Universal Hyperuniform Organization in Looped Leaf Vein Networks.

The leaf vein network is a hierarchical vascular system that transports water and nutrients to the leaf cells. The thick primary veins form a branched network, while the secondary veins can develop closed loops forming a well-defined cellular structure. Through extensive analysis of a variety of distinct leaf species, we discover that the apparently disordered cellular structures of the secondary vein networks exhibit a universal hyperuniform organization and possess a hidden order on large scales. Disorder hyperuniform systems lack conventional long-range order, yet they completely suppress normalized infinite-wavelength density fluctuations like crystals. Specifically, we find that the distributions of the geometric centers associated with the vein network loops possess a vanishing static structure factor in the limit that the wave number k goes to 0, i.e., S(k)∼k^{α}, where α≈0.64±0.021, providing an example of class III hyperuniformity in biology. This hyperuniform organization leads to superior efficiency of diffusive transport, as evidenced by the much faster convergence of the time-dependent spreadability S(t) to its longtime asymptotic limit, compared to that of other uncorrelated or correlated disordered but nonhyperuniform organizations. Our results also have implications for the discovery and design of novel disordered network materials with optimal transport properties.

Transcriptome Changes Reveal the Toxic Mechanism of Cadmium and Lead Combined Exposure on Silk Production and Web-Weaving Behavior of Spider A. ventricosus.

The combined exposure of multiple metals imposes a substantial burden on the ecophysiological functions in organisms; however, the precise mechanism(s) remains largely unknown. Here, adult female A. ventricosus were exposed to single and combined exposure to cadmium (Cd) and lead (Pb) through the food chain. The aim was to explore the combined toxicity of these metals on silk production and web-weaving behavior at physiological, cellular morphological, and transcriptomic levels. The Cd and Pb combined exposure significantly inhibited the ability of silk production and web-weaving, including reduced silk fiber weight and diameter of single strands, lowered weaving position, induced nocturnal weaving, and increased instances of no-web, and showed a dose-response relationship on the Cd and Pb bioaccumulation. Concurrently, severe oxidative stress and degenerative changes in cells were observed. In addition, the combined pollution of Cd and Pb demonstrated synergistic effects, influenced by variations in concentration, on the enrichment of metals, inhibition of silk weight, oxidative damage, and cellular degeneration. At the transcriptome level, the upregulated ampullate spidroin genes and downregulated amino acid anabolic genes, upregulated Far genes and downregulated cytoskeleton-related TUBA genes, and overexpressed AChE and Glu genes may tend to present promising potential as biomarkers for silk protein synthesis, cellular degeneration, and neurotransmitter induction. This study offers an enormous capability for a comprehensive understanding of the eco-toxicological effects and mechanisms of multiheavy metals pollution.

Geometric Dependence of 3D Collective Cancer Invasion.

Metastasis of mesenchymal tumor cells is traditionally considered as a single-cell process. Here, we report an emergent collective phenomenon in which the dissemination rate of mesenchymal breast cancer cells from three-dimensional tumors depends on the tumor geometry. Combining experimental measurements and computational modeling, we demonstrate that the collective dynamics is coordinated by the mechanical feedback between individual cells and their surrounding extracellular matrix (ECM). We find the tissue-like fibrous ECM supports long-range physical interactions between cells, which turn geometric cues into regulated cell dissemination dynamics. Our results suggest that migrating cells in three-dimensional ECM represent a distinct class of an active particle system in which the collective dynamics is governed by the remodeling of the environment rather than direct particle-particle interactions.

Predicting maximally random jammed packing density of non-spherical hard particles via analytical continuation of fluid equation of state.

Dense packings of hard particles are useful models for condensed matters including crystalline and glassy state of solids, simple liquids, granular materials and composites. It is very challenging to devise predictive theories of random packings, due to the intrinsic non-equilibrium and non-local nature of the system. Here, we develop a formalism for accurately predicting the density (i.e., fraction of space covered by the particles) ηMRJ of the maximally random jammed (MRJ) packing state of a wide spectrum of congruent non-spherical hard particles in three-dimensional Euclidean space [Doublestruck R]3, via analytical continuation of the corresponding fluid equation of state (EOS). This formalism is based on the assumption that the fluid branch of the EOS can be analytically extended into the meta-stable region, which leads to a diverging pressure at the jamming point (i.e., the MRJ state). This allows us to estimate ηMRJ as the pole in the EOS, which can be expressed in terms of the virial coefficients encoding intrinsic local n-body packing information of the particles, and depending alone on particle shape. The accuracy of our formalism is verified using the hard sphere system and is subsequently applied to a wide spectrum of non-spherical shapes. The predictions are compared to numerical results whenever possible, and excellent agreements are found.

Performance of the asymptotic expansion method to derive equations of state for hard polyhedron fluids.

The asymptotic expansion method is used to derive analytical expressions for the equations of state of 14 hard polyhedron fluids such as cube, octahedron, rhombic dodecahedron, etc., by knowing the values of only the first eight virial coefficients. The results for the compressibility factor were compared with the most recent ones reported in the literature and obtained by computer simulations. Good results (averaged deviations below 1%) are found for the 8 fluids studied. On the other hand, the method seems to be inadequate, at least with the presently available values for the virial coefficients and compressibility factors, for 4 polyhedron fluids. Unfortunately, sometimes the method does not give low deviations at high densities or it gives excessively high values for the location of the pole. As an advantage, the value of the pole for the compressibility factor is always positive, which is not observed when other methods are used.

Correction: Equations of the state of hard sphere fluids based on recent accurate virial coefficients B5-B12.

Correction for 'Equations of the state of hard sphere fluids based on recent accurate virial coefficients B5-B12' by Jianxiang Tian et al., Phys. Chem. Chem. Phys., 2019, 21, 13070-13077. DOI.

Absorbing-active transition in a multi-cellular system regulated by a dynamic force network.

Collective cell migration in 3D extracellular matrix (ECM) is crucial to many physiological and pathological processes. Migrating cells can generate active pulling forces via actin filament contraction, which are transmitted to the ECM fibers and lead to a dynamically evolving force network in the system. Here, we elucidate the role of this force network in regulating collective cell behaviors using a minimal active-particle-on-network (APN) model, in which active particles can pull the fibers and hop between neighboring nodes of the network following local durotaxis. Our model reveals a dynamic transition as the particle number density approaches a critical value, from an "absorbing" state containing isolated stationary small particle clusters, to an "active" state containing a single large cluster undergoing constant dynamic reorganization. This reorganization is dominated by a subset of highly dynamic "radical" particles in the cluster, whose number also exhibits a transition at the same critical density. The transition is underlaid by the percolation of "influence spheres" due to the particle pulling forces. Our results suggest a robust mechanism based on ECM-mediated mechanical coupling for collective cell behaviors in 3D ECM.

Equations of the state of hard sphere fluids based on recent accurate virial coefficients B5-B12.

By using the recently published simulation data for the compressibility factor (M. N. Bannerman, L. Lue and L. V. Woodcock, J. Chem. Phys., 2010, 132, 084507; S. Pieprzyk, M. N. Bannerman, A. C. Branka, M. Chudak and D. Heyes, Phys. Chem. Chem. Phys., 2019, 21, 6886) and the recently published numerical virial coefficients B5-B12 (R. J. Wheatley, Phys. Rev. Lett., 2013, 110, 200601; C. Zhang and B. M. Pettitt, Mol. Phys., 2014, 112, 1427; A. J. Schultz and D. A. Kofke, Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys., 2014, 90, 023301) of hard sphere fluids, we herein report the updated versions of the equations of the state of hard sphere fluids based on the asymptotic expansion method (J. Tian, H. Jiang, Y. Gui and A. Mulero, Phys. Chem. Chem. Phys., 2009, 11, 11213), the Padé approximants (N. Clisby and B. McCoy, J. Stat. Phys., 2006, 122, 15) and the exponential approximants (N. S. Barlow, A. J. Schultz, S. J. Weinstein and D. A. Kofke, J. Chem. Phys., 2012, 137, 204102) and compare them with other recently published equations. It is found that the so-called mKLM equation describes the relation of the compressibility factor versus the packing fraction with the highest accuracy. The asymptotic expansion method based equation Z(-5, 2) is recommended to well describe both the virial coefficients and the compressibility factor.

New equations of state for the hard polyhedron fluids.

In this paper, we derived a new equation of state for hard polyhedron fluids that is obtained by the knowledge of virial coefficients and a fit to the computer simulation data for the compressibility factor, and which contains two adjustable parameters. This equation reproduces exactly the correct known virial coefficients up to the ninth one and also the compressibility factor data with high accuracy, the absolute average deviations (AADs) being 0.05% for the stable state and 1.12% for both stable and metastable states for the hard tetrahedron fluid. For 12 of the other hard polyhedron fluids, it reproduces exactly the correct known virial coefficients up to the eighth one and also the compressibility factor data in the stable state with AADs less than 0.25%, with the only exception being the triangular prism polyhedron fluid.

Oriented collagen fibers direct tumor cell intravasation.

In this work, we constructed a Collagen I-Matrigel composite extracellular matrix (ECM). The composite ECM was used to determine the influence of the local collagen fiber orientation on the collective intravasation ability of tumor cells. We found that the local fiber alignment enhanced cell-ECM interactions. Specifically, metastatic MDA-MB-231 breast cancer cells followed the local fiber alignment direction during the intravasation into rigid Matrigel (∼10 mg/mL protein concentration).

Metatranscriptome analysis of the intestinal microorganisms in Pardosa pseudoannulata in response to cadmium stress.

Cadmium (Cd) generates a variety of physiological and ecological toxicity to spiders. However, little is known about the effects of Cd on symbiotic bacteria of spiders. Metatranscriptomics is increasing our knowledge of microorganisms in environment. To better understand the impact of Cd on the symbiotic bacteria of spiders, we generated and compared the metatranscriptomes of the intestinal microorganisms of Pardosa pseudoannulata with and without Cd stress. The community structure of intestinal microorganisms in P. pseudoannulata was composed of 4 kingdoms, namely bacteria, viruses, eukaryotes and archaea, including 46 phyla, 97 classes, 184 orders, 339 families, 470 genera, and 598 species. The abundance of eukaryotes, bacteria and viruses was decreased by 0.14%, 1.22% and 2.52% respectively while the archaea was increased by 99.16% when under Cd stress. We identified 1519 differentially expressed genes (DEGs), including 770 up-regulated and 749 down-regulated genes. The results of KEGG annotation revealed that the expression of genes that are involved in the carbon metabolism, protein and amino acid metabolism and synthesis, glucose metabolism, oxidative phosphorylation, and glutathione metabolism were influenced by Cd. Collectively, these findings showed that Cd significantly impacted the community structure and expression of related functional genes of intestinal microorganisms in P. pseudoannulata.

Transcriptome assembly and expression profiling of the molecular responses to cadmium toxicity in cerebral ganglia of wolf spider Pardosa pseudoannulata (Araneae: Lycosidae).

Cadmium (Cd) is a heavy metal that can cause irreversible toxicity to animals, and is an environmental pollutant in farmlands. Spiders are considered to be an excellent model for investigating the impacts of heavy metals on the environment. To date, the changes at the molecular level in the cerebral ganglia of spiders are poorly understood. Cd exposure leads to strong damage in the nervous system, such as apoptosis and necrosis of nerve cells, therefore we conducted a transcriptomic analysis of Pardosa pseudoannulata cerebral ganglia under Cd stress to profile differential gene expression (DGE). We obtained a total of 123,328 assembled unigenes, and 1441 Cd stress-associated DEGs between the Cd-treated and control groups. Expression profile analysis demonstrated that many genes involved in calcium signaling, cGMP-PKG signaling, tyrosine metabolism, phototransduction-fly, melanogenesis and isoquinoline alkaloid biosynthesis were up-regulated under Cd stress, whereas oxidative phosphorylation-related, nervous disease-associated, non-alcoholic fatty liver disease-associated, and ribosomal-associated genes were down-regulated. Here, we provide a comprehensive set of DEGs influenced by Cd stress, and heavy metal stress, and provide new information for elucidating the neurotoxic mechanisms of Cd stress in spiders.

Review: biosafety assessment of Bt rice and other Bt crops using spiders as example for non-target arthropods in China.

Since the birth of transgenic crops expressing Bacillus thuringiensis (Bt) toxin for pest control, the public debate regarding ecological and environmental risks as well as benefits of Bt crops has continued unabated. The impact of Bt crops, especially on non-target invertebrates, has received particular attention. In this review, we summarize and analyze evidences for non-target effects of Bt rice on spiders, major predators in rice fields. Bt rice has been genetically modified to express the Bt protein, which has been shown to be transferred and accumulate in spiders as part of their food chain. Moreover, the Bt protein exhibits unintended effects on the physiology of spiders and spreads to higher trophic levels. Spiders possess unique physiological and ecological characteristics, revealing traits of surrogate species, and are thus considered to be excellent non-target arthropod model systems for study of Bt protein impacts. Due to the complexities of Bt protein transfer and accumulation mechanisms, as well as the apparent lack of information about resulting physiological, biochemical, and ecological effects on spiders, we raise questions and provide recommendations for promising further research.

Structural, electronic, and photophysical properties of thieno-expanded tricyclic purine analogs: a theoretical study.

Modified forms of DNA are under intense research because of their potential applications in nanotechnology and medical science. In the present work, comprehensive theoretical investigations into the structural, electronic, and optical properties of four newly designed thieno-expanded base analogs, namely ttA, ttG, ttX, and ttHX, have been performed. The results are compared against the findings obtained for the natural ones. Geometrically, ttA and ttG have nonplanar ground-state geometries caused by the pyramidalization of the amino groups, while ttX and ttHX have planar geometries. Electronically, the ionization potentials and HOMO-LUMO gaps are smaller than natural ones, while the electron affinities are larger than natural ones. The nature of the low-lying excited states is discussed, and it was found that the lowest transitions are of ππ* nature and were mainly dominated by the configuration HOMO → LUMO. The calculated excitation maxima are 283, 302, 294, and 290 nm for ttA, ttG, ttX, and ttHX, respectively, and they are greatly red-shifted compared with natural bases. In the gas phase, the fluorescence from them would be expected to occur around 291, 331, 317, and 323 nm, respectively. The effects of micro-hydration, bulk water solution, and base pairing with their complementary natural bases on the low-lying electronic transitions of these modified bases were also examined.

Artificial Neural Network Model for the Prediction of Thermal Conductivity of Saturated Liquid Refrigerants and n-Alkanes.

In this paper, a feed-forward back-propagation artificial neural network (ANN) is proposed to correlate and predict the thermal conductivity from the triple point temperature up to 0.98 times critical temperature (T c) for 23 refrigerants and 11 n-alkanes. It requires the temperature (T) as well as the molecular mass (M), acentric factor (ω), critical temperature, and critical pressure (P c) as input variables. The optimal ANN model is obtained by a trial-and-error procedure and consists of the input layer and the output layer together with one hidden layer with seven neurons. This ANN model can not only correlate the thermal conductivity but also accurately predict the thermal conductivity of refrigerants and n-alkanes. The correlation coefficients (R) in the training and testing phases are 0.9994 and 0.9993, respectively. Furthermore, the average absolute deviation (AAD) values are less than 1% for 14 out of 34 fluids, less than 2% for 28 fluids, and less than 4.5% for all the considered fluids.

Surface Tension for Silanes, Refrigerants, and Carboxylic Acids: Simple Corresponding State Correlations versus DIPPR Data.

A simple corresponding state-based correlation, whose analytical expression contains just one term with an exponential function, is proposed to calculate the surface tension of 36 silanes, 29 carboxylic acids, and 81 refrigerants as a function of temperature. This correlation only requires critical temperature, maximum value of surface tension, and its corresponding temperature in the DIPPR database as inputs for each liquid considered. The correlation allows us to calculate the accepted DIPPR data for silanes with a mean absolute average deviation (AAD) of 2.75%, 2.42% for acids, and 3.32% for refrigerants. Moreover, it gives AADs below 3% for 99 fluids. The mean deviation for the 146 fluids is 3.0%, which is practically equal to the results obtained when two terms are used in the analytical expression.

Cadmium-induced oxidative stress and transcriptome changes in the wolf spider Pirata subpiraticus.

Spiders are believed to have enormous potential for indicating heavy metal pollution in ecosystems. The diversity of influencing factors caused significant differences in the toxicities of cadmium (Cd) on spiders. There is limited understanding of the underlying mechanism and response to acute Cd exposure at different concentrations and different poisoning times. We exposed adult female P. subpiraticus to 0.2 mM and 2 mM Cd for 6 and 12 h, respectively, to explore acute Cd toxicities by RNA-seq. We measured the bioaccumulation levels in P. subpiraticus and tested the activities of superoxide dismutase (SOD) and glutathione S-transferase (GST). There were 187, 292, 101 and 155 differentially expressed genes (DEGs) after exposure to 0.2 mM and 2 mM Cd for 6 and 12 h, respectively. The results revealed that Cd accumulated in P. subpiraticus, changed the SOD and GST activities, and caused significant adverse effects at the molecular level on metabolism and immune and oxidative stress, with time- and concentration-dependent differences. Transcriptome analysis showed that acute Cd exposure depressed lipid metabolism and induced protein metabolism, especially serine metabolism. Genes encoding lipoproteins were depressed when exposed to 0.2 mM Cd, while fatty acid-related genes were downregulated under 2 mM Cd stress. In total, 46 cuticle-related genes were upregulated, and 6 cytoskeleton-related genes changed notably in the immune process. Peroxidase-related genes were further upregulated significantly. Meanwhile, the pathways related to metabolism, immunity and oxidative stress were significantly enriched. This report illustrated that acute Cd exposure exerts toxicities on P. subpiraticus and the spiders against acute Cd toxicities by selective differential expression of the genes associated with the physiological process of metabolism and immune and antioxidant stress. This study provides a comprehensive transcriptional basis for understanding the response of the P. sublimations to heavy metals at different concentrations and different treatment times.

Asymptotic expansion based equation of state for hard-disk fluids offering accurate virial coefficients.

Despite the fact that more than 30 analytical expressions for the equation of state of hard-disk fluids have been proposed in the literature, none of them is capable of reproducing the currently accepted numeric or estimated values for the first eighteen virial coefficients. Using the asymptotic expansion method, extended to the first ten virial coefficients for hard-disk fluids, fifty-seven new expressions for the equation of state have been studied. Of these, a new equation of state is selected which reproduces accurately all the first eighteen virial coefficients. Comparisons for the compressibility factor with computer simulations show that this new equation is as accurate as other similar expressions with the same number of parameters. Finally, the location of the poles of the 57 new equations shows that there are some particular configurations which could give both the accurate virial coefficients and the correct closest packing fraction in the future when higher than the tenth virial coefficients are numerically calculated.

New virial equation of state for hard-disk fluids.

Although many equations of state of hard-disk fluids have been proposed, none is capable of reproducing the currently calculated or estimated values of the first eighteen virial coefficients at the same time as giving very good accuracy when compared with computer simulation values for the compressibility factor over the whole fluid range. A new virial-based expression is here proposed which achieves these aims. For that, we use the fact that the currently accepted estimated values for the highest virial coefficients behave linearly with their order, and also that virial coefficients must have a limiting behaviour that permits the closest packing limit in the compressibility factor to be also adequately reproduced.

Equation of state for hard-sphere fluids offering accurate virial coefficients.

The asymptotic expansion method is extended by using currently available accurate values for the first ten virial coefficients for hard sphere fluids. It is then used to yield an equation of state for hard sphere fluids, which accurately represents the currently accepted values for the first sixteen virial coefficients and compressibility factor data in both the stable and the metastable regions of the phase diagram.