Article

Development of molecular tools for the detection of freshwater diatoms.

Department of Biosciences and Biotechnology, University of Camerino, Via Gentile III da Varano, 62032 Camerino, Italy.
Journal of microbiological methods (Impact Factor: 2.43). 10/2010; 84(1):33-40. DOI: 10.1016/j.mimet.2010.10.008
Source: PubMed

ABSTRACT This study was undertaken to develop a reliable and reproducible procedure for the detection and quantitative determination of diatoms in environmental samples. A comparative study of seven different DNA extraction kits was carried out to establish conditions for analysis of diatom containing samples. The best performers were identified using both standard and real-time PCR. We show that the yield of diatom DNA is generally quite low when using commercially available extraction kits; in addition, a new protocol was devised to obtain samples suitable for DNA amplification without the need to perform all the steps required for DNA extraction. This method was tested on environmental samples spiked, in a wide range of total cell mass, with the rarely occurring diatom Neidium affine together with a highly species-specific oligonucleotide designed on the small subunit (SSU) rRNA gene. Thus, we propose a fast and effective procedure that, combined with the use of species-specific oligonucleotide probes can detect minute amounts of a spiked diatom within a complex diatom community. This study provides experimental conditions for a fast and accurate detection of diatoms, and demonstrates the feasibility of the use of molecular tools in the evaluation of water quality.

1 Bookmark
 · 
196 Views
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Instruments to assess everyday functioning have utilized self-report, proxy report, clinician ratings, or direct observation of performance. Each of these methods has strengths and weaknesses. In this article we argue for the inclusion of performance-based measures of functional capacity in studies of severely mentally ill persons and describe a new measure, the UCSD Performance-Based Skills Assessment (UPSA). We administered the UPSA to 50 middle-aged and older outpatients with schizophrenia or schizoaffective disorder, and 20 normal comparison subjects. Participants' performance in five domains of functioning (Household Chores; Communication; Finance; Transportation; and Planning Recreational Activities) was assessed in standardized role-play situations. Administration of the UPSA required an average of 30 minutes to complete. Interrater reliability of ratings was excellent. Patients' performance was significantly more impaired than that of normal subjects. Among patients, the UPSA performance correlated significantly with severity of negative symptoms and of cognitive impairment but not with that of positive or depressive symptoms. The UPSA scores correlated highly with those on another performance-based measure. We believe that UPSA would be useful for assessing everyday functioning in severely mentally ill adults.
    Schizophrenia Bulletin 02/2001; 27(2):235-45. · 8.49 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Benthic diatoms represent an important element of global nutritional productivity; to raise attention on their role, which is often neglected due to analytical difficulties, surface (1 cm top layer) coastal sediments from Gerlache inlet to Penguin Bay at Terra Nova Bay were collected and stored at -20 °C. DNA amplification by real-time PCR, based on diatom-specific oligonucleotide primers designed on small-subunit rRNA (SSU rRNA), was performed in addition to diatom conventional cell counting and spectrophotometric determination of photo-pigments. Moreover, cations and anions were determined in sediments with the aim to identify factors involved in the control of diatom abundance. Diatom distribution was found quite heterogeneous displaying significant differences from site to site. The salinity in sediments ranged from 45.1 at Gerlache inlet to 76.2 at Penguin Bay and it was correlated with cell abundance, biodiversity, amount of pigments and amplified DNA. The dominant species, Fragilariopsis curta, was associated to sediment salinity brines.
    Marine environmental research 02/2011; 71(4):304-11. · 2.34 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: A simple agar diffusion method is developed where pure colony of Chlamydomonas sp. CRP7 was isolated from Chlorella sp. CB4 mixtures by passing through agar migration with a light exposure of 6,000 lux for 7 h. The main concept behind it is that Chlamydomonas has flagella and the rhodopsin pigment is attracted towards light. Thus the above two microalgae species can be separated from the mixtures as eye spot serves as a navigator and flagella serves as a propeller for Chlamydomonas spp. Further the genomic DNA was isolated and purified from the above mentioned two species after the separation from the mixtures. PCR amplification was carried out for ITS1, 5.8S and ITS2 regions. The amplified products were sequenced and the sequence analysis confirmed that they belong to Chlamydomonas sp. and Chlorella sp. This is an important augmentation for isolation and separation of microalgae.
    Indian Journal of Microbiology 52(4). · 0.46 Impact Factor

Full-text

View
90 Downloads
Available from
Jun 5, 2014