A multi-species co-occurrence index to avoid type II errors in null model testing

Community structure is determined by the interplay among different processes, including biotic interactions, abiotic filtering, and dispersal. Their effects can be detected by comparing observed patterns of co-occurrence between different species (e.g. C-score and the natural metric) to patterns generated by null models based on permutations of species-by-site matrices under constraints on row or column sums. These comparisons enable us to detect significant signals of species association or dissociation, from which the type of biotic interactions between species (e.g. facilitative or antagonistic) can be inferred. Commonly used patterns are based on the levels of co-occurrence between randomly paired species. The level of co-occurrence for three or more species is rarely considered, ignoring the potential existence of functional guilds or motifs composed of multiple species within the community. Null model tests that do not consider multi-species co-occurrence could therefore generate false negatives (Type II error) in detecting non-random forces at play that would only be apparent for such guilds. Here, we propose a multi-species co-occurrence index (hereafter, joint occupancy) that measures the number of sites jointly occupied by multiple species simultaneously, of which the pairwise metric of co-occurrence is a special case. Using this joint occupancy index along with standard permutation algorithms for null model testing, we illustrate nine archetypes of multi-species co-occurrence and explore how frequent they are in the seminal database of 289 species-by-site community matrices published by Atmar and Patterson in 1995. We show that null model testing using pairwise co-occurrence metrics could indeed lead to severe Type II errors in one specific archetype, accounting for 2.4% of the tested community matrices.

Mutual spectral densities calculation of the moments of resistance on the peat milling unit working bodies

When performing technological operations in the peat industry, various units with milling-type working bodies are used. They differ in design, layout, number and type of cutting elements, operating modes, and may have one or more working bodies. During operation, random forces and moments act on the cutters, which have a dramatically variable nature, which is associated with the periodic interaction of the knives with the peat deposit, its structural heterogeneity, variations in the milling depth, physical and mechanical properties of peat, the rotational speed of the cutter and the movement speed of the machine. In this case, significant dynamic loads arise in the structural elements, which leads to a decrease in their reliability, deterioration of the energy characteristics of the engine operation and technical and economic indicators of use. In the dynamic analysis of drive elements, when using machines with several working bodies, it is necessary to know both spectral and mutual spectral load densities. For their calculation, expressions were obtained that take into account the physical and mechanical properties of peat, the operating modes of the unit and their probabilistic characteristics, as well as the design features of the working body. The expressions are obtained for the case when there are several working bodies with the same diameters and the number of knives in the cutting plane. In this case, the number of planes, width, type of cutting element and type of cutting (locked, semi-locked, etc.) may differ. As an example of using the developed approaches, the calculation of spectral and mutual spectral densities of moments on cutters and loads in the drive elements of the machine for surface-layer milling MTF-14 is presented.

Power Spectral Density Analysis of Nanowire-Anchored Fluctuating Microbead Reveals a Double Lorentzian Distribution

In this work, we investigate the properties of a stochastic model, in which two coupled degrees of freedom are subordinated to viscous, elastic, and also additive random forces. Our model, which builds on previous progress in Brownian motion theory, is designed to describe water-immersed microparticles connected to a cantilever nanowire prepared by polymerization using two-photon direct laser writing (TPP-DLW). The model focuses on insights into nanowires exhibiting viscoelastic behavior, which defines the specific conditions of the microbead. The nanowire bending is described by a three-parameter linear model. The theoretical model is studied from the point of view of the power spectrum density of Brownian fluctuations. Our approach also focuses on the potential energy equipartition, which determines random forcing parametrization. Analytical calculations are provided that result in a double-Lorentzian power density spectrum with two corner frequencies. The proposed model explained our preliminary experimental findings as a result of the use of regression analysis. Furthermore, an a posteriori form of regression efficiency evaluation was designed and applied to three typical spectral regions. The agreement of respective moments obtained by integration of regressed dependences as well as by summing experimental data was confirmed.

Two timescales control the creation of large protein aggregates in cells

Protein aggregation is of particular interest due to its connection with many diseases and disorders. Many factors can alter the dynamics and result of this process, one of them being the diffusivity of the monomers and aggregates in the system. Here, we study experimentally and theoretically an aggregation process in cells, and we identify two distinct physical timescales that set the number and size of aggregates. The first timescale involves fast aggregation of small clusters freely diffusing in the cytoplasm, while, in the second one, the aggregates are larger than the pore size of the cytoplasm and thus barely diffuse, and the aggregation process is slowed down. However, the process is not entirely halted, potentially reflecting a myriad of active but random forces forces that stir the aggregates. Such slow timescale is essential to account for the experimental results of the aggregation process. These results could also have implications in other processes of spatial organization in cell biology, such as phase-separated droplets.

Cytoplasmic forces functionally reorganize nuclear condensates in oocytes

Cells remodel their cytoplasm with force-generating cytoskeletal motors1. Their activity generates random forces that stir the cytoplasm, agitating and displacing membrane-bound organelles like the nucleus in somatic2–4 and germ5–7 cells. These forces are transmitted inside the nucleus4,7, yet their consequences on liquid-like biomolecular condensates8–10 residing in the nucleus remain unexplored. Here, we probe experimentally and computationally diverse nuclear condensates, that include splicing speckles, Cajal bodies, and nucleoli, during cytoplasmic remodeling of female germ cells named oocytes. We discover that growing mammalian oocytes deploy cytoplasmic forces to timely impose multiscale reorganization of condensates inside the nucleus. We determine that cytoplasmic forces accelerate nuclear condensate collision-coalescence and molecular kinetics within condensates. Inversely, disrupting the forces decelerates nuclear condensate reorganization on both scales. We link the molecular deceleration found in mRNA-processing splicing speckles to reduced and altered splicing of mRNA, which in oocytes impedes fertility11. We establish that different sources of cytoplasmic forces can reorganize nuclear condensates and that this cytoplasmic aptitude for subnuclear reorganization is evolutionary conserved in insects. Our work implies that cells evolved a mechanism, based on cytoplasmic force tuning, to functionally regulate a broad range of nuclear condensates across scales. This finding opens new perspectives when studying condensate-associated pathologies like cancer, neurodegeneration and viral infections12.One sentence summaryCytoplasmic random forces in growing oocytes drive multiscale reorganization of nuclear liquid-like biomolecular condensates.

Macroevolution and megaclimate: revealing the domains of the Court Jester and biotic equilibration

<p>The fundamental question of the biodiversity dynamics field is whether global diversity of organisms is driven by multiple random forces resulting in unsteady pattern or is it constrained by sufficiently strong biotic interactions. The first set of hypotheses is combined under the umbrella of the “Court Jester”, reflecting non-steady nature of the process. The latter set of hypotheses is sometimes combined under the header of the “Red Queen”, an epitomization of perpetual change at constant equilibrium diversity level. Based on the Haar fluctuation analyses of the classical Sepkoski database and Paleobiology Database occurrence based biodiversity data, it was revealed that both datasets show that marine animal genus level diversity is characterized by the two regimes.  The first, up to time scales of 30 to 40 Myrs, has a positive scaling exponent implying that fluctuations diverging with time scale i.e. behaviour like the Court Jester that is apparently unstable. The second regime, at longer time scales has a negative fluctuation exponent so that on average anomalies converge, the system is appears stable: a biodiversity regulating Red Queen regime. The smaller scale diverging regime (unstable) is characterized by nearly the same scaling exponent as megaclimate paleotemperatures, suggests a causal connection with diversity.</p><p>To investigate this further, we use a new multi-scale Haar fluctuation correlation analysis to quantify the scale by scale correlations.   We found a persistent trend of increasing correlation of macroevolutionary rates with the surface water temperatures with increasing time scales. At the same time, the diversity shows increasingly negative correlations with the temperatures at longer time scales, which suggest that positive largest scale temperature fluctuations although increased biotic turnover had a regulating effect on the global marine animal diversity levels.</p><p>Based on the consideration of dominant processes at the longest time scales we propose that the equilibration of biota is a result of continuous geodispersal and consequently mixing and competition of regional biotas, which becomes increasingly more likely on the deca-million-year time scales.</p><p>We conclude that the Earth system processes play a significant role in driving both diverging and equilibrating global biodiversity regimes: both Court Jester and Red Queen regimes may operate, with the former dominant up to ≈ 40 Myrs, and the latter at longer time scales.</p>

Enhanced diffusion by reversible binding to active polymers

Cells are known to use reversible binding to active biopolymer networks to allow diffusive transport of particles in an otherwise impenetrable mesh. We here determine the motion of a particle that experiences random forces during binding and unbinding events while being constrained by attached polymers. Using Monte-Carlo simulations and a statistical mechanics model, we find that enhanced diffusion is possible with active polymers. However, this is possible only under optimum conditions that has to do with the relative length of the chains to that of the plate. For example, in systems where the plate is shorter than the chains, diffusion is maximum when many chains have the potential to bind but few remain bound at any one time. Interestingly, if the chains are shorter than the plate, we find that diffusion is maximized when more active chains remain transiently bound. The model provides insight into these findings by elucidating the mechanisms for binding-mediated diffusion in biology and design rules for macromolecular transport in transient synthetic polymers.