Historical and Philosophical Perspectives on Contemporary Biology
Keller EF
Evelyn Fox Keller introduces a new series that aims to promote productive dialogue between laboratory researchers and historians and philosophers of science to address the challenges arising from the rapid pace of biological discovery.
doi:10.1371/journal.pbio.0060321
Synopses
Lessons on Life from SENP2
Sedwick C
doi:10.1371/journal.pbio.0060312
Loopy Chromatin Brings Distant DNA to Bear on Silencing Promoter Genes
Hoff M
doi:10.1371/journal.pbio.0060313
Gal4 Gets Genes to Loosen Up
Sedwick C
doi:10.1371/journal.pbio.1000006
Essay
Towards an Integrated Framework for Assessing the Vulnerability of Species to Climate Change
Williams SE, Shoo LP, Isaac JL, Hoffmann AA, Langham G
Climate change is a major threat to global biodiversity. A novel integrated framework to assess vulnerability and prioritize research and management action aims to improve our ability to respond to this emerging crisis.
doi:10.1371/journal.pbio.0060325
Historical and Philosophical Perspectives
“It's Ok, We're Not Cousins by Blood”: The Cousin Marriage Controversy in Historical Perspective
Paul DB, Spencer HG
Marriage between first cousins is highly stigmatized in the West and, indeed, is illegal in 31 US states. But is the hostility to such marriage scientifically well-grounded?
doi:10.1371/journal.pbio.0060320
Primers
The Role of Auxin Transport in Plant Patterning Mechanisms
Smith RS
In plants, many patterning processes involve the phytohormone auxin, and controlling how it moves around plays a critical role in pattern formation.
Research Article: Root System Architecture from Coupling Cell Shape to Auxin Transport
doi:10.1371/journal.pbio.0060323
Caenorhabditis elegans Meets Microsporidia: The Nematode Killers from Paris
Hodgkin J, Partridge FA
A newly discovered species of Microsporidia, which are obligate intracellular parasitic fungi, has been found able to infect the intestinal cells of the nematode C. elegans and subvert their cytoskeletal architecture.
Research Article: Microsporidia Are Natural Intracellular Parasites of the Nematode Caenorhabditis elegans
doi:10.1371/journal.pbio.1000005
Animal Defenses against Infectious Agents: Is Damage Control More Important Than Pathogen Control
Read AF, Graham AL, Råberg L
The ability of hosts to withstand a given number of pathogens is a critical component of health. Now playing catch-up with plant biologists, animal biologists are starting to formally separate this form of defense from classical resistance.
Research Article: A Signaling Protease Required for Melanization in Drosophila Affects Resistance and Tolerance of Infections
doi:10.1371/journal.pbio.1000004
Research Articles
Mutualistic Interactions Drive Ecological Niche Convergence in a Diverse Butterfly Community
Elias M, Gompert Z, Jiggins C, Willmott K
Müllerian mimicry, a classic mutualism, is associated with microhabitat convergence in tropical butterflies, outweighing both common ancestry and competition. Positive interactions may thus be more important in community assembly than commonly assumed.
Author Summary
doi:10.1371/journal.pbio.0060300
The Worldwide Variation in Avian Clutch Size across Species and Space
Jetz W, Sekercioglu CH, Böhning-Gaese K
Why do some bird species lay only one egg in their nest, and others ten? An analysis combining comparative and macroecological approaches across more than half of all bird species explains the global variation in this trait with high confidence.
Author Summary
doi:10.1371/journal.pbio.0060303
High Functional Diversity in Mycobacterium tuberculosis Driven by Genetic Drift and Human Demography
Hershberg R, Lipatov M, Small PM, Sheffer H, Niemann S, et al.
DNA sequence analysis of a global collection of M. tuberculosis strains reveals high functional diversity, severely reduced selective constraint, and global spread through both ancient and recent human migrations.
Author Summary
doi:10.1371/journal.pbio.0060311
Timing Precision in Population Coding of Natural Scenes in the Early Visual System
Desbordes G, Jin J, Weng C, Lesica NA, Stanley GB, et al.
Early neural representation of visual scenes occurs with a temporal precision on the order of 10 ms, which is precise enough to strongly drive downstream neurons in the visual pathway. Unlike individual neurons, the neural population code is largely insensitive to pronounced changes in visual contrast.
Author Summary
doi:10.1371/journal.pbio.0060324
Identifying Neural Drivers with Functional MRI: An Electrophysiological Validation
David O, Guillemain I, Saillet S, Reyt S, Deransart C, et al.
Neural long-range interactions can be distinguished from hemodynamic confounds in functional magnetic resonance imaging using new data analysis techniques that will allow experimental validation of models of brain function.
Author Summary
doi:10.1371/journal.pbio.0060315
PKMζ Maintains Spatial, Instrumental, and Classically Conditioned Long-Term Memories
Serrano P, Friedman EL, Kenney J, Taubenfeld SM, Zimmerman JM, et al.
The persistent activity of a brain enzyme, PKMζ, stores specific associations, both unpleasant and rewarding, for places, events, and actions, and is thus a general mechanism for memory storage.
Author Summary
doi:10.1371/journal.pbio.0060318
The Maternally Expressed WRKY Transcription Factor TTG2 Controls Lethality in Interploidy Crosses of Arabidopsis
Dilkes BP, Spielman M, Weizbauer R, Watson B, Burkart-Waco D, et al.
Hybrid lethality in crosses between diploids and tetraploids, plants with whole genome duplication, is determined by an epidermal regulator expressed in the maternal tissue that envelops the seed.
Author Summary
doi:10.1371/journal.pbio.0060308
Root System Architecture from Coupling Cell Shape to Auxin Transport
Laskowski M, Grieneisen VA, Hofhuis H, Hove CAt, Hogeweg P, et al.
Experimental data and computer modeling show that lateral root positioning can be controlled by the physical stimulus of root curvature, which triggers self-organizing alterations in auxin transport.
Author Summary
Primer: The Role of Auxin Transport in Plant Patterning Mechanisms
doi:10.1371/journal.pbio.0060307
Microsporidia Are Natural Intracellular Parasites of the Nematode Caenorhabditis elegans
Troemel ER, Félix MA, Whiteman NK, Barrière A, Ausubel FM
A newly identified intracellular pathogen of wild-caught Caenorhabditis elegans represents a new microsporidian species that will provide a model to study this class of pathogen in humans.
Author Summary
Primer: Caenorhabditis elegans Meets Microsporidia: The Nematode Killers from Paris
doi:10.1371/journal.pbio.0060309
The Bacterial Symbiont Wolbachia Induces Resistance to RNA Viral Infections in Drosophila melanogaster
Teixeira L, Ferreira A, Ashburner M
Wolbachia are one of the most widespread intracellular bacteria. In Drosophila melanogaster, the presence of Wolbachia increases resistance to infection by RNA viruses.
Author Summary
doi:10.1371/journal.pbio.1000002
A Signaling Protease Required for Melanization in Drosophila Affects Resistance and Tolerance of Infections
Ayres JS, Schneider DS
It isn't easy to predict how mutations will affect a host's immune response. Mutations that affect the interaction of a fly with one pathogen can increase or decrease resistance or tolerance to other pathogens.
Author Summary
Primer: Animal Defenses against Infectious Agents: Is Damage Control More Important Than Pathogen Control?
doi:10.1371/journal.pbio.0060305
The Communication Factor EDF and the Toxin–Antitoxin Module mazEF Determine the Mode of Action of Antibiotics
Kolodkin-Gal I, Sat B, Keshet A, Kulka HE
The mode of action of certain antibiotics is revealed in a study using different strains of E. coliM, which implicates mazEF-mediated cell death and the formation of reactive oxygen species.
Author Summary
doi:10.1371/journal.pbio.0060319
Twist-2 Controls Myeloid Lineage Development and Function
Sharabi AB, Aldrich M, Sosic D, Olson EN, Friedman AD, et al.
The transcription factor Twist-2 is a new regulator that inhibits the proliferation and differentiation of granulocyte macrophage progenitors. Twist-2 also inhibits proinflammatory cytokine production, while stimulating IL-10 by myeloid cells.
Author Summary
doi:10.1371/journal.pbio.0060316
SUMO-Specific Protease 2 Is Essential for Modulating p53-Mdm2 in Development of Trophoblast Stem Cell Niches and Lineages
Chiu SY, Asai N, Costantini F, Hsu W
Targeted disruption of SUMO-specific protease 2 in mice reveals that SUMO modulation of the p53/Mdm2 pathway is pivotal for G/S transition of mitosis and endoreduplication during trophoblast development.
Author Summary
Synopsis: Lessons on Life from SENP2
doi:10.1371/journal.pbio.0060310
Nutrient-Regulated Antisense and Intragenic RNAs Modulate a Signal Transduction Pathway in Yeast
Nishizawa M, Komai T, Katou Y, Shirahige K, Ito T, et al.
During nutritional adaptation, transcriptional activation in yeast produces noncoding RNAs that allow the formation of a positive-feedback regulatory loop.
Author Summary
doi:10.1371/journal.pbio.0060326
Modeling a Snap-Action, Variable-Delay Switch Controlling Extrinsic Cell Death
Albeck JG, Burke JM, Spencer SL, Lauffenburger DA, Sorger PK
A combination of single-cell experiments and mathematical modeling reveals the mechanisms underlying all-or-none caspase activation during receptor-induced apoptosis.
Author Summary
doi:10.1371/journal.pbio.0060299
Senescence-Associated Secretory Phenotypes Reveal Cell-Nonautonomous Functions of Oncogenic RAS and the p53 Tumor Suppressor
Coppé JP, Patil CK, Rodier F, Sun Y, Muñoz DP, et al.
By controlling how damaged cells modify their surrounding tissue environment, a tumor suppressor gene can restrain, and an oncogene can promote, the development of cancer.
Author Summary
doi:10.1371/journal.pbio.0060301
Tissue-Specific Genetic Control of Splicing: Implications for the Study of Complex Traits
Heinzen EL, Ge D, Cronin KD, Maia JM, Shianna KV, et al.
We investigated tissue-specific genetic control of gene expression and alternative splicing in primary human cells, and we describe here the implications for understanding how genetic variation influences human disease.
Author Summary
doi:10.1371/journal.pbio.1000001
Epigenomic Consequences of Immortalized Plant Cell Suspension Culture
Tanurdzic M, Vaughn MW, Jiang H, Lee TJ, Slotkin RK, et al.
Immortalized plant cells undergo epigenomic changes, reminiscent of immortalized animal cell lines and cancer cells, accompanied by shifts in small RNA classes, implicating a role for the RNAi machinery in regulating the epigenome.
Author Summary
doi:10.1371/journal.pbio.0060302
BEAF Regulates Cell-Cycle Genes through the Controlled Deposition of H3K9 Methylation Marks into Its Conserved Dual-Core Binding Sites
Emberly E, Blattes R, Schuettengruber B, Hennion M, Jiang N, et al.
Chromatin Dual-Cores define new potent nucleosome-associated cis-regulatory elements that regulate the accessibility of promoters of genes controlling chromosome organization/segregation and the cell cycle.
Author Summary
doi:10.1371/journal.pbio.0060327
PcG Proteins, DNA Methylation, and Gene Repression by Chromatin Looping
Tiwari VK, McGarvey KM, Licchesi JD, Ohm JE, Herman JG, et al.
Chromatin regions enriched for Polycomb group proteins physically interact in a series of loops around a single gene in mammalian cells. This higher order structure maintains a poised, low transcription state in embryonic cancer cells and, with addition of DNA methylation, a completely repressed transcription in adult cancer cells.
Author Summary
Synopsis: Loopy Chromatin Brings Distant DNA to Bear on Silencing Promoter Genes
doi:10.1371/journal.pbio.0060306
Activator Control of Nucleosome Occupancy in Activation and Repression of Transcription
Bryant GO, Prabhu V, Floer M, Wang X, Spagna D, et al.
A new nucleosome-occupancy technique reveals how the transcriptional activator Gal4 determines chromatin structure as genes are activated and repressed.
Author Summary
Synopsis: Gal4 Gets Genes to Loosen Up
doi:10.1371/journal.pbio.0060317
Corrections
Correction: Fish Invasions in the World's River Systems: When Natural Processes Are Blurred by Human Activities
Leprieur F, Beauchard O, Blanchet S, Oberdorff T, Brosse S
doi:10.1371/journal.pbio.0060322
Correction: Survival of Migrating Salmon Smolts in Large Rivers With and Without Dams
Welch DW, Rechisky EL, Melnychuk MC, Porter AD, Walters CJ, et al.
doi:10.1371/journal.pbio.0060314
All journal content, except where otherwise noted, is licensed under a Creative Commons Attribution License.
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