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Single-Molecule Analysis by Biological Nanopores
Published in Shuo Huang, Single-Molecule Tools for Bioanalysis, 2022
In 2012, Oxford Nanopore Technologies released the first nanopore-based DNA sequencer, named MinION (Figure 1.3B,C) [81]. As advertised, this disposable sequencing gadget, which costs <$1000, is capable of exporting a gigabase of DNA sequences per day [74, 75, 82, 83]. However, the poor accuracy of the base identification remains a major drawback, limiting its broad implementation over existing sequencing technologies. In 2016, based on several measurements of replicated circular DNAs, the latest MinION successfully sequenced the Ebola virus genomes stemming directly from patients’ samples [84]. Acknowledging a portable size and a constantly improved accuracy, a nanopore-based sequencer is anticipated to be widely applied as a diagnosis tool in clinical trials.
Fundamentals of silicene
Published in Klaus D. Sattler, Silicon Nanomaterials Sourcebook, 2017
Gian G. Guzmán-Verri, Lok C. Lew Yan Voon, Morten Willatzen
The original motivation for silicene is its relation and compatibility to silicon electronics and the potential of pushing Moore’s Law to the ultimate limit of a single monolayer of silicon. Nonetheless, silicene is qualitatively very different from silicon, particularly with respect to the dimensionality of the material. Thus, the monolayer thickness motivates its potential use as a DNA sequencer when such an application would not make sense for bulk Si. Indeed, what is being envisioned for silicene is similar to what has been considered for graphene. To date, only one possible device has been realized in the lab, a silicene-based field-effect transistor (FET).607 In addition to discussing the latter application, we provide a brief survey of a few other potential applications.
Biological Synthesis of Nanomaterials
Published in M. H. Fulekar, Bhawana Pathak, Environmental Nanotechnology, 2017
Water samples were collected and stored in sterilized bottles in refrigerator at 4°C. After that water samples were serially diluted in sterile 0.8% sodium chloride (NaCl) solution and cultured on nutrient agar containing 2% agar, 1% peptone, 0.5% yeast extract, 0.5% beef extract and 1% NaCl and then supplemented with 3.5 mM silver nitrate (AgNO3). Then they were incubated for 4 days at 30°C. Colonies with dark brown colour on the plate were isolated and evaluated as AgNO3 resistant. The morphological examination of individual colonies including colony and cell characterization, Gram-staining test, shape, size and acid-fast staining were carried out as described in Bergey's Manual of Systematic Bacteriology. The molecular identification of the selected isolate was performed by the amplification of 16S rDNA with eubacterial universal primers 27F and 1492R. Sequencing was performed using ABI PRISM dye terminator cycle sequencing kit with Ampli Taq DNA polymerase and DNA Sequencer. The sequence was analyzed using the ribosomal database (BLAST program) to determine the closest available database sequences. The production of silver nanoparticles by strain 39M investigated by UV–Vis spectroscopy, XRD, TEM, SEM and EDX. The results of UV–Vis spectroscopy demonstrated a peak at 420 nm corresponding to the plasmon absorbance of silver nanoparticles. SEM micrograph showed the formation of silver nanoparticles in the range of 5–50 nm. XRD spectrum exhibited 2θ values corresponding to the silver nanocrystal that are produced in hexagonal and cubic crystal configurations with different planes of orientation. In addition, the signals of the silver atoms were observed by EDS spectrum analysis that confirms the presence of silver nanoparticles.
Biodegradation of low density polyethylene (LDPE) by mesophilic fungus ‘Penicillium citrinum’ isolated from soils of plastic waste dump yard, Bhopal, India
Published in Environmental Technology, 2023
Shazia Khan, Sharique A. Ali, Ayesha S. Ali
The screened fungal isolate was identified based on morphological characteristics like colour, form, elevation, pigmentation, margins and microscopic characteristics using lactophenol blue stain. For further identification nucleotide sequence analysis of internal transcribed space (ITS) region by partial ITS-rDNA gene sequencing method was used. The Genomic DNA was isolated using Kit AmpurE Fungal gDNA Mini Kit (Amnion Biosciences Pvt. Ltd. Bangalore, India). The ITS-rDNA partial gene was successfully amplified using ITS4 & ITS5 primers. The sequencing PCR was set up with ABI-BigDye® Terminatorv3.1 Cycle Sequencing Kit. The raw sequence obtained from ABI 3100 automated DNA sequencer was manually edited for inconsistency. The sequence data was aligned with publicly available sequences & analyzed to reach identity. The phylogenetic & evolutionary analyses were conducted in MEGA X [32].
Dye degradation potential of Acinetobacter baumannii strain VITVB against commercial azo dyes
Published in Bioremediation Journal, 2021
Veena Sreedharan, Purbasha Saha, Kokati Venkata Bhaskara Rao
Potential bacterial isolate was identified by molecular characterization based on 16 s rRNA sequencing. Genomic DNA of the potent bacterium was isolated using the DNA Isolation Kit (InstaGeneTM Matrix Genomic). The fragments were amplified using the forward primer (5′AGAGTTTGATCMTGGCTCAG-3′) and reverse primer (5′- TACGGYTACCTTGTTACGACTT -3′) using polymerase chain reaction (PCR) (MJ Research Peltier Thermal Cycler). Analysis of the sequences was done by using ABI 3730xl capillary DNA sequencer (ABI Prism 310 Genetic Analyzer, Tokyo, Japan). Finally, the consensus sequence was observed for similarity using NCBI Basic Local Alignment Search Tool (BLAST) in the National Center for Biotechnology Information (NCBI) GenBank. (Altschul et al. 1997). A phylogenetic tree was then created with the help of the software Mega 7.
Novel attacin from Hermetia illucens: cDNA cloning, characterization, and antibacterial properties
Published in Preparative Biochemistry and Biotechnology, 2019
To prepare the cDNA library, total RNA was isolated from the induced fat bodies of H. illucens using Trizol (Invitrogen), according to the manufacturer’s protocol and was dissolved in water treated with diethyl pyrocarbonate. The full-length sequence of the H. illucens attacin (HI-attacin) gene was revealed by RACE. The first-strand cDNA was synthesized from 1 µg of total RNA using a SMARTer RACE cDNA Amplification Kit (Clontech, USA). For 3′-RACE, a DNA fragment encoding a portion of HI-attacin was amplified by PCR using the Advantage 2 PCR Kit (Clontech) with forward primers (Table 1) and a universal primer mix (UPM) for the reverse primers. The 3′-RACE forward primer was designed based on high degree of homology in the amino acid sequences of dipteran attacins. The RACE-PCR product was cloned into the TA topo vector (Doctor protein) and the nucleotide sequence was determined from both the ends using an ABI-3700 automatic DNA sequencer (Applied Biosystems, USA). For 5′-RACE, a gene-specific primer (Table 1) was designed from the internal sequence obtained from the previous 3′-RACE-PCR. The nucleotide sequencing was conducted as described above. The sequence alignment was carried out using the Clustal W multiple sequence alignment program and phylogenetic tree was generated using the MEGA 6 program.