Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution,new validation tools,and implications for the future

As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) “Resolution Revolution” made possible by convergence of robust cryo-preservation of vitrified biological materials, sample handling systems, and measurement stages operating a liquid nitrogen temperature, improvements in electron optics that preserve phase information at the atomic level, direct electron detectors (DEDs), high-speed computing with graphics processing units, and rapid advances in data acquisition and processing software. 3DEM structure information (atomic coordinates and related metadata) are archived in the open-access Protein Data Bank (PDB), which currently holds more than 11,000 3DEM structures of proteins and nucleic acids, and their complexes with one another and small-molecule ligands (~ 6% of the archive). Underlying experimental data (3DEM density maps and related metadata) are stored in the Electron Microscopy Data Bank (EMDB), which currently holds more than 21,000 3DEM density maps. After describing the history of the PDB and the Worldwide Protein Data Bank (wwPDB) partnership, which jointly manages both the PDB and EMDB archives, this review examines the origins of the resolution revolution and analyzes its impact on structural biology viewed through the lens of PDB holdings. Six areas of focus exemplifying the impact of 3DEM across the biosciences are discussed in detail (icosahedral viruses, ribosomes, integral membrane proteins, SARS-CoV-2 spike proteins, cryogenic electron tomography, and integrative structure determination combining 3DEM with complementary biophysical measurement techniques), followed by a review of 3DEM structure validation by the wwPDB that underscores the importance of community engagement.     

Validation of elk resource selection models with spatially independent data

Knowledge of how landscape features affect wildlife resource use is essential for informed management. Resource selection functions often are used to make and validate predictions about landscape use; however, resource selection functions are rarely validated with data from landscapes independent of those from which the models were built. This problem has severely limited the application of resource selection functions over larger geographic areas for widely distributed species. North American elk (Cervus elaphus) is an example of a widely-distributed species of keen interest to managers and for which validation of resource selection functions over large geographic areas is important. We evaluated the performance of resource selection functions developed for elk on one landscape in northeast Oregon with independent data from a different landscape in the same region. We compared predicted versus observed elk resource use for 9 monthly or seasonal periods across 3 yr. Results showed strong, positive agreement between predicted and observed use for 2 spring and 3 late summer-early fall models (3-yr r = 0.81–0.95). Predicted versus observed use was negatively or weakly positively correlated for 3 summer models and 1 mid-fall model (3-yr r = −0.57–0.14). Predicted and observed use correlated well when forage was limited (spring and late summer or early fall), corresponding to important biological stages for elk (parturition and breeding seasons). For these seasonal periods, model covariates such as rate of motorized traffic and canopy closure often were effective predictors of elk resource selection. The models we validated for spring and late summer-early fall may be used to evaluate management activities in areas with similar landscape characteristics. © 2010 The Wildlife Society.     

Carrying capacity in a heterogeneous environment with habitat connectivity

A large body of theory predicts that populations diffusing in heterogeneous environments reach higher total size than if non‐diffusing, and, paradoxically, higher size than in a corresponding homogeneous environment. However, this theory and its assumptions have not been rigorously tested. Here, we extended previous theory to include exploitable resources, proving qualitatively novel results, which we tested experimentally using spatially diffusing laboratory populations of yeast. Consistent with previous theory, we predicted and experimentally observed that spatial diffusion increased total equilibrium population abundance in heterogeneous environments, with the effect size depending on the relationship between r and K. Refuting previous theory, however, we discovered that homogeneously distributed resources support higher total carrying capacity than heterogeneously distributed resources, even with species diffusion. Our results provide rigorous experimental tests of new and old theory, demonstrating how the traditional notion of carrying capacity is ambiguous for populations diffusing in spatially heterogeneous environments.     

不同光强对吴茱萸生长动态和光合日变化的影响

报道了不同生长光强(透光率分别为15%、30%、50%、100%)对吴茱萸的生长和光合日变化的影响。结果表明:生长环境光强对吴茱萸苗期株高、地径和冠面积的影响较大,100%RI下的株高、地径和冠面积明显小于各遮荫处理,其中30%RI下吴茱萸的株高、地径和冠面积最大,这表明苗期强光不利于吴茱萸的生长。随着光强的减弱,吴茱萸增大冠面积与株高有利于截获更多光能。10月下旬,100%RI下吴茱萸净光合速率(Pn)日变化曲线呈"双峰型",11:30～14:30,吴茱萸的Pn、胞间二氧化碳浓度与气孔导度均下降,表明此时的光合午休现象是由气孔部分关闭造成的。各遮荫处理下,吴茱萸的Pn日变化均呈"单峰型",并无第二峰的出现,可能与遮荫条件下,下午光强较弱,环境温度较高,空气相对湿度较低有关。     

Multicolour Fluorescence Imaging of Sugar Beet Leaves with Different Nitrogen Status by Flash Lamp UV-Excitation

Fluorescence images of leaves of sugar beet plants (Beta vulgaris L. cv. Patricia) grown on an experimental field with different fertilisation doses of nitrogen [0, 3, 6, 9, 12, 15 g(N) m^–2] were taken, applying a new multicolour flash-lamp fluorescence imaging system (FL-FIS). Fluorescence was excited by the UV-range (280–400 nm, _max = 340 nm) of a pulsed Xenon lamp. The images were acquired successively in the four fluorescence bands of leaves near 440, 520, 690, and 740 nm (F₄₄₀, F₅₂₀, F₆₉₀, F₇₄₀) by means of a CCD-camera. Parallel measurements were performed to characterise the physiological state of the leaves (nitrogen content, invert-sugars, chlorophylls and carotenoids as well as chlorophyll fluorescence induction kinetics and beet yield). The fluorescence images indicated a differential local patchiness across the leaf blade for the four fluorescence bands. The blue (F₄₄₀) and green fluorescence (F₅₂₀) were high in the leaf veins, whereas the red (F₆₉₀) and far-red (F₇₄₀) chlorophyll (Chl) fluorescences were more pronounced in the intercostal leaf areas. Sugar beet plants with high N supply could be distinguished from beet plants with low N supply by lower values of F₄₄₀/F₆₉₀ and F₄₄₀/F₇₄₀. Both the blue-green fluorescence and the Chl fluorescence rose at a higher N application. This increase was more pronounced for the Chl fluorescence than for the blue-green one. The results demonstrate that fluorescence ratio imaging of leaves can be applied for a non-destructive monitoring of differences in nitrogen supply. The FL-FIS is a valuable diagnostic tool for screening site-specific differences in N-availability which is required for precision farming.     

Parallelism in adaptive radiations of experimental Escherichia coli populations

Adaptive radiations are major contributors to species diversity. Although the underlying mechanisms of adaptive radiations, specialization and trade‐offs, are relatively well understood, the tempo and repeatability of adaptive radiations remain elusive. Ecological specialization can occur through the expansion into novel niches or through partitioning of an existing niche. To test how the mode of resource specialization affects the tempo and repeatability of adaptive radiations, we selected replicate bacterial populations in environments that promoted the evolution of diversity either through niche expansion or through niche partitioning, and in a third low‐quality single‐resource environment, in which diversity was not expected to evolve. Colony size diversity evolved equally fast in environments that provided ecological opportunities regardless of the mode of resource specialization. In the low‐quality environments, diversity did not consistently evolve. We observed the largest fitness improvement in the low‐quality environment and the smallest the glucose‐limited environment. We did not observe a change in the rate of evolutionary change in either trait or environment, suggesting that the pool of beneficial mutations was not exhausted. Overall, the mode of resource specialization did not affect the tempo or repeatability of adaptive radiations. These results demonstrate the limitations of eco‐evolutionary feedbacks to affect evolutionary outcomes.     

A new method to measure and calculate light intensity and light quality simultaneously by using portable spectrometer

The influence of light intensity and light quality on plants is highly concerned in the field of plant physiology and ecology. However, the calibrated quantum meter for measurement of light intensity cannot measure light quality, and vice versa. Here we developed an empirical formula to convert light energy to photon flux density, based on the measurement conditions of spectrometer. Under the guide of the formula, a portable spectrometer (AvaSpec-ULS2048×64) was calibrated by using four narrowband light emitting diode (LEDs) in combination with a calibrated quantum meter (LI-190SB). After calibration of the spectrometer, we can calculate photosynthetic photon flux density (PPFD or PAR) and measure spectrum of radiation flux simultaneously. Under natural light conditions, the errors between measured and calculated PPFDs are in the range from -2% to 5%, indicating the reliability of the method. With this new approach, the application of portable spectrometer can be greatly broadened: 1) the light intensity and quality of light source and plant growth light environment can be obtained simultaneously, 2) PPFD can be obtained within any specified wavelength range, and 3) there is no need to use standard light source to obtain the absolute light/radiation flux of a spectrum measured by spectrometer. In conclusion, this method has potential applications for the study of plant physiology and ecology.     

Photosynthetic net O<Subscript>2</Subscript> evolution enhancement as a sign of acclimation to phosphorus deficiency in bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.) leaves

Primary leaves of bean (Phaseolus vulgaris L.) seedlings cultivated for 14 days in a growth chamber on complete (control) and phosphate deficient (−P) Knop liquid medium were used for measurements. The −P leaves were smaller and showed an increased specific leaf area (SLA). Their inorganic phosphate (P_i) concentration was considerably lowered. They did not show any significant changes in chlorophyll (Chl) (a + b) concentration and in their net CO₂ assimilation rate when it was estimated under the conditions close to those of the seedlings growth. Light response curves of photosynthetic net O₂ evolution (P _NO₂) of the leaves for the irradiation range up to 500 μmol(photon) m⁻² s⁻¹ were determined, using the leaf-disc Clark oxygen electrode. The measurements were taken under high CO₂ concentration of about 1 % and O₂ concentrations of 21 % or lowered to about 3 % at the beginning of measurement. The results obtained at 21 % O₂ and the irradiations close to or higher than those used during the seedlings growth revealed the phosphorus stress suppressive effect on the leaf net O₂ evolution, however, no such effect was observed at lower irradiations. Other estimated parameters of P _NO₂ such as: apparent quantum requirement (QR_A) and light compensation point (LCP) for the control and −P leaves were similar. However, with a high irradiation and lowered O₂ concentration the rate of P _NO₂ for the −P leaves was markedly higher than that for the control, in relation to both the leaf area and leaf fresh mass. This difference also disappeared at low irradiations, but the estimated reduced QR_A values indicate, under those conditions, the increased yield of photosynthetic light reaction, especially in the −P leaves. The presented results confirm the suggestion that during the initial phase of insufficient phosphate feeding the acclimations in the light phase of photosynthesis, both structural and functional appear. They correspond, probably, to the increased energy costs of carbon assimilation under phosphorus stress, e.g. connected with raised difficulties in phosphate uptake and turnover and enhanced photorespiration. Under the experimental conditions especially advantageous for the dark phase of photosynthesis (saturating CO₂ and PAR, low O₂ concentration), those acclimations may be manifested as an enhancement of photosynthetic net O₂ evolution.     

Influence of galls of Phanacis taraxaci on carbon partitioning within common dandelion, Taraxacum officinale

We examined how leaf galls, induced by the cynipid wasp Phanacis taraxaci, influence the partitioning of photoassimilates within the host, the common dandelion, Taraxacum officinale. Galled and ungalled plants were exposed to ¹⁴CO₂ and the labelled photoassimilates accumulating within galls and other parts of the host were measured. During the growth phase of the gall they were physiological sinks for photoassimilates, accumulating 9% to 70% of total carbon produced by the host, depending upon the number of galls per plant. High levels of ¹⁴C assimilation in the leaves of galled plants compared to controls, suggest that galls actively redirect carbon resources from unattacked leaves of their host plant. This represents a significant drain on the carbon resources of the host, which increases with the number and size of galls per plant. Active assimilation of ¹⁴C by the gall is greatest in the growth phase and is several orders of magnitude lower in the maturation phase. This finding is consistent with physiological and anatomical changes that occur during the two phases of gall development and represents a key developmental strategy by cynipids to ensure adequate food resources before larval growth begins.     

Interspecific Differences of Leaf Gas Exchange and Water Relations of Three Evergreen Mediterranean Shrub Species

Leaf gas exchange and plant water relations of three co-occurring evergreen Mediterranean shrubs species, Quercus ilex L. and Phillyrea latifolia L. (typical evergreen sclerophyllous shrubs) and Cistus incanus L. (a drought semi-deciduous shrub), were investigated in order to evaluate possible differences in their adaptive strategies, in particular with respect to drought stress. C. incanus showed the highest annual rate of net photosynthetic rate (P _N) and stomatal conductance (g _s) decreasing by 67 and 69 %, respectively, in summer. P. latifolia and Q. ilex showed lower annual maximum P _N and g _s, although P _N was less lowered in summer (40 and 37 %, respectively). P. latifolia reached the lowest midday leaf water potential (₁) during the drought period (–3.54±0.36 MPa), 11 % lower than in C. incanus and 19 % lower than in Q. ilex. Leaf relative water content (RWC) showed the same trend as ₁. C. incanus showed the lowest RWC values during the drought period (60 %) while they were never below 76 % in P. latifolia and Q. ilex; moreover C. incanus showed the lowest recovery of ₁ at sunset. Hence the studied species are well adapted to the prevailing environment in Mediterranean climate areas, but they show different adaptive strategies that may be useful for their co-occurrence in the same habitat. However, Q. ilex and P. latifolia by their water use strategy seem to be less sensitive to drought stress than C. incanus.