4 research outputs found
Naturalization of Escherichia coli in New Zealand freshwater streams
No full textEscherichia coli is used internationally as a faecal indicator of water quality based on the assumption that this bacterium is exclusively a commensal of the vertebrate gut. However, recent findings show that E. coli can also grow and multiply in water and soils, either in tropical and temperate climates in different parts of the world. It is becoming clear that some strains of E.coli are able to naturalize in the environment and that these populations persist and expand over weeks or months before resolving and being replaced by new apparently naturalized strains. The process by which this naturalization takes place is as yet undescribed and an approach to discriminating naturalized from contaminating commensal E.coli in an aquatic environment is also not available. This research focuses on defining the specific characteristics of naturalized E. coli strains and determining what makes them different from commensal E. coli strains, by using multi-omic tools. The first step of this project was to select potentially naturalized E. coli isolates characterized by a similar genetic profile and retrieved from freshwater stream biofilms overtime at the same location. Then in the second step, the genetic, transcriptomic, metabolic and phenotypic characteristics of this group of isolates have been extensively studied and compared with the corresponding features of commensal E. coli using Affymetrix microarrays, qPCR, carbon substrate utilization assays, metabolomics analyses and phenotypic assays. Results show similarities and differences with commensal E. coli. While both E. coli categories show similar growth rates, catalase and glycogen production, the naturalized isolates possess enhanced biofilm formation capabilities and a red dry and rough (rdar) morphotype. Transcriptomic analyses demonstrate a lower expression of rpoS, the gene encoding the general stress sigma factor (S), the key component of the general stress response for the naturalized strains compared to the commensal strains. Microarray analyses revealed over-expression of 160 genes mostly involved in motility, chemotaxis, energy production and conversion, amino-acid and inorganic ion metabolisms and reduced expression of 87 genes coding for proteins involved in transcription, translation or in unknown functions. Phenotypic macroarrays show that the naturalized isolates use a broader range of substrates although their nutrient utilization profiles are still very close to some human strain profiles. The metabolomic analyses confirm that the naturalized strains favour different metabolic pathways and metabolites indicating different strategies in relation to the different lifestyles. All together these results suggest that naturalized isolates have better abilities to sense, and to move to, an area with greater nutrient resources (chemotaxis and motility), to remain to these areas by colonizing biofilms (via surface appendages) and to incorporate and use different compounds (carbohydrate and amino acids) in an energy-efficient manner. These capabilities would allow a better survival and growth in a stream environment reflecting a more variable environment with stressors such as variations in nutrient availability, temperature and light. Down regulation of rpoS may facilitate the metabolic flexibility of environmental isolates by reducing the energy and resource requirements devoted to the stress responses, in line whith bacteria favouring the less costly metabolic pathways
The efficacy of combined therapy of arsenic trioxide and alpha interferon in human T-cell leukemia virus type-1-infected squirrel monkeys (Saimiri sciureus)
No full textHuman T-cell lymphotropic virus type 1 (HTLV-1)-associated adult T-cell leukemia-lymphoma (ATLL) has a poor prognosis owing to its intrinsic resistance to chemotherapy. Although zidovudine (AZT) and alpha interferon (IFN-α) give rise to some response and improve the prognosis of ATLL, alternative therapies are needed. Arsenic trioxide (As2O3) has been shown to synergize with IFN-α in arresting cell growth and inducing apoptosis of ATLL cells in vitro. In this study, we evaluated the toxicity and the efficacy of this combined treatment in HTLV-1-infected squirrel monkeys (Saimiri sciureus) and HTLV-1 infected cell lines derived therefrom. We first show that treatment with As2O3 and IFN-α can induce growth arrest in HTLV-1-transformed monkey T-cell lines in vitro. We then show that treatment of squirrel monkeys with As2O3 in vivo is highly toxic at 0.9 or 0.3 mg-day but not at 0.14 mg-day for up to 2 weeks. Although the combination of As2O3 and IFN-α did not affect significantly the HTLV-1 proviral load in infected monkeys, it reduced the absolute numbers of CD3+, CD4+ and CD8+ cells during treatment, with a significant reduction in the total number of circulating HTLV-1 flower cells in the infected monkeys with chronic ATLL-like disease. © 2006 Elsevier B.V. All rights reserved.Arnulf B, 2004, LEUKEMIA, V18, P126, DOI 10.1038-sj.leu.2403176; Bangham CRM, 2000, CURR OPIN IMMUNOL, V12, P397, DOI 10.1016-S0952-7915(00)00107-2; Bazarbachi A, 1999, BLOOD, V93, P278; BENVENISTY N, 1992, ONCOGENE, V7, P2399; Cavrois M, 1996, ONCOGENE, V12, P2419; Cavrois M, 1998, ONCOGENE, V17, P77, DOI 10.1038-sj.onc.1201906; Cavrois M, 1996, BLOOD, V88, P4646; CHEN YX, 1995, INT J CANCER, V60, P798; Debacq C, 2005, ONCOGENE, V24, P7514, DOI 10.1038-sj.onc.1208896; El-Sabban ME, 2000, BLOOD, V96, P2849; FURUTA Y, 1989, J VIROL, V63, P3185; GREEN JE, 1989, MOL CELL BIOL, V9, P4731; Hanon E, 2000, BLOOD, V95, P1386; HERMINE O, 1995, NEW ENGL J MED, V332, P1749, DOI 10.1056-NEJM199506293322604; Hermine O, 2004, HEMATOL J, V5, P130, DOI 10.1038-sj.thj.6200374; HINUMA Y, 1982, INT J CANCER, V29, P631, DOI 10.1002-ijc.2910290606; IBRAHIM F, 1994, INT J CANCER, V58, P446, DOI 10.1002-ijc.2910580324; Kazanji M, 1997, INT J CANCER, V73, P131; Kazanji M, 2000, AIDS RES HUM RETROV, V16, P1741, DOI 10.1089-08892220050193245; Kazanji M, 1997, INT J CANCER, V71, P300, DOI 10.1002-(SICI)1097-0215(19970410)71:2300::AID-IJC273.0.CO;2-J; Kazanji M, 2000, J VIROL, V74, P4860, DOI 10.1128-JVI.74.10.4860-4867.2000; Kazanji M, 1997, VIROLOGY, V231, P258, DOI 10.1006-viro.1997.8528; Leclercq I, 1998, BRIT J HAEMATOL, V101, P500, DOI 10.1046-j.1365-2141.1998.00743.x; Leclercq I, 1999, BRIT J HAEMATOL, V105, P743, DOI 10.1046-j.1365-2141.1999.01389.x; Li XH, 1999, GENE EXPRESSION, V7, P233; Mahieux R, 2001, BLOOD, V98, P3762, DOI 10.1182-blood.V98.13.3762; Mortreux F, 2001, J VIROL, V75, P1083, DOI 10.1128-JVI.75.2.1083-1089.2001; Nagai M, 1998, J NEUROVIROL, V4, P586, DOI 10.3109-13550289809114225; NAKADA K, 1987, INT J CANCER, V40, P145, DOI 10.1002-ijc.2910400203; Nasr R, 2003, BLOOD, V101, P4576, DOI 10.1182-blood-2002-09-2986; SHIMOYAMA M, 1991, BRIT J HAEMATOL, V79, P428, DOI 10.1111-j.1365-2141.1991.tb08051.x; Soignet SL, 1998, NEW ENGL J MED, V339, P1341, DOI 10.1056-NEJM199811053391901; Taylor GP, 1999, J ACQ IMMUN DEF SYND, V22, P92; Tsukasaki K, 1997, BLOOD, V89, P948; WALDMANN TA, 1993, BLOOD, V82, P1701; YAMAMOTO H, 1993, ARTHRITIS RHEUM, V36, P1612, DOI 10.1002-art.1780361117; YOSHIDA M, 1984, P NATL ACAD SCI-BIOL, V81, P2534, DOI 10.1073-pnas.81.8.253465
Arbitrarily primed PCR to type Vibrio spp. pathogenic for shrimp
No full textA molecular typing study on Vibrio strains implicated in shrimp disease outbreaks in New Caledonia and Japan was conducted by using AP-PCR (arbitrarily primed PCR). It allowed rapid identification of isolates at the genospecies level and studies of infraspecific population structures of epidemiological interest. Clusters identified within the species Vibrio penaeicida were related to their area of origin, allowing discrimination between Japanese and New Caledonian isolates, as well as between those from two different bays in New Caledonia separated by only 50 km. Other subclusters of New Caledonian V. penaeicida isolates could be identified, but it was not possible to link those differences to accurate epidemiological features. This contribution of AP-PCR to the study of vibriosis in penaeid shrimps demonstrates its high discriminating power and the relevance of the epidemiological information provided. This approach would contribute to better knowledge of the ecology of Vibrio spp. and their implication in shrimp disease in aquaculture.Source type: Electronic(1
Analiza javno dostupnih alata za geokodiranje i njihova primjena u AKM ustanovama
No full textPurpose. The paper aims to present to the broader ALM community the available geocoding tools that can be useful for presenting diverse collections related to a particular area. The paper will discuss a few publicly available tools and outline their advantages and disadvantages, application possibilities, and accessibility.
Approach/methodology/design. The paper theoretically defines the basic terms that the authors of virtual exhibitions and interactive maps encounter (GIS, mapping, geocoding, and geolocation). The paper presents a comparison of seventeen publicly available geocoding tools using an analysis that considers the advantages, disadvantages, institutions for which they are intended, and price.
Findings. There were 17 geocoding tools analyzed. Of the 17 observed tools, 10 of them have a wide spectrum of application, which, in the author\u27s opinion, also includes the ALM community. The results provide information on the advantages, disadvantages, price and purpose (that is, users) of the observed tools, and the possibilities of their application. Performances of the mentioned tools, such as simplicity of the user interface, open code, transparency, the durability of access and the price ranges were taken in consideration.
Research limitations/implications. The large number of publicly available geocoding tools as well as their continuous development make analysis difficult. Despite the detailed familiarization, not all analyzed geocoding tools were used by the authors, only some of them, which leaves the possibility that some advantages or disadvantages were overlooked.
Practical implications. The paper presents publicly available geocoding tools that can be useful for the promotion of digital collections in an interactive and popular way.
Originality/value. The value of this paper is reflected in the fact that publicly available geocoding tools are included and analyzed in one place. The analysis can be used as a template for comparison before deciding on the selection of the appropriate geocoding tool for creating an interactive map based on the digital collection of a certain ALM institution.Cilj. Cilj je rada široj AKM zajednici predstaviti javno dostupne alate geokodiranja koji mogu biti korisni za predstavljanje raznolikih zbirki vezanih za pojedino područje. Rad će predstaviti neke od javno dostupnih alata te iznijeti njihove prednosti i nedostatke, mogućnosti primjene i pristupačnost.
Pristup/metodologija/dizajn. Teorijski su razgraničeni osnovni pojmovi s kojima se autori virtualnih izložbi i interaktivnih karata susreću (GIS, mapiranje, geokodiranje, geolociranje). Uz pomoć analize koja razmatra prednosti, nedostatke, ustanove kojima je namijenjen te cijenu, napravljena je usporedba sedamnaest javno dostupnih alata za geokodiranje.
Rezultati. Analizirano je 17 alata za geokodiranje. Od 17 promatranih alata, njih 10 ima širok spektar primjene koji, po mišljenju autora, uključuje i AKM zajednicu. Rezultati donose prednosti, nedostatke, cijenu i namjenu (odnosno korisnike) promatranih alata, a proučene su mogućnosti primjene, jednostavnost korisničkog sučelja, otvorenost koda, preglednost, trajnost pristupa i cjenovni rangovi.
Ograničenja. Velik broj javno dostupnih alata za geokodiranje kao i njihov kontinuirani razvoj onemogućuju nam analizu svih. Također, usprkos podrobnom upoznavanju, svi analizirani alati za geokodiranje nisu korišteni od strane autora, samo pojedini, što ostavlja mogućnost da su se pojedine prednosti ili nedostaci previdjeli.
Praktična primjena. U radu su predstavljeni javno dostupni alati za geokodiranja koji mogu biti korisni za promociju digitalnih zbirki na interaktivan i popularan način.
Originalnost/vrijednost. Vrijednost ovoga rada ogleda se u činjenici da su na jednom mjestu obuhvaćeni i analizirani javno dostupni alati za geokodiranje koji mogu poslužiti ustanovama AKM zajednice za njihovu usporedbu prije odlučivanja o odabiru alata za izradu interaktivne karte na temelju vlastitih digitalnih zbirki
