Aquaglyceroporin AQP7's affinity for its substrate glycerol

AQP7 is one of the four human aquaglyceroporins that facilitate glycerol transport across the cell membrane, a biophysical process that is essential in human physiology. Therefore, it is interesting to compute AQP7s affinity for its substrate (glycerol) with reasonable certainty to compare with the experimental data suggesting high affinity in contrast with most computational studies predicting low affinity. In this study aimed at computing the AQP7-glycerol affinity with high confidence, we implemented a direct computation of the affinity from unbiased equilibrium molecular dynamics (MD) simulations of three all-atom systems constituted with 0.16M, 4.32M, and 10.23M atoms, respectively. These three sets of simulations manifested a fundamental physics law that the intrinsic fluctuations of pressure in a system are inversely proportional to the system size (the number of atoms in it). These simulations showed that the computed values of glycerol-AQP7 affinity are dependent upon the system size (the inverse affinity estimations were, respectively, 47.3 mM, 1.6 mM, and 0.92 mM for the three model systems). In this, we obtained a lower bound for the AQP7-glycerol affinity (an upper bound for the dissociation constant). Namely, the AQP7-glycerol affinity is stronger than 1087/M (the dissociation constant is less than 0.92 mM). Additionally, we conducted hyper steered MD (hSMD) simulations to map out the Gibbs free-energy profile. From the free-energy profile, we produced an independent computation of the AQP7-glycerol dissociation constant being approximately 0.18 mM.

Non-uniform tropical forest responses to the ‘Columbian Exchange’ in the Neotropics and Asia-Pacific

It has been suggested that Iberian arrival in the Americas in 1492 and subsequent dramatic depopulation led to forest regrowth that had global impacts on atmospheric CO2 concentrations and surface temperatures. Despite tropical forests representing the most important terrestrial carbon stock globally, systematic examination of historical afforestation in these habitats in the Neotropics is lacking. Additionally, there has been no assessment of similar depopulation–afforestation dynamics in other parts of the global tropics that were incorporated into the Spanish Empire. Here, we compile and semi-quantitatively analyse pollen records from the regions claimed by the Spanish in the Atlantic and Pacific to provide pan-tropical insights into European colonial impacts on forest dynamics. Our results suggest that periods of afforestation over the past millennium varied across space and time and depended on social, economic and biogeographic contexts. We argue that this reveals the unequal and divergent origins of the Anthropocene as a socio-political and biophysical process, highlighting the need for higher-resolution, targeted analyses to fully elucidate pre-colonial and colonial era human–tropical landscape interactions.

Preservation or reconstruction of the Peri-implant bone- A Review

The main biological and biophysical process that has made dental implant therapy predictably successful for replacing missing teeth is Osseointegration. Teeth extraction is done for several purposes, often without any consideration for the preservation of the alveolar ridge. Alveolar bone post-extraction changes have been estimated to cause a 50% decrease in alveolar bone buccolingual width, and a further loss in height. This review will go through various techniques of ARP and bone regeneration techniques and explore the best way to obtain the best outcomes after implant placement.

Correlating solvation with conformational pathways of proteins in alcohol-water mixtures: A THz spectroscopic insight

Water being an active participant in most of the biophysical process, it is important to trace how protein solvation changes as its conformations evolves in presence of solutes or co-solvents....

Divergent climate feedbacks in the growing period and the dormancy period to sowing date shift of winter wheat in the North China Plain

The land cover and management changes have strong feedbacks to climate through surface biophysical and biochemical processes. Agricultural phenology dynamic exerted measurable impacts on land surface properties, biophysical process and climate feedback in particular times at local/regional scale. But the responses of climate feedback through surface biophysical process to sowing date shift in the winter wheat ecosystem have been overlooked, especially at winter dormancy period. Considering the large cultivation area, unique surface property and phenology shift of winter wheat in the North China Plain, we first validated the SiBcrop model. Then, we used it to investigate the dynamics of leaf area index (LAI) and canopy temperature (Tc) under two planting date scenarios (Early Sowing: EP; Late Sowing: LP) of winter wheat at 10 selected stations. Finally, the surface energy budget was analyzed and interpreted. The results showed that the SiBcrop with a modified crop phenology scheme better simulated the seasonal dynamic of LAI, Tc, phenology, and surface heat fluxes. Earlier sowing date had higher LAI with earlier development than later sowing date. But the response of Tc to sowing date exhibited opposite patterns during the dormancy and active growth periods: EP led to higher Tc (0.05 K) than LP in the dormancy period and lower Tc (−0.2 K) in the growth period. The highest difference (0.6 K) between EP and LP happened at the time when wheat was sown in EP but wasn't in LP. The higher LAI captured more net radiation with lower surface albedo for warming, whist surface energy partitioning exerted cooling effect. The relative contributions of albedo-radiative process and partitioning-non-radiative process determined the climate effect of sowing date shift. The spatial pattern of the climate response to sowing date was influence by precipitation and air temperature. The study highlight that the climate effects of the sowing date shift in winter dormancy period are worthy of attention.

Cargo crowding contributes to sorting stringency in COPII vesicles

Accurate maintenance of organelle identity in the secretory pathway relies on retention and retrieval of resident proteins. In the endoplasmic reticulum (ER), secretory proteins are packaged into COPII vesicles that largely exclude ER residents and misfolded proteins by mechanisms that remain unresolved. Here we combined biochemistry and genetics with correlative light and electron microscopy (CLEM) to explore how selectivity is achieved. Our data suggest that vesicle occupancy contributes to ER retention: in the absence of abundant cargo, nonspecific bulk flow increases. We demonstrate that ER leakage is influenced by vesicle size and cargo occupancy: overexpressing an inert cargo protein or reducing vesicle size restores sorting stringency. We propose that cargo recruitment into vesicles creates a crowded lumen that drives selectivity. Retention of ER residents thus derives in part from the biophysical process of cargo enrichment into a constrained spherical membrane-bound carrier.

Cargo crowding drives sorting stringency in COPII vesicles

Accurate maintenance of organelle identity in the secretory pathway relies on retention and retrieval of resident proteins. In the endoplasmic reticulum (ER), secretory proteins are packaged into COPII vesicles that largely exclude ER residents and misfolded proteins by mechanisms that remain unresolved. Here we combined biochemistry and genetics with correlative light and electron microscopy (CLEM) to explore how selectivity is achieved. Our data suggest that vesicle occupancy dictates ER retention: in the absence of abundant cargo, non-specific bulk flow increases. We demonstrate that ER leakage is influenced by vesicle size and cargo occupancy: overexpressing an inert cargo protein, or reducing vesicle size restores sorting stringency. We propose that cargo recruitment into vesicles creates lumenal steric pressure that drives selectivity. Sorting stringency is thus an emergent property of the biophysical process of cargo enrichment into a constrained spherical membrane-bound carrier.SummaryCombining correlative light and electron microscopy with yeast genetics and biochemistry, Gomez-Navarro, Melero and colleagues show that cargo recruitment into a constrained COPII vesicle restricts bulk flow, thereby contributing to sorting stringency and ER quality control.

Shaping the zebrafish myotome by intertissue friction and active stress

Organ formation is an inherently biophysical process, requiring large-scale tissue deformations. Yet, understanding how complex organ shape emerges during development remains a major challenge. During zebrafish embryogenesis, large muscle segments, called myotomes, acquire a characteristic chevron morphology, which is believed to aid swimming. Myotome shape can be altered by perturbing muscle cell differentiation or the interaction between myotomes and surrounding tissues during morphogenesis. To disentangle the mechanisms contributing to shape formation of the myotome, we combine single-cell resolution live imaging with quantitative image analysis and theoretical modeling. We find that, soon after segmentation from the presomitic mesoderm, the future myotome spreads across the underlying tissues. The mechanical coupling between the future myotome and the surrounding tissues appears to spatially vary, effectively resulting in spatially heterogeneous friction. Using a vertex model combined with experimental validation, we show that the interplay of tissue spreading and friction is sufficient to drive the initial phase of chevron shape formation. However, local anisotropic stresses, generated during muscle cell differentiation, are necessary to reach the acute angle of the chevron in wild-type embryos. Finally, tissue plasticity is required for formation and maintenance of the chevron shape, which is mediated by orientated cellular rearrangements. Our work sheds light on how a spatiotemporal sequence of local cellular events can have a nonlocal and irreversible mechanical impact at the tissue scale, leading to robust organ shaping.

A critically modern ecological economics for the Anthropocene

Ecological economics recognizes economic activity as a biophysical process mediated by social systems and ultimately subject to the constraints of a finite earth system. The Anthropocene discourse appears as validation of the central concerns of ecological economics yet throws into relief its limits as a normative transdiscipline oriented toward social transformation. We review ecological economics in light of two overarching challenges: first, negotiating between biophysical reality and plural constructed social realities, so as to create legitimate grounds for a sustainability transition; second, accounting for multi-level, multi-scale social and political action, which demands a means for arbitrating among competing normative propositions. We argue that attempts to address these challenges within ecological economics have been inconsistent and relatively scarce, reflecting an unresolved tension regarding modern and postmodern social theory. We demonstrate that a critically modern ecological economics could draw on aligned social movements and build on deliberative theory as a foundation for social and political change fit for navigating the Anthropocene.