In vivo labeling and specific magnetic bead separation of RNA for biofilm characterization and stress-induced gene expression analysis in bacteria

2009 ◽  
Vol 79 (3) ◽  
pp. 344-352 ◽  
Author(s):  
Nikolai Stankiewicz ◽  
Andrea Gold ◽  
Yousra Yüksel ◽  
Sonja Berensmeier ◽  
Thomas Schwartz
BioTechniques ◽  
2021 ◽  
Author(s):  
Jyotsnamayee Sabat ◽  
Subhra Subhadra ◽  
Sonalika Rath ◽  
Lal Mohan Ho ◽  
Srikanta Kanungo ◽  
...  

Purity and integrity are two important criteria for any RNA extraction process to qualify the RNA for meaningful gene expression analysis. This study compares four commercially available RNA extraction kits using silica membrane and magnetic bead separation methods. The performance was evaluated in terms of both quantity (total RNA amount in μg/μl) and purity (260/280 ratio). The concentration and purity of each kit was significantly different from those of the others (p < 0.001). Although quantity obtained from Mag MAX is comparatively lower than QIAGEN, the quality is comparable as evident from real-time PCR performance. This study suggests that there are practical differences between these RNA extraction kits that should be taken into account while isolating RNA required for gene expression analysis.


2012 ◽  
Vol 87 (Suppl_1) ◽  
pp. 192-192
Author(s):  
Callie V. Barnwell ◽  
Christopher M. Ashwell ◽  
Peter W. Farin ◽  
William T. Farmer ◽  
Charlotte E. Farin

2003 ◽  
Vol 144 ◽  
pp. s102
Author(s):  
H. Hildebrand ◽  
G. Kempka ◽  
H. Ellinger ◽  
B. Stuart ◽  
B. Wahle ◽  
...  

2005 ◽  
Vol 441 (1) ◽  
pp. 1-15 ◽  
Author(s):  
Paul Gallagher ◽  
Yongde Bao ◽  
Solange M.T. Serrano ◽  
Gavin D. Laing ◽  
R. David G. Theakston ◽  
...  

Blood ◽  
2009 ◽  
Vol 113 (17) ◽  
pp. 3953-3960 ◽  
Author(s):  
Andrea Ditadi ◽  
Paolo de Coppi ◽  
Olivier Picone ◽  
Laetitia Gautreau ◽  
Rim Smati ◽  
...  

Abstract We have isolated c-Kit+Lin− cells from both human and murine amniotic fluid (AF) and investigated their hematopoietic potential. In vitro, the c-Kit+Lin− population in both species displayed a multilineage hematopoietic potential, as demonstrated by the generation of erythroid, myeloid, and lymphoid cells. In vivo, cells belonging to all 3 hematopoietic lineages were found after primary and secondary transplantation of murine c-Kit+Lin− cells into immunocompromised hosts, thus demonstrating the ability of these cells to self-renew. Gene expression analysis of c-Kit+ cells isolated from murine AF confirmed these results. The presence of cells with similar characteristics in the surrounding amnion indicates the possible origin of AF c-Kit+Lin− cells. This is the first report showing that cells isolated from the AF do have hematopoietic potential; our results support the idea that AF may be a new source of stem cells for therapeutic applications.


2021 ◽  
Vol 11 (5) ◽  
pp. 12877-12885

Pseudomonas aeruginosa is one of the most common pathogenic bacteria that cause nosocomial infection. Unfortunately, the irrational use of antibiotics has created a surge in P. aeruginosa resistance nowadays. To overcome this situation, new antibacterial compounds are urgently needed. One of the potential sources to obtain such antibacterial compounds is roselle calyx. This research was carried out using two experimental approaches, survival assay and gene expression analysis, to examine the in vivo antibacterial effect of water fraction of roselle calyx (WFR) against Pseudomonas aeruginosa in Drosophila model of infection. Survival assay was used to demonstrate the impact of treatment on the lifespan of the infected host. The measurement of immune-related Dpt mRNA levels by reverse-transcriptase quantitative PCR (RT-qPCR) was used to assess whether immunostimulation is involved in the antibacterial protection of WFR against P. aeruginosa. The result demonstrated that WFR at concentrations of 0.8% and 2% were able to enhance P. aeruginosa-infected flies' survival. Furthermore, gene expression analysis showed the insignificant difference between WFR-treated flies and healthy control flies at all tested concentrations, implying the non-involvement of Imd-Dpt-mediated pathway immunity in the antipseudomonal protection of WFR. Taken together, our data suggested the in vivo antibacterial activity of WFR against P. aeruginosa in the fruit fly model of infection.


2019 ◽  
Vol 85 (18) ◽  
Author(s):  
Massimiliano Lucidi ◽  
Daniela Visaggio ◽  
Elisa Prencipe ◽  
Francesco Imperi ◽  
Giordano Rampioni ◽  
...  

ABSTRACT The Acinetobacter genus includes species of opportunistic pathogens and harmless saprophytes. The type species, Acinetobacter baumannii, is a nosocomial pathogen renowned for being multidrug resistant (MDR). Despite the clinical relevance of infections caused by MDR A. baumannii and a few other Acinetobacter spp., the regulation of their pathogenicity remains elusive due to the scarcity of adequate genetic tools, including vectors for gene expression analysis. Here, we report the generation and testing of a series of Escherichia coli-Acinetobacter promoter-probe vectors suitable for gene expression analysis in Acinetobacter spp. These vectors, named pLPV1Z, pLPV2Z, and pLPV3Z, carry both gentamicin and zeocin resistance markers and contain lux, lacZ, and green fluorescent protein (GFP) reporter systems downstream of an extended polylinker, respectively. The presence of a toxin-antitoxin gene system and the high copy number allow pLPV plasmids to be stably maintained even without antibiotic selection. The pLPV plasmids can easily be introduced by electroporation into MDR A. baumannii belonging to the major international lineages as well as into species of the Acinetobacter calcoaceticus-A. baumannii complex. The pLPV vectors have successfully been employed to study the regulation of stress-responsive A. baumannii promoters, including the DNA damage-inducible uvrABC promoter, the ethanol-inducible adhP and yahK promoters, and the iron-repressible promoter of the acinetobactin siderophore biosynthesis gene basA. A lux-tagged A. baumannii ATCC 19606T strain, carrying the iron-responsive pLPV1Z::PbasA promoter fusion, allowed in vivo and ex vivo monitoring of the bacterial burden in the Galleria mellonella infection model. IMPORTANCE The short-term adaptive response to environmental cues greatly contributes to the ecological success of bacteria, and profound alterations in bacterial gene expression occur in response to physical, chemical, and nutritional stresses. Bacteria belonging to the Acinetobacter genus are ubiquitous inhabitants of soil and water though some species, such as Acinetobacter baumannii, are pathogenic and cause serious concern due to antibiotic resistance. Understanding A. baumannii pathobiology requires adequate genetic tools for gene expression analysis, and to this end we developed user-friendly shuttle vectors to probe the transcriptional responses to different environmental stresses. Vectors were constructed to overcome the problem of antibiotic selection in multidrug-resistant strains and were equipped with suitable reporter systems to facilitate signal detection. By means of these vectors, the transcriptional response of A. baumannii to DNA damage, ethanol exposure, and iron starvation was investigated both in vitro and in vivo, providing insights into A. baumannii adaptation during stress and infection.


2013 ◽  
Vol 25 (1) ◽  
pp. 212
Author(s):  
G. Machado ◽  
A. Ferreira ◽  
I. Pivato ◽  
A. Fidelis ◽  
J. F. Srpicigo ◽  
...  

This study aimed to compare post-hatching development of Day 7 in vitro and in vivo embryos cultured in recipient uterus until Day 14. For producing in vitro embryos (IVP), oocytes were matured, fertilized (Day 0) and cultured in vitro for 6 days (Day 7) in synthetic oviduct fluid medium supplemented with 5% of fetal bovine serum and incubated at 39°C in 5% CO2 in air. At Day 7, part of IVP blastocysts was transferred to recipient uterus and part was stored for gene expression analysis. As a control group, in vivo embryos were produced after ovarian stimulation, insemination and uterine flushing on Day 7 post insemination. Similarly to the IVP embryos, part of embryos was transferred to recipient uterus and part was stored for gene expression analysis. Day 7 in vivo (n = 53) and IVP (n = 64) expanded blastocysts were transferred to synchronized recipients (10/horn) and were collected by uterine flushing 7 days after transfer (Day 14). Recovered embryos were measured using Motic Image Plus software and evaluated for presence and size of embryonic disc (ED). A trophoblast biopsy was removed and stored for gene expression analysis. For the molecular profile evaluation of Day 7 and Day 14 in vivo and in vitro embryos, 8 genes related with placentation, implantation, oxidative stress, and glucose metabolism (PLAC8, CD9, GLUT-1, GLUT-3, KRT8, MnSOD, HSP70, and INFT, respectively) were quantified by RT-qPCR using ΔΔCT method and CYC-A gene as endogenous control. The recovery rate of Day 14 embryos, analyzed by chi-square test, was higher (P < 0.05) for in vitro than for in vivo embryos, being 50.0% (64/128) and 38.6% (53/137), respectively. No differences (P > 0.05; t-test) were observed in embryo length when comparing Day 14 in vitro (19.1 ± 2.4 mm) and in vivo embryos (24.2 ± 3.7 mm). ED was detected in 25% (16/64) of in vitro and in 26% (14/53) of in vivo embryos. No differences were found (P > 0.05; t-test) in diameter between the two types of embryos (0.3 ± 0.0 mm/in vitro and 0.3 ± 0.0 mm/in vivo). Regarding gene expression, Day 7 IVP embryos showed higher (P < 0.05, Mann–Whitney test) expression of HSP70 and SCL2A1 than in vivo embryos. However, at Day 14 no differences between embryos were observed in transcript levels for any of the studied genes. Therefore, the present study showed that although differences in Day 7 in vitro embryos were observed at the molecular level compared to in vivo counterpart, after transfer to the uterine environment, they showed similar morphology and gene expression profile. These results highlight the importance of evaluating embryos produced by assisted reproductive techniques in later stages of development to have a more precise evaluation of their quality. Financial support: Embrapa, CNPq, CAPES.


2016 ◽  
Vol 311 (5) ◽  
pp. G794-G806 ◽  
Author(s):  
Egle Juskeviciute ◽  
Rachael P. Dippold ◽  
Anil N. Antony ◽  
Aditi Swarup ◽  
Rajanikanth Vadigepalli ◽  
...  

Liver regeneration is a clinically significant tissue repair process that is suppressed by chronic alcohol intake through poorly understood mechanisms. Recently, microRNA-21 (miR-21) has been suggested to serve as a crucial microRNA (miRNA) regulator driving hepatocyte proliferation after partial hepatectomy (PHx) in mice. However, we reported recently that miR-21 is significantly upregulated in ethanol-fed rats 24 h after PHx, despite inhibition of cell proliferation, suggesting a more complex role for this miRNA. Here, we investigate how inhibition of miR-21 in vivo affects the early phase of liver regeneration in ethanol-fed rats. Chronically ethanol-fed rats and pair-fed control animals were treated with AM21, a mixed locked nucleic acid-DNA analog antisense to miR-21 that inhibited miR-21 in vivo to undetectable levels. Liver regeneration after PHx was followed by cell proliferation marker and gene expression analysis, miRNA profiling, and cell signaling pathway analysis. Although liver regeneration was not significantly impaired by AM21 in chow-fed rats, AM21 treatment in ethanol-fed animals completely restored regeneration and enhanced PHx-induced hepatocyte proliferation to levels comparable to those of untreated or chow-fed animals. In addition, a marked deposition of α-smooth muscle actin, a marker of stellate cell activation, which was evident in ethanol-treated animals after PHx, was effectively suppressed by AM21 treatment. Gene expression analysis further indicated that suppression of stellate cell-specific profibrogenic profiles and the Notch signaling contributed to AM21-mediated rescue from deficient hepatocyte proliferation in ethanol-fed animals. Our results indicate that the impact of miR-21 balances proproliferative effects with antiproliferative profibrogenic actions in regulating distinctive regenerative responses in normal vs. disease conditions.


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