22 posts · 18,881 views
The American Biotechnologist is a place where PIs, Graduate Students, Technicians and Science Educators can network, post and view articles, videos, seminars, techniques etc of interest and generally find subject matter relevant to them.
In a recent review article published in the New England Journal of Medicine, authors Liewei Wang and a team from the Mayo Clinic discuss recent advances in the field of pharmacogenomics and the potential value that it holds for patient care with proper uptake by the medical community. Pharmacogenomics is the study of a patient’s [...]... Read more »
Most of my graduate work focused on transcriptional regulation of a vasoregulatory gene and all the nitty-gritty work that goes along with these types of molecular protocols. As such, I am always on the lookout for techniques that improve upon current transcriptional regulation protocols especially if they show a propensity for doing the job either [...]... Read more »
L. Stirling Churchman, & Jonathan S. Weissman. (2011) Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature, 368-373. info:/doi:10.1038/nature09652
We found a great post this past weekend on fastcompany.com which we thought we’d share with you. Author David Zax describes an interactive video game designed by researchers in the bioengineering department of Stanford University that uses living cells as part of the game mechanics. These “Biotic Games” are played much like any arcade classic [...]... Read more »
Towards the end of last week, NASA announced that it would reveal a stunning scientific report in a live press conference that would surely be the scientific breakthrough of the year. Watching the conference later in the day, I was amazed to hear Felisa Wolfe-Simon of the NASA Astrobiology Institute explain that she found a [...]... Read more »
Wolfe-Simon F, Blum JS, Kulp TR, Gordon GW, Hoeft SE, Pett-Ridge J, Stolz JF, Webb SM, Weber PK, Davies PC.... (2010) A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science (New York, N.Y.). PMID: 21127214
What does the domesticated Turkey have in common with the mouse, rat, chimpanzee and Human? Give up? The answer is that its genome can now be added to the long list of species that have had their genomes sequenced thanks to advances in Next Generation Sequencing.
Earlier this year, a team of 34 scientists published their [...]... Read more »
Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Ann Blomberg L, Bouffard P, Burt DW, Crasta O, Crooijmans RP.... (2010) Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS biology, 8(9). PMID: 20838655
If you think that genetic evolutionary processes take Milena….think again. Scientists at Allegheny General Hospital’s Center for Genomic Sciences have found that through a process known as horizontal gene transfer (HGT), bacterial pathogens can mutate multiple times during the course of a bacterial infection. In a study published by Hiller et. al. in PLoS Pathogens [...]... Read more »
Hiller NL, Ahmed A, Powell E, Martin DP, Eutsey R, Earl J, Janto B, Boissy RJ, Hogg J, Barbadora K.... (2010) Generation of genic diversity among Streptococcus pneumoniae strains via horizontal gene transfer during a chronic polyclonal pediatric infection. PLoS pathogens, 6(9). PMID: 20862314
If you watched the video on real time quantitative PCR data analysis, you should have a good understanding of real-time quantitative PCR basics and the associated data analysis techniques. Classical quantification techniques such as Livak, delta CT and the Pfaffl rely on linear regression analysis and are currently the most widely accepted methodologies for quantitative [...]... Read more »
Bernth Jensen JM, Petersen MS, Stegger M, Ostergaard LJ, & Møller BK. (2010) Real-Time Relative qPCR without Reference to Control Samples and Estimation of Run-Specific PCR Parameters from Run-Internal Mini-Standard Curves. PloS one, 5(7). PMID: 20661435
MIT scientists Matthew Angel and Mehmet Fatih Yanik have discovered a method for transfecting mRNA into fibroblasts without triggering the immune response that normally defends cells against exogenous RNA infection. Cells are usually able to differentiate between endogenous and exogenous RNA through activation of pattern-recognition receptors (PRRs) that initiate a subsequent immune response. While this [...]... Read more »
Angel M, & Yanik MF. (2010) Innate Immune Suppression Enables Frequent Transfection with RNA Encoding Reprogramming Proteins. PLoS ONE, 5(7). info:/
At the risk of developing a complex that all I talk about is fecal matter, for the second time this week I would like to bring your attention to another study that focuses on the gut and its microbial habitat. A couple of days ago I discussed the challenge of identifying the huge number of [...]... Read more »
Alejandro Reyes, Matthew Haynes, Nicole Hanson, Florent E. Angly, Andrew C. Heath, Forest Rohwer, & Jeffrey I. Gordon. (2010) Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature, 334-338. info:/10.1038/nature09199
A recent study published in the New England Journal of Medicine reported that autologous limbal stem cells can be used to permanently reverse the loss of vision caused by ocular burn induced limbal stem-cell deficiency (limbal stem cells function to replace dead corneal cells).
It is important to note that in the cases reported, eyesight [...]... Read more »
Rama, P., Matuska, S., Paganoni, G., Spinelli, A., De Luca, M., & Pellegrini, G. (2010) Limbal Stem-Cell Therapy and Long-Term Corneal Regeneration. New England Journal of Medicine. DOI: 10.1056/NEJMoa0905955
One of my favorite pastimes is reading about situations where experts from different (and seemingly divergent) disciplines get together to discuss interdisciplinary cooperation and mutual progress. All too often scientists segregate themselves according to their area of expertise and only make use of the techniques that they are familiar with or have access to in [...]... Read more »
Finney, L., Chishti, Y., Khare, T., Giometti, C., Levina, A., Lay, P., & Vogt, S. (2010) Imaging Metals in Proteins by Combining Electrophoresis with Rapid X-ray Fluorescence Mapping. ACS Chemical Biology, 5(6), 577-587. DOI: 10.1021/cb1000263
If you’ve been following the Diabetes news lately, you likely noticed that two stories have dominated the news over the last couple of days. The first is a widely published study that implicates the consumption of white rice (as opposed to brown rice) in increased incidents of diabetes and the second relates to emerging evidence [...]... Read more »
Transfecting cells can be a difficult task for even the most seasoned of cell biologists. Sure there are easy-to-transfect cell lines such as A10 Smooth Muscle Cells, COS Cells or p19 cells, but what about those pesky, hard to isolate primary cells? Or better yet, what about cells embedded in living tissue on animals or [...]... Read more »
Woods, G., & Zito, K. (2008) Preparation of Gene Gun Bullets and Biolistic Transfection of Neurons in Slice Culture. Journal of Visualized Experiments. DOI: 10.3791/675
Enteroviruses such as Poliovirus and Hepatitis are notorious for the disastrous effects they cause upon infection. A study recent published in Cell contributes a significant finding to the field of RNA virus replication. The Altan-Bonnet lab at Rutgers University has shown how that upon infection, RNA viruses generate specialized RNA replication organelles enriched in phosphatidylinositol-4-phosphate [...]... Read more »
Hsu, N., Ilnytska, O., Belov, G., Santiana, M., Chen, Y., Takvorian, P., Pau, C., van der Schaar, H., Kaushik-Basu, N., & Balla, T. (2010) Viral Reorganization of the Secretory Pathway Generates Distinct Organelles for RNA Replication. Cell, 141(5), 799-811. DOI: 10.1016/j.cell.2010.03.050
According to popular thought, Charles Darwin’s Origin of the Species was heavily influenced by his grandfather Erasmus Darwin (1). The impact that a grandparent can have upon an impressionable child should never be underestimated. To what extent do you think that Dana Carvey was influenced by his grandfather?
Dana Carvey is “DARWIN” – watch more funny [...]... Read more »
C. U. M. Smith, . (2010) Like Grandfather, Like Grandson: Erasmus and Charles Darwin on evolution. Perspectives in Biology and Medicine, 53(2), 186-199. DOI: 10.1353/pbm.0.0152
The Allen Institute for Brain Science initiated the Allen Brain Atlas in 2003 with a goal to create a genomic map of the mouse brain. The mouse brain atlas was successfully completed in 2006 using 85 million images containing 600 terabytes of data and identifying 21,000 active genes in the mouse brain. The atlas has [...]... Read more »
Lein, E., Hawrylycz, M., Ao, N., Ayres, M., Bensinger, A., Bernard, A., Boe, A., Boguski, M., Brockway, K., Byrnes, E.... (2006) Genome-wide atlas of gene expression in the adult mouse brain. Nature, 445(7124), 168-176. DOI: 10.1038/nature05453
Davis FP, & Eddy SR. (2009) A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas. Bioinformatics (Oxford, England), 25(13), 1647-54. PMID: 19414530
As scientists we are “naturally obsessed.” We have a need to find the answer and can’t stop working until we get it. So how do we find the time to watch this one hour dramatic story by Richard and Carole Rifkind about life in a molecular biology lab? Although there are many health related stories [...]... Read more »
Wang, Z., & Gantz, W. (2010) Health Content in Local Television News: A Current Appraisal. Health Communication, 25(3), 230-237. DOI: 10.1080/10410231003698903
As a proteomics fan in general and a 2D Gel Electrophoresis fan specifically, I have been following the Ludesi Blog which I have found to be a resource rich in 2D information including a knowledgebase, webinars and an great tool that pulls together all proteomics related tweets from twitter. For those of you who [...]... Read more »
Chevalier, F. (2010) Highlights on the capacities of "Gel-based" proteomics. Proteome Science, 8(1), 23. DOI: 10.1186/1477-5956-8-23
Gibson et. al. from the Venter Institute have just published a report in Science Express (online only) that sounds very cool, but whose implications don’t seem to be well understood yet from experts in the field. Essentially the group synthesized the genome of one bacterial species and transplanted it into another bacterial species. What resulted [...]... Read more »
Lartigue, C., Vashee, S., Algire, M., Chuang, R., Benders, G., Ma, L., Noskov, V., Denisova, E., Gibson, D., Assad-Garcia, N.... (2009) Creating Bacterial Strains from Genomes That Have Been Cloned and Engineered in Yeast. Science, 325(5948), 1693-1696. DOI: 10.1126/science.1173759
Lartigue, C., Glass, J., Alperovich, N., Pieper, R., Parmar, P., Hutchison, C., Smith, H., & Venter, J. (2007) Genome Transplantation in Bacteria: Changing One Species to Another. Science, 317(5838), 632-638. DOI: 10.1126/science.1144622
If you’ve ever done gene knockdown experiments, you know that the process can be complicated and involve many steps. siRNA design, cell culture, perfect cell confluency, transfection or electroporation, downstream analysis etc. Bio-Rad now has a plethora of instruments and reagents to help you simplify the process. In a recently published article in the Journal [...]... Read more »
McCoy, A., Litterst, C., Collins, M., & Ugozzoli, L. (2010) Using an Automated Cell Counter to Simplify Gene Expression Studies: siRNA Knockdown of IL-4 Dependent Gene Expression in Namalwa Cells. Journal of Visualized Experiments. DOI: 10.3791/1904
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