Digestion efficiency differences of restriction enzymes frequently used for genotype-by-sequencing technology

2017 ◽  
Vol 44 (3) ◽  
Keyword(s):  
Restriction Enzymes ◽  
Sequencing Technology ◽  
Digestion Efficiency ◽  
Genotype By Sequencing

scholarly journals Would an RRS by any other name sound as RAD?

2018 ◽  
Author(s):  
Erin O Campbell ◽  
Bryan M T Brunet ◽  
Julian R Dupuis ◽  
Felix A H Sperling
Keyword(s):  
Literature Review ◽  
Restriction Enzyme ◽  
Restriction Enzymes ◽  
Shotgun Sequencing ◽  
Sequencing Technology ◽  
Reduced Representation ◽  
Minor Elements ◽  
Scientific Innovation ◽  
A Genome ◽  
Unique Method

ABSTRACTSampling markers throughout a genome with restriction enzymes emerged in the 2000s as reduced representation shotgun sequencing (RRS). Rapid advances in sequencing technology have since spurred modifications of RRS, giving rise to many derivatives with unique names, such as RADseq. But naming conventions have often been more creative than consistent, with unclear criteria for recognition as a unique method resulting in a proliferation of names characterized by ambiguity. We conducted a literature review to assess methodological and etymological relationships among 36 restriction enzyme-based methods, as well as rates of correct referencing of commonly-used methods. We identify several instances of methodological convergence or misattribution in the literature, and note that many published derivatives have modified only minor elements of parent protocols. We urge greater restraint in naming derivative methods, to strike a better balance between clarity, recognition of scientific innovation, and correct attribution.

scholarly journals FN-Identify: Novel Restriction Enzymes-Based Method for Bacterial Identification in Absence of Genome Sequencing

2015 ◽  
Vol 2015 ◽  
pp. 1-14 ◽  
Author(s):  
Mohamed Awad ◽  
Osama Ouda ◽  
Ali El-Refy ◽  
Fawzy A. El-Feky ◽  
Kareem A. Mosa ◽  
...  
Keyword(s):  
16S Rrna ◽  
Genome Sequencing ◽  
Restriction Analysis ◽  
Restriction Enzymes ◽  
Rrna Gene ◽  
Bacterial Identification ◽  
Rapid Progress ◽  
Restriction Maps ◽  
Sequencing Technology ◽  
Bacterial Populations

Sequencing and restriction analysis of genes like 16S rRNA and HSP60 are intensively used for molecular identification in the microbial communities. With aid of the rapid progress in bioinformatics, genome sequencing became the method of choice for bacterial identification. However, the genome sequencing technology is still out of reach in the developing countries. In this paper, we propose FN-Identify, a sequencing-free method for bacterial identification. FN-Identify exploits the gene sequences data available in GenBank and other databases and the two algorithms that we developed, CreateScheme and GeneIdentify, to create a restriction enzyme-based identification scheme. FN-Identify was tested using three different and diverse bacterial populations (members of Lactobacillus, Pseudomonas, and Mycobacterium groups) in an in silico analysis using restriction enzymes and sequences of 16S rRNA gene. The analysis of the restriction maps of the members of three groups using the fragment numbers information only or along with fragments sizes successfully identified all of the members of the three groups using a minimum of four and maximum of eight restriction enzymes. Our results demonstrate the utility and accuracy of FN-Identify method and its two algorithms as an alternative method that uses the standard microbiology laboratories techniques when the genome sequencing is not available.

Exploring the usefulness of microhaplotypes in forensic identification using massive parallel sequencing technology

2020 ◽  
Vol 140 (1) ◽  
Author(s):  
Chiara Turchi ◽  
Filomena Melchionda ◽  
Mauro Pesaresi ◽  
Eleonora Ciarimboli ◽  
Carla Bini ◽  
...  
Keyword(s):  
Forensic Identification ◽  
Massive Parallel Sequencing ◽  
Sequencing Technology ◽  
Parallel Sequencing

Gut Microbiota and Antipsychotics Induced Metabolic Alteration

2019 ◽  
pp. 131-143
Author(s):  
Dong-Yu Kan ◽  
Su-Juan Li ◽  
Chen-Chen Liu ◽  
Ren-Rong Wu
Keyword(s):  
Gut Microbiota ◽  
Body Weight Gain ◽  
Neuropsychiatric Disorders ◽  
Elevated Risk ◽  
Metabolic Disturbance ◽  
Metabolic Dysfunction ◽  
Sequencing Technology ◽  
Severe Mental Disorder ◽  
Metabolic Alteration

Schizophrenia is a chronic and severe mental disorder with antipsychotics as primary medications, but the antipsychotic-induced metabolic side effects may contribute to the elevated risk of overall morbidity and mortality in patients with psych-iatric diseases. With the development in sequencing technology and bioinformatics, dysbiosis has been shown to contribute to body weight gain and metabolic dysfunction. However, the role of gut microbiota in the antipsychotic-induced metabolic alteration remains unknown. In this paper, we reviewed the recent studies of the gut microbiota with psychiatric disorders and antipsychotic-induced metabolic dysfunction. Patients with neuropsychiatric disorders may have a different composi-tion of gut microbiota compared with healthy controls. In addition, it seems that the use of antipsychotics is concurrently associated with both altered composition of gut microbiota and metabolic disturbance. Further study is needed to address the role of gut microbiota in the development of neuropsychiatric disorders and antipsychotic-induced metabolic disturbance, to develop novel therapeutics for both neuropsychiatric disorders and metabolic dysfunction.

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