Single-Molecule Reaction-Diffusion.

We propose to capture reaction-diffusion on a molecule-by-molecule basis from the fastest acquirable timescale, namely individual photon arrivals. We illustrate our method on intrinsically disordered human proteins, the linker histone H1.0 as well as its chaperone prothymosin α, as these diffuse through an illuminated confocal spot and interact forming larger ternary complexes on millisecond timescales. Most importantly, single-molecule reaction-diffusion, smRD, reveals single molecule properties without trapping or otherwise confining molecules to surfaces. We achieve smRD within a Bayesian paradigm and term our method Bayes-smRD. Bayes-smRD is further free of the average, bulk, results inherent to the analysis of long photon arrival traces by fluorescence correlation spectroscopy. In learning from thousands of photon arrivals continuous spatial positions and discrete conformational and photophysical state changes, Bayes-smRD estimates kinetic parameters on a molecule-by-molecule basis with two to three orders of magnitude less data than tools such as fluorescence correlation spectroscopy thereby also dramatically reducing sample photodamage.

Two-state swimming: Strategy and survival of a model bacterial predator in response to environmental cues.

Bdellovibrio bacteriovorus is a predatory bacterium preying upon Gram-negative bacteria. As such, B. bacteriovorus has the potential to control antibiotic-resistant pathogens and biofilm populations. To survive and reproduce, B. bacteriovorus must locate and infect a host cell. However, in the temporary absence of prey, it is largely unknown how B. bacteriovorus modulate their motility patterns in response to physical or chemical environmental cues to optimize their energy expenditure. To investigate B. bacteriovorus' predation strategy, we track and quantify their motion by measuring speed distributions as a function of starvation time. While an initial unimodal speed distribution relaxing to one for pure diffusion at long times may be expected, instead we observe a bimodal speed distribution with one mode centered around that expected from diffusion and the other centered at higher speeds. What is more, for an increasing amount of time over which B. bacteriovorus is starved, we observe a progressive reweighting from the active swimming state to an apparent diffusive state in the speed distribution. Distributions of trajectory-averaged speeds for B. bacteriovorus are largely unimodal, indicating switching between a faster swim speed and an apparent diffusive state within individual observed trajectories rather than there being distinct active swimming and apparent diffusive populations. We also find that B. bacteriovorus' apparent diffusive state is not merely caused by the diffusion of inviable bacteria as subsequent spiking experiments show that bacteria can be resuscitated and bimodality restored. Indeed, starved B. bacteriovorus may modulate the frequency and duration of active swimming as a means of balancing energy consumption and procurement. Our results thus point to a reweighting of the swimming frequency on a trajectory basis rather than a population level basis.

BNP-Track: A framework for superresolved tracking.

Assessing dynamic processes at single molecule scales is key toward capturing life at the level of its molecular actors. Widefield superresolution methods, such as STORM, PALM, and PAINT, provide nanoscale localization accuracy, even when distances between fluorescently labeled single molecules ("emitters") fall below light's diffraction limit. However, as these superresolution methods rely on rare photophysical events to distinguish emitters from both each other and background, they are largely limited to static samples. In contrast, here we leverage spatiotemporal correlations of dynamic widefield imaging data to extend superresolution to simultaneous multiple emitter tracking without relying on photodynamics even as emitter distances from one another fall below the diffraction limit. We simultaneously determine emitter numbers and their tracks (localization and linking) with the same localization accuracy per frame as widefield superresolution does for immobilized emitters under similar imaging conditions (≈50nm). We demonstrate our results for both in cellulo data and, for benchmarking purposes, on synthetic data. To this end, we avoid the existing tracking paradigm relying on completely or partially separating the tasks of emitter number determination, localization of each emitter, and linking emitter positions across frames. Instead, we develop a fully joint posterior distribution over the quantities of interest, including emitter tracks and their total, otherwise unknown, number within the Bayesian nonparametric paradigm. Our posterior quantifies the full uncertainty over emitter numbers and their associated tracks propagated from origins including shot noise and camera artefacts, pixelation, stochastic background, and out-of-focus motion. Finally, it remains accurate in more crowded regimes where alternative tracking tools cannot be applied.

[Clinical analysis of the correlation between gallbladder adenomyomatosis and occult pancreaticobiliary reflux].

Objective: To explore the association between gallbladder adenomyomatosis (GA) and occult pancreaticobiliary reflux (OPBR). Methods: A total of 81 patients with GA who underwent cholecystectomy in Shanghai East Hospital from December 2020 to January 2022 were enrolled, including 48 cases of fundal type, 28 cases of segmental type and 5 cases of diffuse type. Patient's intraoperative bile was coltected and tested for amylase. According to gallbladder bile amylase level, patients were divided into OPBR group (bile amylase>110 U/L) and the control group (bile amylase≤110 U/L). Results: Among 81 patients, 32 were male and 49 were female, and aged (49.1±13.2) years; there were 66 cases in control group, including 27 males and 39 females, and aged (50.0±12.9)years; there were 15 patients in the OPBR group, including 5 males and 10 females, and aged (45.1±14.2) years. In terms of the clinical features of the two groups, there was no significant difference (all P>0.05), except for a significant increase in biliary amylase in the OPBR group compared with the control group (P<0.001). However, the incidence of OPBR was significantly different in the three types of GA, with a lower incidence of OPBR in the fundal type (10.4%, 5/48) than in the segmental type (28.6%, 8/28) and diffuse type (2/5) (P=0.038). In addition, segmental GA was more likely to be combined with gallbladder stones (85.7%, 24/28) than fundal GA (58.3%, 28/48) and diffuse GA (3/5) (P=0.031). Univariate and multivariate logistic regression analyses showed OPBR [OR (95%CI)=3.410 (1.010 to 11.513), P=0.048] and combined gallbladder stones [OR (95%CI)=2.974 (1.011 to 8.745), P=0.048] indepenclently correlated with segmental and diffuse GA. Conclusions: The incidence of OPBR is higher in segmental and diffuse GA, and gallstones and OPBR are independently associated with the occurrence of segmental and diffuse GA. These results suggest that OPBR may be the initiating factor for the occurrence and carcinogenesis of segmental and diffuse GA.

Computational Proposal for Tracking Multiple Molecules in a Multifocus Confocal Setup.

Tracking single molecules continues to provide new insights into the fundamental rules governing biological function. Despite continued technical advances in fluorescent and non-fluorescent labeling as well as data analysis, direct observations of trajectories and interactions of multiple molecules in dense environments remain aspirational goals. While confocal methods provide a means to deduce dynamical parameters with high temporal resolution, such as diffusion coefficients, they do so at the expense of spatial resolution. Indeed, on account of a confocal volume's symmetry, typically only distances from the center of the confocal spot can be deduced. Motivated by the need for true three dimensional high speed tracking in densely labeled environments, we propose a computational tool for tracking many fluorescent molecules traversing multiple, closely spaced, confocal measurement volumes providing independent observations. Various realizations of this multiple confocal volumes strategy have previously been used for long term, large area, tracking of one fluorescent molecule in three dimensions. What is more, we achieve tracking by directly using single photon arrival times to inform our likelihood and exploit Hamiltonian Monte Carlo to efficiently sample trajectories from our posterior within a Bayesian nonparametric paradigm. A nonparametric paradigm here is warranted as the number of molecules present are, themselves, a priori unknown. Taken together, we provide a computational framework to infer trajectories of multiple molecules at once, below the diffraction limit (the width of a confocal spot), in three dimensions at sub-millisecond or faster time scales.

Neuronal activities in the rostral ventromedial medulla associated with experimental occlusal interference-induced orofacial hyperalgesia.

The imbalanced conditions of pronociceptive ON-cells and antinociceptive OFF-cells in the rostral ventromedial medulla (RVM) alter nociceptive transmission and play an important role in the development of chronic pain. This study aimed to explore the neuroplastic mechanisms of the RVM ON-cells and OFF-cells in a male rat model of experimental occlusal interference (EOI)-induced nociceptive behavior reflecting orofacial hyperalgesia and in modified models involving EOI removal at early and later stages. We recorded the mechanical head withdrawal thresholds (HWTs), orofacial operant behaviors, and the activity of identified RVM ON-cells and OFF-cells in these rats. EOI-induced orofacial hyperalgesia could be relieved by EOI removal around postoperative day 3; this effect could be inhibited by intra-RVM microinjection of the kappa-opioid receptor agonist U-69593. EOI removal around postoperative day 8 did not relieve the orofacial hyperalgesia which could however be reversed by intra-RVM microinjection of the NK-1 receptor antagonist L-733060. The activity of ON-cells and OFF-cells did not change during both the initial 3 and 6 days of EOI. When EOI was removed on postoperative day 3, OFF-cell responses decreased, contributing to the reversal of hyperalgesia. When EOI lasted for 8 days or was removed on postoperative day 8, spontaneous activity and stimulus-evoked responses of ON-cell increased, contributing to the maintained hyperalgesia. In contrast, when the EOI lasted for 14 days, OFF-cell responses decreased, possibly participating in the maintenance of hyperalgesia with persistent EOI. Our results reveal that adaptive changes in the RVM were associated with orofacial pain following EOI placement and removal.SIGNIFICANCE STATEMENTA considerable proportion of patients suffered from chronic orofacial pain throughout life despite the therapies given or removal of potential etiological factors. However, current therapies lack effectiveness due to limited knowledge of the chronicity mechanisms. Using electrophysiological recording, combined with a behavioral test, we found that the prevailing descending facilitation in the rostral ventromedial medulla (RVM) participates in the maintenance of orofacial hyperalgesia following late removal of nociceptive stimuli, while the prevailing descending inhibition from the RVM may contribute to the reversal of orofacial hyperalgesia following early removal of nociceptive stimuli. Thus, variable clinical outcomes of orofacial pain may be associated with descending modulation and an optimal window of time may exist in the management of chronic orofacial pain.

Novel Genomic Insights into Body Size Evolution in Cetaceans and a Resolution of Peto's Paradox.

AbstractCetaceans (whales, dolphins, and porpoises) have undergone a radical transformation from the typical terrestrial mammalian body plan to a streamlined body, while exhibiting dramatic interspecific size differences. However, the molecular mechanisms underlying the diversification of cetacean body size are largely unknown. Here, by using genomic and phenotypic data for 22 cetaceans, we performed phylogenetic genome-body size analysis and explored the genetic basis of the high diversity of body size in cetaceans. A functional enrichment analysis showed that body size-related genes in cetaceans are enriched in pathways associated with immunity, cell growth, and metabolism, suggesting that they contributed to body size diversification. Genes showing correlated evolution with body size were mainly involved in immune surveillance, tumor suppression function, and development of hypertumors. The role of these genes in tumor control resolves Peto's paradox (i.e., the lack of a correspondence between an expansion in body size and, thereby, cell number and an increased cancer incidence). Our results provide novel insights into the evolution of substantial body size variation in cetaceans.

Knockout of the NONO Gene Inhibits Neointima Formation in a Mouse Model of Vascular Injury.

[Figure: see text].