängigen Regulation der
Genexpression. Während bei C. coli und C. lari jeweils 9 % der Gene eine
signifikante Expressionsänderung zeigen, beträgt dieser Anteil bei C. jejuni
nur 3 %. Bei C. jejuni weisen 89 % der regulierten Gene eine erhöhte
Transkriptionsrate auf, während bei C. coli 69 % und bei C. lari 45 % der
regulierten Gene eine gesteigerte Expression zeigen. Der Anteil an Genen,
deren Expression in allen drei Spezies gleichermaßen reguliert wird, ist sehr
gering. Kategorisiert man die differentiell exprimierten Gene, so wird
deutlich, dass deren Produkte aus nahezu allen funktionellen Gruppen stammen.
Besonders Gene, die für die Zellhülle, den Proteinstoffwechsel, die
Proteinbiosythese als auch für Transport- und Bindungsproteine kodieren,
zeigen eine gesteigerte Expression Die eigentliche Stärke der RNA-Seq liegt
nicht in der genauen quantitativen Ermittlung der Genexpression, sondern in
ihrem Potential, die Architektur des Transkriptoms und mögliche regulatorische
Komponenten zu entschlüsseln. RNA-Seq-Experimente als zukünftiger Standard auf
dem Gebiet der Genexpressionsanalysen könnten auch in der
Lebensmittelmikrobiologie eine wichtige Rolle spielen, um Informationen über
das Überleben von Mikroorganismen in der Lebensmittelkette und deren Anpassung
an subletale Faktoren zu generieren.The aim of this study was to characterize the stress response of C. jejuni, C.
coli and C. lari to elevated temperatures. C. coli and C. lari show a
decreased ability to survive at 46 °C in comparison to C. jejuni. The
differential expression of heat-shock genes by real-time qPCR could not
explain the phenotypic differences. Therefore, the changes in global gene
expression at 46 °C compared to 37 °C in C. jejuni, C. coli and C. lari was
investigated by RNA sequencing (RNA-Seq). This analysis confirmed and extended
the knowledge of the heat-shock response of C. jejuni generated in earlier
studies by using other methods such as microarray and RT-qPCR. Furthermore,
this work provides first insights on the heat shock response on the
transcriptional level of C. coli and C. lari. The RNA-Seq data show
significant differences in the temperature-dependent regulation of gene
expression. While in C. coli and C. lari 9 % of the genes showed a significant
change in expression, this proportion in C. jejuni is only 3 %. In C. jejuni
89 % of the regulated genes show an increased transcription rate, while 45 %
of the regulated genes in C. coli and 69 % in C. lari are upregulated. The
percentage of genes whose expression is regulated in all three species alike,
is very low. A categorization of the differentially expressed genes reveals
that their products were distributed over almost all functional groups.
Particularly genes encoding cell membrane proteins, protein metabolism, the
protein biosynthesis and transport and binding proteins, show an increased
expression. The potential of RNA-Seq is not the precise quantitative
determination of gene expression, but in its potential to decipher the
architecture of the transcriptome and possible regulatory components. RNA-Seq
experiments, as the future standard in the field of gene expression analysis,
could also play an important role in food microbiology to understand the
survival of microorganisms and their adaptation to sublethal factors in the
food chain
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
Konventionelle PCR- und Real-Time PCR-Verfahren zum Nachweis von thermophilen Campylobacter jejuni, C. coli, und C. lari : ein Überblick
No full textEine Vielzahl von PCR-Nachweismethoden für Campylobacter jejuni und C. coli wurden bereits publiziert. Hier wird eine Zusammenfassung von aktuellen PCR-Nachweismethoden für thermophile Campylobacter spp. präsentiert, die dem Anwender exemplarisch eine schnelle tabellarische übersicht über aktuelle Methoden bietet sowie über deren Zielgene und Spezifitäten. Es wurden vier konventionelle und sieben Real-Time PCR-Methoden zur Identifizierung von Campylobacter spp. verglichen. Bei den konventionellen Methoden handelt es sich um eine auf dem 16S rRNA-Gen basierende PCR, die spezifisch mit C. jejuni, C. coli und C. lari reagiert, zwei auf dem Flagellin-Gen beruhende PCR-Typisierungsmethoden, die in modifizierter Form für C. jejuni, C. coli und zusätzlich für C. lari durchgeführt wurden. Als vierte Methode wurde eine Duplex-PCR zur Identifzierung von C. jejuni und C. coli mit einbezogen. Unter den getesteten Real-Time PCR-Methoden befanden sich drei 5´-Nuklease Assays, die spezifisch C. jejuni detektieren, zwei Assays, die auf dem Flagellin-Gen beruhen und C. jejuni und C. coli gemeinsam erfassen, eine Duplex-PCR, die C. jejuni (mapA-Gen) und C. coli (ceu-EGen) identifizieren kann und noch mit einer unveröffentlichten internen Kontrolle kombiniert wurde, sowie eine Lightcycler-Methode, die auf dem 16S rRNA-Gen basiert und C. jejuni, C. coli und C. lari gemeinsam detektiert, aber nicht differenziert. Die Methoden sind entweder unverändert aus Publikationen übernommen oder auch nach Datenbankanalysen modifziert worden. Zum Testen wurden 65 Campylobacter-Stämme aus 12 verschiedenen Spezies eingesetzt. Die Inklusivität war insgesamt bei allen Methoden sehr gut, bei der Exklusivität gab es Unsicherheiten. Real-Time PCR-Methoden, die auf dem Flagellin-Gen beruhen, können in manchen Fällen die verwandten Arten C. lari oder C. upsaliensis mit erfassen. Der enge Verwandte C. hyoilei wird in fast allen Fällen gleichzeitig mit C. coli detektiert.Many PCR-techniques have already been published for the detection of thermophilic Campylobacters. In order to provide a practical overview for the user – without laying claim to completeness – we present a collection of actual PCR detection methods, some of them were modified and some are still unpublished. They are listed along with their target genes and specificities. Four conventional and seven real-time PCR methods were tested and compared using a panel of 65 Campylobacter strains belonging to 12 different more or less related species. The regular PCR methodes tested include the 16S rRNA gene based technique that specifically detects C. jejuni, C. coli and C. lari without differenciating to species level, two flaA gene based typing-methods, one for C. jejuni and C. coli in combination, which was slightly modified according to Nachamkin et al. (1993, 1996), and additionally for C. lari. Another duplex PCR was carried out which allows identification of the two species C. jejuni and C. coli simultaneously. Among the real-time methods tested there were three techniques allowing identification of C. jejuni alone, two assays based on the flagellin A gene capable to identify C. jejuni and C. coli in combination, a duplex PCR performed as triplex PCR combined with an internal amplification control that detected C. jejuni and C. coli separately, and a Lightcycler method that detected C. jejuni, C. coli and C. lari simultaneously. Inclusivity and exclusivity were shown for each of the methods. In most cases inclusivity was good, but some techniques raised problems concerning exclusivity. Flagellin based real-time PCR techniques partially crossreacted either with C. lari or C. upsaliensis. C. hyoilei which is very closely related to C. coli reacted in almost all methods applied like C. coli
Analysis of some variables concerning guidelines adopted in a hospital in Milan: quantity, quality and physicians' attitude; which is the reciprocal influence of these factors?
No full textStarting in 1998 the Italian NHS promoted the adoption of practice guidelines without, however, launching directions on how they should be produced and adopted. The aim of the current work was to explore the relationship between number and quality of guidelines and physicians' attitudes towards them.
METHODS:
All documents named 'guidelines' adopted after 1998 by each unit at the San Paolo Hospital (SPH), a 600-bed university hospital were collected. The quality of these guidelines was assessed according to a seven point scale looking at methodological quality and completeness of reporting. A 16-item questionnaire was delivered to all physicians of the SPH investigating barriers affecting their attitude towards adopting guidelines. The correlation between quantity and quality of guidelines and physicians' attitude was explored.
RESULTS:
In total, 319 documents from 19 units were examined. The overall quality varied across units and was generally poor (range: 0.5-3 items satisfied per guideline). Of the 392 physicians sampled, 301 filled in the questionnaire, and a positive attitude to guidelines was found. None of the relationships analysed--quantity, quality and attitude--turned out to be significantly associated.
CONCLUSIONS:
this study highlights contrasting results. The number of recorded documents and physicians' attitude indicate a vivacious interest in guidelines even if the quantitative production was extremely variable among units and the quality was unsatisfactory. This scenario may suggest a transition period in which the lack of a solid methodological background in the production and adoption of guidelines runs into the need to be compliant to a new rule
Specific PCR identification and differentiation of the thermophilic campylobacters, Campylobacter jejuni, C-coli, C-lari, and C-upsaliensis
No full textA sensitive PCR assay that detects the thermophilic campylobacters C.jejuni, C. coli, C. lari, and C. upsaliensis is reported. Furthermore, by digestion of the PCR products with two restriction enzymes, species differentiation was demonstrated. Thus, the</p
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
FREQUENCY AND GENETIC DIVERSITY OF Campylobacter jejuni AND C. lari IN YELLOW-LEGGED GULLS, Larus michahellis, (Naumann, 1840) IN CROATIA
No full textBakterije roda Campylobacter su jedni od najčešćih zoonotskih patogena u ljudi, a ptice
se smatraju važnim rezervoarom. Ova disertacija istražuje prevalenciju i genetičku raznolikost
C. jejuni i C. lari u galebova klaukavaca koji gnijezde na jadranskim otocima i krovovima
zgrada u gradovima. Uzorci kloake prikupljeni su od odraslih ptica i mladunaca u prirodnim i
urbanim kolonijama te na odlagalištima otpada zimi. Zbog svoje bliske povezanosti s ljudima i
pokretljivosti, galebovi mogu širiti bakterije roda Campylobacter. Za proučavanje korištenja
urbanih staništa, korišteni su GPS-GSM uređaji za praćenje kretanja galebova koji se hrane na
moru, u gradovima, na poljoprivrednim površinama i na odlagalištima otpada. Bakterije roda
Campylobacter su pronađene u galebova iz prirodnih kolonija i u galebovima koji se hrane na
odlagalištima. Zabilježena je velika genetička raznolikost C. jejuni i C. lari, što pokazuje da su
ove bakterije još uvijek nedovoljno neistražene. Galebovi klaukavci imaju uglavnom genotipove
specifične za galebove, što ukazuje na nizak rizik od širenja bakterija roda Campylobacter na
čovjeka.Species of the genus Campylobacter are among the most common zoonotic pathogens
in humans, and birds are considered an important reservoir. This dissertation
investigates the prevalence and genetic diversity of C. jejuni and C. lari in Yellowlegged
Gulls breeding on Adriatic islands and urban rooftops. Cloacal swabs were
collected from adults and nestlings in natural and urban colonies and on landfills in
winter. Due to their close association with humans and their mobility, gulls can spread
Campylobacter bacteria. To study the use of urban habitats, GPS-GSM devices were
used to track the movements of gulls foraging at sea, in cities, on farmland and in
landfills. Campylobacter bacteria were found in gulls breeding in natural colonies and
in wintering gulls feeding on landfills. A high genetic diversity of C. jejuni and C. lari
was found, indicating that these bacteria are still largely unexplored. The Yellow-legged
Gulls have mainly gull-specific genotypes, indicating a low risk for the spread of the
Campylobacter pathogen
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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