Environmental and genetic influence on the rate and spectrum of spontaneous mutations in Escherichia coli.

Spontaneous mutations are the ultimate source of novel genetic variation on which evolution operates. Although mutation rate is often discussed as a single parameter in evolution, it comprises multiple distinct types of changes at the level of DNA. Moreover, the rates of these distinct changes can be independently influenced by genomic background and environmental conditions. Using fluctuation tests, we characterized the spectrum of spontaneous mutations in Escherichia coli grown in low and high glucose environments. These conditions are known to affect the rate of spontaneous mutation in wild-type MG1655, but not in a ΔluxS deletant strain - a gene with roles in both quorum sensing and the recycling of methylation products used in E. coli's DNA repair process. We find an increase in AT>GC transitions in the low glucose environment, suggesting that processes relating to the production or repair of this mutation could drive the response of overall mutation rate to glucose concentration. Interestingly, this increase in AT>GC transitions is maintained by the glucose non-responsive ΔluxS deletant. Instead, an elevated rate of GC>TA transversions, more common in a high glucose environment, leads to a net non-responsiveness of overall mutation rate for this strain. Our results show how relatively subtle changes, such as the concentration of a carbon substrate or loss of a regulatory gene, can substantially influence the amount and nature of genetic variation available to selection.

Impaired performance of rapid grip in people with Parkinson's disease and motor segmentation.

Bradykinesia, or slow movement, is a defining symptom of Parkinson's disease (PD), but the underlying neuromechanical deficits that lead to this slowness remain unclear. People with PD often have impaired rates of motor output accompanied by disruptions in neuromuscular excitation, causing abnormal, segmented, force-time curves. Previous investigations using single-joint models indicate that agonist electromyogram (EMG) silent periods cause motor segmentation. It is unknown whether motor segmentation is evident in more anatomically complex and ecologically important tasks, such as handgrip tasks. Aim 1 was to determine how handgrip rates of force change compare between people with PD and healthy young and older adults. Aim 2 was to determine whether motor segmentation is present in handgrip force and EMG measures in people with PD. Subjects performed rapid isometric handgrip pulses to 20-60% of their maximal voluntary contraction force while EMG was collected from the grip flexors and extensors. Dependent variables included the time to 90% peak force, the peak rate of force development, the duration above 90% of peak force, the number of segments in the force-time curve, the number of EMG bursts, time to relaxation from 90% of peak force, and the peak rate of force relaxation. People with PD had longer durations and lower rates of force change than young and older adults. Six of 22 people with PD had motor segmentation. People with PD had more EMG bursts compared to healthy adults and the number of EMG bursts covaried with the number of segments. Thus, control of rapid movement in Parkinson's disease can be studied using isometric handgrip. People with PD have impaired rate control compared to healthy adults and motor segmentation can be studied in handgrip.

Cost-effectiveness of nivolumab versus surveillance for the adjuvant treatment of patients with urothelial carcinoma who are at high risk of recurrence: a US payer perspective.

AIM: To evaluate the cost-effectiveness of adjuvant nivolumab compared with surveillance for the treatment of patients with high-risk muscle-invasive urothelial carcinoma (MIUC) after radical resection from a US healthcare payer perspective and to investigate the impact of alternative modeling approaches on the cost-effectiveness results. MATERIAL AND METHODS: A four-state, semi-Markov model consisting of disease free, local recurrence, distant recurrence, and death health states was developed to investigate the cost-effectiveness of nivolumab compared with surveillance over a 30-year time horizon. The model used data from the randomized CheckMate 274 trial (NCT02632409) and published literature to inform transitions among health states, and inputs on cost, utility, adverse event, and disease management. Scenario analyses were conducted to investigate the impact of model structure and key assumptions on the results. One-way deterministic and probabilistic sensitivity analysis were conducted to investigate the robustness of the results. RESULTS: Total expected costs were higher with nivolumab ($162,278) compared with surveillance ($63,027). Nivolumab was associated with improved survival (1.61 life-years gained compared with surveillance) and an incremental gain of 0.98 quality-adjusted life-years (QALYs). Although total treatment costs were higher for nivolumab, cost offsets were observed because of delayed or avoided recurrences and deaths experienced with nivolumab compared with observation. The incremental cost-effectiveness and cost-utility ratios were $61,462/life-year and $100,930/QALY. LIMITATIONS: At the time of analysis, CheckMate 274 had limited follow-up on disease-free survival and no overall survival data. The limited evidence necessitated assumptions on modeling survival after each type of recurrence. CONCLUSIONS: Nivolumab is estimated to be a life-extending and cost-effective option for adjuvant treatment of MIUC for patients who are at high risk of recurrence after undergoing radical resection in the United States. Using a threshold of $150,000/QALY, the cost-effectiveness conclusions remained consistent across the scenario and sensitivity analyses conducted.

Novel Colorimetric and Light Scatter Methods to Identify and Manage Peritoneal Dialysis-Associated Peritonitis at the Point-of-Care.

Introduction: Peritoneal dialysis (PD)-related peritonitis (PDRP) is a common cause of transfer to hemodialysis, patient morbidity, and is a risk factor for mortality. Associated patient anxiety can deter selection of PD for renal replacement therapy. Diagnosis relies on hospital laboratory tests; however, this might be achieved earlier if such information was available at the point-of-care (POC), thereby significantly improving outcomes. The presence of culturable microbes and the concentration of leukocytes in effluent both aid peritonitis diagnosis, as specified in the International Society for Peritoneal Dialysis (ISPD) diagnostic guidelines. Here, we report the development of 2 new methods providing such information in simple POC tests. Methods: One approach uses a tetrazolium-based chemical reporting system, primarily focused on detecting bacterial contamination and associated vancomycin-sensitivity. The second approach uses a novel forward light-scatter device (QuickCheck) to provide an instant quantitative cell count directly from PD patient effluent. Results: The tetrazolium approach detected and correctly distinguished laboratory isolates, taking 10 hours to provide non-quantitative results. We compared the technical performance of the light scatter leukocyte counting approach with spectrophotometry, hemocytometer counting and flow cytometry (Sysmex) using patient effluent samples. QuickCheck had high accuracy (94%) and was the most precise (coefficient of variation <4%), showing minimal bias, overall performing similarly to flow cytometry. Conclusion: These complementary new approaches provide a simple means to obtain information to assist diagnosis at the POC. The first provides antibiotic sensitivity following 10 hours incubation, whereas the second optical approach (QuickCheck), provides instant accurate total leukocyte count.

Challenges, considerations, and approaches for developing a cost-effectiveness model for the adjuvant treatment of muscle-invasive urothelial carcinoma: with a spotlight on nivolumab versus placebo.

AIMS: To present alternative approaches related to both structural assumptions and data sources for the development of a decision analytic model for evaluating the cost-effectiveness of adjuvant nivolumab compared with surveillance in patients with high-risk muscle-invasive urothelial carcinoma (MIUC) after radical resection. METHODS AND RESULTS: Alternative approaches related to both structural assumptions and data sources are presented to address challenges and data gaps, as well as discussion of strengths and limitations of each approach. Specifically, challenges and considerations related to the following are presented: (1) selection of a modeling approach (partitioned survival model or state transition model) given the available evidence, (2) choice of health state structure (three- or four-state) to model disease progression and subsequent therapy, (3) modeling of outcomes from subsequent therapy using tunnel states to account for time-dependent transition probabilities or absorbing health states with one-off costs and outcomes applied, and (4) methods for modeling health-state transitions in a setting where treatment has curative intent and available survival data are immature. CONCLUSIONS: Multiple considerations must be taken into account when developing an economic model for new, emerging oncology treatments in early lines of therapy, all of which can affect the model's overall ability to estimate (quality-adjusted) survival benefits over a lifetime horizon. This paper identifies a series of key structural and analytic considerations regarding modeling of nivolumab treatment in the adjuvant MIUC setting. Several alternative approaches with regard to structure and data have been included in a flexible cost-effectiveness model so the impact of the alternative approaches on model results can be explored. The impact of these alternative approaches on cost-effectiveness results are presented in a companion article. Our findings may also help inform the development of future models for other treatments and settings in early-stage cancer.

Large-scale molecular dynamics simulations of bubble collapse in water: Effects of system size, water model, and nitrogen.

Molecular dynamics simulations in the microcanonical ensemble are performed to study the collapse of a bubble in liquid water using the single-site mW and the four-site TIP4P/2005 water models. To study system size effects, simulations for pure water systems are performed using periodically replicated simulation boxes with linear dimensions, L, ranging from 32 to 512 nm with the largest systems containing 8.7 × 106 and 4.5 × 109 molecules for the TIP4P/2005 and mW water models, respectively. The computationally more efficient mW water model allows us to reach converging behavior when the bubble dynamics results are plotted in reduced units, and the limiting behavior can be obtained through linear extrapolation in L-1. Qualitative differences are observed between simulations with the mW and TIP4P/2005 water models, but they can be explained by the models' differences in predicted viscosity and surface tension. Although bubble collapse occurs on time scales of only hundreds of picoseconds, the system sizes used here are sufficiently large to obtain bubble dynamics consistent with the Rayleigh-Plesset equation when using the models' thermophysical properties as input. For the conditions explored here, extreme heating of the interfacial water molecules near the time of collapse is observed for the larger mW water systems (but the model underpredicts the viscosity), whereas heating is less pronounced for the TIP4P/2005 water systems because its larger viscosity contribution slows the collapse dynamics. The presence of nitrogen within the bubble only starts to affect bubble dynamics near the very end of the initial collapse, leading to an incomplete collapse and strong rebound for the mW water model. Although nitrogen is non-condensable at 300 K, it becomes highly compressed and reaches a liquid-like density near the collapse point. We find that the dissolution of nitrogen is much slower than the movement of the collapsing water front, and the re-expansion of the dense nitrogen droplet gives rise to bubble rebound. The incompatibility of the collapse and dissolution time scales should be considered for continuum-scale modeling of bubble dynamics. We also confirm that the diffusion coefficient for dissolved nitrogen is insensitive to pressure as the liquid transitions from a compressed to a stretched state.

MBX: A many-body energy and force calculator for data-driven many-body simulations.

Many-Body eXpansion (MBX) is a C++ library that implements many-body potential energy functions (PEFs) within the "many-body energy" (MB-nrg) formalism. MB-nrg PEFs integrate an underlying polarizable model with explicit machine-learned representations of many-body interactions to achieve chemical accuracy from the gas to the condensed phases. MBX can be employed either as a stand-alone package or as an energy/force engine that can be integrated with generic software for molecular dynamics and Monte Carlo simulations. MBX is parallelized internally using Open Multi-Processing and can utilize Message Passing Interface when available in interfaced molecular simulation software. MBX enables classical and quantum molecular simulations with MB-nrg PEFs, as well as hybrid simulations that combine conventional force fields and MB-nrg PEFs, for diverse systems ranging from small gas-phase clusters to aqueous solutions and molecular fluids to biomolecular systems and metal-organic frameworks.

The Helicobacter pylori CagA oncoprotein disrupts Wnt/PCP signaling and promotes hyperproliferation of pyloric gland base cells.

Helicobacter pylori strains that deliver the oncoprotein CagA into gastric epithelial cells are the major etiologic agents of upper gastric diseases including gastric cancer. CagA promotes gastric carcinogenesis through interactions with multiple host proteins. Here, we show that CagA also disrupts Wnt-dependent planar cell polarity (Wnt/PCP), which orients cells within the plane of an epithelium and coordinates collective cell behaviors such as convergent extension to enable epithelial elongation during development. Ectopic expression of CagA in Xenopus laevis embryos impaired gastrulation, neural tube formation, and axis elongation, processes driven by convergent extension movements that depend on the Wnt/PCP pathway. Mice specifically expressing CagA in the stomach epithelium had longer pyloric glands and mislocalization of the tetraspanin proteins VANGL1 and VANGL2 (VANGL1/2), which are critical components of Wnt/PCP signaling. The increased pyloric gland length was due to hyperproliferation of cells at the gland base, where Lgr5+ stem and progenitor cells reside, and was associated with fewer differentiated enteroendocrine cells. In cultured human gastric epithelial cells, the N terminus of CagA interacted with the C-terminal cytoplasmic tails of VANGL1/2, which impaired Wnt/PCP signaling by inducing the mislocalization of VANGL1/2 from the plasma membrane to the cytoplasm. Thus, CagA may contribute to the development of gastric cancer by subverting a Wnt/PCP-dependent mechanism that restrains pyloric gland stem cell proliferation and promotes enteroendocrine differentiation.

Mutators can drive the evolution of multi-resistance to antibiotics.

Antibiotic combination therapies are an approach used to counter the evolution of resistance; their purported benefit is they can stop the successive emergence of independent resistance mutations in the same genome. Here, we show that bacterial populations with 'mutators', organisms with defects in DNA repair, readily evolve resistance to combination antibiotic treatment when there is a delay in reaching inhibitory concentrations of antibiotic-under conditions where purely wild-type populations cannot. In populations of Escherichia coli subjected to combination treatment, we detected a diverse array of acquired mutations, including multiple alleles in the canonical targets of resistance for the two drugs, as well as mutations in multi-drug efflux pumps and genes involved in DNA replication and repair. Unexpectedly, mutators not only allowed multi-resistance to evolve under combination treatment where it was favoured, but also under single-drug treatments. Using simulations, we show that the increase in mutation rate of the two canonical resistance targets is sufficient to permit multi-resistance evolution in both single-drug and combination treatments. Under both conditions, the mutator allele swept to fixation through hitch-hiking with single-drug resistance, enabling subsequent resistance mutations to emerge. Ultimately, our results suggest that mutators may hinder the utility of combination therapy when mutators are present. Additionally, by raising the rates of genetic mutation, selection for multi-resistance may have the unwanted side-effect of increasing the potential to evolve resistance to future antibiotic treatments.

Three-Dimensional Analysis of Water Dynamics in Human Skin by Stimulated Raman Scattering.

The stratum corneum (SC), the outermost layer of the skin, has an important function to provide a barrier against dry environments. To evaluate the barrier function and the skin condition, it is crucial to investigate the ability of SC to absorb and retain water. In this study, we demonstrate stimulated Raman scattering (SRS) imaging of three-dimensional SC structure and water distribution when water is absorbed into dried SC sheets. Our results show that the process of water absorption and retention is dependent on the specific sample and can be spatially heterogeneous. We also found that acetone treatment leads to spatially homogeneous retention of water. These results suggest the great potential of SRS imaging in diagnosing skin conditions.

Inhibitory and excitatory alcohol-seeking cues distinct roles in behavior, neurochemistry, and mesolimbic pathway in alcohol preferring (P) rats.

Cues associated with alcohol use can readily enhance self-reported cravings for alcohol, which increases the likelihood of reusing alcohol. Understanding the neuronal mechanisms involved in alcohol-seeking behavior is important for developing strategies to treat alcohol use disorder. In all experiments, adult female alcohol-preferring (P) rats were exposed to three conditioned odor cues; CS+ associated with EtOH self-administration, CS- associated with the absence of EtOH (extinction training), and a CS0, a neutral stimulus. The data indicated that presentation of an excitatory conditioned cue (CS+) can enhance EtOH- seeking while the CS- can inhibit EtOH-seeking under multiple test conditions. Presentation of the CS+ activates a subpopulation of dopamine neurons within the interfascicular nucleus of the posterior ventral tegmental area (posterior VTA) and basolateral amygdala (BLA). Pharmacological inactivation of the BLA with GABA agonists inhibits the ability of the CS+ to enhance EtOH-seeking but does not alter context-induced EtOH-seeking or the ability of the CS- to inhibit EtOH-seeking. Presentation of the conditioned odor cues in a non-drug-paired environment indicated that presentation of the CS+ increased dopamine levels in the BLA. In contrast, presentation of the CS- decreased both glutamate and dopamine levels in the BLA. Further analysis revealed that presentation of a CS+ EtOH-associated conditioned cue activates GABA interneurons but not glutamate projection neurons. Overall, the data indicate that excitatory and inhibitory conditioned cues can contrarily alter EtOH-seeking behaviors and that different neurocircuitries are mediating these distinct cues in critical brain regions. Pharmacotherapeutics for craving should inhibit the CS+ and enhance the CS- neurocircuits.

Imaging the lower limb network in Parkinson's disease.

BACKGROUND: Despite the significant impact of lower limb symptoms on everyday life activities in Parkinson's disease (PD), knowledge of the neural correlates of lower limb deficits is limited. OBJECTIVE: We ran an fMRI study to investigate the neural correlates of lower limb movements in individuals with and without PD. METHODS: Participants included 24 PD and 21 older adults who were scanned while performing a precisely controlled isometric force generation task by dorsiflexing their ankle. A novel MRI-compatible ankle dorsiflexion device that limits head motion during motor tasks was used. The PD were tested on their more affected side, whereas the side in controls was randomized. Importantly, PD were tested in the off-state, following overnight withdrawal from antiparkinsonian medication. RESULTS: The foot task revealed extensive functional brain changes in PD compared to controls, with reduced fMRI signal during ankle dorsiflexion within the contralateral putamen and M1 foot area, and ipsilateral cerebellum. The activity of M1 foot area was negatively correlated with the severity of foot symptoms based on the Movement Disorder Society-Sponsored Revision of the Unified Parkinson's Disease Rating Scale (MDS-UPDRS-III). CONCLUSION: Overall, current findings provide new evidence of brain changes underlying motor symptoms in PD. Our results suggest that pathophysiology of lower limb symptoms in PD appears to involve both the cortico-basal ganglia and cortico-cerebellar motor circuits.

Rate control deficits during pinch grip and ankle dorsiflexion in early-stage Parkinson's disease.

BACKGROUND: Much of our understanding of the deficits in force control in Parkinson's disease (PD) relies on findings in the upper extremity. Currently, there is a paucity of data pertaining to the effect of PD on lower limb force control. OBJECTIVE: The purpose of this study was to concurrently evaluate upper- and lower-limb force control in early-stage PD and a group of age- and gender-matched healthy controls. METHODS: Twenty individuals with PD and twenty-one healthy older adults participated in this study. Participants performed two visually guided, submaximal (15% of maximum voluntary contractions) isometric force tasks: a pinch grip task and an ankle dorsiflexion task. PD were tested on their more affected side and after overnight withdrawal from antiparkinsonian medication. The tested side in controls was randomized. Differences in force control capacity were assessed by manipulating speed-based and variability-based task parameters. RESULTS: Compared with controls, PD demonstrated slower rates of force development and force relaxation during the foot task, and a slower rate of relaxation during the hand task. Force variability was similar across groups but greater in the foot than in the hand in both PD and controls. Lower limb rate control deficits were greater in PD with more severe symptoms based on the Hoehn and Yahr stage. CONCLUSIONS: Together, these results provide quantitative evidence of an impaired capacity in PD to produce submaximal and rapid force across multiple effectors. Moreover, results suggest that force control deficits in the lower limb may become more severe with disease progression.

Distinct microbiome profiles in convergent wisdom tooth impactions.

AIMS: Long-term retention of impacted third molars (wisdom teeth) is associated with plaque stagnation and the development of caries on the adjacent surface of the neighboring second molar. While caries and tooth loss are common outcomes of impaction, there is currently insufficient evidence to support the pre-emptive removal of asymptomatic wisdom teeth. Emerging evidence suggests that convergently growing impactions are associated with caries. We have therefore investigated the composition of dental plaque on the distal surface of the mandibular second molar at various impaction angles. METHODS AND RESULTS: We have compared the microbiome of these surfaces at four impaction angulations using short-read sequencing of the bacterial 16S rRNA gene: two convergent (horizontal and mesial) and two divergent (distal and vertical) angulations, and in cases where the wisdom tooth is missing. Horizontal angulations exhibited lower microbial diversity than mesial impactions. Amplicon Sequence Variants (ASVs) associated with Veillonella were significantly more abundant at impactions with angulations toward the midline. Using machine learning, a random forest classifier trained to distinguish microbiome profiles was used to predict the native angulations for a subset of samples, with samples from the two convergent impactions estimated with the greatest accuracy. CONCLUSIONS: Differences in microbial diversity were apparent between caries-associated convergent (horizontal and mesial) impacted wisdom teeth, as well as greater abundances of Veillonella ASVs at horizontal impactions.