Temporal declines in fecundity: A study of southern Gulf of St. Lawrence Atlantic herring (Clupea harengus) and implications for potential reproductive output.

Individuals must reproduce to survive and thrive from generation to generation. In fish, the fecundity of individuals and estimates of total reproductive output are critical for evaluating reproductive success and understanding population dynamics. Estimating fecundity is an onerous task; therefore, many populations lack contemporary estimates of fecundity and size-fecundity relationships. However, reproductive dynamics are not static in time; therefore, it is important to develop contemporary fecundity estimates to better inform conservation and management action. To highlight the importance of contemporary fecundity estimates, we examined the fecundity of southern Gulf of St. Lawrence (sGSL) spring and fall spawning Atlantic herring in 2022, developed size-fecundity models, and compared these to historical fecundity estimates and models. Our results suggest that the average fecundity of sGSL spring and fall herring has undergone a substantial temporal decline of approximately 47% and 58%, respectively, since the 1970s and 1980s. The size-fecundity relationships for fall spawning herring have shifted, with fish of a given size exhibiting lower fecundity in 2022 compared to the 1970s. Alternatively, the size-fecundity relationships for spring spawning herring have remained relatively static. Furthermore, simulations highlighted a substantial reduction in potential reproductive output in 2022 compared to 1970 of approximately 32% and 68% for spring and fall spawners, respectively, based on a fixed number of mature females, which may have negative implications for stock rebuilding. Overall, our study provides support for periodic estimates of fecundity in fish populations to better understand temporal changes in reproductive and population dynamics.

Synergistic defects in pre-rRNA processing from mutations in the U3-specific protein Rrp9 and U3 snoRNA.

U3 snoRNA and the associated Rrp9/U3-55K protein are essential for 18S rRNA production by the SSU-processome complex. U3 and Rrp9 are required for early pre-rRNA cleavages at sites A0, A1 and A2, but the mechanism remains unclear. Substitution of Arg 289 in Rrp9 to Ala (R289A) specifically reduced cleavage at sites A1 and A2. Surprisingly, R289 is located on the surface of the Rrp9 ß-propeller structure opposite to U3 snoRNA. To understand this, we first characterized the protein-protein interaction network of Rrp9 within the SSU-processome. This identified a direct interaction between the Rrp9 ß-propeller domain and Rrp36, the strength of which was reduced by the R289A substitution, implicating this interaction in the observed processing phenotype. The Rrp9 R289A mutation also showed strong synergistic negative interactions with mutations in U3 that destabilize the U3/pre-rRNA base-pair interactions or reduce the length of their linking segments. We propose that the Rrp9 ß-propeller and U3/pre-rRNA binding cooperate in the structure or stability of the SSU-processome. Additionally, our analysis of U3 variants gave insights into the function of individual segments of the 5'-terminal 72-nt sequence of U3. We interpret these data in the light of recently reported SSU-processome structures.

Implication of the box C/D snoRNP assembly factor Rsa1p in U3 snoRNP assembly.

The U3 box C/D snoRNA is one key element of 90S pre-ribosome. It contains a 5΄ domain pairing with pre-rRNA and the U3B/C and U3C΄/D motifs for U3 packaging into a unique small nucleolar ribonucleoprotein particle (snoRNP). The RNA-binding protein Snu13/SNU13 nucleates on U3B/C the assembly of box C/D proteins Nop1p/FBL and Nop56p/NOP56, and the U3-specific protein Rrp9p/U3-55K. Snu13p/SNU13 has a much lower affinity for U3C΄/D but nevertheless forms on this motif an RNP with box C/D proteins Nop1p/FBL and Nop58p/NOP58. In this study, we characterized the influence of the RNP assembly protein Rsa1 in the early steps of U3 snoRNP biogenesis in yeast and we propose a refined model of U3 snoRNP biogenesis. While recombinant Snu13p enhances the binding of Rrp9p to U3B/C, we observed that Rsa1p has no effect on this activity but forms with Snu13p and Rrp9p a U3B/C pre-RNP. In contrast, we found that Rsa1p enhances Snu13p binding on U3C΄/D. RNA footprinting experiments indicate that this positive effect most likely occurs by direct contacts of Rsa1p with the U3 snoRNA 5΄ domain. In light of the recent U3 snoRNP cryo-EM structures, our data suggest that Rsa1p has a dual role by also preventing formation of a pre-mature functional U3 RNP.

New Atom Probe Tomography Reconstruction Algorithm for Multilayered Samples: Beyond the Hemispherical Constraint.

Accuracy of atom probe tomography measurements is strongly degraded by the presence of phases that have different evaporation fields. In particular, when there are perpendicular interfaces to the tip axis in the specimen, layers thicknesses are systematically biased and the resolution is degraded near the interfaces. Based on an analytical model of field evaporated emitter end-form, a new algorithm dedicated to the 3D reconstruction of multilayered samples was developed. Simulations of field evaporation of bilayer were performed to evaluate the effectiveness of the new algorithm. Compared to the standard state-of-the-art reconstruction methods, the present approach provides much more accurate analyzed volume, and the resolution is clearly improved near the interface. The ability of the algorithm to handle experimental data was also demonstrated. It is shown that the standard algorithm applied to the same data can commit an error on the layers thicknesses up to a factor 2. This new method is not constrained by the classical hemispherical specimen shape assumption.

A Meshless Algorithm to Model Field Evaporation in Atom Probe Tomography.

An alternative approach for simulating the field evaporation process in atom probe tomography is presented. The model uses the electrostatic Robin's equation to directly calculate charge distribution over the tip apex conducting surface, without the need for a supporting mesh. The partial ionization state of the surface atoms is at the core of the method. Indeed, each surface atom is considered as a point charge, which is representative of its evaporation probability. The computational efficiency is ensured by an adapted version of the Barnes-Hut N-body problem algorithm. Standard desorption maps for cubic structures are presented in order to demonstrate the effectiveness of the method.

Interplay of structure and photophysics of individualized rod-shaped graphene quantum dots with up to 132 sp² carbon atoms.

Nanographene materials are promising building blocks for the growing field of low-dimensional materials for optics, electronics and biophotonics applications. In particular, bottom-up synthesized 0D graphene quantum dots show great potential as single quantum emitters. To fully exploit their exciting properties, the graphene quantum dots must be of high purity; the key parameter for efficient purification being the solubility of the starting materials. Here, we report the synthesis of a family of highly soluble and easily processable rod-shaped graphene quantum dots with fluorescence quantum yields up to 94%. This is uncommon for a red emission. The high solubility is directly related to the design of the structure, allowing for an accurate description of the photophysical properties of the graphene quantum dots both in solution and at the single molecule level. These photophysical properties were fully predicted by quantum-chemical calculations.

The structure of cellulose nanofibril networks at low concentrations and their stabilizing action on colloidal particles.

The structure and dynamics of networks formed by rod-shaped particles can be indirectly investigated by measuring the diffusion of spherical tracer particles. This method was used to characterize cellulose nanofibril (CNF) networks in both dispersed and arrested states, the results of which were compared with coarse-grained Brownian dynamics simulations. At a CNF concentration of 0.2 wt% a transition was observed where, below this concentration tracer diffusion is governed by the increasing macroscopic viscosity of the dispersion. Above 0.2 wt%, the diffusion of small particles (20-40 nm) remains viscosity controlled, while particles (100-500 nm) become trapped in the CNF network. Sedimentation of silica microparticles (1-5 µm) in CNF dispersions was also determined, showing that sedimentation of larger particles is significantly affected by the presence of CNF. At concentrations of 0.2 wt%, the sedimentation velocity of 5 µm particles was reduced by 99 % compared to pure water.

New Patchy Particle Model with Anisotropic Patches for Molecular Dynamics Simulations: Application to a Coarse-Grained Model of Cellulose Nanocrystal.

Self-assembly is ubiquitous in nature and underlies the formation of many complex systems from the molecular to the macroscopic scale. Kern-Frenkel-like patchy particles are powerful models to investigate this phenomenon by computational methods such as Monte Carlo or molecular dynamics simulations. However, in these models the interactions are mediated by circular patches at the particle surface, which can be hardly mapped to realistic systems, containing for instance faceted particles with rectangular surfaces. In this paper we extend the model to take into account such geometries, and we use it to build a supra coarse-grained model of the cellulose nanocrystal where the interactions are parametrized against all-atomistic molecular dynamics simulations. The formation of cholesteric ribbons and defects in cholesteric droplets of the cellulose nanocrystal are investigated and confirm experimental behavior reported in the literature. The flexibility of this new patchy particle model makes it a powerful tool to develop supra coarse-grained models of self-assembly for large space and time scales and should find a broad range of applications for self-assembly in chemical and biological systems.

Substrate-Dependent Morphology and Its Effect on Electrical Mobility of Doped Poly(3,4-ethylenedioxythiophene) (PEDOT) Thin Films.

Deposition dynamics, crystallization, molecular packing, and electronic mobility of poly(3,4-ethylenedioxythiophene) (PEDOT) thin films are affected by the nature of the substrate. Computational microscopy has been carried out to reveal the morphology-substrate dependence for PEDOT thin films doped with molecular tosylate deposited on different substrates including graphite, Si3N4, silicon, and amorphous SiO2. It is shown that the substrate is instrumental in formation of the lamellar structure. PEDOT films on the ordered substrates (graphite, Si3N4, and silicon) exhibit preferential face-on orientation, with graphite showing the most ordered and pronounced face-on packing. In contrast, PEDOT on amorphous SiO2 exhibits the dominant edge-on orientation, except in the dry state where both packings are equally presented. The role of water and the porosity of the substrate in formation of the edge-on structure on SiO2 is outlined. On the basis of the calculated morphology, the multiscale calculations of the electronic transport and percolative analysis are performed outlining how the character of the substrate affects the electron mobility. It is demonstrated that good crystallinity (PEDOT on graphite substrate) and high content of edge-on (PEDOT on SiO2 substrate) are not enough to achieve the highest electrical in-plane mobility. Instead, the least ordered material with lower degree of the edge-on content (PEDOT on silicon substrate) provides the highest mobility because it exhibits an efficient network of π-π stacked chain extending throughout the entire sample.