Structure of a phage 434 Cro/DNA complex

Comparison of the crystal structure of a complex of the phage 434 Cro protein and a synthetic DNA operator with the complex of the same operator and the 434 repressor DNA-binding domain shows different DNA conformations in the two structures. Binding of the protein determines the precise conformation of the DNA in each case.     

Models in Biology and Physics: What’s the Difference?

In Making Sense of Life, Keller emphasizes several differences between biology and physics. Her analysis focuses on significant ways in which modelling practices in some areas of biology, especially developmental biology, differ from those of the physical sciences. She suggests that natural models and modelling by homology play a central role in the former but not the latter. In this paper, I focus instead on those practices that are importantly similar, from the point of view of epistemology and cognitive science. I argue that concrete and abstract models are significant in both disciplines, that there are shared selection criteria for models in physics and biology, e.g. familiarity, and that modelling often occurs in a similar fashion.     

Improving seed germination of Salicornia rubra (Chenopodiaceae) under saline conditions using germination-regulating chemicals

Salicornia rubra Nels. (Chenopodiaceae) is a salt-tolerant annual species occurring in salt playas of the Great Basin desert in western United States. It forms pioneer communities on the most saline location of an inland salt playa at Goshen, Utah. Seeds of Salicornia rubra are capable of germinating at 1000 mM NaCl at 25-35° C alternating temperature regime. Dormancy-regulating chemicals were evaluated for their ability to alleviate the innate and salinityenforced dormancy in seeds of Salicornia rubra . Betaine, GA3, kinetin, fusicoccin, ethephon, thiourea, proline, and nitrate had no effect in alleviating primary dormancy. Increases in NaCl concentration progressively inhibited germination of Salicornia rubra seeds. Ethephon, fusicoccin, GA3, kinetin, thiourea, and nitrate promoted germination under low saline conditions. At high salinity fusicoccin had no effect, whereas GA3, kinetin, and ethephon substantially alleviated salinity effects. Application of these dormancy-regulating compounds could be of practical value in seeding a saline area for restoration purposes, particularly under high saline conditions.     

The decline and fate of an iron-induced subarctic phytoplankton bloom

Iron supply has a key role in stimulating phytoplankton blooms in high-nitrate low-chlorophyll oceanic waters. However, the fate of the carbon fixed by these blooms, and how efficiently it is exported into the ocean's interior, remains largely unknown. Here we report on the decline and fate of an iron-stimulated diatom bloom in the Gulf of Alaska. The bloom terminated on day 18, following the depletion of iron and then silicic acid, after which mixed-layer particulate organic carbon (POC) concentrations declined over six days. Increased particulate silica export via sinking diatoms was recorded in sediment traps at depths between 50 and 125 m from day 21, yet increased POC export was not evident until day 24. Only a small proportion of the mixed-layer POC was intercepted by the traps, with more than half of the mixed-layer POC deficit attributable to bacterial remineralization and mesozooplankton grazing. The depletion of silicic acid and the inefficient transfer of iron-increased POC below the permanent thermocline have major implications both for the biogeochemical interpretation of times of greater iron supply in the geological past, and also for proposed geo-engineering schemes to increase oceanic carbon sequestration.     

Structure of an auxilin-bound clathrin coat and its implications for the mechanism of uncoating

Clathrin-coated pits invaginate from specific membrane compartments and pinch off as coated vesicles. These vesicles then uncoat rapidly once released. The Hsc70 molecular chaperone effects the uncoating reaction, and is guided to appropriate locations on clathrin lattices by the J-domain-containing co-chaperone molecule auxilin. This raises the question of how a local event such as ATP hydrolysis by Hsc70 can catalyse a global disassembly. Here, we have used electron cryomicroscopy to determine 12-A-resolution structures of in-vitro-assembled clathrin coats in association with a carboxy-terminal fragment of auxilin that contains both the clathrin-binding region and the J domain. We have located the auxilin fragment by computing differences between these structures and those lacking auxilin (described in an accompanying paper). Auxilin binds within the clathrin lattice near contacts between an inward-projecting C-terminal helical tripod and the crossing of two 'ankle' segments; it also contacts the terminal domain of yet another clathrin 'leg'. It therefore recruits Hsc70 to the neighbourhood of a set of critical interactions. Auxilin binding produces a local change in heavy-chain contacts, creating a detectable global distortion of the clathrin coat. We propose a mechanism by which local destabilization of the lattice promotes general uncoating.     

Unified spatial scaling of species and their trophic interactions

Two largely independent bodies of scaling theory address the quantitative relationships between habitat area, species diversity and trophic interactions. Spatial theory within macroecology addresses how species richness scales with area in landscapes, while typically ignoring interspecific interactions. Complexity theory within community ecology addresses how trophic links scale with species richness in food webs, while typically ignoring spatial considerations. Recent studies suggest unifying these theories by demonstrating how spatial patterns influence food-web structure and vice versa. Here, we follow this suggestion by developing and empirically testing a more unified scaling theory. On the basis of power-law species-area relationships, we develop link-area and non-power-law link-species models that accurately predict how trophic links scale with area and species richness of microcosms, lakes and streams from community to metacommunity levels. In contrast to previous models that assume that species richness alone determines the number of trophic links, these models include the species' spatial distribution, and hence extend the domain of complexity theory to metacommunity scales. This generality and predictive success shows how complexity theory and spatial theory can be unified into a much more general theory addressing new domains of ecology.     

Structural rearrangements in the membrane penetration protein of a non-enveloped virus

Non-enveloped virus particles (those that lack a lipid-bilayer membrane) must breach the membrane of a target host cell to gain access to its cytoplasm. So far, the molecular mechanism of this membrane penetration step has resisted structural analysis. The spike protein VP4 is a principal component in the entry apparatus of rotavirus, a non-enveloped virus that causes gastroenteritis and kills 440,000 children each year. Trypsin cleavage of VP4 primes the virus for entry by triggering a rearrangement that rigidifies the VP4 spikes. We have determined the crystal structure, at 3.2 A resolution, of the main part of VP4 that projects from the virion. The crystal structure reveals a coiled-coil stabilized trimer. Comparison of this structure with the two-fold clustered VP4 spikes in a approximately 12 A resolution image reconstruction from electron cryomicroscopy of trypsin-primed virions shows that VP4 also undergoes a second rearrangement, in which the oligomer reorganizes and each subunit folds back on itself, translocating a potential membrane-interaction peptide from one end of the spike to the other. This rearrangement resembles the conformational transitions of membrane fusion proteins of enveloped viruses.     

Structure of the repressor-operator complex of bacteriophage 434

The crystal structure of a specific complex between the DNA-binding domain of phage 434 repressor and a synthetic 434 operator DNA shows interactions that determine sequence-dependent affinity. The repressor recognizes its operators by its complementarity to a particular DNA conformation as well as by direct interaction with base pairs in the major groove.