Super-resolution microscopy reveals the number and distribution of topoisomerase IIα and CENH3 molecules within barley metaphase chromosomes

Chromosoma - Topoisomerase IIα (Topo IIα) and the centromere-specific histone H3 variant CENH3 are key proteins involved in chromatin condensation and centromere determination,...     

Using averaged models from 4D ultrasound strain imaging allows to significantly differentiate local wall strains in calcified regions of abdominal aortic aneurysms

Abdominal aortic aneurysms are a degenerative disease of the aorta associated with high mortality. To date, in vivo information to characterize the individual elastic properties of the aneurysm wall in terms of rupture risk is lacking. We have used time-resolved 3D ultrasound strain imaging to calculate spatially resolved in-plane strain distributions characterized by mean and local maximum strains, as well as indices of local variations in strains. Likewise, we here present a method to generate averaged models from multiple segmentations. Strains were then calculated for single segmentations and averaged models. After registration with aneurysm geometries based on CT-A imaging, local strains were divided into two groups with and without calcifications and compared. Geometry comparison from both imaging modalities showed good agreement with a root mean squared error of 1.22 ± 0.15 mm and Hausdorff Distance of 5.45 ± 1.56 mm (mean ± sd, respectively). Using averaged models, circumferential strains in areas with calcifications were 23.2 ± 11.7% (mean ± sd) smaller and significantly distinguishable at the 5% level from areas without calcifications. For single segmentations, this was possible only in 50% of cases. The areas without calcifications showed greater heterogeneity, larger maximum strains, and smaller strain ratios when computed by use of the averaged models. Using these averaged models, reliable conclusions can be made about the local elastic properties of individual aneurysm (and long-term observations of their change), rather than just group comparisons. This is an important prerequisite for clinical application and provides qualitatively new information about the change of an abdominal aortic aneurysm in the course of disease progression compared to the diameter criterion.

     

Application of an Escherichia coli triple reporter strain for at-line monitoring of single-cell physiology during L-phenylalanine production

Biotechnological production processes are sustainable approaches for the production of biobased components such as amino acids for food and feed industry. Scale-up from ideal lab-scale bioreactors to large-scale processes is often accompanied by loss in productivity. This may be related to population heterogeneities of cells originating from isogenic cultures that arise due to dynamic non-ideal conditions in the bioreactor. To better understand this phenomenon, deeper insights into single-cell physiologies in bioprocesses are mandatory before scale-up. Here, a triple reporter strain (3RP) was developed by chromosomally integrating the fluorescent proteins mEmerald, CyOFP1, and mTagBFP2 into the L-phenylalanine producing Escherichia coli strain FUS4 (pF81_kan) to allow monitoring of growth, oxygen availability, and general stress response of the single cells. Functionality of the 3RP was confirmed in well-mixed lab-scale fed-batch processes with glycerol as carbon source in comparison to the strain without fluorescent proteins, leading to no difference in process performance. Fluorescence levels could successfully reflect the course of related process state variables, revealed population heterogeneities during the transition between different process phases and potentially subpopulations that exhibit superior process performance. Furthermore, indications were found for noise in gene expression as regulation strategy against environmental perturbation.     

Novel Miscanthus hybrids: Modelling productivity on marginal land in Europe using dynamics of canopy development determined by light interception

New biomass crop hybrids for bioeconomic expansion require yield projections to determine their potential for strategic land use planning in the face of global challenges. Our biomass growth simulation incorporates radiation interception and conversion efficiency. Models often use leaf area to predict interception which is demanding to determine accurately, so instead we use low-cost rapid light interception measurements using a simple laboratory-made line ceptometer and relate the dynamics of canopy closure to thermal time, and to measurements of biomass. We apply the model to project the European biomass potentials of new market-ready hybrids for 2020–2030. Field measurements are easier to collect, the calibration is seasonally dynamic and reduces influence of weather variation between field sites. The model obtained is conservative, being calibrated by crops of varying establishment and varying maturity on less productive (marginal) land. This results in conservative projections of miscanthus hybrids for 2020–2030 based on 10% land use conversion of the least (productive) grassland and arable for farm diversification, which show a European potential of 80.7–89.7 Mt year⁻¹ biomass, with potential for 1.2–1.3 EJ year⁻¹ energy and 36.3–40.3 Mt year⁻¹ carbon capture, with seeded Miscanthus sacchariflorus × sinensis displaying highest yield potential. Simulated biomass projections must be viewed in light of the field measurements on less productive land with high soil water deficits. We are attempting to model the results from an ambitious and novel project combining new hybrids across Europe with agronomy which has not been perfected on less productive sites. Nevertheless, at the time of energy sourcing issues, seed-propagated miscanthus hybrids for the upscaled provision of bioenergy offer an alternative source of renewable energy. If European countries provide incentives for growers to invest, seeded hybrids can improve product availability and biomass yields over the current commercial miscanthus variety.     

LEAF GAS EXCHANGE IN QUERCUS MACROCARPA (FAGACEAE): RAPID STOMATAL RESPONSES TO VARIABILITY IN SUNLIGHT IN A TREE GROWTH FORM

Responses in net photosynthesis (A), stomatal conductance to water vapor (g), and leaf xylem pressure potential (ψ) were measured in the deciduous tree Quercus macrocarpa during alternating periods of sun (photosynthetic photon flux, PPF > 1,500 μmol m^-2 sec^-1) and shade (ca. 350 μmol m^-2 sec^-1 simulating cloud cover). Measurements were made on trees growing at the gallery forest-prairie edge on the Konza Prairie Research Natural Area in northeast Kansas. The region is near the westernmost extension of the range of Q. macrocarpa where this species experiences significant seasonal water stress (minimum ψ < -2.9 MPa). Quercus macrocarpa was chosen for study because it has relatively high A (15 μmol m^-2 sec^-1) and g (300 mmol m^-2 sec^-1) in contrast to the deciduous and evergreen subalpine trees previously studied. Both trees and large saplings of Q. macrocarpa responded to alternating several minute periods of sun and shade with relatively rapid changes in A and g. Reductions in g (110 mmol m^-2 sec^-1) during shade periods lowered transpirational water losses (E) by 13% (and reduced A by 5%) relative to estimates of A and E made assuming g remained constant. Partial stomatal closure during shade was correlated with moderate enhancement in ψ (0.31 MPa) in Q. macrocarpa. However, greater increases in ψ were measured in adjacent prairie grasses exposed to similar periods of shade (0.72 MPa in Andropogon gerardii, 0.61 MPa in Sorghastrum nutans). Reduced variability in ψ in tree growth forms may reflect greater buffering of water relations associated with the large size of trees, the amount of tissue devoted to water storage, and differences in hydraulic resistance relative to herbs. Nonetheless, the gas exchange and water relations responses in Q. macrocarpa were much more similar to those previously measured in herbaceous subalpine and grassland species than to those documented for subalpine trees. Thus, rapid gas exchange responses to variable PPF may also occur in tree growth forms.     

Migratory Orientation of Blackcaps (Sylvia atricapilla): Population-specific Shifts of Direction during the Autumn

The population-specific orientation of two groups of blackcaps (Sylvia atricapilla), one from southwest Germany, the other from easternmost Austria, was studied outdoors in Emlen funnels. We investigated whether a seasonal shift in the migratory direction — as expected for the Austrian birds from ringing recoveries — occurs under experimental conditions and in a seasonally constant magnetic field. The West German birds, for which no shift was expected, oriented southwest during the entire season. The Austrian birds oriented southeast in October and southsouthwest in November. The clockwise shift by about 60° occurred within a 10-day period. The results indicate that in this species seasonal changes of migratory direction are probably based on an endogenous program, occur without the birds actually migrating and are independent of changes in the magnetic field. Our results provide further evidence that directional shifts in Sylvia warblers may be controlled by a different mechanism than in pied flycatchers (Ficedula hypoleuca).     

Accurate detection of very sparse sequence motifs.

Protein sequence alignments are more reliable the shorter the evolutionary distance. Here, we align distantly related proteins using many closely spaced intermediate sequences as stepping stones. Such transitive alignments can be generated between any two proteins in a connected set, whether they are direct or indirect sequence neighbors in the underlying library of pairwise alignments. We have implemented a greedy algorithm, MaxFlow, using a novel consistency score to estimate the relative likelihood of alternative paths of transitive alignment. In contrast to traditional profile models of amino acid preferences, MaxFlow models the probability that two positions are structurally equivalent and retains high information content across large distances in sequence space. Thus, MaxFlow is able to identify sparse and narrow active-site sequence signatures which are embedded in high-entropy sequence segments in the structure based multiple alignment of large diverse enzyme superfamilies. In a challenging benchmark based on the urease superfamily, MaxFlow yields better reliability and double coverage compared to available sequence alignment software. This promises to increase information returns from functional and structural genomics, where reliable sequence alignment is a bottleneck to transferring the functional or structural characterization of model proteins to entire protein superfamilies.     

Tumor necrosis factor-alpha converting enzyme is processed by proprotein-convertases to its mature form which is degraded upon phorbol ester stimulation.

Tumor necrosis factor-alpha converting enzyme (TACE or ADAM17) is a member of the ADAM (a disintegrin and metalloproteinase) family of type I membrane proteins and mediates the ectodomain shedding of various membrane-anchored signaling and adhesion proteins. TACE is synthesized as an inactive zymogen, which is subsequently proteolytically processed to the catalytically active form. We have identified the proprotein-convertases PC7 and furin to be involved in maturation of TACE. This maturation is negatively influenced by the phorbol ester phorbol-12-myristate-13-acetate (PMA), which decreases the cellular amount of the mature form of TACE in PMA-treated HEK293 and SH-SY5Y cells. Furthermore, we found that stimulation of protein kinase C or protein kinase A signaling pathways did not influence long-term degradation of mature TACE. Interestingly, PMA treatment of furin-deficient LoVo cells did not affect the degradation of mature TACE. By examination of furin reconstituted LoVo cells we were able to exclude the possibility that PMA modulates furin activity. Moreover, the PMA dependent decrease of the mature enzyme form is specific for TACE, as the amount of mature ADAM10 was unaffected in PMA-treated HEK293 and SH-SY5Y cells. Our results indicate that the activation of TACE by the proprotein-convertases PC7 and furin is very similar to the maturation of ADAM10 although there is a significant difference in the cellular stability of the mature enzyme forms after phorbol ester treatment.     

Responses in stomatal conductance to elevated CO2 in 12 grassland species that differ in growth form

Responses in stomatal conductance (g _st ) and leaf xylem pressure potential ( _leaf ) to elevated CO₂ (2x ambient) were compared among 12 tallgrass prairie species that differed in growth form and growth rate. Open-top chambers (OTCs, 4.5 m diameter, 4.0 m in height) were used to expose plants to ambient and elevated CO₂ concentrations from April through November in undisturbed tallgrass prairie in NE Kansas (USA). In June and August, _leaf was usually higher in all species at elevated CO₂ and was lowest in adjacent field plots (without OTCs). During June, when water availability was high, elevated CO₂ resulted in decreased g _st in 10 of the 12 species measured. Greatest decreases in g _st (ca. 50%) occurred in growth forms with the highest potential growth rates (C₃ and C₄ grasses, and C₃ ruderals). In contrast, no significant decrease in g _st was measured in the two C₃ shrubs. During a dry period in September, reductions in g _st at elevated CO₂ were measured in only two species (a C₃ ruderal and a C₄ grass) whereas increased g _st at elevated CO₂ was measured in the shrubs and a C₃ forb. These increases in g _st were attributed to enhanced _leaf in the elevated CO₂ plants resulting from increased soil water availability and/or greater root biomass. During a wet period in September, only reductions in g _st were measured in response to elevated CO₂. Thus, there was significant interspecific variability in stomatal responses to CO₂ that may be related to growth form or growth rate and plant water relations. The effect of growth in the OTCs, relative to field plants, was usually positive for g _st and was greatest (>30%) when water availability was low, but only 6–12% when _leaf was high.The results of this study confirm the importance of considering interactions between indirect effects of high CO₂ of plant water relations and direct effects of elevated CO₂ on g _st , particularly in ecosystems such as grasslands where water availability often limits productivity. A product of this interaction is that the potential exists for either positive or negative responses in g _st to be measured at elevated levels of CO₂.