Habib Maroon

57 posts · 26,089 views

Biobabel
57 posts

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  • January 22, 2013
  • 01:06 PM
  • 291 views

Supergenes, Sociality, and Sex Chromosomes

by Habib Maroon in Biobabel

A new paper in Nature shows that the social structure of fire ant colonies is determined by a ‘supergene’ – a single non-recombining cluster of hundreds of genes. The supergene makes up more than 50% of a pair of divergent … Continue reading →... Read more »

Wang, J., Wurm, Y., Nipitwattanaphon, M., Riba-Grognuz, O., Huang, Y., Shoemaker, D., & Keller, L. (2013) A Y-like social chromosome causes alternative colony organization in fire ants. Nature. DOI: 10.1038/nature11832  

  • December 11, 2012
  • 07:52 PM
  • 299 views

The Transposon/piRNA/Chromatin Nexus

by Habib Maroon in Biobabel

Close observation of chromatin states at piRNA-silenced genomic loci demonstrates the power of transposons to change native gene expression. As reviewed in an earlier post, the Drosophila Piwi/piRNA transposon silencing pathway can be divided into two facets; a complex pathway … Continue reading →... Read more »

  • December 6, 2012
  • 02:39 PM
  • 299 views

Breaking Neuronal Symmetry by Chromatin Memories

by Habib Maroon in Biobabel

The asymmetric fates of two bilaterally symmetrical neurons are determined by a two-step activation program at a miRNA locus. Very low levels of transcription ‘prime’ the locus many cell generations before the final fate determination is imposed by a bilateral … Continue reading →... Read more »

  • November 23, 2012
  • 07:52 PM
  • 335 views

The Heterodox Dinokaryon

by Habib Maroon in Biobabel

The nuclei of dinoflagellates display a highly derived organisation; chromosomes are permanently condensed and seem to lack histone proteins. A new study in Current Biology links the emergence of these characters to the importation of a novel family of nuclear … Continue reading →... Read more »

  • November 11, 2012
  • 10:08 AM
  • 306 views

Uploading piRNAs to the Cloud.

by Habib Maroon in Biobabel

A new paper finds a protein linking piRNA transcription with processing in nuage. The Piwi/piRNA system is responsible for protecting the germline from the mutagenic effects of transposon mobilisation. As summarised in an earlier post, in Drosophila large arrays of … Continue reading →... Read more »

  • November 3, 2012
  • 12:45 PM
  • 307 views

A chimeric fusion of RNA and DNA viruses.

by Habib Maroon in Biobabel

The discovery of a new family of viruses leads to speculations on possible modes recombination between RNA and DNA viruses. The virosphere can be divided into three major classes; viruses with DNA genomes, retroviruses that reverse-transcribe their RNA genome into … Continue reading →... Read more »

  • October 25, 2012
  • 11:07 AM
  • 359 views

Beating a Toxin-Antitoxin System; Evading Suicide

by Habib Maroon in Biobabel

Bacteria have evolved many different systems to evade viral predation. One strategy, abortive infection (Abi), involves altruistic suicide. Mediated by a toxin-antitoxin (TA) system, the suicide of the infected cell protects the clonal bacterial population by preventing the spread of … Continue reading →... Read more »

  • October 23, 2012
  • 06:37 PM
  • 323 views

Barcoding the Brain

by Habib Maroon in Biobabel

A new DNA-sequencing based idea for mapping the connectome is presented in Plos biology. The defining purpose of neurons is information transmission and processing within a network. Hence, to appreciate neural function we must look at the interactions between neurons; … Continue reading →... Read more »

Zador, A.M., Dubnau, J., Oyibo, H.K., Zhan, H., Cao, G.,Peikon, I.D. (2012) Sequencing the Connectome. Plos Biology, 10(10). info:/10.1371/journal.pbio.1001411

  • October 2, 2012
  • 03:09 PM
  • 299 views

Opening up the RNA-chromatin network

by Habib Maroon in Biobabel

In eukaryotic nuclei, DNA is coiled around histone proteins to form nucleosomes. The pattern by which nucleosomes are compacted into higher-order structures determines the accessibility of chromatin and hence it’s transcriptional activity. Many different factors, including the linker histone H1, … Continue reading →... Read more »

Schubert T, Pusch MC, Diermeier S, Benes V, Kremmer E, Imhof A, & Längst G. (2012) Df31 Protein and snoRNAs Maintain Accessible Higher-Order Structures of Chromatin. Molecular cell. PMID: 23022379  

Filion GJ, van Bemmel JG, Braunschweig U, Talhout W, Kind J, Ward LD, Brugman W, de Castro IJ, Kerkhoven RM, Bussemaker HJ.... (2010) Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell, 143(2), 212-24. PMID: 20888037  

  • September 26, 2012
  • 08:42 AM
  • 314 views

The CSR-1 siRNA pathway gets more enigmatic

by Habib Maroon in Biobabel

A recent paper forces a reappraisal of the role of CSR-1 its associated 22G-RNAs, and demonstrates a positive regulatory role for this RNAi pathway in C. elegans. As described in a previous post, depletion of the Argonaute protein CSR-1, or … Continue reading →... Read more »

Claycomb JM, Batista PJ, Pang KM, Gu W, Vasale JJ, van Wolfswinkel JC, Chaves DA, Shirayama M, Mitani S, Ketting RF.... (2009) The Argonaute CSR-1 and its 22G-RNA cofactors are required for holocentric chromosome segregation. Cell, 139(1), 123-34. PMID: 19804758  

  • September 24, 2012
  • 11:34 AM
  • 341 views

Chromosomal Flip-Flop

by Habib Maroon in Biobabel

A study describes how phenotypic switching in Staphylococcus aureus is caused by a reversible large-scale genomic inversion. Clonal bacterial populations often display various phenotypes. This diversity is most obviously identifiable as colony variation. Many different bacterial genera display ‘small colony … Continue reading →... Read more »

Cui L, Neoh HM, Iwamoto A, & Hiramatsu K. (2012) Coordinated phenotype switching with large-scale chromosome flip-flop inversion observed in bacteria. Proceedings of the National Academy of Sciences of the United States of America, 109(25). PMID: 22645353  

  • September 20, 2012
  • 11:29 AM
  • 289 views

Expanding the Conjugative Realm

by Habib Maroon in Biobabel

A recent paper demonstrates that a broader range of plasmids can be transferred by conjugation than previously thought. Integrative and conjugative elements (ICEs, aka conjugative transposons) are a variety of bacterial mobile element generally found integrated into the host genome, … Continue reading →... Read more »

  • September 18, 2012
  • 07:12 PM
  • 321 views

Epigenetic Licensing of a Sex Determination Gene

by Habib Maroon in Biobabel

A recent series of papers describing interacting small RNA pathways in C. elegans, posited the existence of an anti-silencing pathway responsible for licensing the expression of germline transcripts. Johnson and Spence (Science. 2011) published the first paper suggesting such a … Continue reading →... Read more »

  • September 6, 2012
  • 06:40 AM
  • 386 views

Trans-Extremophile Para-Sex

by Habib Maroon in Biobabel

More than twenty years ago, an extra-ordinary mode of para-sexual genetic exchange was found to occur between cells of the halophilic archaeon Haloferax volcanii, an extremophile isolated from the Dead Sea. This process involves first, cell fusion producing heterodiploid cells. … Continue reading →... Read more »

  • August 31, 2012
  • 01:52 PM
  • 393 views

Genomic Rearrangement in Lampreys 2

by Habib Maroon in Biobabel

As discussed in a recent post, during lamprey embryogenesis programmed genomic rearrangements lead to deletion of ~20% of the germline genome in the soma. Smith, Amemiya and co-workers have now published a follow-up study in which they further characterise the … Continue reading →... Read more »

Smith JJ, Baker C, Eichler EE, & Amemiya CT. (2012) Genetic consequences of programmed genome rearrangement. Current biology : CB, 22(16), 1524-9. PMID: 22818913  

  • August 26, 2012
  • 11:33 AM
  • 666 views

Upstream ORFs and Regulation of Translation

by Habib Maroon in Biobabel

Protein expression can be rapidly and responsively regulated at the level of translation. Translational regulation commonly involves trans-acting factors such as miRNA complexes or RNA-binding proteins, specifically binding cis-regulatory sequences. A study from last year – Medenbach et al. – … Continue reading →... Read more »

  • August 19, 2012
  • 04:42 PM
  • 344 views

Interacting small RNA pathways in worms 5: Global Genome Surveillance

by Habib Maroon in Biobabel

As discussed previously, in C. elegans more than 15,000 21U-RNAs are expressed from two large clusters on chromosome IV. As very few of these piRNAs exhibit perfect sequence complementarity with other endogenous sequences within in the C. elegans genome, it’s … Continue reading →... Read more »

Bagijn MP, Goldstein LD, Sapetschnig A, Weick EM, Bouasker S, Lehrbach NJ, Simard MJ, & Miska EA. (2012) Function, targets, and evolution of Caenorhabditis elegans piRNAs. Science (New York, N.Y.), 337(6094), 574-8. PMID: 22700655  

Ashe A, Sapetschnig A, Weick EM, Mitchell J, Bagijn MP, Cording AC, Doebley AL, Goldstein LD, Lehrbach NJ, Le Pen J.... (2012) piRNAs Can Trigger a Multigenerational Epigenetic Memory in the Germline of C. elegans. Cell, 150(1), 88-99. PMID: 22738725  

Shirayama M, Seth M, Lee HC, Gu W, Ishidate T, Conte D Jr, & Mello CC. (2012) piRNAs Initiate an Epigenetic Memory of Nonself RNA in the C. elegans Germline. Cell, 150(1), 65-77. PMID: 22738726  

  • August 2, 2012
  • 01:40 PM
  • 345 views

Interacting small RNAs in worms 4: 21U-RNAs.

by Habib Maroon in Biobabel

A survey of C. elegans small RNAs from 2006 (Ruby et al) first reported the discovery of a large class of 21nt RNAs with 5’ uridines – 21U-RNAs. The majority of these RNAs mapped to two distinct regions of the … Continue reading →... Read more »

  • August 2, 2012
  • 01:40 PM
  • 281 views

Interacting small RNA pathways in worms 4: 21U-RNAs.

by Habib Maroon in Biobabel

A survey of C. elegans small RNAs from 2006 (Ruby et al) first reported the discovery of a large class of 21nt RNAs with 5’ uridines – 21U-RNAs. The majority of these RNAs mapped to two distinct regions of the … Continue reading →... Read more »

  • July 26, 2012
  • 05:51 PM
  • 416 views

Interacting small RNA pathways in worms 3: CSR-1 associated 22G-RNAs

by Habib Maroon in Biobabel

During mitosis, duplicated chromosomes are separated and segregated into two daughter cells. This is achieved by the action of spindle microtubules. In metaphase, microtubules radiating from centrosomes at two poles in the cell, attach to the condensed chromosomes at proteinaceous … Continue reading →... Read more »

Claycomb JM, Batista PJ, Pang KM, Gu W, Vasale JJ, van Wolfswinkel JC, Chaves DA, Shirayama M, Mitani S, Ketting RF.... (2009) The Argonaute CSR-1 and its 22G-RNA cofactors are required for holocentric chromosome segregation. Cell, 139(1), 123-34. PMID: 19804758  

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