Size-dependent Changes Research Articles

A numerical study of the effect of graphene nanoparticle size on brownian displacement, thermophoresis, and thermal performance of graphene/water nanofluid by molecular dynamics simulation

Brownian motion, often known as BM, is an inherent characteristic of minute particles suspended in a fluid. It plays an important role in several physical and chemical processes. Thermophoresis refers to the process where particles in a fluid are carried along with a gradient in temperature (Temp). This feature has significant importance in several applications, including microfluidics, thermal control, and energy conversion. Through the examination of the thermophoresis phenomenon in water/graphene nanofluid (NF), researchers might get valuable knowledge on the potential uses of these materials. The current study examined the effect of various sizes of graphene nanoparticles (NPs) (5, 6, 9, and 10 Å) on the thermal behavior (TB), BM, and thermophoresis of water/graphene NF using molecular dynamics (MD) simulation. This study reported the changes in heat flux (HF), thermal conductivity (TC), average Brownian displacement (BD), and thermophoresis. It is concluded that by increasing the size of graphene NPs from 5 to 10 Å, the average BD and thermophoresis increased from 3.06 Å and 23.88 Å to 4.16 Å and 31.46 Å, respectively. Due to their higher kinetic energy (KE) and momentum, larger graphene NPs experienced more BM, enabling them to withstand random thermal fluctuations more effectively than smaller particles. In addition, as the size of graphene NPs increased, the HF and TC values ​​increased from 39.54 W/m2 and 0.36 W/(m.K) to 47.19 W/m2 and 0.51 W/(m.K) after 10 ns. Therefore, the size-dependent changes in BD and thermophoretic effects led to a simultaneous increase in HF and TC of the NF, which was attributed to the larger heat transfer (HT) surface area, improved HT properties, and synergistic effects of larger graphene NPs. The maximum (Max) temperature increases from 1415 K to 1504 K. These findings were useful in a variety of industries, particularly for improving TB in different NFs.

Relationship between stable cesium concentration and body size of Japanese flounder Paralichthys olivaceus and the effect of a size-dependent shift in diet.

To understand the relationship between the radioactive cesium (Cs) concentration in muscle of Japanese flounder Paralichthys olivaceus and the species' biological characteristics (size, sex, and age) under conditions of ecological equilibrium (i.e., distributed among ecosystem components over sufficient time, and with nearly constant ratios of Cs concentration in organisms to the concentration in water) as existed before the accident at the Fukushima Dai-ichi Nuclear Power Station (FDNPS), Japan, in 2011, we examined stable Cs, as it is thought to exist in equilibrium in the environment and behave similarly to radioactive Cs in aquatic animals. The concentration of stable Cs in 241 P. olivaceus (range 216-782 mm total length [TL]) collected in Sendai Bay, approximately 90 km north of the FDNPS, in June-July 2015 was expressed as an exponential function with size as an independent variable; the results show the concentration of stable Cs doubled with an increase in TL of 442 mm. Next, to evaluate the cause of the size-dependent change in stable Cs concentration, we examined 909 individuals (200-770 mm TL) collected in September 2013-July 2015 to determine their feeding habit based on size. Analysis of the frequency of occurrence of prey organisms in stomach contents showed that sand lance Ammodytes japonicus (55-180 mm standard length [SL]) was the most consistently consumed across size classes. Analysis on a wet-mass basis showed that A. japonicus and anchovy Engraulis japonicus (65-130 mm SL) were the main food of P. olivaceus sized 200-599 mm TL, whereas chub mackerel Scomber japonicus (120-230 mm SL) and two species of flatfishes (180-205 mm SL) were abundant in the diet of P. olivaceus sized ≥600 mm TL. All these prey items were presumed to have similar concentrations of stable Cs. Based on the above, the effect of diet on the relationship between stable Cs in muscle and fish size was considered negligible. That the diet of P. olivaceus largely did not change with size was also confirmed by C and N stable isotope ratios in P. olivaceus and their prey species. Therefore, the Cs-size relationship is probably determined by changes in the balance between the rate of Cs intake from food and seawater and the excretion rate during growth, both of which change as functions of body mass. Values of stable Cs concentrations among environmental components and animals appear to be a valid indicator for understanding the radioactive Cs distribution in the marine environment and aquatic animals under the equilibrium state, as existed before the 2011 nuclear accident.

Modeling the Progression of Placental Transport from Early- to Late-Stage Pregnancy by Tuning Trophoblast Differentiation and Vascularization.

The early-stage placental barrier is characterized by a lack of fetal circulation and by a thick trophoblastic barrier, whereas the later-stage placenta consists of vascularized chorionic villi encased in a thin, differentiated trophoblast layer, ideal for nutrient transport. In this work, predictive models of early- and late-stage placental transport are created using blastocyst-derived placental stem cells (PSCs) by modulating PSC differentiation and model vascularization. PSC differentiation results in a thinner, fused trophoblast layer, as well as an increase in human chorionic gonadotropin secretion, barrier permeability, and secretion of certain inflammatory cytokines, which are consistent with in vivo findings. Further, gene expression confirms this shift toward a differentiated trophoblast subtype. Vascularization results in a molecule type- and size-dependent change in dextran and insulin permeability. These results demonstrate that trophoblast differentiation and vascularization have critical effects on placental barrier permeability and that this model can be used as a predictive measure to assess fetal toxicity of xenobiotic substances at different stages of pregnancy.

Size-dependent distribution of metal(loid)s in recent marine sediments of the Adriatic sea

This paper investigates occurrence of metal(loid)s, and size-dependent changes in their concentration in recent marine sediments from coastal and open-sea environments in the eastern Adriatic. Size fractionation of sediments was performed after removal of organic matter (OM), and the individual fractions, comprising particles below 8 μm, 4 μm, 2 μm, 1 μm and 0.45 μm, were analysed using HR ICP-MS. The concentrations of most elements increased with decreasing particle size, as a result of accumulation of clay minerals and Fe and Mn (oxyhydr)oxides. A decrease in concentrations was observed for Ba, Sr, Ti and U, due to lowering of the carbonate content and presence in the coarse-grained and heavy mineral fraction. The highest element concentrations were determined in the fraction comprising particles below 1 μm. Occasionally, depending on the sedimentological environment and/or the element in question, the peak concentrations occurred in the <2 μm or <0.45 μm fraction. The lowest size-dependent enrichment was observed for elements associated with aluminosilicates (Al, Be, Cs, Co, Fe, K, Li, Rb). A different size-dependent behaviour of the elements was observed between deep-sea areas and shallow environments under greater coastal influence, mainly due to differences in sediment sorting, and between the northern and central vs. southern Adriatic due to the different catchment geologies. The Fe and Mn (oxyhydr)oxides, abundant in the deep-sea sediments, played an important role in the geochemical cycle of As, Cd, Co, Mo, Sb and V.

Stable isotopes in eye lenses reveal migration and mixing patterns of diamond squid in the western North Pacific and its marginal seas

Abstract Knowledge of the movements of marine organisms is essential for effective conservation schemes. Here, we investigated the lifetime habitat use of diamond squid, Thysanoteuthis rhombus, collected in the western North Pacific and its marginal seas (the Sea of Japan and the East China Sea) during 2021–2022, whose migratory ecology is poorly known, using bulk stable nitrogen and carbon isotope ratios in eye lenses. From the eye lens isotope profiles, the chronology of the isotopic baseline of squid habitat was estimated by removing the effect of size-dependent changes of trophic position. Then, the baseline estimates were compared to the isoscapes of particulate organic matter. The baseline chronologies showed fluctuations during the paralarval and juvenile stages, becoming stable during the adult stage, suggesting that significant movements mainly occur during the early life stages due to current transport, with adults potentially not undertaking long-distance migrations. The squids in the marginal seas mostly originated from outside the subtropical gyre, while the squids in the subtropical gyre had various sources, including outside the gyre and southern and northern parts within the gyre, revealing a complex mixing pattern of the species. These results show that isotope chronology combined with baseline isoscapes are effective tools to understand animal migrations, which can help managing various cephalopods and fish.

Size-dependent colouration balances conspicuous aposematism and camouflage.

Colour is an important component of many different defensive strategies, but signal efficacy and detectability will also depend on the size of the coloured structures, and how pattern size interacts with the background. Consequently, size-dependent changes in colouration are common among many different species as juveniles and adults frequently use colour for different purposes in different environmental contexts. A widespread strategy in many species is switching from crypsis to conspicuous aposematic signalling as increasing body size can reduce the efficacy of camouflage, while other antipredator defences may strengthen. Curiously, despite being chemically defended, the gold-striped frog (Lithodytes lineatus, Leptodactylidae) appears to do the opposite, with bright yellow stripes found in smaller individuals, whereas larger frogs exhibit dull brown stripes. Here, we investigated whether size-dependent differences in colour support distinct defensive strategies. We first used visual modelling of potential predators to assess how colour contrast varied among frogs of different sizes. We found that contrast peaked in mid-sized individuals while the largest individuals had the least contrasting patterns. We then used two detection experiments with human participants to evaluate how colour and body size affected overall detectability. These experiments revealed that larger body sizes were easier to detect, but that the colours of smaller frogs were more detectable than those of larger frogs. Taken together our data support the hypothesis that the primary defensive strategy changes from conspicuous aposematism to camouflage with increasing size, implying size-dependent differences in the efficacy of defensive colouration. We discuss our data in relation to theories of size-dependent aposematism and evaluate the evidence for and against a possible size-dependent mimicry complex with sympatric poison frogs (Dendrobatidae).

Experimental evidence of a size-dependent sign change of the Seebeck coefficient of Bi nanowire arrays

The electrical transport in bismuth nanowires is strongly influenced by both sample geometry and crystallinity. Compared to bulk bismuth, the electrical transport in nanowires is dominated by size effects and influenced by surface states, which gain increasing relevance with increasing surface-to-volume ratios, i.e. with decreasing wire diameter. Bismuth nanowires with tailored diameter and crystallinity constitute, therefore, excellent model systems, allowing to study the interplay of the different transport phenomena. Here, we present temperature-dependent Seebeck coefficient and relative electrical resistance measurements of parallel bismuth nanowire arrays with diameters between 40 and 400 nm synthesized by pulsed electroplating in polymer templates. Both electrical resistance and Seebeck coefficient exhibit a non-monotonic temperature dependence, with the sign of the Seebeck coefficient changing from negative to positive with decreasing temperature. The observed behavior is size-dependent and is attributed to limitations of the mean free path of the charge carriers within the nanowires. The observed size-dependent Seebeck coefficient and in particular the size-dependent sign change opens a promising avenue for single-material thermocouples with p- and n-legs made from nanowires with different diameters.

Delineation of proteome changes driven by cell size and growth rate.

Increasing cell size drives changes to the proteome, which affects cell physiology. As cell size increases, some proteins become more concentrated while others are diluted. As a result, the state of the cell changes continuously with increasing size. In addition to these proteomic changes, large cells have a lower growth rate (protein synthesis rate per unit volume). That both the cell’s proteome and growth rate change with cell size suggests they may be interdependent. To test this, we used quantitative mass spectrometry to measure how the proteome changes in response to the mTOR inhibitor rapamycin, which decreases the cellular growth rate and has only a minimal effect on cell size. We found that large cell size and mTOR inhibition, both of which lower the growth rate of a cell, remodel the proteome in similar ways. This suggests that many of the effects of cell size are mediated by the size-dependent slowdown of the cellular growth rate. For example, the previously reported size-dependent expression of some senescence markers could reflect a cell’s declining growth rate rather than its size per se. In contrast, histones and other chromatin components are diluted in large cells independently of the growth rate, likely so that they remain in proportion with the genome. Finally, size-dependent changes to the cell’s growth rate and proteome composition are still apparent in cells continually exposed to a saturating dose of rapamycin, which indicates that cell size can affect the proteome independently of mTORC1 signaling. Taken together, our results clarify the dependencies between cell size, growth, mTOR activity, and the proteome remodeling that ultimately controls many aspects of cell physiology.

Increasing cell size remodels the proteome and promotes senescence

Cell size is tightly controlled in healthy tissues, but it is unclear how deviations in cell size affect cell physiology. To address this, we measured how the cell's proteome changes with increasing cell size. Size-dependent protein concentration changes are widespread and predicted by subcellular localization, size-dependent mRNA concentrations, and protein turnover. As proliferating cells grow larger, concentration changes typically associated with cellular senescence are increasingly pronounced, suggesting that large size may be a cause rather than just a consequence of cell senescence. Consistent with this hypothesis, larger cells are prone to replicative, DNA-damage-induced, and CDK4/6i-induced senescence. Size-dependent changes to the proteome, including those associated with senescence, are not observed when an increase in cell size is accompanied by an increase in ploidy. Together, our findings show how cell size could impact many aspects of cell physiology by remodeling the proteome and provide a rationale for cell size control and polyploidization.

Real-Time Nanoparticle Characterization Through Optofluidic Force Induction

We propose and demonstrate a scheme for optical nanoparticle characterization, optofluidic force induction (OF2i), which achieves real-time optical counting with single-particle sensitivity, high throughput, and for particle sizes ranging from tens of nanometers to several micrometers. The particles to be analyzed flow through a microfluidic channel alongside a weakly focused laser vortex beam, which accomplishes two-dimensional trapping of the particles in the transverse directions and size-dependent velocity changes due to the optical forces in the longitudinal direction. Upon monitoring the trajectories and velocity changes of each individually tracked particle, we obtain detailed information about the number-based particle size distribution. A parameter-free model based on Maxwell’s equations and Mie theory is shown to provide very good agreement with the experimental results for standardized particles of spherical shape. Our results prove that OF2i can provide a flexible work bench for numerous pharmaceutical and technological applications, as well as for medical diagnostics.Received 25 April 2022Revised 24 June 2022Accepted 27 June 2022DOI:https://doi.org/10.1103/PhysRevApplied.18.024056© 2022 American Physical SocietyPhysics Subject Headings (PhySH)Research AreasClassical opticsLight-matter interactionMetrologyMicrofluidicsOptical forcesPhysical SystemsColloidsNanoparticlesSuspensionsAtomic, Molecular & OpticalCondensed Matter, Materials & Applied PhysicsFluid DynamicsPolymers & Soft Matter

Substrate size-dependent conformational changes of bacterial pectin-binding protein crucial for chemotaxis and assimilation

Gram-negative Sphingomonas sp. strain A1 exhibits positive chemotaxis toward acidic polysaccharide pectin. SPH1118 has been identified as a pectin-binding protein involved in both pectin chemotaxis and assimilation. Here we show tertiary structures of SPH1118 with six different conformations as determined by X-ray crystallography. SPH1118 consisted of two domains with a large cleft between the domains and substrates bound to positively charged and aromatic residues in the cleft through hydrogen bond and stacking interactions. Substrate-free SPH1118 adopted three different conformations in the open form. On the other hand, the two domains were closed in substrate-bound form and the domain closure ratio was changed in response to the substrate size, suggesting that the conformational change upon binding to the substrate triggered the expression of pectin chemotaxis and assimilation. This study first clarified that the solute-binding protein with dual functions recognized the substrate through flexible conformational changes in response to the substrate size.

Investigation of Quantum Size Effects on the Optical Absorption in Ultrathin Single Quantum Well Solar Cell Embedded as a Nanophotonic Resonator

Subwavelength optical nanocavity using semiconductor nanostructures is a key nanophotonic approach for various optoelectronic devices. In such low-dimensional systems, size-dependent changes can arise due to quantum confinement (QC). In this article, the implications of quantum-size effects on the light harvesting in ultrathin single quantum well solar cell (SQWSC) are analyzed. This device is based on silicon (barrier)/germanium (QW) nanostructures integrated as a deep-subwavelength nanophotonic resonator. Compared with the state-of-the-art, the novelty of this article consists of the investigation of the synergy between photonic and electronic confinements at both functional materials and device levels. It is shown that QC effects enhance the optical absorption efficiency in both low-dimensional germanium single layers and QW structures. However, this is affected by the barrier heights and the interface states. In the SQWSC devices, the changes of the photocurrent output, the resonance condition and the absorption edge as a function of QW thickness are explained based on the optical field and the local absorption distributions. Shorter nanocavity lengths with thinner QW nanoabsorbers result in blue-shifted resonance wavelength, suitable maximum optical field intensity in the visible wavelengths range as well as promoted photonic confinement. This enables an enhancement of the optical absorption efficiency relative to thick counterparts. The nonlinearity in the thickness-related photocurrent implies a drastic reduction in QW thickness while preserving a high photocurrent level. The presented considerations in SQWC could be extended as design rules for the optimization of the photocurrent in derived multiple quantum well systems and for relevant color-neutral semitransparent devices.

Multiomics Data Integration Identifies New Molecular Signatures for Abdominal Aortic Aneurysm and Aortic Occlusive Disease: Implications for Early Diagnosis, Prognosis, and Therapeutic Targets.

Cardiovascular disease (CVD) is the leading cause of death among adults in developed countries. Among CVDs, abdominal aortic aneurysm (AAA) and aortic occlusive disease (AOD) are of great public health importance because of the high mortality rate in the elderly population. Despite significant molecular insights into AAA and AOD, the molecular mechanisms of these diseases remain unclear, and the current lack of robust diagnostic and prognostic biomarkers requires novel approaches to biomarker discovery and molecular targeting. In this study, we performed a comparative analysis of genome-wide expression data from patients with large AAA (n = 29), small AAA (n = 20), AOD (n = 9), and controls (n = 10). Specifically, we identified the differentially expressed genes and associated molecular pathways and biological processes (BPs) in each disease. Using a systems science approach, these data were linked to comprehensive human biological networks (i.e., protein-protein interaction, transcriptional regulatory, and metabolic networks) to identify molecular signatures of the salient mechanisms of AAA and AOD. Significant alterations in lipid metabolism and valine, leucine, and isoleucine metabolism, as well as neurodegenerative diseases and sex differences in the pathogenesis of AAA and AOD were identified. In the presence of aneurysm, size-dependent changes in lipid metabolism were observed. In addition, molecules and signaling pathways related to immunity, inflammation, infectious disease, and oxidative phosphorylation were identified in common. The results of the comparative and integrative analyzes revealed important clues to disease mechanisms and reporter molecules at various levels that warrant future development as potential prognostic biomarkers and putative therapeutic targets.

Explanation of the Opposing Shifts in the Absorption Edge and the Optical Resonance in CuFeS2 Nanoparticles

Size-dependent change of the electronic band structure is one of the key features of nanoparticles in the quantum confinement region. CuFeS2 nanoparticles have a strong absorption feature in the visible region that has, controversially, been described as neither an excitonic transition nor a free carrier plasmon oscillation. Instead, the absorption feature in CuFeS2 nanoparticles has been attributed to quasi-static optical resonances from inter-band transitions between the valence band (VB), intermediate band (IB), and conduction band (CB). As such, we hypothesized that the feature should be subject to quantum confinement effects through modification of the electronic bands. In this paper, we show experimentally that the optical resonance absorption peak red-shifts and the optical band gap blue-shifts as the particle size decreases. Through density functional theory (DFT) and the tight binding (TB) modeling, we elucidate the size dependence of the band structure, especially focusing on the change in the IB. Using a Lorentzian oscillator optical model to simulate the absorption spectrum with inputs from the DFT-calculated band structure and band shifts from the TB model, we find that the size-dependent shifts of the optical resonance peak position in CuFeS2 are due to a tri-band quantum confinement effect that results in both the VB to IB and IB to CB gap expansion that accompanies a decrease in particle size. We also find that the transitions between the IB and CB play only a minor role in the optical spectrum. Moreover, the linear optical Lorentzian model predicts that the optical resonance peak is tunable across the visible range by partially filling the IB, lowering the CB, or expanding the IB.

Spatial and Temporal Resolution of Luminescence Quenching in Small Upconversion Nanocrystals.

Luminescent upconversion nanocrystals (UCNCs) have become one of the most promising nanomaterials for biosensing, imaging, and theranostics. However, their ultimate translation into robust luminescent probes for daily use in biological and medical laboratories requires comprehension and control of the many possible deactivation pathways that cause upconversion luminescence (UCL) quenching. Here, we demonstrate that thorough modeling of UCL rise and decay kinetics using a freely accessible software can identify the UCL quenching mechanisms in small (<40 nm) UCNCs with spatial and temporal resolution. Applied to the most relevant β-NaYF4:Yb3+,Er3+ UCNCs, our model showed that only a few distinct nonradiative low-energy transitions were deactivated via specific solvent and ligand vibrations with a strong downstream effect on the population and depopulation dynamics of the emitting states. UCL quenching could penetrate ca. 4 nm inside the UCNC, which resulted in significant size-dependent changes of UCL intensities and spectra. Despite the large surface-to-volume ratios and UCL quenching via the UCNC surface, we found strong contributions of the outer layers to the overall UCL, which will be highly important for the design of UCNPs to investigate biomolecular interactions via distance-dependent energy transfer methods. Our advanced kinetic model is easily scalable to different UCNC architectures, environments, and energy transfer interactions such that relatively simple modeling of UCL kinetics can be used for efficiently optimizing UCNCs for their final application as practical luminescent probes.

Two-Dimensional CdSe-PbSe Heterostructures and PbSe Nanoplatelets: Formation, Atomic Structure, and Optical Properties.

Cation exchange enables the preparation of nanocrystals (NCs), which are not reachable by direct synthesis methods. In this work, we applied Pb2+-for-Cd2+ cation exchange on CdSe nanoplatelets (NPLs) to prepare two-dimensional CdSe-PbSe heterostructures and PbSe NPLs. Lowering the reaction temperature slowed down the rate of cation exchange, making it possible to characterize the intermediary NCs ex situ with atomically resolved high-angle annular dark-field scanning transmission electron microscopy and optical spectroscopy. We observe that the Pb2+-for-Cd2+ cation exchange starts from the vertices of the NPLs and grows into the zinc blende CdSe (zb-CdSe) lattice as a rock salt PbSe phase (rs-PbSe), while the anion (selenium) sublattice is being preserved. In agreement with previous works on CdTe-PbTe films, the interfaces between zb-CdSe and rs-PbSe consist of shared {001} and {011} planes. The final PbSe NPLs are highly crystalline and contain protrusions at the edges, which are slightly rotated, indicating an atomic reconfiguration of material. The growth of PbSe domains into CdSe NPLs could also be monitored by the emission peak shift as a function of the exchange time. Temperature-dependent emission measurements confirm a size-dependent change of the band gap energy with temperature and reveal a strong influence of the anisotropic shape. Time-resolved photoluminescence measurements between 4 and 30 K show a dark-bright exciton-state splitting different from PbSe QDs with three-dimensional quantum confinement.

Functionalization of Gold Nanoparticles with Monosaccharide Mannose

Gold nanoparticles have found a wide range of application in biomedical sciences. Unique properties of these metal nanoparticles include surface plasmon resonance and size dependent colour change. Various molecules have been functionalized on the gold nanoparticles surface but carbohydrates have garnered attention due to their properties and their role in living systems. However certain challenges make carbohydrate-gold nanoparticles association difficult to obtain and stabilize. This study was carried out to chemically remodel gold nanoparticles by adding a monosaccharide mannose to its surface. A modified phase transfer method was used to synthesize gold nanoparticles. The surface of the nanoparticles was fixed with cyanuric chloride to serve as a linker. Mannose was then linked to the linker molecule. All three stages of the process, gold nanoparticles, and gold nanoparticles with linker and gold nanoparticles with the carbohydrate were analyzed for size and stability. Zeta potential and UV-vis data exhibited stable gold nanoparticles dispersion, successful binding of linker molecule as well as the carbohydrate. This study shows a simple, cost-effective and robust method of glycomodification of gold nanoparticles surface which can further find use in wide ranging applications.

Ontogenetic changes in limb posture, kinematics, forces and joint moments in American alligators (Alligator mississippiensis).

As animals increase in size, common patterns of morphological and physiological scaling may require them to perform behaviors such as locomotion while experiencing a reduced capacity to generate muscle force and an increased risk of tissue failure. Large mammals are known to manage increased mechanical demands by using more upright limb posture. However, the presence of such size-dependent changes in limb posture has rarely been tested in animals that use non-parasagittal limb kinematics. Here, we used juvenile to subadult American alligators (total length 0.46-1.27 m, body mass 0.3-5.6 kg) and examined their limb kinematics, forces, joint moments and center of mass (CoM) to test for ontogenetic shifts in posture and limb mechanics. Larger alligators typically walked with a more adducted humerus and femur and a more extended knee. Normalized peak joint moments reflected these postural patterns, with shoulder and hip moments imposed by the ground reaction force showing relatively greater magnitudes in the smallest individuals. Thus, as larger alligators use more upright posture, they incur relatively smaller joint moments than smaller alligators, which could reduce the forces that the shoulder and hip adductors of larger alligators must generate. The CoM shifted nonlinearly from juveniles through subadults. The more anteriorly positioned CoM in small alligators, together with their compliant hindlimbs, contributes to their higher forelimb and lower hindlimb normalized peak vertical forces in comparison to larger alligators. Future studies of alligators that approach maximal adult sizes could give further insight into how animals with non-parasagittal limb posture modulate locomotor patterns as they increase in mass and experience changes in the CoM.

Allosteric Regulation of 3CL Protease of SARS-CoV-2 and SARS-CoV Observed in the Crystal Structure Ensemble

The 3C-like protease (3CLpro) of SARS-CoV-2 is a potential therapeutic target for COVID-19. Importantly, it has an abundance of structural information solved as a complex with various drug candidate compounds. Collecting these crystal structures (83 Protein Data Bank (PDB) entries) together with those of the highly homologous 3CLpro of SARS-CoV (101 PDB entries), we constructed the crystal structure ensemble of 3CLpro to analyze the dynamic regulation of its catalytic function. The structural dynamics of the 3CLpro dimer observed in the ensemble were characterized by the motions of four separate loops (the C-loop, E-loop, H-loop, and Linker) and the C-terminal domain III on the rigid core of the chymotrypsin fold. Among the four moving loops, the C-loop (also known as the oxyanion binding loop) causes the order (active)–disorder (collapsed) transition, which is regulated cooperatively by five hydrogen bonds made with the surrounding residues. The C-loop, E-loop, and Linker constitute the major ligand binding sites, which consist of a limited variety of binding residues including the substrate binding subsites. Ligand binding causes a ligand size dependent conformational change to the E-loop and Linker, which further stabilize the C-loop via the hydrogen bond between the C-loop and E-loop. The T285A mutation from SARS-CoV 3CLpro to SARS-CoV-2 3CLpro significantly closes the interface of the domain III dimer and allosterically stabilizes the active conformation of the C-loop via hydrogen bonds with Ser1 and Gly2; thus, SARS-CoV-2 3CLpro seems to have increased activity relative to that of SARS-CoV 3CLpro.

The evolution of size-dependent competitive interactions promotes species coexistence.

Theory indicates that competing species coexist in a community when intraspecific competition is stronger than interspecific competition. When body size determines the outcome of competitive interactions between individuals, coexistence depends also on how resource use and the ability to compete for these resources change with body size. Testing coexistence theory in size-structured communities, therefore, requires disentangling the effects of size-dependent competitive abilities and niche shifts. Here, we tested the hypothesis that the evolution of species- and size-dependent competitive asymmetries increased the likelihood of coexistence between interacting species. We experimentally estimated the effects of size-dependent competitive interactions on somatic growth rates of two interacting fish species, Trinidadian guppies Poecilia reticulata and killifish Rivulus hartii. We controlled for the effects of size-dependent changes in the niche at two competitive settings representing the early (allopatric) and late (sympatric) evolutionary stages of a killifish-guppy community. We fitted the growth data to a model that incorporates species- and size-dependent competitive asymmetries to test whether changes in the competitive interactions across sizes increased the likelihood of species coexistence from allopatry to sympatry. We found that guppies are competitively superior to killifish but were less so in sympatric populations. The decrease in the effects of interspecific competition on the fitness of killifish and increase in the interspecific effect on guppies' fitness increased the likelihood that sympatric guppies and killifish will coexist. However, while the competitive asymmetries between the species changed consistently between allopatry and sympatry between drainages, the magnitude of the size-dependent competitive asymmetries varied between drainages. These results demonstrate the importance of integrating evolution and trait-based interactions into the research on how species coexist.