How does radiation damage in protein crystals depend on X-ray dose?

Is radiation damage to cryopreserved protein crystals strictly proportional to accumulated dose at the high-flux density of beams from undulators at third-generation synchrotron sources? The answer is "yes," for overall damage to several different kinds of protein crystals at flux densities up to 10(15) ph/sec/mm(2) (APS beamline 19-ID). We find that, at 12 keV (1 A wavelength), about ten absorbed photons are sufficient to "kill" a unit cell. As this corresponds to about one elastically scattered photon, each unit cell can contribute only about one photon to total Bragg diffraction. The smallest crystal that can yield a full data set to 3.5 A resolution has a diameter of about 20 microm (100 A unit cell).     

How does averaging affect protein structure comparison on the ensemble level?

Recent algorithmic advances and continual increase in computational power have made it possible to simulate protein folding and dynamics on the level of ensembles. Furthermore, analyzing protein structure by using ensemble representation is intrinsic to certain experimental techniques, such as nuclear magnetic resonance. This creates a problem of how to compare an ensemble of molecules with a given reference structure. Recently, we used distance-based root-mean-square deviation (dRMS) to compare the native structure of a protein with its unfolded-state ensemble. We showed that for small, mostly alpha-helical proteins, the mean unfolded-state Calpha-Calpha distance matrix is significantly more nativelike than the Calpha-Calpha matrices corresponding to the individual members of the unfolded ensemble. Here, we give a mathematical derivation that shows that, for any ensemble of structures, the dRMS deviation between the ensemble-averaged distance matrix and any given reference distance matrix is always less than or equal to the average dRMS deviation of the individual members of the ensemble from the same reference matrix. This holds regardless of the nature of the reference structure or the structural ensemble in question. In other words, averaging of distance matrices can only increase their level of similarity to a given reference matrix, relative to the individual matrices comprising the ensemble. Furthermore, we show that the above inequality holds in the case of Cartesian coordinate-based root-mean-square deviation as well. We discuss this in the context of our proposal that the average structure of the unfolded ensemble of small helical proteins is close to the native structure, and demonstrate that this finding goes beyond the above mathematical fact.     

How does inactivation change timing of replication in the human X chromosome?

Summary The kinetics of replication of the inactive (late replicating) X chromosome (LRX) were studied in karyotypically normal lymphocytes and human amniotic fluid cells. Both cell types were successively pulse labeled with 1-h or 1/2-h thymidine pulses in an otherwise BrdU-substituted S phase after partial synchronization of the cultures at G₁/S. For the first time with this technique, the entire sequence of replication was analyzed for the LRX from the beginning to the end of the S phase, with special reference to mid S (R-band to G-band transition replication). The inactive X is the last chromosome of the metaphase to start replication, with a delay of 1 or 2h, after which time a thymidine pulse results in R-type patterns. In mid S, the inactive X is the first chromosome to switch to G-type replication (without overlapping of both types and without any detectable replication pause). Until the end of S, a thymidine pulse results in G-type patterns. To rule out artifacts that might arise by the synchronization of cultures in these experiments, controls were carried out with BrdU pulses and the BrdU antibody technique without synchronization. In the course of replication, no fundamental difference was seen between the two different cell types examined. In contrast to studies using continuos labeling, this study did not reveal an interindividual difference of replication kinetics in the LRXs of the seven individuals studied; thus it is concluded that the inactive X chromosome shows only one characteristic course of replication.     

Bergmann's Rule – what's in a name?

Despite the great interest it generates, the definition of Bergmann's Rule is vague and often contested. Debate focuses on whether the rule should be described in terms of pattern or process, what taxa it should apply to and what taxonomic level it should be associated with. Here I review the historical development of studies of Bergmann's Rule. I suggest that Bergmann thought that his rule should be strongest at the intra‐specific level, rather than between closely related species as is usually thought. I argue that the rule is a pattern that can be studied regardless of mechanism in any taxon and at any taxonomic level.     

How does habitat diversity affect the species–area relationship?

Aim   To examine the way in which 'area' and 'habitat diversity' interact in shaping species richness and to find a simple and valid way to express this interaction.
Location   The Natura 2000 network of terrestrial protected areas in Greece, covering approximately 16% of the national territory.
Methods   We used the Natura 2000 framework, which provides a classification scheme for natural habitat types, to quantify habitat heterogeneity. We analysed data for the plant species composition in 16,143 quadrats in which 5044 species and subspecies of higher plants were recorded. We built a simple mathematical model that incorporates the effect of habitat diversity on the species–area relationship (SAR).
Results   Our analysis showed that habitat diversity was correlated with area. However, keeping habitat diversity constant, species richness was related to area; while keeping area constant, species richness was related to habitat diversity. Comparing the SAR of the 237 sites we found that the slope of the species–area curve was related to habitat diversity.
Main conclusions   Discussion of the causes of the SAR has often focused on the primacy of area per se versus habitat heterogeneity, even though the two mechanisms are not mutually exclusive and should be considered jointly. We find that increasing habitat diversity affects the SAR in different ways, but the dominant effect is to increase the slope of the SAR. While a full model fit typically includes a variety of terms involving both area and habitat richness, we find that the effect of habitat diversity can be reduced to a linear perturbation of the slope of the species accumulation curve.     

Life on the edge – to which degree does phreatic water sustain vegetation in the periphery of the Taklamakan Desert?

Questions: Do the vegetation‐specific patterns in the forelands of river oases of the Taklamakan Desert provide clues to the degree to which a vegetation type depends on unsaturated soil moisture, brought about by extensive floodings, or phreatic water? Location: Foreland of the Qira oasis on the southern rim of the Taklamakan Desert, Xinjiang Uygur Autonomous Region, China. Methods: A vegetation map was prepared using a SPOT satellite image and ground truthing. Measurements of soil water contents were obtained from a flooding experiment and transformed into water potentials. Sum excedance values were calculated as the percentage of days on which different thresholds of soil water potentials were transgressed. Groundwater depth was mapped by drilling 30 groundwater holes and extrapolating the distances to the whole study area. Results: The vegetation was characterized by only six dominant or codominant species: Alhagi sparsifolia, Karelinia caspia, Populus euphratica, Tamarix ramosissima, Calligonum caput‐medusae and Phragmites australis. The vegetation patterns encountered lacked any linear features typical of phreatophytes, thus not allowing direct conclusions on the type of the sustaining water sources. Soil water potentials never transgressed a threshold of pF 5 (?10 MPa) in horizons above the capillary fringe during periods without inundation, thus representing water not accessible for plants. Depth to the groundwater ranged between 2.3 and 17.5 m among plots and varied between 1.7 and 8.0 m within a plot owing to dune relief. The seven main vegetation types showed distinct niches of groundwater depths, corresponding to the observed concentric arrangement of vegetation types around the oasis. Conclusions: Inundation by flooding and unsaturated soil moisture are irrelevant for the foreland vegetation water supply. Although distances to the groundwater table can reach about 20 m, which is exceptionally large for phreatophytes, groundwater is the only water source for all vegetation types in the oasis foreland. In consequence, successful maintenance of oasis foreland vegetation will crucially depend on providing non‐declining ground water tables.     

How long does it take to equilibrate the unfolded state of a protein?

How long does it take to equilibrate the unfolded state of a protein? The answer to this question has important implications for our understanding of why many small proteins fold with two state kinetics. When the equilibration within the unfolded state U is much faster than the folding, the folding kinetics will be two state even if there are many folding pathways with different barriers. Yet the mean first passage times (MFPTs) between different regions of the unfolded state can be much longer than the folding time. This seems to imply that the equilibration within U is much slower than the folding. In this communication we resolve this paradox. We present a formula for estimating the time to equilibrate the unfolded state of a protein. We also present a formula for the MFPT to any state within U, which is proportional to the average lifetime of that state divided by the state population. This relation is valid when the equilibration within U is very fast as compared with folding as it often is for small proteins. To illustrate the concepts, we apply the formulas to estimate the time to equilibrate the unfolded state of Trp-cage and MFPTs within the unfolded state based on a Markov State Model using an ultra-long 208 microsecond trajectory of the miniprotein to parameterize the model. The time to equilibrate the unfolded state of Trp-cage is ∼100 ns while the typical MFPTs within U are tens of microseconds or longer.     

Changes in a deep lake following sewage diversion – a challenge to the orthodoxy of external phosphorus control as a restoration strategy?

1. The restoration of deep lakes has traditionally focused on reducing the external phosphorus loading. 2. Following the diversion of sewage effluent, that led to marked reductions in nutrient concentrations in its main inflow, Rostherne Mere has shown no reduction in phosphorus or chlorophyll a concentrations. A shallow lake upstream (Little Mere), however, has shown a marked response to effluent diversion. 3. Nutrient budgets for Rostherne Mere reveal that sewage effluent was by far the most significant external source of total phosphorus and that diffuse drainage from the catchment was the most significant external source of dissolved inorganic nitrogen. Phosphorus loads from groundwater and a bird roost were insignificant. Internal sources of phosphorus were, however, considerable and were largely responsible for the observed delay in recovery. 4. Phosphorus limitation of phytoplankton biomass may never be attainable because of substantial internal and diffuse sources of phosphorus, combined with a long retention time. Nitrogen is likely to be more important in limiting phytoplankton biomass. Control of diffuse nitrogen sources may therefore be more effective in the restoration of the deeper lakes of this region.     

How does hunger affect convergence on prey patches in a social forager?

Internal state, in this case hunger, is known to influence both the organisation of animal groups and the social foraging interactions that occur within them. In this study, we investigated the effects of hunger upon the time taken to locate and converge upon hidden simulated prey patches in a socially foraging fish, the threespine stickleback (Gasterosteus aculeatus). We predicted that groups of food‐deprived fish would find and recruit to prey patches faster than recently fed groups, reasoning that they might search more rapidly and be more attentive to inadvertent social information produced by other foragers. Instead we saw no difference between the two groups in the time taken to find the patches and found that in fact, once prey patches had been discovered, it was the recently fed fish that converged on them most rapidly. This finding is likely due to the fact that recently fed fish tend to organise themselves into fewer but larger subgroups, which arrived at the food patch together. Hunger has a significant impact upon the social organisation of the fish shoals, and it appears that this has a stronger effect upon the rate at which they converged upon the food patches than does internal state itself.     

Spermatogenic ultrastructure in the anomalodesmatan bivalve Myochama anomioides (Mollusca: Myochamidae) – does the nucleus help position the ‘temporary’ acrosome?

Spermatogenic ultrastructure in the marine bivalve mollusc Myochama anomioides (Myochamidae) is described and contrasted with other bivalves, especially other euheterodonts. Small (0.1 μm diameter), primary proacrosomal vesicles produced in spermatocytes give rise to much larger (0.4 μm diameter) secondary proacrosomal vesicles in early spermatids, which in turn form the dished‐shaped, definitive acrosomal vesicle (diameter 1.0 μm) of later spermatids. The acrosomal vesicle acquires a deposit of subacrosomal material and comes to lie close to or in contact with the plasma membrane. The acrosomal complex (acrosomal vesicle + subacrosomal material) initially positions itself at the apex of the condensing, fibrous nucleus (the so‐called temporary acrosome position), but subsequently begins to move posteriorly. The condensing nucleus becomes markedly folded so that its apex is posteriorly orientated towards the migrating acrosomal complex and the midpiece (mitochondria and centrioles). The close spatial relationship of nuclear apex to acrosomal complex during this folding strongly suggests that acrosomal migration in M. anomioides is assisted, at least in part, by movement of the late spermatid nucleus. Similar nuclear folding has previously been demonstrated in an early stage of fertilization in another anomalodesmatan (Laternula limicola) raising the possibility that one event might be a reversal of the other.     

Using connectivity metrics in conservation planning – when does habitat quality matter?

Aim The objective of conservation planning is often to prioritize patches based on their estimated contribution to metapopulation or metacommunity viability. The contribution that an individual patch makes will depend on its intrinsic characteristics, such as habitat quality, as well as its location relative to other patches, its connectivity. Here we systematically evaluate five patch value metrics to determine the importance of including an estimate of habitat quality into the metrics. Location We tested the metrics in landscapes designed to represent different degrees of variability in patch quality and different levels of patch aggregation. Methods In each landscape, we simulated population dynamics using a spatially explicit, continuous time metapopulation model linked to within patch logistic growth models. We tested five metrics that are used to estimate the contribution that a patch makes to metapopulation viability: two versions of the probability of connectivity index, two versions of patch centrality (a graph theory metric) and the metapopulation capacity metric. Results All metrics performed best in environments where patch quality was very variable and high quality patches were aggregated. Metrics that incorporated some measure of patch quality did better in all environments, but did particularly well in environments with high variance of patch quality and spatial aggregation of good quality patches. Main conclusions Including an estimate of patch quality significantly increased the ability of a given connectivity metric to rank correctly habitat patches according to their contribution to metapopulation viability. Incorporating patch quality is particularly important in landscapes where habitat quality is highly variable and good quality patches are spatially aggregated. However, caution should be used when applying patch metrics to homogeneous landscapes, even if good estimates of patch quality are available. Our results demonstrate that landscape structure and the degree of variability in patch quality need to be assessed prior to selecting a suitable method for estimating patch value.