First Attempt at Spectroscopic Detection of Gravity Modes in a Long-Period Pulsating Subdwarf B Star -- PG 1627+017

In the first spectroscopic campaign for a PG 1716 variable (or long-period pulsating subdwarf B star), we succeeded in detecting velocity variations due to g-mode pulsations at a level of 1.0-1.5 km/s.The observations were obtained during 40 nights on 2-m class telescopes in Arizona, South Africa,and Australia. The target,PG1627+017, is one of the brightest and largest amplitude stars in its class.It is also the visible component of a post-common envelope binary.Our final radial velocity data set includes 84 hours of time-series spectroscopy over a time baseline of 53 days. Our derived radial velocity amplitude spectrum, after subtracting the orbital motion, shows three potential pulsational modes 3-4 sigma above the mean noise level, at 7201.0s,7014.6s and 7037.3s.Only one of the features is statistically likely to be real,but all three are tantalizingly close to, or a one day alias of, the three strongest periodicities found in the concurrent photometric campaign. We further attempted to detect pulsational variations in the Balmer line amplitudes. The single detected periodicity of 7209 s, although weak, is consistent with theoretical expectations as a function of wavelength.Furthermore, it allows us to rule out a degree index of l= 3 or l= 5 for that mode. Given the extreme weakness of g-mode pulsations in these stars,we conclude that anything beyond simply detecting their presence will require larger telescopes,higher efficiency spectral monitoring over longer time baselines,improved longitude coverage, and increased radial velocity precision.Comment: 39 pages, 9 figures, 4 tables, ApJ accepted. See postscript for full abtrac

Measurement of Subcellular Force Generation in Neurons

AbstractForces are important for neuronal outgrowth during the initial wiring of the nervous system and after trauma, yet subcellular force generation over the microtubule-rich region at the rear of the growth cone and along the axon has never, to our knowledge, been directly measured. Because previous studies have indicated microtubule polymerization and the microtubule-associated proteins Kinesin-1 and dynein all generate forces that push microtubules forward, a major question is whether the net forces in these regions are contractile or expansive. A challenge in addressing this is that measuring local subcellular force generation is difficult. Here we develop an analytical mathematical model that describes the relationship between unequal subcellular forces arranged in series within the neuron and the net overall tension measured externally. Using force-calibrated towing needles to measure and apply forces, in combination with docked mitochondria to monitor subcellular strain, we then directly measure force generation over the rear of the growth cone and along the axon of chick sensory neurons. We find the rear of the growth cone generates 2.0 nN of contractile force, the axon generates 0.6 nN of contractile force, and that the net overall tension generated by the neuron is 1.3 nN. This work suggests that the forward bulk flow of the cytoskeletal framework that occurs during axonal elongation and growth-cone pauses arises because strong contractile forces in the rear of the growth cone pull material forward

Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences

BACKGROUND: More than 2 million SARS-CoV-2 genome sequences have been generated and shared since the start of the COVID-19 pandemic and constitute a vital information source that informs outbreak control, disease surveillance, and public health policy. The Pango dynamic nomenclature is a popular system for classifying and naming genetically-distinct lineages of SARS-CoV-2, including variants of concern, and is based on the analysis of complete or near-complete virus genomes. However, for several reasons, nucleotide sequences may be generated that cover only the spike gene of SARS-CoV-2. It is therefore important to understand how much information about Pango lineage status is contained in spike-only nucleotide sequences. Here we explore how Pango lineages might be reliably designated and assigned to spike-only nucleotide sequences. We survey the genetic diversity of such sequences, and investigate the information they contain about Pango lineage status. RESULTS: Although many lineages, including the main variants of concern, can be identified clearly using spike-only sequences, some spike-only sequences are shared among tens or hundreds of Pango lineages. To facilitate the classification of SARS-CoV-2 lineages using subgenomic sequences we introduce the notion of designating such sequences to a “lineage set”, which represents the range of Pango lineages that are consistent with the observed mutations in a given spike sequence. CONCLUSIONS: We find that many lineages, including the main variants-of-concern, can be reliably identified by spike alone and we define lineage-sets to represent the lineage precision that can be achieved using spike-only nucleotide sequences. These data provide a foundation for the development of software tools that can assign newly-generated spike nucleotide sequences to Pango lineage sets. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08358-2

Exomoon simulations

We introduce and describe our newly developed code that simulates light curves and radial velocity curves for arbitrary transiting exoplanets with a satellite. The most important feature of the program is the calculation of radial velocity curves and the Rossiter-McLaughlin effect in such systems. We discuss the possibilities for detecting the exomoons taking the abilities of Extremely Large Telescopes into account. We show that satellites may be detected also by their RM effect in the future, probably using less accurate measurements than promised by the current instrumental developments. Thus, RM effect will be an important observational tool in the exploration of exomoons.Comment: 5 pages, 2 figures with 9 figure panels, accepted by EM&

Clustered Regularly Interspaced Short Palindromic Repeat-Dependent, Biofilm-Specific Death of Pseudomonas aeruginosa Mediated by Increased Expression of Phage-Related Genes

The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (CRISPR/Cas) system is an adaptive immune system present in many archaea and bacteria. CRISPR/Cas systems are incredibly diverse, and there is increasing evidence of CRISPR/Cas systems playing a role in cellular functions distinct from phage immunity. Previously, our laboratory reported one such alternate function in which the type 1-F CRISPR/Cas system of the opportunistic pathogen Pseudomonas aeruginosa strain UCBPP-PA14 (abbreviated as P. aeruginosa PA14) inhibits both biofilm formation and swarming motility when the bacterium is lysogenized by the bacteriophage DMS3. In this study, we demonstrated that the presence of just the DMS3 protospacer and the protospacer-adjacent motif (PAM) on the P. aeruginosa genome is necessary and sufficient for this CRISPR-dependent loss of these group behaviors, with no requirement of additional DMS3 sequences. We also demonstrated that the interaction of the CRISPR system with the DMS3 protospacer induces expression of SOS-regulated phage-related genes, including the well-characterized pyocin operon, through the activity of the nuclease Cas3 and subsequent RecA activation. Furthermore, our data suggest that expression of the phage-related genes results in bacterial cell death on a surface due to the inability of the CRISPR-engaged strain to downregulate phage-related gene expression, while these phage-related genes have minimal impact on growth and viability under planktonic conditions. Deletion of the phage-related genes restores biofilm formation and swarming motility while still maintaining a functional CRISPR/Cas system, demonstrating that the loss of these group behaviors is an indirect effect of CRISPR self-targeting

Slowing down atomic diffusion in subdwarf B stars: mass loss or turbulence?

Subdwarf B stars show chemical peculiarities that cannot be explained by diffusion theory alone. Both mass loss and turbulence have been invoked to slow down atomic diffusion in order to match observed abundances. The fact that some sdB stars show pulsations gives upper limits on the amount of mass loss and turbulent mixing allowed. Consequently, non-adiabatic asteroseismology has the potential to decide which process is responsible for the abundance anomalies. We compute for the first time seismic properties of sdB models with atomic diffusion included consistently during the stellar evolution. The diffusion equations with radiative forces are solved for H, He, C, N, O, Ne, Mg, Fe and Ni. We examine the effects of various mass-loss rates and mixed surface masses on the abundances and mode stability. It is shown that the mass-loss rates needed to simulate the observed He abundances (10^{-14}<=Mdot [Msun/yr]<=10^{-13}) are not consistent with observed pulsations. We find that for pulsations to be driven the rates should be Mdot<=10^{-15} Msun/yr. On the other hand, weak turbulent mixing of the outer 10^{-6} Msun can explain the He abundance anomalies while still allowing pulsations to be driven. The origin of the turbulence remains unknown but the presence of pulsations gives tight constraints on the underlying turbulence model.Comment: 12 pages, 8 figures, 1 table, accepted for publication in MNRA

Multicolour correlative imaging using phosphor probes

Correlative light and electron microscopy exploits the advantages of optical methods, such as multicolour probes and their use in hydrated live biological samples, to locate functional units, which are then correlated with structural details that can be revealed by the superior resolution of electron microscopes. One difficulty is locating the area imaged by the electron beam in the much larger optical field of view. Multifunctional probes that can be imaged in both modalities and thus register the two images are required. Phosphor materials give cathodoluminescence (CL) optical emissions under electron excitation. Lanthanum phosphate containing thulium or terbium or europium emits narrow bands in the blue, green and red regions of the CL spectrum; they may be synthesised with very uniform-sized crystals in the 10- to 50-nm range. Such crystals can be imaged by CL in the electron microscope, at resolutions limited by the particle size, and with colour discrimination to identify different probes. These materials also give emissions in the optical microscope, by multiphoton excitation. They have been deposited on the surface of glioblastoma cells and imaged by CL. Gadolinium oxysulphide doped with terbium emits green photons by either ultraviolet or electron excitation. Sixty-nanometre crystals of this phosphor have been imaged in the atmospheric scanning electron microscope (JEOL ClairScope). This probe and microscope combination allow correlative imaging in hydrated samples. Phosphor probes should prove to be very useful in correlative light and electron microscopy, as fiducial markers to assist in image registration, and in high/super resolution imaging studies

A Hierarchical Cascade of Second Messengers Regulates Pseudomonas aeruginosa Surface Behaviors

Biofilms are surface-attached multicellular communities. Using single-cell tracking microscopy, we showed that apilY1 mutant of Pseudomonas aeruginosa is defective in early biofilm formation. We leveraged the observation that PilY1 pro- tein levels increase on a surface to perform a genetic screen to identify mutants altered in surface-grown expression of this pro- tein. Based on our genetic studies, we found that soon after initiating surface growth, cyclic AMP (cAMP) levels increase, depen- dent on PilJ, a chemoreceptor-like protein of the Pil-Chp complex, and the type IV pilus (TFP). cAMP and its receptor protein Vfr, together with the FimS-AlgR two-component system (TCS), upregulate the expression of PilY1 upon surface growth. FimS and PilJ interact, suggesting a mechanism by which Pil-Chp can regulate FimS function. The subsequent secretion of PilY1 is dependent on the TFP assembly system; thus, PilY1 is not deployed until the pilus is assembled, allowing an ordered signaling cascade. Cell surface-associated PilY1 in turn signals through the TFP alignment complex PilMNOP and the diguanylate cyclase SadC to activate downstream cyclic di-GMP (c-di-GMP) production, thereby repressing swarming motility. Overall, our data support a model whereby P. aeruginosa senses the surface through the Pil-Chp chemotaxis-like complex, TFP, and PilY1 to reg- ulate cAMP and c-di-GMP production, thereby employing a hierarchical regulatory cascade of second messengers to coordinate its program of surface behaviors

Particulate matter concentrations in residences: an intervention study evaluating stand‐alone filters and air conditioners

This study, a randomized controlled trial, evaluated the effectiveness of free‐standing air filters and window air conditioners (ACs) in 126 low‐income households of children with asthma. Households were randomized into a control group, a group receiving a free‐standing HEPA filter placed in the child’s sleeping area, and a group receiving the filter and a window‐mounted AC. Indoor air quality (IAQ) was monitored for week‐long periods over three to four seasons. High concentrations of particulate matter (PM) and carbon dioxide were frequently seen. When IAQ was monitored, filters reduced PM levels in the child’s bedroom by an average of 50%. Filter use varied greatly among households and declined over time, for example, during weeks when pollutants were monitored, filter use was initially high, averaging 84 ± 27%, but dropped to 63 ± 33% in subsequent seasons. In months when households were not visited, use averaged only 34 ± 30%. Filter effectiveness did not vary in homes with central or room ACs. The study shows that measurements over multiple seasons are needed to characterize air quality and filter performance. The effectiveness of interventions using free‐standing air filters depends on occupant behavior, and strategies to ensure filter use should be an integral part of interventions. Practical Implications Environmental tobacco smoke (ETS) increased particulate matter (PM) levels by about 14 μg/m 3 and was often detected using ETS‐specific tracers despite restrictions on smoking in the house as reported on questionnaires administered to caregivers. PM concentrations depended on season, filter usage, relative humidity, air exchange ratios, number of children, outdoor PM levels, sweeping/dusting, and presence of a central air conditioner (AC). Free‐standing air filters can be an effective intervention that provides substantial reductions in PM concentrations if the filters are used. However, filter use was variable across the study population and declined over the study duration, and thus strategies are needed to encourage and maintain use of filters. The variability in filter use suggests that exposure misclassification is a potential problem in intervention studies using filters. The installation of a room AC in the bedroom, intended to limit air exchange ratios, along with an air filter, did not lower PM levels more than the filter alone.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/91183/1/j.1600-0668.2011.00761.x.pd

Residential Proximity to Major Roadways Is Associated With Increased Levels of AC133+ Circulating Angiogenic Cells

Objectives: Previous studies have shown that residential proximity to a roadway is associated with increased cardiovascular disease risk. Yet, the nature of this association remains unclear, and its effect on individual cardiovascular disease risk factors has not been assessed. The objective of this study was to determine whether residential proximity to roadways influences systemic inflammation and the levels of circulating angiogenic cells. Approach and Results: In a cross-sectional study, cardiovascular disease risk factors, blood levels of C-reactive protein, and 15 antigenically defined circulating angiogenic cell populations were measured in participants (n=316) with moderate-to-high cardiovascular disease risk. Attributes of roadways surrounding residential locations were assessed using geographic information systems. Associations between road proximity and cardiovascular indices were analyzed using generalized linear models. Close proximity (\u3c50 m) to a major roadway was associated with lower income and higher rates of smoking but not C-reactive protein levels. After adjustment for potential confounders, the levels of circulating angiogenic cells in peripheral blood were significantly elevated in people living in close proximity to a major roadway (CD31+/AC133+, AC133+, CD34+/AC133+, and CD34+/45dim/AC133+ cells) and positively associated with road segment distance (CD31+/AC133+, AC133+, and CD34+/AC133+ cells), traffic intensity (CD31+/AC133+ and AC133+ cells), and distance-weighted traffic intensity (CD31+/34+/45+/AC133+ cells). Conclusions: Living close to a major roadway is associated with elevated levels of circulating cells positive for the early stem marker AC133+. This may reflect an increased need for vascular repair. Levels of these cells in peripheral blood may be a sensitive index of cardiovascular injury because of residential proximity to roadways