How river rocks round: resolving the shape-size paradox.
Ontology highlight
ABSTRACT:
SUBMITTER: Domokos G
PROVIDER: S-EPMC3922984 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:For almost a century, thermoelectricity in superconductors has been one of the most intriguing topics in physics. During its early stages in the 1920s, the mere existence of thermoelectric effects in superconductors was questioned. In 1944, it was demonstrated that the effects may occur in inhomogeneous superconductors. Theoretical breakthrough followed in the 1970s, when the generation of a measurable thermoelectric magnetic flux in superconducting loops was predicted; however, a major crisis developed when experiments showed puzzling discrepancies with the theory. Moreover, different experiments were inconsistent with each other. This led to a stalemate in bringing theory and experiment into agreement. With this work, we resolve this stalemate, thus solving this long-standing "paradox," and open prospects for exploration of novel thermoelectric phenomena predicted recently.
| S-EPMC4771438 | biostudies-literature
Project description:The genetic paradox of biological invasions is complex and multifaceted. In particular, the relative role of disparate propagule sources and genetic adaptation through postintroduction hybridization has remained largely unexplored. To add resolution to this paradox, we investigate the genetic architecture responsible for the invasion of two invasive Asian carp species, bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) (bigheaded carps) that experience extensive hybridization in the Mississippi River Basin (MRB). We sequenced the genomes of bighead and silver carps (~1.08G bp and ~1.15G bp, respectively) and their hybrids collected from the MRB. We found moderate-to-high heterozygosity in bighead (0.0021) and silver (0.0036) carps, detected significantly higher dN/dS ratios of single-copy orthologous genes in bigheaded carps versus 10 other species of fish, and identified genes in both species potentially associated with environmental adaptation and other invasion-related traits. Additionally, we observed a high genomic similarity (96.3% in all syntenic blocks) between bighead and silver carps and over 90% embryonic viability in their experimentally induced hybrids. Our results suggest intrinsic genomic features of bigheaded carps, likely associated with life history traits that presumably evolved within their native ranges, might have facilitated their initial establishment of invasion, whereas ex-situ interspecific hybridization between the carps might have promoted their range expansion. This study reveals an alternative mechanism that could resolve one of the genetic paradoxes in biological invasions and provides invaluable genomic resources for applied research involving bigheaded carps.
| S-EPMC6976960 | biostudies-literature
Project description:BackgroundDespite their notorious diversity, biological cells are mechanically well characterized by only a few robust and universal laws. Intriguingly, the law characterizing the nonlinear response to stretch appears self-contradictory. Various cell types have been reported to both stiffen and soften, or "fluidize" upon stretch. Within the classical paradigm of cells as viscoelastic bodies, this constitutes a paradox.Principal findingsOur measurements reveal that minimalistic reconstituted cytoskeletal networks (F-actin/HMM) exhibit a similarly peculiar response. A mathematical model of transiently crosslinked polymer networks, the so-called inelastic glassy wormlike chain (iGwlc) model, can simulate the data and resolve the apparent contradiction. It explains the observations in terms of two antagonistic physical mechanisms, the nonlinear viscoelastic resistance of biopolymers to stretch, and the breaking of weak transient bonds between them.ConclusionsOur results imply that the classical paradigm of cells as viscoelastic bodies has to be replaced by such an inelastic mechanical model.
| S-EPMC3397976 | biostudies-literature
Project description:Carcinogenesis is one of the leading health concerns afflicting presumably every single animal species, including humans. Currently, cancer research expands considerably beyond medicine, becoming a focus in other branches of natural science. Accumulating evidence suggests that a proportional scale of tumor deaths involves domestic and wild animals and poses economical or conservation threats to many species. Therefore, understanding the genetic and physiological mechanisms of cancer initiation and its progression is essential for our future action and contingent prevention. From this perspective, I used an evolutionary-based approach to re-evaluate the baseline for debate around Peto's paradox. First, I review the background of information on which current understanding of Peto's paradox and evolutionary concept of carcinogenesis have been founded. The weak points and limitations of theoretical modeling or indirect reasoning in studies based on intraspecific, comparative studies of carcinogenesis are highlighted. This is then followed by detail discussion of an effect of the body mass in cancer research and the importance of cell size in consideration of body architecture; also, I note to the ambiguity around cell size invariance hypothesis and hard data for variability of cell size across species are provided. Finally, I point to the new research area that is driving concepts to identify exact molecular mechanisms promoting the process of tumorigenesis, which in turn may provide a proximate explanation of Peto's paradox. The novelty of the approach proposed therein lies in intraspecies testing of the effect of differentiation of cell size/number on the probability of carcinogenesis while controlling for the confounding effect of body mass/size.
| S-EPMC9746147 | biostudies-literature
Project description:Blue is a favored color of many humans. While blue skies and oceans are a common visual experience, this color is less frequently observed in flowers. We first review how blue has been important in human culture, and thus how our perception of blue has likely influenced the way of scientifically evaluating signals produced in nature, including approaches as disparate as Goethe's Farbenlehre, Linneaus' plant taxonomy, and current studies of plant-pollinator networks. We discuss the fact that most animals, however, have different vision to humans; for example, bee pollinators have trichromatic vision based on UV-, Blue-, and Green-sensitive photoreceptors with innate preferences for predominantly short-wavelength reflecting colors, including what we perceive as blue. The subsequent evolution of blue flowers may be driven by increased competition for pollinators, both because of a harsher environment (as at high altitude) or from high diversity and density of flowering plants (as in nutrient-rich meadows). The adaptive value of blue flowers should also be reinforced by nutrient richness or other factors, abiotic and biotic, that may reduce extra costs of blue-pigments synthesis. We thus provide new perspectives emphasizing that, while humans view blue as a less frequently evolved color in nature, to understand signaling, it is essential to employ models of biologically relevant observers. By doing so, we conclude that short wavelength reflecting blue flowers are indeed frequent in nature when considering the color vision and preferences of bees.
| S-EPMC7859648 | biostudies-literature
Project description:A wealth of evidence indicates that humans can engage two types of mechanisms to solve category-learning tasks: declarative mechanisms, which involve forming and testing verbalizable decision rules, and associative mechanisms, which involve gradually linking stimuli to appropriate behavioral responses.1,2,3 In contrast to declarative mechanisms, associative mechanisms have received surprisingly little attention in the broader category-learning literature. Although various forms of associatively driven artificial intelligence (AI) have matched-and even surpassed-humans' performance on several challenging problems,3,4,5,6 associative learning is routinely dismissed as being too simple to power the impressive cognitive achievements of both humans and non-human species.6,7,8,9 Here, we attempt to resolve this paradox by demonstrating that pigeons-which appear to rely solely on associative learning mechanisms in several tasks that promote declarative rule use by humans3,10,11,12-succeed at learning a novel, highly demanding category structure that ought to hinder declarative rule use: the sectioned-rings task. Our findings highlight the power and flexibility that associative mechanisms afford in the realm of category learning.
| S-EPMC10050111 | biostudies-literature
Project description:Periplasmic chaperone/usher machineries are used for assembly of filamentous adhesion organelles of Gram-negative pathogens in a process that has been suggested to be driven by folding energy. Structures of mutant chaperone-subunit complexes revealed a final folding transition (condensation of the subunit hydrophobic core) on the release of organelle subunit from the chaperone-subunit pre-assembly complex and incorporation into the final fibre structure. However, in view of the large interface between chaperone and subunit in the pre-assembly complex and the reported stability of this complex, it is difficult to understand how final folding could release sufficient energy to drive assembly. In the present paper, we show the X-ray structure for a native chaperone-fibre complex that, together with thermodynamic data, shows that the final folding step is indeed an essential component of the assembly process. We show that completion of the hydrophobic core and incorporation into the fibre results in an exceptionally stable module, whereas the chaperone-subunit pre-assembly complex is greatly destabilized by the high-energy conformation of the bound subunit. This difference in stabilities creates a free energy potential that drives fibre formation.
| S-EPMC1180718 | biostudies-literature
Project description:During the 1930s Dust Bowl drought in the central United States, species with the C3 photosynthetic pathway expanded throughout C4-dominated grasslands. This widespread increase in C3 grasses during a decade of low rainfall and high temperatures is inconsistent with well-known traits of C3 vs. C4 pathways. Indeed, water use efficiency is generally lower, and photosynthesis is more sensitive to high temperatures in C3 than C4 species, consistent with the predominant distribution of C3 grasslands in cooler environments and at higher latitudes globally. We experimentally imposed extreme drought for 4 y in mixed C3/C4 grasslands in Kansas and Wyoming and, similar to Dust Bowl observations, also documented three- to fivefold increases in C3/C4 biomass ratios. To explain these paradoxical responses, we first analyzed long-term climate records to show that under nominal conditions in the central United States, C4 grasses dominate where precipitation and air temperature are strongly related (warmest months are wettest months). In contrast, C3 grasses flourish where precipitation inputs are less strongly coupled to warm temperatures. We then show that during extreme drought years, precipitation-temperature relationships weaken, and the proportion of precipitation falling during cooler months increases. This shift in precipitation seasonality provides a mechanism for C3 grasses to respond positively to multiyear drought, resolving the Dust Bowl paradox. Grasslands are globally important biomes and increasingly vulnerable to direct effects of climate extremes. Our findings highlight how extreme drought can indirectly alter precipitation seasonality and shift ecosystem phenology, affecting function in ways not predictable from key traits of C3 and C4 species.
| S-EPMC7486763 | biostudies-literature
Project description:Granular materials do not perform Brownian motion, yet diffusion can be observed in such systems when agitation causes inelastic collisions between particles. It has been suggested that axial diffusion of granular matter in a rotating drum might be "anomalous" in the sense that the mean squared displacement of particles follows a power law in time with exponent less than unity. Further numerical and experimental studies have been unable to definitively confirm or disprove this observation. We show two possible resolutions to this apparent paradox without the need to appeal to anomalous diffusion. First, we consider the evolution of arbitrary (non-point-source) initial data towards the self-similar intermediate asymptotics of diffusion by deriving an analytical expression for the instantaneous collapse exponent of the macroscopic concentration profiles. Second, we account for the concentration-dependent diffusivity in bidisperse mixtures, and we give an asymptotic argument for the self-similar behavior of such a diffusion process, for which an exact self-similar analytical solution does not exist. The theoretical arguments are verified through numerical simulations of the governing partial differential equations, showing that concentration-dependent diffusivity leads to two intermediate asymptotic regimes: one with an anomalous scaling that matches the experimental observations for naturally polydisperse granular materials, and another with a "normal" diffusive scaling (consistent with a "normal" random walk) at even longer times.
| S-EPMC3479569 | biostudies-literature
Project description:While colorectal cancers (CRC) are paradigmatic tumors invaded by effector memory lymphocytes, the mechanisms accounting for the relative resistance of MSI negative CRC to immunogenic cell death mediated by oxaliplatin and immune checkpoint inhibitors has remained an open conundrum. Here, we propose the viewpoint where its microenvironmental contexture could be explained -at least in part- by macroenvironmental cues constituted by the complex interplay between the epithelial barrier, its microbial ecosystem, and the local immune system. Taken together this dynamic ménage-à-trois offers novel coordinated actors of the humoral and cellular immune responses actionable to restore sensitivity to immune checkpoint inhibition. Solving this paradox involves breaking tolerance to crypt stem cells by inducing the immunogenic apoptosis of ileal cells in the context of an ileal microbiome shifted towards immunogenic bacteria using cytotoxicants. This manoeuver results in the elicitation of a productive Tfh and B cell dialogue in mesenteric lymph nodes culminating in tumor-specific memory CD8+ T cell responses sparing the normal epithelium.
| S-EPMC7768083 | biostudies-literature