Browsing by Subject "detection"

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  • Gonzalez Ramos, Victor Manuel (Helsingin yliopisto, 2020)
    Yeasts are a major spoilage threat in carbonated and fermented beverages, causing considerable economic losses for the manufacturers. Dekkera bruxellensis and Zygosaccharomyces bailii are the two most common spoilage yeast in beverages due to their high tolerance towards beverage-related stress factors. For industry, early and reliable detection of contamination is necessary to minimize spoilage potential and maintain product quality. Cultivation on selective/differential media remains the main method for detection of these organisms, with incubation times from 3 to 15 days. Beverage-related stresses may generate sub-population of injured yeast cells and further delay or even prevent the detection in regular media. PCR, flow cytometry and other alternative detection methods also rely on enrichment cultivation to achieve the required sensitivity for the industry. Therefore, reduced incubation time of sample enrichment and improved detection of injured cells is crucial for a more rapid and reliable detection method. Modification of specific compounds in the culture medium composition has been reported to improve recovery of bacteria after stress. As analogue studies have not been performed on spoilage yeast, modification of the culture medium composition offers a possibility to improve the growth of injured and healthy yeast cells. The aim of this study is to reduce cultivation time required for detection of healthy and injured Dekkera bruxellensis and Zygosaccharomyces bailii cells. Initially, conditions for inducing organic acid and heat injury in D. bruxellensis, D. anomala and Z. bailii cells were studied in an artificial beverage containing basic components of soft drinks. Selective and non-selective plate cultivation and fluorescent viability stains were used to assess the level of injury. The organic acid treatments resulted in inconsistent injury of spoilage yeasts, and thus, recovery from organic acid injury could not be screened. The heat treatments resulted in consistent 1-3 log reduction of viable cell counts. Altogether, 46 potential injury-relieving or growth-enhancing supplements were screened for their effects on the growth rate and lag time of heat-treated and untreated cells in non-selective YM broth using high-throughput automated turbidometry. During individual screening, the growth of Z. bailii strains was significantly improved (p<0.05) only by supplementation with three ion sources: calcium chloride, potassium chloride, and magnesium sulphate. Synergistic effects of the three ion sources was optimized for D. bruxellensis and Z. bailii individually using surface response analysis. Optimized D. bruxellensis YM medium showed no consistent impact on healthy or heat-treated D. bruxellensis strains. On the other hand, two out of the three Z. bailii strains showed significant lag time reduction of 63-66% in untreated cells and 34% in heat-treated cells when incubated in optimized Z. bailii YM medium. The lack of differentiation between improvement of growth of untreated and heat-treated cells point to a generalized ionic deficiency in YM medium. In conclusion, the optimized Z. bailii YM medium is a promising candidate for reducing the detection time of the common spoilage yeast, but it would still require validation with additional Z. bailii strains and quality control samples. It would be also interesting to study the benefits of the medium for cultivation of other spoilage yeasts and in the presence of Z. bailii selective compounds. The information about the importance of various salts for growth of Z. bailii may also prove useful in biotechnological applications of this yeast.
  • Kashif, Muhammad (Helsingfors universitet, 2012)
    Sweetpotato is a subsistence crop for many thousands of families across the globe. The present studies in the thesis provide basic knowledge about Sweet potato chlorotic stunt virus (SPCSV) and Sweet potato feathery mottle virus (SPFMV) that were detected and characterized from sweetpotatoes in Guatemala and Honduras. Sweetpotato plants from Central American countries were showing typical virus-like symptoms. Different strategies were adopted for virus detection. SPCSV and SPFMV were found to be infecting sweetpotato plants. SPFMV was detected only in sweetpotato plants from Honduras. SPFMV infection was detected serologically and results were confirmed by RT-PCR and sequencing. A recently developed detection method, based on restrictotypes of PCR products by two different endonucleases, revealed co-infection of SPFMV strains C and RC in a sweetpotato plant from Honduras which was corroborated by sequencing 3'-proximal end (1.8 kb) of the genome and the coat protein (CP) ~940 nt based phylogenetic analysis. SPCSV was detected by double-stranded RNA extraction, confirmed by RT-PCR and subsequent sequencing of the partial HSP70h gene of genomic RNA2 gene of SPCSV. Phylogenetic analysis was done by constructing neighbour-joining tree of aligned nucleotide sequences, including SPCSV-EA isolates and SPCSV-WA isolates from database that clearly differentiated SPCSV isolates of Central American countries. These isolates from Guatemala and Honduras were grouped together with SPCSV-WA isolates from Argentina, United States, Spain, Israel, Nigeria and Egypt. Additionally, the RNase3 gene with UTR at 3´ end of genomic RNA1 gene of SPCSV was sequenced (1264 nt) and aligned against other WA isolates. It was found that the gene for the silencing suppressor protein p22 (676nt) was missing, reflecting intraspecific variation in the genomic structure of SPCSV. These findings revealed the two most important sweetpotato viruses in Guatemala, Honduras, and Central America for the first time and urge further studies of sweetpotato viruses in the region.
  • Ivaska, Lotta E.; Christensen, Andreas; Waris, Matti; Puhakka, Tuomo; Vuorinen, Tytti; Allander, Tobias; Söderlund-Venermo, Maria; Jartti, Tuomas (2019)
    Human bocavirus 1 (HBoV1) can persist in nasopharynx and tonsils. Using HBoV1 serology, reverse-transcription polymerase chain reaction (PCR) for detecting messenger RNA (mRNA) and quantitative PCR for HBoV1 genome load count, we studied to what extent the HBoV1 DNA loads in nasopharynx correlate with acute infection markers. Tonsillar tissue, nasopharyngeal aspirate, and serum were obtained from 188 elective adeno-/tonsillectomy patients. Relatively high loads of HBoV1 DNA were detected in the nasopharynx of 14 (7%) primarily asymptomatic subjects with negative mRNA and/or serodiagnostic results. Quantitative HBoV1 DNA PCR may have lower specificity than HBoV1 mRNA detection for diagnosing symptomatic infection.
  • Oristo, S.; Lee, H. -J.; Maunula, L. (2018)
    AimsDetection/Quantification of RNA viruses is mostly done by reverse-transcriptase (RT)-(q)PCR, but it does not distinguish between infectious and noninfectious viruses. Our aim was to test, how different pretreatments before RT-qPCR could eliminate positivity originated from external nucleic acids or genomes of damaged particles. Methods and ResultsHeat-inactivated (80 degrees C for 10min) rotavirus Wa strain and faecal samples containing rotavirus or norovirus were treated with PMA/PMAxx, benzonase or crude extract RNase prior to RT-qPCR. PMA/PMAxx pretreatments were not consistently efficient for RV, although they seemed to work to some extent for heat-inactivated norovirus. Benzonase and RNase provided consistently 22-28 log(10) reductions in the titre of faecal rotavirus. ConclusionsAll pretreatments need to be further validated for each virus separately, taking into account sample matrix and inactivation conditions. Although none of the pretreatments could completely render inactivated viruses undetectable, RNase worked most consistently for both rota- and norovirus. Significance and Impact of the StudyThis study sheds light on capacity of the most common pre-RT-qPCR treatments to eliminate damaged, noninfectious rotaviruses and noroviruses after thermal treatment. To our knowledge, this is the first time, when benzonase has been used in this context.
  • Lehtola, Ville; Hyyti, Heikki; Keränen, Pekka; Kostamovaara, Juha (Copernicus Publications, 2019)
    The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences
    Single photon lidars (in solid state form) offer several benefits over pulsed lidars, such as independence of micro-mechanical moving parts or rotating joints, lower power consumption, faster acquisition rate, and reduced size. When mass produced, they will be cheaper and smaller and thus very attractive for mobile laser scanning applications. However, as these lidars operate by receiving single photons, they are very susceptible to background illumination such as sunlight. In other words, the observations contain a significant amount of noise, or to be specific, outliers. This causes trouble for measurements done in motion, as the sampling rate (i.e. the measurement frequency) should be low and high at the same time. It should be low enough so that target detection is robust, meaning that the targets can be distinguished from the single-photon avalanche diode (SPAD) triggings caused by the background photons. On the other hand, the sampling rate should be high enough to allow for measurements to be done from motion. Quick sampling reduces the probability that a sample gathered during motion would contain data from more than a single target at a specific range. Here, we study the exploitation of spatial correlations that exist between the observations as a mean to overcome this sampling rate paradox. We propose computational methods for short and long range. Our results indicate that the spatial correlations do indeed allow for faster and more robust sampling of measurements, which makes single photon lidars more attractive in (daylight) mobile laser scanning.
  • Xie, Long (Helsingfors universitet, 2014)
    Glomus intraradices and Bacillus amyloliquefaciens are two commercially used plant growth promoting micro-organisms. They associate with plant roots to facilitate host plants to absorb nutrients, induce resistance against pathogens and pests, and regulate growth through phytohormones. Growth conditions for plants on green roofs are often unfavorable. In order to test whether growth and development of green roof plants could be enhanced via improving the microbial interface, G. intraradices and B. amyloliquefaciens were inoculated on experimental plots on a green roof in the summer of 2012. The experimental plots were marked as R (inoculated with B. amyloliquefaciens from Rhizocell), M (inoculated with G. intraradices from MYC4000), and C (control). The green roof was made of sedum-herb-grass mats. The plants included e.g. stonecrops, bluegrasses, yellow rockets, white clover, mullein, pennycress, and moss. The survival and development of G. intraradices and B. amyloliquefaciens were studied respectively from Poa alpina roots and soils in the summers of 2012 and 2013. G. intraradices was not detected in P alpina roots according to root staining and microscopy. Probable reasons for the lacking of G. intraradices include high phosphorus content in the soils, high soil temperature, and low soil moisture. PCR and qPCR were used to detect Bacillus content in green roof soils. The abundance of B. amyloliquefaciens was related to soil water content and soil temperature. During the last two measurements in 2012, 4 weeks of high moisture content in the soil resulted in large increase of B. amyloliquefaciens content in both M and R groups, but then decreased substantially due to drought and heat in 2013. In 2013, Only R group increased from the third to the last measurement, indicating probable resistance of the B. amyloliquefaciens strain from Rhizocell additive. The synergistic effect of B. amyloliquefaciens and G. intraradices might be responsible for the thousand-fold increase of Bacillus content in M group in 2012.
  • Rahman, Saifur; Alwadie, Abdullah S.; Irfan, Muhammed; Nawaz, Rabia; Raza, Mohsin; Javed, Ehtasham; Awais, Muhammad (2020)
    Gas sensors are critical components when adhering to health safety and environmental policies in various manufacturing industries, such as the petroleum and oil industry; scent and makeup production; food and beverage manufacturing; chemical engineering; pollution monitoring. In recent times, gas sensors have been introduced to medical diagnostics, bioprocesses, and plant disease diagnosis processes. There could be an adverse impact on human health due to the mixture of various gases (e.g., acetone (A), ethanol (E), propane (P)) that vent out from industrial areas. Therefore, it is important to accurately detect and differentiate such gases. Towards this goal, this paper presents a novel electronic nose (e-nose) detection method to classify various explosive gases. To detect explosive gases, metal oxide semiconductor (MOS) sensors are used as reliable tools to detect such volatile gases. The data received from MOS sensors are processed through a multivariate analysis technique to classify different categories of gases. Multivariate analysis was done using three variants-differential, relative, and fractional analyses-in principal components analysis (PCA). The MOS sensors also have three different designs: loading design, notch design, and Bi design. The proposed MOS sensor-based e-nose accurately detects and classifies three different gases, which indicates the reliability and practicality of the developed system. The developed system enables discrimination of these gases from the mixture. Based on the results from the proposed system, authorities can take preventive measures to deal with these gases to avoid their potential adverse impacts on employee health.