42 posts · 27,003 views
We highlight and comment selected stand-out papers, techniques, tools, websites and news in molecular biology.
Alejandro Montenegro-Montero
42 posts
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- April 6, 2009
- 09:50 PM
- 1,230 views
What is Epigenetics? An operational definition
by Alejandro Montenegro-Montero in MolBio Research Highlights
Epigenetics is a hot topic; its usage in articles included in PubMed has increased by more than tenfold in the last 10 years.This trend, however, could be explained, to some degree, by its loose usage. Although there is a clear meaning to the concept, it has been used to define things that are not exactly epigenetics per se, but rather something else.Indeed, on a recent News Feature1 in Nature... Read more »
Berger, S., Kouzarides, T., Shiekhattar, R., & Shilatifard, A. (2009) An operational definition of epigenetics. Genes , 23(7), 781-783. DOI: 10.1101/gad.1787609
- February 16, 2009
- 12:00 AM
- 1,004 views
ChIP-seq accurately predicts tissue-specific activity of enhancers
by Francisco Barriga in MolBio Research Highlights
An interesting paper highlighting the use of new technologies in studying regulatory elements on a genome-wide scale. ... Read more »
Axel Visel, Matthew J. Blow, Zirong Li, Tao Zhang, Jennifer A. Akiyama, Amy Holt, Ingrid Plajzer-Frick, Malak Shoukry, Crystal Wright, Feng Chen.... (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature, 457(7231), 854-858. DOI: 10.1038/nature07730
- July 27, 2009
- 11:59 AM
- 958 views
JANE: Journal and Author Name Estimator
by Alejandro Montenegro-Montero in MolBio Research Highlights
I've just read over at Scienceroll about two tools that “help you determine which journal you should choose for publication”, based on your abstract or keywords [See Journal and Author Name Estimator and Huge Steps in Changing Science].The first one is part of ResearchGATE (a “scientific network that connects researchers”) and the second one (which has been around for some time, since early 2008)... Read more »
Schuemie, M., & Kors, J. (2008) Jane: suggesting journals, finding experts. Bioinformatics, 24(5), 727-728. DOI: 10.1093/bioinformatics/btn006
- March 21, 2009
- 07:14 PM
- 939 views
Are we training pit bulls to review our manuscripts?
by Alejandro Montenegro-Montero in MolBio Research Highlights
Virgina Walbot has recently published an article in the Journal of Biology discussing the idea that grad students and postdocs can turn out to be excessively (and in some cases unjustifiably) critical and even ‘savage’ in their review of articles (when asked to referee), and that this issue is a result of their training. She argues that this "problem" may be addressed by some exercises during... Read more »
Walbot, V. (2009) Are we training pit bulls to review our manuscripts?. Journal of Biology, 8(3), 24. DOI: 10.1186/jbiol125
- March 15, 2010
- 09:23 AM
- 936 views
Surveying the gut microbiota, cross dressing chickens and more, in my Picks of the Week, from RB
by Alejandro Montenegro-Montero in MolBio Research Highlights
Another week has gone by and some very interesting molbio blog posts have been aggregated to Researchblogging.org. Every week [see my opening post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used], briefly describe them and list them here for you to check out.Note that I'm ... Read more »
Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T.... (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464(7285), 59-65. DOI: 10.1038/nature08821
Vijay-Kumar, M., Aitken, J., Carvalho, F., Cullender, T., Mwangi, S., Srinivasan, S., Sitaraman, S., Knight, R., Ley, R., & Gewirtz, A. (2010) Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5. Science. DOI: 10.1126/science.1179721
Zhao, D., McBride, D., Nandi, S., McQueen, H., McGrew, M., Hocking, P., Lewis, P., Sang, H., & Clinton, M. (2010) Somatic sex identity is cell autonomous in the chicken. Nature, 464(7286), 237-242. DOI: 10.1038/nature08852
- June 30, 2009
- 03:13 PM
- 931 views
Cancer Stem Cells: the root of all evil?
by Francisco Barriga in MolBio Research Highlights
A recent series of papers [1-3] have prompted me to write about the cancer stem cell (CSC) hypothesis, since during the last years there has been a lot of controversy regarding the existence, function and clinical implications of cancer stem cells. This confusion stems (no pun intended) from the lack of clarity in the field nowadays, arising mainly from misconceptions regarding the origin and... Read more »
Jordan, C. (2009) Cancer Stem Cells: Controversial or Just Misunderstood?. Cell Stem Cell, 4(3), 203-205. DOI: 10.1016/j.stem.2009.02.003
Rosen, J., & Jordan, C. (2009) The Increasing Complexity of the Cancer Stem Cell Paradigm. Science, 324(5935), 1670-1673. DOI: 10.1126/science.1171837
Visvader, J., & Lindeman, G. (2008) Cancer stem cells in solid tumours: accumulating evidence and unresolved questions. Nature Reviews Cancer, 8(10), 755-768. DOI: 10.1038/nrc2499
- September 14, 2009
- 06:41 PM
- 928 views
Targeting cancer stem cells: chemical style
by Francisco Barriga in MolBio Research Highlights
In a previous post I tried to summarize the major points underlying the Cancer Stem Cell Hypothesis, which states that tumors are hierarchically structured and that a particular subpopulation of cells, cancer stem cells (CSCs), are capable of initiating and sustaining the growth of the tumor [Cancer Stem Cells: the root of all evil?]. This has obvious clinical implications since eliminating ... Read more »
Gupta, P., Onder, T., Jiang, G., Tao, K., Kuperwasser, C., Weinberg, R., & Lander, E. (2009) Identification of Selective Inhibitors of Cancer Stem Cells by High-Throughput Screening. Cell, 138(4), 645-659. DOI: 10.1016/j.cell.2009.06.034
MANI, S., GUO, W., LIAO, M., EATON, E., AYYANAN, A., ZHOU, A., BROOKS, M., REINHARD, F., ZHANG, C., & SHIPITSIN, M. (2008) The Epithelial-Mesenchymal Transition Generates Cells with Properties of Stem Cells. Cell, 133(4), 704-715. DOI: 10.1016/j.cell.2008.03.027
- January 29, 2009
- 12:00 AM
- 830 views
System-wide molecular evidence for phenotypic buffering in Arabidopsis
by Alejandro Montenegro-Montero in MolBio Research Highlights
Phenotypic buffering appears to be a widespread mechanism. In this paper, the authors study this phenomenon using a system-wide genetical genomics approach in the model plant Arabidopsis thaliana. ... Read more »
Jingyuan Fu, Joost J B Keurentjes, Harro Bouwmeester, Twan America, Francel W A Verstappen, Jane L Ward, Michael H Beale, Ric C H de Vos, Martijn Dijkstra, Richard A Scheltema.... (2009) System-wide molecular evidence for phenotypic buffering in Arabidopsis. Nature Genetics, 41(2), 166-167. DOI: 10.1038/ng.308
- December 2, 2009
- 09:21 PM
- 783 views
An alternative cloning strategy: yeast recombinational cloning
by Alejandro Montenegro-Montero in MolBio Research Highlights
As part of my Ph.D thesis, I have to generate a lot of transcriptional fusions (constructs in which a promoter of choice is cloned in front of a reporter gene in order to evaluate transcriptional regulation. Such plasmids can then be transformed into your model organism to study this regulation in vivo).Traditionally, this involves amplifying the region of interest (in my case a promoter region) ... Read more »
MA, H., KUNES, S., SCHATZ, P., & BOTSTEIN, D. (1987) Plasmid construction by homologous recombination in yeast. Gene, 58(2-3), 201-216. DOI: 10.1016/0378-1119(87)90376-3
Oldenburg KR, Vo KT, Michaelis S, & Paddon C. (1997) Recombination-mediated PCR-directed plasmid construction in vivo in yeast. Nucleic acids research, 25(2), 451-2. PMID: 9016579
Gibson, D. (2009) Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides. Nucleic Acids Research, 37(20), 6984-6990. DOI: 10.1093/nar/gkp687
- February 24, 2009
- 12:00 AM
- 773 views
Relapse and Leukemic Evolution: tracing back the newcomer
by Francisco Barriga in MolBio Research Highlights
During the last decade, the improvement of our understanding of the molecular basis of cancer has led to better diagnosis and prognosis for several types of cancer of the hematopoietic system or leukemias, as exemplified by the development of Gleevec (the commercial name of Imatinib), a drug successfully used in the treatment of acute myeloid leukemia (AML). Despite these and several other... Read more »
C. G. Mullighan, L. A. Phillips, X. Su, J. Ma, C. B. Miller, S. A. Shurtleff, & J. R. Downing. (2008) Genomic Analysis of the Clonal Origins of Relapsed Acute Lymphoblastic Leukemia. Science, 322(5906), 1377-1380. DOI: 10.1126/science.1164266
- December 21, 2009
- 04:02 PM
- 772 views
“Chameleon sequences’’, “surveying the human microbiota” and more, in my picks of the week from RB
by Alejandro Montenegro-Montero in MolBio Research Highlights
Another week has gone by and some very interesting molbio blog posts have been aggregated to Researchblogging.org. Every week [see my opening post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used], briefly describe them and list them here for you to check out.Note that I'm ... Read more »
Pleasance, E., Stephens, P., O’Meara, S., McBride, D., Meynert, A., Jones, D., Lin, M., Beare, D., Lau, K., Greenman, C.... (2009) A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature. DOI: 10.1038/nature08629
Alexander, P., He, Y., Chen, Y., Orban, J., & Bryan, P. (2009) From the Cover: A minimal sequence code for switching protein structure and function. Proceedings of the National Academy of Sciences, 106(50), 21149-21154. DOI: 10.1073/pnas.0906408106
Costello, E., Lauber, C., Hamady, M., Fierer, N., Gordon, J., & Knight, R. (2009) Bacterial Community Variation in Human Body Habitats Across Space and Time. Science, 326(5960), 1694-1697. DOI: 10.1126/science.1177486
- October 12, 2009
- 10:32 AM
- 754 views
Omics-dominated issue! Genomics, metagenomics, reactomics and more, in my picks of the week from RB
by Alejandro Montenegro-Montero in MolBio Research Highlights
Another week has gone by and some very interesting molbio blog posts have been aggregated to Researchblogging.org. Every week [see my inaugural post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used], briefly describe them and list them here for you to check out.Note that ... Read more »
Quince, C., Lanzén, A., Curtis, T., Davenport, R., Hall, N., Head, I., Read, L., & Sloan, W. (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nature Methods, 6(9), 639-641. DOI: 10.1038/nmeth.1361
Tan CS, Pasculescu A, Lim WA, Pawson T, Bader GD, & Linding R. (2009) Positive selection of tyrosine loss in metazoan evolution. Science (New York, N.Y.), 325(5948), 1686-8. PMID: 19589966
Beloqui, A., Guazzaroni, M., Pazos, F., Vieites, J., Godoy, M., Golyshina, O., Chernikova, T., Waliczek, A., Silva-Rocha, R., Al-ramahi, Y.... (2009) Reactome Array: Forging a Link Between Metabolome and Genome. Science, 326(5950), 252-257. DOI: 10.1126/science.1174094
Shah, S., Morin, R., Khattra, J., Prentice, L., Pugh, T., Burleigh, A., Delaney, A., Gelmon, K., Guliany, R., Senz, J.... (2009) Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature, 461(7265), 809-813. DOI: 10.1038/nature08489
- February 17, 2010
- 08:33 AM
- 750 views
The Almighty Fungi: The Revolutionary Neurospora crassa
by Alejandro Montenegro-Montero in MolBio Research Highlights
On January 11 2010, a new series of blog posts was born over at Benchfly: BenchFly’s Model Organism Week. The idea was to invite fellow science bloggers to discuss and present some of the many model organism used in biology to the rest of the science blogosphere.In that post, a poll was displayed asking people´s model organism of choice, and offered the following alternatives:* Mice* Flies* Rats*... Read more »
Perkins DD. (1992) Neurospora: the organism behind the molecular revolution. Genetics, 130(4), 687-701. PMID: 1582553
- September 17, 2009
- 09:54 PM
- 735 views
Ninja viruses, a (free) radical take on aging and more in my picks of the week from RB
by Alejandro Montenegro-Montero in MolBio Research Highlights
Another week has gone by and some very interesting molbio blog posts have been aggregated into Researchblogging.org. Every week [see my inaugural post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used], briefly describe them and list them here for you to check out.Note that... Read more »
Moltedo, B., Lopez, C., Pazos, M., Becker, M., Hermesh, T., & Moran, T. (2009) Cutting Edge: Stealth Influenza Virus Replication Precedes the Initiation of Adaptive Immunity. The Journal of Immunology, 183(6), 3569-3573. DOI: 10.4049/jimmunol.0900091
Lapointe, J., & Hekimi, S. (2009) When a theory of aging ages badly. Cellular and Molecular Life Sciences. DOI: 10.1007/s00018-009-0138-8
Gupta, P., Onder, T., Jiang, G., Tao, K., Kuperwasser, C., Weinberg, R., & Lander, E. (2009) Identification of Selective Inhibitors of Cancer Stem Cells by High-Throughput Screening. Cell, 138(4), 645-659. DOI: 10.1016/j.cell.2009.06.034
- April 5, 2010
- 10:09 AM
- 686 views
Matryoshka dolls in biology, the connection between flowers, stem cells and fat and more, in my Picks of the Week from RB
by Alejandro Montenegro-Montero in MolBio Research Highlights
Another week has gone by and some very interesting molbio blog posts have been aggregated to Researchblogging.org. Every week [see my opening post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used], briefly describe them and list them here for you to check out.Note that I'm ... Read more »
Craddock, N., Hurles, M., Cardin, N., Pearson, R., Plagnol, V., Robson, S., Vukcevic, D., Barnes, C., Conrad, D., Giannoulatou, E.... (2010) Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature, 464(7289), 713-720. DOI: 10.1038/nature08979
Cleveland, L., & Grimstone, A. (1964) The Fine Structure of the Flagellate Mixotricha paradoxa and Its Associated Micro-Organisms. Proceedings of the Royal Society of London. Series B, Biological Sciences (1934-1990), 159(977), 668-686. DOI: 10.1098/rspb.1964.0025
Koretke KK, Lupas AN, Warren PV, Rosenberg M, & Brown JR. (2000) Evolution of two-component signal transduction. Molecular biology and evolution, 17(12), 1956-70. PMID: 11110912
Zhang, Q., Raoof, M., Chen, Y., Sumi, Y., Sursal, T., Junger, W., Brohi, K., Itagaki, K., & Hauser, C. (2010) Circulating mitochondrial DAMPs cause inflammatory responses to injury. Nature, 464(7285), 104-107. DOI: 10.1038/nature08780
Kilian, K., Bugarija, B., Lahn, B., & Mrksich, M. (2010) Geometric cues for directing the differentiation of mesenchymal stem cells. Proceedings of the National Academy of Sciences, 107(11), 4872-4877. DOI: 10.1073/pnas.0903269107
- November 30, 2009
- 08:13 AM
- 634 views
“Bacterial Fortresses” and “gene-trafficking phages”, in my picks of the week from RB
by Alejandro Montenegro-Montero in MolBio Research Highlights
Another week has gone by and some very interesting molbio blog posts have been aggregated to Researchblogging.org. Every week [see my opening post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used], briefly describe them and list them here for you to check out.Note that I'm ... Read more »
Alhede M, Bjarnsholt T, Jensen PØ, Phipps RK, Moser C, Christophersen L, Christensen LD, van Gennip M, Parsek M, Høiby N.... (2009) Pseudomonas aeruginosa recognizes and responds aggressively to the presence of polymorphonuclear leukocytes. Microbiology (Reading, England), 155(Pt 11), 3500-8. PMID: 19643762
Sharon, I., Alperovitch, A., Rohwer, F., Haynes, M., Glaser, F., Atamna-Ismaeel, N., Pinter, R., Partensky, F., Koonin, E., Wolf, Y.... (2009) Photosystem I gene cassettes are present in marine virus genomes. Nature, 461(7261), 258-262. DOI: 10.1038/nature08284
- September 3, 2009
- 11:52 AM
- 629 views
Viral reassortment, genome transplantation and more in my picks of the week from RB
by Alejandro Montenegro-Montero in MolBio Research Highlights
Another week has gone by and some very interesting blog posts have been aggregated into Researchblogging.org. Every week [see my inaugural post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used] and list them here for you to check out.This week, three blog posts made the cut:... Read more »
Ghedin, E., Fitch, A., Boyne, A., Griesemer, S., DePasse, J., Bera, J., Zhang, X., Halpin, R., Smit, M., Jennings, L.... (2009) Mixed Infection and the Genesis of Influenza Virus Diversity. Journal of Virology, 83(17), 8832-8841. DOI: 10.1128/JVI.00773-09
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. DOI: 10.1126/science.1173759
Castellano, L., Giamas, G., Jacob, J., Coombes, R., Lucchesi, W., Thiruchelvam, P., Barton, G., Jiao, L., Wait, R., Waxman, J.... (2009) The estrogen receptor- -induced microRNA signature regulates itself and its transcriptional response. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0906947106
- September 24, 2009
- 12:08 PM
- 608 views
No T-cell left behind, an explanation to why we sleep and more in my picks of the week from RB
by Alejandro Montenegro-Montero in MolBio Research Highlights
Another week has gone by and some very interesting molbio blog posts have been aggregated into Researchblogging.org. Every week [see my inaugural post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used], briefly describe them and list them here for you to check out.Note that ... Read more »
van Heijst, J., Gerlach, C., Swart, E., Sie, D., Nunes-Alves, C., Kerkhoven, R., Arens, R., Correia-Neves, M., Schepers, K., & Schumacher, T. (2009) Recruitment of Antigen-Specific CD8 T Cells in Response to Infection Is Markedly Efficient. Science, 325(5945), 1265-1269. DOI: 10.1126/science.1175455
Ascher, M., Sheppard, H., Jr, W., & Vittinghoff, E. (1993) Does drug use cause AIDS?. Nature, 362(6416), 103-104. DOI: 10.1038/362103a0
Nattrass, N. (2008) AIDS and the Scientific Governance of Medicine in Post-Apartheid South Africa. African Affairs, 107(427), 157-176. DOI: 10.1093/afraf/adm087
Siegel, J. (2009) Sleep viewed as a state of adaptive inactivity. Nature Reviews Neuroscience, 10(10), 747-753. DOI: 10.1038/nrn2697
- March 22, 2010
- 09:06 AM
- 605 views
Dominant transposases, becoming famous for your lab mistakes and more, in my Picks of the Week from RB.
by Alejandro Montenegro-Montero in MolBio Research Highlights
Another week has gone by and some very interesting molbio blog posts have been aggregated to Researchblogging.org. Every week [see my opening post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used], briefly describe them and list them here for you to check out.Note that I'm ... Read more »
Aziz RK, Breitbart M, & Edwards RA. (2010) Transposases are the most abundant, most ubiquitous genes in nature. Nucleic acids research. PMID: 20215432
Christodoulou, F., Raible, F., Tomer, R., Simakov, O., Trachana, K., Klaus, S., Snyman, H., Hannon, G., Bork, P., & Arendt, D. (2010) Ancient animal microRNAs and the evolution of tissue identity. Nature, 463(7284), 1084-1088. DOI: 10.1038/nature08744
- November 16, 2009
- 11:02 AM
- 597 views
Bacterial signaling and studying diseases through exome sequencing, in my picks of the week from RB
by Alejandro Montenegro-Montero in MolBio Research Highlights
Another week has gone by and some very interesting molbio blog posts have been aggregated to Researchblogging.org. Every week [see my opening post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used], briefly describe them and list them here for you to check out.Note that I'm ... Read more »
Galperin MY. (2005) A census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial IQ, extroverts and introverts. BMC microbiology, 35. PMID: 15955239
Ng, S., Buckingham, K., Lee, C., Bigham, A., Tabor, H., Dent, K., Huff, C., Shannon, P., Jabs, E., Nickerson, D.... (2009) Exome sequencing identifies the cause of a mendelian disorder. Nature Genetics. DOI: 10.1038/ng.499
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