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Microtubules form important cytoskeletal structures that play a role in establishing and maintaining neuronal polarity, regulating neuronal morphology, transporting cargo, and scaffolding signaling molecules to form signaling hubs. Within a neuronal cell, microtubules are found to have variable lengths and can be both stable and dynamic. Microtubule associated proteins, post-translational modifications of tubulin subunits, microtubule severing enzymes, and signaling molecules are all known to influence both stable and dynamic pools of microtubules. Microtubule dynamics, the process of interconversion between stable and dynamic pools, and the proportions of these two pools have the potential to influence a wide variety of cellular processes. Reduced microtubule stability has been observed in several neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), Amyotrophic Lateral Sclerosis (ALS), and tauopathies like Progressive Supranuclear Palsy. Hyperstable microtubules, as seen in Hereditary Spastic Paraplegia (HSP), also lead to neurodegeneration. Therefore, the ratio of stable and dynamic microtubules is likely to be important for neuronal function and perturbation in microtubule dynamics might contribute to disease progression.

Economic incentives to harvest a species usually diminish as its abundance declines, because harvest costs increase. This prevents harvesting to extinction. A known exception can occur if consumer demand causes a declining species’ harvest price to rise faster than costs. This threat may affect rare and valuable species, such as large land mammals, sturgeons, and bluefin tunas. We analyze a similar but underappreciated threat, which arises when the geographic area (range) occupied by a species contracts as its abundance declines. Range contractions maintain the local densities of declining populations, which facilitates harvesting to extinction by preventing abundance declines from causing harvest costs to rise. Factors causing such range contractions include schooling, herding, or flocking behaviors—which, ironically, can be predator-avoidance adaptations; patchy environments; habitat loss; and climate change. We use a simple model to identify combinations of range contractions and price increases capable of causing extinction from profitable overharvesting, and we compare these to an empirical review. We find that some aquatic species that school or forage in patchy environments experience sufficiently severe range contractions as they decline to allow profitable harvesting to extinction even with little or no price increase; and some high-value declining aquatic species experience severe price increases. For terrestrial species, the data needed to evaluate our theory are scarce, but available evidence suggests that extinction-enabling range contractions may be common among declining mammals and birds. Thus, factors causing range contraction as abundance declines may pose unexpectedly large extinction risks to harvested species.

Saturation suppressor mutagenesis was used to generate thermostable mutants of the SARS-CoV-2 spike receptor-binding domain (RBD). A triple mutant with an increase in thermal melting temperature of ~7°C with respect to the wild-type B.1 RBD and was expressed in high yield in both mammalian cells and the microbial host, Pichia pastoris , was downselected for immunogenicity studies. An additional derivative with three additional mutations from the B.1.351 (beta) isolate was also introduced into this background. Lyophilized proteins were resistant to high-temperature exposure and could be stored for over a month at 37°C. In mice and hamsters, squalene-in-water emulsion (SWE) adjuvanted formulations of the B.1-stabilized RBD were considerably more immunogenic than RBD lacking the stabilizing mutations and elicited antibodies that neutralized all four current variants of concern with similar neutralization titers. However, sera from mice immunized with the stabilized B.1.351 derivative showed significantly decreased neutralization titers exclusively against the B.1.617.2 (delta) VOC. A cocktail comprising stabilized B.1 and B.1.351 RBDs elicited antibodies with qualitatively improved neutralization titers and breadth relative to those immunized solely with either immunogen. Immunized hamsters were protected from high-dose viral challenge. Such vaccine formulations can be rapidly and cheaply produced, lack extraneous tags or additional components, and can be stored at room temperature. They are a useful modality to combat COVID-19, especially in remote and low-resource settings.

OBJECTIVE Few methods are available for analyzing populations with changing rates. Here hyperstable models are presented and substantially extended to facilitate such analyses. METHODS Hyperstable models, where a known birth trajectory yields a consistent set of age-specific birth rates, are set out in both discrete and continuous form. Mathematical analysis is used to find new relationships between model functions for a range of birth trajectories. RESULTS Hyperstable population projection matrices can create bridges that project any given initial population to any given ending population. New, explicit relationships are found between period and cohort births for exponential, polynomial, and sinusoidal birth trajectories. In quadratic and cubic models, the number of cohort births equals the number of period births a generation later, with a modest adjustment. In sinusoidal models, cohort births equal the number of period births a generation later, modified by a factor related to cycle length. CONTRIBUTION Because of their adaptability, structure, and internal relationships, hyperstable birth models afford a valuable platform for analyzing populations with changing fertility. The new relationships found provide insight into dynamic models and period-cohort connections and offer useful applications to analysts.

The epidermal cells of bracts, petals and sepals of L. (Star-of-Bethlehem, Asparagaceae) contain lipotubuloids, complex aggregates of lipid droplets (LDs) enmeshed by bundles of microtubules (MTs). We investigated lipotubuloid organization and stability through the transient expression of GFP fusion proteins targeted to different subcellular structures and with immunofluorescence and transmission electron microscopy (TEM). Live cell imaging confirmed that lipotubuloids contain LDs, organelles including endomembranes, mitochondria and peroxisomes, a tonoplast-defined vacuole, and that they move through actin microfilament-based streaming. Intriguingly, the different microscopy modes used showed different patterns of MT organization in the lipotubuloid. While MT sheets and bundles were visible by TEM, few MTs were seen with fusion proteins and immunofluorescence. Oryzalin-based MT depolymerization experiments suggest a possible resolution for this paradox: TEM showed that lipotubuloid MTs resisted depolymerization, even after 20 h in oryzalin, while MT polymerization was visible in lipotubuloids with fusion proteins during oryzalin wash-out. These results suggest that the lipotubuloids contain hyperstable MTs, possibly formed with microtubule-associated proteins (MAPs) that normally occlude fusion protein and antibody binding sites.

Background: DNA methylation mediates the gene–environment interactions, with implications for health and disease. Studies with sampling at more than one timepoint revealed the considerable variability of the blood methylome, but comprehensive resources on genome-wide methylation stability are still lacking. We aimed to identify methylation sites that remain the most stable across two timepoints in human whole blood. Methods: Publicly available blood DNA methylation data from three cohorts were analysed, which included methylation profiles at two timepoints >1 year apart. The cohorts included pre-/post-pubertal children (Illumina 450k array), the elderly (Illumina 450k array), and middle-aged adults with obesity (Illumina EPIC array). Two metrics were used for the stability assessment: the mean absolute difference (MAD) of beta values between two measurements and the intraclass correlation coefficient (ICC). We searched for probes demonstrating high stability (low MAD and high ICC) across the three cohorts. Data from 51 children, 86 elderly adults, and 120 middle-aged participants were re-analysed. Results: The median interquartile range (IQR) of the maximum (from three datasets) MAD was 2.1% (1.5–2.9%), and the median of the minimum ICC agreement coefficient was 0.053 (−0.077–0.304). The Pearson’s correlation coefficient for the ICC vs. maximum MAD was low (r = 0.34, p < 2.2 × 10−16). We found only 239 probes that were highly stable based on both the maximum MAD (<5th percentile, <0.01) and ICC criterion (>95th percentile, >0.74). Conclusions: The whole-blood DNA methylation profile, as measured using microarrays, is dynamic over >1 year, but contains a fraction of stable probes, most of which are related to genomic variation. A resource describing probe stability is made publicly available, with the intention to support biomarker studies and the investigation of early epigenetic programming. The absolute error and correlation are two complementary facets of probe stability that may be considered in further research, especially to determine the stability of probes in health and disease across different tissues and populations.

TDP-43 is an essential RNA-binding protein forming aggregates in almost all cases of sporadic amyotrophic lateral sclerosis (ALS) and many cases of frontotemporal lobar dementia (FTLD) and other neurodegenerative diseases. TDP-43 consists of a folded N-terminal domain with a singular structure, two RRM RNA-binding domains, and a long disordered C-terminal region which plays roles in functional RNA regulatory assemblies as well as pernicious aggregation. Evidence from pathological mutations and seeding experiments strongly suggest that TDP-43 aggregates are pathologically relevant through toxic gain-of-harmful-function and/or harmful loss-of-native-function mechanisms. Recent, but not early, microscopy studies and the ability of TDP-43 aggregates to resist harsh treatment and to seed new pathological aggregates and in cells strongly suggest that TDP-43 aggregates have a self-templating, amyloid-like structure. Based on the importance of the Gln/Asn-rich 341-367 residue segment for efficient aggregation of endogenous TDP-43 when presented as a 12X-repeat and extensive spectroscopic and computational experiments, we recently proposed that this segment adopts a beta-hairpin structure that assembles in a parallel with a beta-turn configuration to form an amyloid-like structure. Here, we propose that this conformer is stabilized by an especially strong class of hypercooperative hydrogen bonding unique to Gln and Asn sidechains. The clinical existence of this conformer is supported by very recent LC-MS/MS characterization of TDP-43 from aggregates, which show that residues 341-367 were protected from Ser phosphorylation, Gln/Asn deamidation and Met oxidation. Its distinct pattern of SDS-PAGE bands allows us to link this conformer to the exceptionally stable seed of the Type A TDP-43 proteinopathy.

[This corrects the article on p. 343 in vol. 9, PMID: 26441521.].

Adaptive infinite impulse response (IIR), or recursive, filters are less attractive mainly because of the stability and the difficulties associated with their adaptive algorithms. Hyperstability theory when simplified and adapted for digital signal processing offers a new class of IIR filters, simple hyperstable adaptive recursive filters (SHARFs), which is directly related to strictly positive real (SPR) transfer functions. One of the most important drawbacks of the SHARF algorithm is the presence of the unknown denominator in the transfer function that must be SPR in order to ensure convergence. In this paper, SHARF is investigated with SPR transfer functions designed without any priori knowledge of the filter parameters by the pole-zero placement on the unit circle method and made self-adjusting. To demonstrate self-adjustment of the algorithm, SHARF algorithm using constraint least-mean square (LMS) method is applied to a pure four-pole autoregressive process.