scholarly journals Targeted DNA sequencing and in situ mutation analysis using mobile phone microscopy

2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Malte Kühnemund ◽  
Qingshan Wei ◽  
Evangelia Darai ◽  
Yingjie Wang ◽  
Iván Hernández-Neuta ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Mobile Phone ◽  
Mutation Analysis

In situ detection of point mutations and targeted DNA sequencing using mobile phone microscopy (Conference Presentation)

2018 ◽  
Author(s):  
Malte Kühnemund ◽  
Qingshan Wei ◽  
Evangelia Darai ◽  
Yingjie Wang ◽  
Ivan Hernandez-Neuta ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Mobile Phone ◽  
Point Mutations ◽  
In Situ Detection

An investigation of PIK3CA mutations in isolated macrodactyly

2018 ◽  
Vol 43 (7) ◽  
pp. 756-760 ◽  
Author(s):  
Jingheng Wu ◽  
Wei Tian ◽  
Guanglei Tian ◽  
Kelli Sumner ◽  
Douglas T. Hutchinson ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Molecular Mechanism ◽  
Mutation Analysis ◽  
Detection Rate ◽  
Mutation Detection ◽  
Pik3ca Mutation ◽  
Mutation Detection Rate ◽  
Pik3ca Mutations ◽  
Diagnosis And Classification ◽  
Set Up

Somatic PIK3CA mutations may relate to pathogenesis of isolated macrodactyly. We set up to test the association between PIK3CA mutations with isolated macrodactyly in order to establish a more accurate and molecular mechanism-based diagnosis and classification. DNA extracted from affected tissues in 12 individuals with isolated macrodactyly was tested for PIK3CA mutation using targeted Sanger DNA sequencing. Ten patients had macrodactyly in the foot and two in the hand. Nine of the 12 patients were found to carry a low-level, mosaic PIK3CA mutation. The mutations identified, p.His1047Arg, p.His1047Leu, p.Glu545Lys, and p.Glu542Lys, are codons frequently mutated in cancers. Among all tissues tested, adipose had the highest mutation detection rate, followed by nerve and skin. Our results indicate that a high proportion of isolated macrodactyly patients carry a pathogenic PIK3CA mutation. Affected adipose, nerve and skin tissues are ideal for PIK3CA mutation analysis.

scholarly journals A comparison of ARMS and DNA sequencing for mutation analysis in clinical biopsy samples

2010 ◽  
Vol 29 (1) ◽  
Author(s):  
Gillian Ellison ◽  
Emma Donald ◽  
Gael McWalter ◽  
Lucy Knight ◽  
Lynn Fletcher ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Mutation Analysis

scholarly journals OTOF mutation analysis with massively parallel DNA sequencing in 2,265 Japanese sensorineural hearing loss patients

PLoS ONE ◽  
2019 ◽  
Vol 14 (5) ◽  
pp. e0215932 ◽  
Author(s):  
Yoh-ichiro Iwasa ◽  
Shin-ya Nishio ◽  
Akiko Sugaya ◽  
Yuko Kataoka ◽  
Yukihiko Kanda ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Dna Sequencing ◽  
Sensorineural Hearing Loss ◽  
Mutation Analysis ◽  
Sensorineural Hearing ◽  
Massively Parallel ◽  
Massively Parallel Dna Sequencing

scholarly journals Kethoxal-assisted single-stranded DNA sequencing (KAS-seq) for capturing transcription dynamics and enhancer activity

2020 ◽  
Author(s):  
Tong Wu ◽  
Ruitu Lyu ◽  
Chuan He
Keyword(s):  
Dna Sequencing ◽  
Enhancer Activity ◽  
Single Stranded Dna ◽  
Dna Structures ◽  
Whole Process ◽  
Pol I ◽  
Input Material ◽  
Material Requirement ◽  
Pol Iii

Abstract We describe a rapid and sensitive labeling of single-stranded DNA for sequencing (KAS-seq), based on a kethoxal-guanine reaction. KAS-seq procedure involves N3-kethoxal labeling, DNA isolation, biotinylation, fragmentation and enrichment, library preparation and sequencing. The whole process can be finished in a day. KAS-seq enables rapid measurement of the dynamics of transcriptionally-engaged Pol II, transcribing enhancers, Pol I and Pol III activities, and non-canonical DNA structures involving ssDNA simultaneously in situ, by using as few as 1,000 cells or mice tissues. The robust and tissue-friendly nature coupled with low input material requirement make KAS-seq a method that can be broadly applied. This step-by-step protocol is related to the publication “Kethoxal-assisted single-stranded DNA sequencing captures global transcription dynamics and enhancer activity in situ” in Nature Methods.

scholarly journals Characterisation of the microbial communities present in an anaerobic baffled reactor utilising molecular techniques

2005 ◽  
Author(s):  
◽  
Tharnija Lalbahadur
Keyword(s):  
Dna Sequencing ◽  
Molecular Techniques ◽  
Operating Conditions ◽  
Desulfovibrio Vulgaris ◽  
Total Biomass ◽  
Dapi Staining ◽  
Specific Flow ◽  
Anaerobic Baffled Reactor ◽  
Treatment Processes

The provision of safe and sanitary water is a constitutional right and above all, a necessity of life. As a result of the rapid urbanisation and the past policies of apartheid, a large population of South Africa dwell in informal settlements, where there is very little hope of development, as the government does not possess the resources that are necessary for a full-scale sanitation programme. Therefore, on-site treatments have been considered to provide sanitation in these dense peri-urban areas. The anaerobic baffled reactor (ABR) is one such sanitation system. This reactor utilises the phenomenon of anaerobic digestion to degrade substrates. One of the major disadvantages of any anaerobic treatment processes is the extreme sensitivity of the bacterial communities, thus inducing slow recovery rates following toxic shocks. Therefore, an understanding of these microbial consortia is essential to effectively control, operate and optimise the anaerobic reactor. Fluorescence in situ hybridization, 4’,6-diamidino-2-phenylindole (DAPI) staining and DNA sequencing techniques were applied to determine the microbial consortium, as well as their reactions to daily operating conditions. With an understanding of these populations and their responses to perturbations within the system, it is possible to construct an anaerobic system that is successful in its treatment of domestic wastewater. In situ hybridizations were conducted for three operating periods, each characterised by specific flow rates. Results showed Eubacterial population dominance over the Archaeal population throughout both of the operating periods investigated. However, these cells cumulatively consisted of 50% of the total biomass fraction, as determined by DAPI staining. Group-probes utilised revealed a high concentration of fermentative acidogenic bacteria, which lead to a decrease in the pH values. It was noted that the ABR did not separate the acidogenic and methanogenic phases, as expected. Therefore, the decrease in pH further inhibited the proliferation of Archaeal acetoclastic methanogens, which were not present in the second operating period. DNA sequencing results revealed the occurrence of the hydrogenotrophic Methanobacterium and Methanococcus genera and confirmed the presence of Methanosarcina. Sequencing of the bacterial DNA confirmed the presence of the low G+ C Gram Positives (Streptococcus), the high G+C Gram Positives (Propionibacterium) and the sulfate reducing bacteria (Desulfovibrio vulgaris). However, justifications were highly subjective due to a lack of supportive analytical data, such as acetate, volatile fatty acids and methane concentrations. Despite this, findings served to add valuable information, providing details on the specific microbial groups associated with ABR treatment processes.

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