CRISPR/Cas9 system is a recently developed multi-purpose technology for genome editing [1,2] and its tool CRISPR-ERA/Cas9 is widely used as explained in the previous article . The possible applications of this system have been discussed by its developers  and have been successfully applied for genome editing, gene function identification, and for gene therapy in animals and human cells [5-9]. Recently, a group of Chinese researchers has reported the editing of a genome using the CRISPR/Cas9 system in human embryo for the first time in history . The team has attempted to remove ‘harmful’ genetic codes to be potentially replaced by the ‘good’ ones. The results are published in Protein & Cell journal  but have opened a topic for debate over crossing the ethics of gene editing.
A research group at Sun Yat-Sen University, Guangzhou led by Dr. Junjiu Huang have attempted to cure a fatal blood disorder caused by removing a gene known as β-thalassemia responsible for this disorder. This is done by using a gene-editing technique called CRISPR/Cas9, which can recognize specific region in a DNA and cut and replace it with some other residues which do not code for any disorder. The researchers have modified this gene in a non-viable embryo but they observed some serious obstacles during the application of this method in human embryos.
The team applied this technique to 86 embryos and then waited for 48 hours to act. Out of 86 embryos, 71 survived, out of which 54 were genetically tested. According to their results, only 28 embryos were successfully spliced and only a fraction of them contained the replaced genetic material [10,11]. At this point, the team stopped experimenting quoting
“If you want to do it in normal embryos, you need to be close to 100%. That’s why we stopped. We still think it’s too immature.” says Dr. Huang .
There are several ethical concerns regarding gene editing in the human genome. Modifying the DNA of viable embryos may lead to unpredictable results in the future generation. Most of the researchers think that this technique is not ready to be used for tweaking human embryos. Some concerned scientists have published an article addressing the consequences of editing human germ line using current technologies . A stem-cell biologist George Daley at Harvard Medical School in Boston, Massachusetts, says
“I believe this is the first report of CRISPR/Cas9 applied to human pre-implantation embryos and as such the study is a landmark, as well as a cautionary tale. Their study should be a stern warning to any practitioner who thinks the technology is ready for testing to eradicate disease genes.” 
Due to ethical concerns, this paper was not published by Nature and Science journal, says Dr. Huang [10,13]. The major concern which is most feared by some researchers is that once this technique is employed to tweak human embryos, it will be applied later to create humans with desired traits. This could be a huge step.
This research is questionable due to ethical issues but still being experimented with. Dr. Huang’s team is trying to improve the technique using CRISPR/Cas9 in animal models for now .
- Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., … & Zhang, F. (2013). Multiplex genome engineering using CRISPR/Cas systems. Science, 1231143.
- Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., … & Church, G. M. (2013). RNA-guided human genome engineering via Cas9. Science, 339(6121), 823-826.
- Cho SW, Kim S, Kim JM, Kim JS (2013) Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat Biotechnol 31:230–232
- Jinek M, East A, Cheng A, Lin S, Ma E, Doudna J (2013) RNAprogrammed genome editing in human cells. Elife 2:e00471
- Li D, Qiu Z, Shao Y, Chen Y, Guan Y, Liu M, Li Y, Gao N, Wang L, Lu X et al (2013) Heritable gene targeting in the mouse and rat using a CRISPR-Cas system. Nat Biotechnol 31:681–683
- Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM (2013) RNA-guided human genome engineering via Cas9. Science 339:823–826
- Smith C, Gore A, Yan W, Abalde-Atristain L, Li Z, He C, Wang Y, Brodsky RA, Zhang K, Cheng L et al (2014) Whole-genome sequencing analysis reveals high specificity of CRISPR/Cas9 and TALEN-Based Genome Editing in Human iPSCs. Cell Stem Cell 15:12–13
- Cyranoski, D., & Reardon, S. (2015). Chinese scientists genetically modify human embryos. Nature News.
- Liang, P., Xu, Y., Zhang, X., Ding, C., Huang, R., Zhang, Z., … & Sun, Y. (2015). CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes. Protein & cell, 6(5), 363-372.
- Lanphier, E., Urnov, F., Haecker, S. E., Werner, M., & Smolenski, J. (2015). Don’t edit the human germline. Nature News, 519(7544), 410.
Tutorial: Vina Output Analysis Using PyMol
Video Tutorial: Autodock Vina Result Analysis with PyMol
How to perform docking in a specific binding site using AutoDock Vina?
AutoDock Vina is a bioinformatics tool that is used to perform in-silico docking of proteins with a ligand. It provides many options depending on the needs of a user. This tool offers blind docking and binding in a specific pocket as well, which is sometimes more demanding when the binding site is already known. This article will guide you to dock a protein with a ligand in a specific binding site/ pocket. (more…)
BiR: Impact report – July 2016 & More
As we improve the quality of articles and as we are nearing our first collective birthday, Bioinformatics Review has expanded its reach, opening new avenues. The progress is summarised as below:
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- Bioinformatics Review was visited over 143,801 times in July 2016.
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Deciding the right journal for your paper: 5 things to look for
Considering the amount of effort and hard work that goes into writing a research paper, it is critical to choose the right journal to reach the right scientific audience. It is particularly important not to literally waste your valuable work by falling prey to predatory journals. So we came up with this short guide that will make it easier for you to decide where to publish without getting into problems or without getting duped.
First things first, OA or Not?
Some journals are purely Open Access(OA). Every single paper published in such journals are available without any fees or subscribe directly via the internet. Open access journals are good to go. But making science available to the public for free comes with a cost – they charge the authors for the publication charges. This makes them out of reach for an independent researcher or authors without much financial backing. To overcome this, some journals are partly open access and allow the authors to choose whether they want their paper to be open access by paid Open Access Charge. So decide carefully whether you want to go open access. If so, you can search for the journal of your interest on DOAJ(Directory of Open Access Journals).
Beware of predatory journal
Predatory journals are ‘Fake’ journals that are fraudulently set up to earn some easy cash. These journals attract young researchers by offering close to 100% acceptance rate, namesake/no review. Typically you can know whether a journal is predatory or not by looking into this list or this list (Popularly known as Bealle’s List). Although this is not an absolute list but it may come handy when deciding. You can identify a predatory journal by looking at the general signs such as lack of contact/office address on the website(or having just an email address as contact information). Not mentioning phone number of editors, missing details of the editorial board etc.
- Does your journal participate in archiving programs?
What if the website goes down tomorrow? or maybe the journal goes bankrupt? What will happen to the valuable research that was published in it? The good news is that the most journals participate in an archiving program where they deposit data for permanent storage, i.e. even if the journal shuts down, your paper will not cease to exist. This is done by providing each article with a DOI(digital object identifier) number which is unique and points to the same article, forever. Okay, so what if the data center gets nuked? or maybe what if the data center where all the DOI are stored suddenly catch fire? To prevent such scenarios, a large number of copies of the same content are kept at different locations around the world. This is achieved by a journal participating in LOCKSS (Large Number of Copies Keep Stuff Safe) program. Some journals participate in NCBI PubMed where they deposit published data. So the next time you choose a journal, better make sure it participates in LOCKSS.
Know the scope of the journal you are publishing in
The basic aim & essence of publishing research are to reach scientific fraternity, telling them about the significant work that you have done and what it could be used for(Although there are people who publish to merely gain credits). So better reach the right audience, by selecting a journal whose readership and editorial board comprises of people in a related field. The aims and scopes of the journal should match with your work. For example, the Journal of Theoretical Biology is aimed at theoretical studies and it will not accept your wet lab research work. Furthermore, the areas outlined in the journal’s homepage are the ones that will be accepted. Articles falling out of scope are usually rejected thus the loss of precious time.
Impact (Not Impact Factor)
Ask yourself whether the contents of the journal are accessible via search. Make sure you are able to search the articles published in your selected journal via Google Scholar, PubMed or PubMed Central. You can also consider Impact Factor (by Thomson Reuters) of a journal while deciding buy, try not to overemphasize it. IF is a measure of others work and does not mean it will put any weight to your research. A journal with a good impact factor is likely to be having more readership and thus, citations. You should target a journal that not only publishes your research but also takes strides in publicizing it. What is the point of publishing in a journal that does not really publishes your research?
It is wise to use caution while selecting a journal. It will save you time, money and your efforts that may otherwise go into vain. Emphasizing on these five points may be time taking, but in the end, it pays off to be more cautious.
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