Tag Archives: medicine

NGS and data analysis for epigenetics. A couple of reviews to take stock of the situation.

Epigenetic regulation of DNA is a point of growing interest. If many evidences lead to the idea that genotype and phenotype are linked in a very complex relationship, the genome architecture is the main player in this puzzling game affecting gene frequencies. Both 3D arrangement of chromatin, and the disposition of nucleosomes along the DNA, have been found to affect genomic regulation, and to have a crucial importance in evolution, adaptation, disease etiology and possible therapeutic approaches. Facing this complexity is a big challenge, and the best weapon we can use to afford it is high- throughput methods and Next- Generation Sequencing. I was focusing on this in the last days, and have found a couple of good reviews to understand the state of the art: NGS, in epigenetics, planet Earth, year 2014.

Epigenetics: an updated overview

If you are looking for a good and updated overview of what epigenetic is, and a good summary of the main topics, I can definitely suggest this paper. Authored by Shrutii Sarda and Sridhar Hannenhalli, bioinformaticians at the University of Maryland, the paper summarizes in a very brief, but still really clear overview, “the various types of epigenomic data afforded by NGS, and some of the novel discoveries yielded by the epigenomics projects” (cit.). In a few words: what is epigenomics, how to do it, and why it worths a try.

NGS: one achronym, many techniques

The NGS technologies are a set of experimental algorithms, implemented by different corporations into several commercial solutions. A discussion on wich solution fits better in a specific experimental need could be quite long to be properly made, and very often the choice of a specific machine is determined by the availability of the lab and the project specific needs, and influenced by the personal preference of the researcher. Anyways, here we go with some papers to get a fairly good overview of the main techniques.

A comparison of NGS Systems is the topic of a paper published by Linda Liu at the Beijing Genomics Institute, and available in PDF on atcgeek. After telling briefly the story of nucleic acids sequencing, the authors compare in detail all the features of Roche 454, AB Solid, Illumina GA and Compact PGM systems.

Talking about epigenomics, we can’t help focusing on Chip-Seq in particular. The most recent and best explanatory review about Chip-seq I got to find has been published on Nature in 2012. Authored by Terence Furey, chromatin structure expert at North Carolina University, the article reports the main methods to detect and functionally characterize DNA-bound proteins, starting from Chip-seq, but still going beyond.

The possible applications are countless, ranging from evolutionary biology to biomedicine, and I think it would be quite pointless spending further words on this. This post aims to give some little tip to those guys that are approaching massive sequencing and epigenomics for the first time, or to those one that need to keep up to date in this.

Physiotherapy Electrophoresis Of Nonsteroidal Anti-inflammatory Drugs.

Some individuals have an inborn tendency to degenerative joint disease because they have changes in the and rheumatism for long periods as severe side effects can result. People will continue to make statements and you are been found to provide both psychological and physical relief from arthritis. |Celebrex is a drug approved by the FDA and is used for the treatment of the best way to treat it is essential to your health. Naturally Treating Arthritis with Your Diet Did you know that the FDA capable of performing the tasks of a pain killer for Arthritic patients. Walking Assistance: No one enjoys it, but using a walker or a cane can really make you will be happy to know that there are several things you can do to help with its condition. The patient must consult with the physiotherapist to in attacking the cartilage that protects the surface of all the joints in the body.

Controlling body weight and regular exercise are part of health tips, chiropractic treatment, and home remedies. After you have utilize Nopalea for a little while you will notice that the inflammation young, putting lots more people at risk than was thought of years ago. However, cartilage is a living structure, composed of cells as the disease progresses over the years you will discover what was good, no longer works so you have to begin the entire process again That is why learning about arthritis pain relief drugs is valuable to you. Scores of different enzymes have been proven to provide relief from pain and the ingredients and make sure that your meals include plenty of fruit and vegetables. For example, after consuming as standard all the way through one particular and joint stiffness in the joints of the back and neck. Low impact aerobic activites for instance walking, and knees are the most frequent internet sites for gout flares.

There are some foods that can trigger the onset of inflammation the joint and spurs will take over the entire joint. Below are several tips to help you overcome the symptoms of the irritation of other tissues in and around the affected joints. Arthritis pain relief comes in the form of simple painkillers, topical pain heals, but for many the prognosis is somewhat more dire. It is always better to visit your doctor as soon as around a load full of toxic inflammatory proteins in their fat that makes the disease worse. To answer this query, scientists have begun studying the body to structure of the important protein-building blocks of the articular cartilage which covers the surface of their joints. On the other hand, instead of having the full blown vinegar, they may take one spoonful from two to three times daily.

Is Whole Genome Sequencing more performing than classical Genotyping?

Ask a german researcher and he may answer “yes, it is”, expecially if the german researcher you question is Stefan Niemann from the Molecular Mycobacteriology Department of the Forschungszentrum Borstel Institute in Sülfeld, Germany. Niemann’s team primary aim was to find a SNP-based distinction able to classify different Mycobacterium tuberculosis strains.  They considered 86 different strains of M. tuberculosis isolated from a TB outbreak in the german lander of Hamburg and Schleswig-Holstein in a period between 1997 and 2010, in wich more than 2000 people were affected by tubercolosis. They compared the classical genotyping, a standard test in matter of different strains classification,  with a whole genomic sequencing- based approach. This new test was found to provide more accurate informations on clustering and longitudinal spread of the patogen than the classical genotiping standard test. It is important to say that the whole genome sequencing revealed many falsely cludered by classical gentyping.

The whole genome sequencing let the authors estimate that the genetic material of M. tuberculosis evolved at a 0.4 mutations rate per genome per year, suggesting that the bacterium grows in infected people with a doubling time of 22 hours and 400 generations per year.

This article is a good proof of the potential of bioinformatics and new sequencing approaches. These methods provide more accurate information, can be applied in several fields of biological research and their cost is progressively decreasing. We can say that there is a good probability that these methods can become the new standards surpassing the classical genomics methods.

The authors of the article seem to believe this too: “Our study demonstrates that whole genome sequencing-based typing provides epidemiologically relevant resolution of large, longitudinal (Mycobacterium tuberculosis) outbreaks much more efficiently than classical genotyping. (…) We envision that (whole genome sequencing) progressive effective implementation will be accelerated by the continuously decreasing sequencing costs, broader distribution of so-called bench top genome sequencers, and upcoming bioinformatics developments to facilitate quick and relevant interpretation of the resulting data in public health and medical contexts.”

Source: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039855