42 posts · 34,312 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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- November 8, 2010
- 09:59 AM
- 508 views
Oh, so I guess they just couldn't do the experiment again...
by Alejandro Montenegro-Montero in MolBio Research Highlights
In 20051, the Liu lab described a new central element in the Neurospora circadian clock. They found that an RNA helicase with similarity to the yeast exosome cofactor Dob1p/Mtr4p, associated with FRQ, a core clock component essential for circadian clock function in this fungus (it was termed FRH, for "FRQ-interacting RNA helicase"). Their evidence suggested that FRH played an important role in ... Read more »
Cheng P, He Q, He Q, Wang L, & Liu Y. (2005) Regulation of the Neurospora circadian clock by an RNA helicase. Genes , 19(2), 234-41. PMID: 15625191
- August 2, 2010
- 02:25 PM
- 812 views
The MolBio Carnival: the first edition
by Alejandro Montenegro-Montero in MolBio Research Highlights
I’m pleased to host the very first edition of the MolBio Carnival, your monthly roundup of interesting posts in molecular biology from the science blogosphere. There has been a great response to this initiative and I had a great time reviewing submissions and writing this post.
You can read all about this Carnival here (submission guidelines, scope, etc), but right now, let’s get down to ... Read more »
Niethammer, P., Grabher, C., Look, A., & Mitchison, T. (2009) A tissue-scale gradient of hydrogen peroxide mediates rapid wound detection in zebrafish. Nature, 459(7249), 996-999. DOI: 10.1038/nature08119
Quyn, A., Appleton, P., Carey, F., Steele, R., Barker, N., Clevers, H., Ridgway, R., Sansom, O., & Näthke, I. (2010) Spindle Orientation Bias in Gut Epithelial Stem Cell Compartments Is Lost in Precancerous Tissue. Cell Stem Cell, 6(2), 175-181. DOI: 10.1016/j.stem.2009.12.007
van Bakel H, Nislow C, Blencowe BJ, & Hughes TR. (2010) Most "dark matter" transcripts are associated with known genes. PLoS biology, 8(5). PMID: 20502517
Altschuler, S., & Wu, L. (2010) Cellular Heterogeneity: Do Differences Make a Difference?. Cell, 141(4), 559-563. DOI: 10.1016/j.cell.2010.04.033
- July 19, 2010
- 04:13 PM
- 815 views
[Direct Connection] Sweet and Sour: Glucose-6-Phosphate, Anoxia, and Enzyme Regulation
by Alejandro Montenegro-Montero in MolBio Research Highlights
The “Direct Connection” section of MolBio Research Highlights includes blog posts discussing primary research articles in the field, but the interesting thing about it is that these posts are written by the authors themselves. This allows them to discuss the background, results and implications of their work with a wider audience and in a more relaxed format. Further, as it provides a direct link... Read more »
Dieni CA, & Storey KB. (2010) Regulation of glucose-6-phosphate dehydrogenase by reversible phosphorylation in liver of a freeze tolerant frog. Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology. PMID: 20532891
- June 28, 2010
- 02:32 PM
- 675 views
A clever genetic strategy for the study of circadian output pathways
by Alejandro Montenegro-Montero in MolBio Research Highlights
Circadian clocks control a large number of daily processes in most organisms. These endogenous cellular timekeepers regulate rhythms in gene expression, physiology and behaviour and enable organisms to anticipate predictable environmental variations.
Circadian clocks are composed of a central oscillator and two signaling pathways: input pathways convey external signals to the oscillator, so ... Read more »
Vitalini MW, Morgan LW, March IJ, & Bell-Pedersen D. (2004) A genetic selection for circadian output pathway mutations in Neurospora crassa. Genetics, 167(1), 119-29. PMID: 15166141
- April 5, 2010
- 10:09 AM
- 1,007 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
- March 22, 2010
- 09:06 AM
- 852 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
- March 15, 2010
- 09:23 AM
- 1,187 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
- March 8, 2010
- 08:53 AM
- 699 views
Non-inherited antibiotic resistance, jumping viruses 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 »
Balaban NQ, Merrin J, Chait R, Kowalik L, & Leibler S. (2004) Bacterial persistence as a phenotypic switch. Science (New York, N.Y.), 305(5690), 1622-5. PMID: 15308767
Jancovich, J., Bremont, M., Touchman, J., & Jacobs, B. (2009) Evidence for Multiple Recent Host Species Shifts among the Ranaviruses (Family Iridoviridae). Journal of Virology, 84(6), 2636-2647. DOI: 10.1128/JVI.01991-09
Gross J, & Bhattacharya D. (2009) Revaluating the evolution of the Toc and Tic protein translocons. Trends in plant science, 14(1), 13-20. PMID: 19042148
- March 2, 2010
- 10:19 AM
- 592 views
Molecular machines and memorable African genomes 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 »
Clements, A., Bursac, D., Gatsos, X., Perry, A., Civciristov, S., Celik, N., Likic, V., Poggio, S., Jacobs-Wagner, C., Strugnell, R.... (2009) The reducible complexity of a mitochondrial molecular machine. Proceedings of the National Academy of Sciences, 106(37), 15791-15795. DOI: 10.1073/pnas.0908264106
Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J.... (2010) Complete Khoisan and Bantu genomes from southern Africa. Nature, 463(7283), 943-7. PMID: 20164927
- February 17, 2010
- 08:33 AM
- 976 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
- February 1, 2010
- 08:18 AM
- 720 views
GWAS under attack?, historical evolutionary constraints, and a lot 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.This week's ... Read more »
Durrant, J., Amaro, R., Xie, L., Urbaniak, M., Ferguson, M., Haapalainen, A., Chen, Z., Di Guilmi, A., Wunder, F., Bourne, P.... (2010) A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology. PLoS Computational Biology, 6(1). DOI: 10.1371/journal.pcbi.1000648
Falkowski PG. (2006) Evolution. Tracing oxygen's imprint on earth's metabolic evolution. Science (New York, N.Y.), 311(5768), 1724-5. PMID: 16556831
KEELING, P., BURGER, G., DURNFORD, D., LANG, B., LEE, R., PEARLMAN, R., ROGER, A., & GRAY, M. (2005) The tree of eukaryotes. Trends in Ecology , 20(12), 670-676. DOI: 10.1016/j.tree.2005.09.005
Milinkovitch, M., Helaers, R., & Tzika, A. (2009) Historical Constraints on Vertebrate Genome Evolution. Genome Biology and Evolution, 13-18. DOI: 10.1093/gbe/evp052
Dickson, S., Wang, K., Krantz, I., Hakonarson, H., & Goldstein, D. (2010) Rare Variants Create Synthetic Genome-Wide Associations. PLoS Biology, 8(1). DOI: 10.1371/journal.pbio.1000294
- January 18, 2010
- 09:02 AM
- 705 views
Protein dancing partners, yeast as our allies, 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 »
Brückner A, Polge C, Lentze N, Auerbach D, & Schlattner U. (2009) Yeast two-hybrid, a powerful tool for systems biology. International journal of molecular sciences, 10(6), 2763-88. PMID: 19582228
Hughes, J., Skaletsky, H., Pyntikova, T., Graves, T., van Daalen, S., Minx, P., Fulton, R., McGrath, S., Locke, D., Friedman, C.... (2010) Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Nature. DOI: 10.1038/nature08700
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
- January 13, 2010
- 03:36 PM
- 761 views
Fourth time is the charm: the quest for the final plasmid
by Alejandro Montenegro-Montero in MolBio Research Highlights
In a previous post, I highlighted the wonders of using yeast recombinational cloning (YRC) as an alternative to “classic” cloning, particularly when under a high-throughput approach [See An alternative cloning strategy: yeast recombinational cloning].Just to refresh your memory, and in a nutshell, the idea is to co-transform the DNA segment to be cloned into yeast along with the linearized target... Read more »
Sobanski, M., & Dickinson, J. (1995) A simple method for the direct extraction of plasmid DNA from yeast. Biotechnology Techniques, 9(3), 225-230. DOI: 10.1007/BF00157083
Ward AC. (1990) Single-step purification of shuttle vectors from yeast for high frequency back-transformation into E. coli. Nucleic acids research, 18(17), 5319. PMID: 2205843
Robzyk K, & Kassir Y. (1992) A simple and highly efficient procedure for rescuing autonomous plasmids from yeast. Nucleic acids research, 20(14), 3790. PMID: 1641351
- January 12, 2010
- 07:11 AM
- 657 views
Hybrid sterility in fruit flies, regulating the mammalian circadian clock 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 »
Bayes, J., & Malik, H. (2009) Altered Heterochromatin Binding by a Hybrid Sterility Protein in Drosophila Sibling Species. Science, 326(5959), 1538-1541. DOI: 10.1126/science.1181756
Sahar, S., Zocchi, L., Kinoshita, C., Borrelli, E., & Sassone-Corsi, P. (2010) Regulation of BMAL1 Protein Stability and Circadian Function by GSK3β-Mediated Phosphorylation. PLoS ONE, 5(1). DOI: 10.1371/journal.pone.0008561
Bonetta, L. (2009) Should You Be Tweeting?. Cell, 139(3), 452-453. DOI: 10.1016/j.cell.2009.10.017
- December 27, 2009
- 10:34 PM
- 719 views
“Filling the gaps in the tree of life” and “Stochasticity in gene expression” 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 »
Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N., Kunin, V., Goodwin, L., Wu, M., Tindall, B.... (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature, 462(7276), 1056-1060. DOI: 10.1038/nature08656
Maamar H, Raj A, & Dubnau D. (2007) Noise in gene expression determines cell fate in Bacillus subtilis. Science (New York, N.Y.), 317(5837), 526-9. PMID: 17569828
- December 21, 2009
- 04:02 PM
- 971 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
- December 14, 2009
- 12:11 PM
- 695 views
"A tale of two membranes", "follow the (Spliced) Leader" 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 »
Gusarov I, Shatalin K, Starodubtseva M, & Nudler E. (2009) Endogenous nitric oxide protects bacteria against a wide spectrum of antibiotics. Science (New York, N.Y.), 325(5946), 1380-4. PMID: 19745150
Cavalier-Smith T. (2006) Rooting the tree of life by transition analyses. Biology direct, 19. PMID: 16834776
Douris V, Telford MJ, & Averof M. (2009) Evidence for multiple independent origins of trans-splicing in Metazoa. Molecular biology and evolution. PMID: 19942614
- December 7, 2009
- 10:07 AM
- 706 views
"Moving through mucus", "quick death-tagging" 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 »
Celli, J., Turner, B., Afdhal, N., Keates, S., Ghiran, I., Kelly, C., Ewoldt, R., McKinley, G., So, P., Erramilli, S.... (2009) Helicobacter pylori moves through mucus by reducing mucin viscoelasticity. Proceedings of the National Academy of Sciences, 106(34), 14321-14326. DOI: 10.1073/pnas.0903438106
Pierce, N., Kleiger, G., Shan, S., & Deshaies, R. (2009) Detection of sequential polyubiquitylation on a millisecond timescale. Nature, 462(7273), 615-619. DOI: 10.1038/nature08595
Benard G, & Karbowski M. (2009) Mitochondrial fusion and division: Regulation and role in cell viability. Seminars in cell , 20(3), 365-74. PMID: 19530306
- December 2, 2009
- 09:21 PM
- 1,114 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
- November 30, 2009
- 08:13 AM
- 790 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
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