Chromosome fusion and programmed DNA elimination shape karyotypes of nematodes.

An increasing number of metazoans undergo programmed DNA elimination (PDE), where a significant amount of DNA is selectively lost from the somatic genome during development. In some nematodes, PDE leads to the removal and remodeling of the ends of all germline chromosomes. In several species, PDE also generates internal breaks that lead to sequence loss and increased numbers of somatic chromosomes. The biological significance of these karyotype changes associated with PDE and the origin and evolution of nematode PDE remain largely unknown. Here, we assembled the single germline chromosome of the nematode Parascaris univalens and compared the karyotypes, chromosomal gene organization, and PDE features among other nematodes. We show that PDE in Parascaris converts an XX/XY sex-determination system in the germline into an XX/XO system in the somatic cells. Comparisons of Ascaris, Parascaris, and Baylisascaris ascarid chromosomes suggest that PDE existed in the ancestor of these nematodes, and their current distinct germline karyotypes were derived from fusion events of smaller ancestral chromosomes. The DNA breaks involved in PDE resolve these fused germline chromosomes into their pre-fusion karyotypes. These karyotype changes may lead to alterations in genome architecture and gene expression in the somatic cells. Cytological and genomic analyses further suggest that satellite DNA and the heterochromatic chromosome arms are dynamic and may play a role during meiosis. Overall, our results show that chromosome fusion and PDE have been harnessed in these ascarids to sculpt their karyotypes, altering the genome organization and serving specific functions in the germline and somatic cells.

Echolocating Bats Have Evolved Decreased Susceptibility to Noise-Induced Temporary Hearing Losses.

Glenis Long championed the application of quantitative psychophysical methods to understand comparative hearing abilities across species. She contributed the first psychophysical studies of absolute and masked hearing sensitivities in an auditory specialist, the echolocating horseshoe bat. Her data demonstrated that this bat has hyperacute frequency discrimination in the 83-kHz range of its echolocation broadcast. This specialization facilitates the bat's use of Doppler shift compensation to separate echoes of fluttering insects from concurrent echoes of non-moving objects. In this review, we discuss another specialization for hearing in a species of echolocating bat that contributes to perception of echoes within a complex auditory scene. Psychophysical and behavioral studies with big brown bats show that exposures to long duration, intense wideband or narrowband ultrasonic noise do not induce significant increases in their thresholds to echoes and do not impair their ability to orient through a naturalistic sonar scene containing multiple distracting echoes. Thresholds of auditory brainstem responses also remain low after intense noise exposures. These data indicate that big brown bats are not susceptible to temporary threshold shifts as measured in comparable paradigms used with other mammals, at least within the range of stimulus parameters that have been tested so far. We hypothesize that echolocating bats have evolved a decreased susceptibility to noise-induced hearing losses as a specialization for echolocation in noisy environments.

Echo detection thresholds in big brown bats (Eptesicus fuscus) vary with echo spectral content.

Echolocating big brown bats (Eptesicus fuscus) broadcast downward frequency-modulated sweeps covering the ultrasonic range from 100-23 kHz in two harmonics. They perceive target range from the time delay between each broadcast and its returning echo. Previous experiments indicated that the bat's discrimination acuity for broadcast-echo delay declines when the lowest frequencies (23-35 kHz) in the first harmonic of an echo are removed. This experiment examined whether echo detection is similarly impaired. Results show that detection thresholds for echoes missing these lowest frequencies are raised. Increased thresholds for echoes differing in spectra facilitates the bat's ability to discriminate against clutter.

Left atrial strain, embolic stroke of undetermined source, and atrial fibrillation detection.

BACKGROUND: Atrial cardiopathy is a proposed mechanism of embolic stroke of undetermined source (ESUS). Left atrial (LA) strain may identify early atrial cardiopathy prior to structural changes. We aim to study the associations between LA strain, ESUS, and atrial fibrillation (AF) detection in ESUS. METHODS: The study population included patients with ESUS and noncardioembolic (NCE) stroke presenting to the Rhode Island Hospital Stroke Center between January 2016 and June 2017 who underwent transthoracic echocardiography. Speckle tracking echocardiography (STE) was used to measure the three phases of LA strain (reservoir, conduit, and contractile). Binary logistic regression analysis was performed to determine the associations between LA strain and stroke subtype (ESUS vs. NCE) as well as follow-up detection of AF in ESUS patients. RESULTS: We identified 656 patients, 307 with ESUS and 349 with NCE. In binary logistic regression, the lowest tertiles of LA reservoir (adjusted OR 1.944, 95% CI 1.266-2.986, p = .002), contractile (aOR 1.568, 95% CI 1.035-2.374, p = .034), and conduit strain (aOR 2.288, 95% CI 1.448-3.613, p = .001) were more likely to be significantly associated with ESUS compared to NCE stroke. Among all ESUS patients, the lowest tertiles of LA reservoir strain (OR 2.534, 95% CI 1.029-6.236, p = .043), contractile strain (OR 2.828, 95% CI 1.158-6.903, p = .022), and conduit strain (OR 2.614, 95% CI 1.003-6.815, p = .049) were significantly associated with subsequent detection of AF. CONCLUSION: Reduced LA strain is associated with ESUS occurrence and AF detection in ESUS patients. Therefore, quantification of LA strain in ESUS patients may improve risk stratification and guide secondary prevention strategies.

Temporal coherence of harmonic frequencies affects echo detection in the big brown bat, Eptesicus fuscus.

Echolocating big brown bats (Eptesicus fuscus) broadcast frequency modulated (FM) ultrasonic pulses containing two prominent harmonic sweeps (FM1, FM2). Both harmonics typically return as echoes at the same absolute time delay following the broadcast, making them coherent. Electronically splitting FM1 and FM2 allows their time delays to be controlled separately, making them non-coherent. Earlier work shows that big brown bats discriminate coherent from split harmonic, non-coherent echoes and that disruptions of harmonic coherence produce blurry acoustic images. A psychophysical experiment on two trained big brown bats tested the hypothesis that detection thresholds for split harmonic, non-coherent echoes are higher than those for coherent echoes. Thresholds of the two bats for detecting 1-glint echoes with coherent harmonics were around 35 and 36 dB sound pressure level, respectively, while thresholds for split harmonic echoes were about 10 dB higher. When the delay of FM2 in split harmonic echoes is shortened by 75 µs to offset neural amplitude-latency trading and restore coherence in the auditory representation, thresholds decreased back down to those estimated for coherent echoes. These results show that echo detection is affected by loss of harmonic coherence, consistent with the proposed broader role of coherence across frequencies for auditory perception.

Representation of frequency-modulated sweeps in the cochlear nucleus of the big brown bat.

The cochlear nucleus (CN) receives ipsilateral input from the auditory nerve and projects to other auditory brainstem nuclei. Little is known about CN processing of signals used for echolocation. This study recorded multiple unit activity in the CN of anesthetized big brown bats (Eptesicus fuscus) to ultrasonic frequency-modulated (FM) sweeps differing in sweep direction. FM up-sweeps evoke larger peak amplitudes at shorter onset latencies and with smaller amplitude-latency trading ratios than FM down-sweeps. Variability of onset latencies is in the tens of microsecond ranges, indicating sharp temporal precision in the CN for coding of FM signals.

Connexin36 RNA Expression in the Cochlear Nucleus of the Echolocating Bat, Eptesicus fuscus.

PURPOSE: The echolocating bat is used as a model for studying the auditory nervous system because its specialized sensory capabilities arise from general mammalian auditory percepts such as pitch and sound source localization. These percepts are mediated by precise timing within neurons and networks of the lower auditory brainstem, where the gap junction protein Connexin36 (CX36) is expressed. Gap junctions and electrical synapses in the central nervous system are associated with fast transmission and synchronous patterns of firing within neuronal networks. The purpose of this study was to identify areas where CX36 was expressed in the bat cochlear nucleus to shed light on auditory brainstem networks in a hearing specialist animal model. METHODS: We investigated the distribution of CX36 RNA throughout the cochlear nucleus complex of the echolocating big brown bat, Eptesicus fuscus, using in situ hybridization. As a qualitative comparison, we visualized Gjd2 gene expression in the cochlear nucleus of transgenic CX36 reporter mice, species that hear ultrasound but do not echolocate. RESULTS: In both the bat and the mouse, CX36 is expressed in the anteroventral and in the dorsal cochlear nucleus, with more limited expression in the posteroventral cochlear nucleus. These results are generally consistent with previous work based on immunohistochemistry. CONCLUSION: Our data suggest that the anatomical substrate for CX36-mediated electrical neurotransmission is conserved in the mammalian CN across echolocating bats and non-echolocating mice.

Oscillatory discharges in the auditory midbrain of the big brown bat contribute to coding of echo delay.

Subsequent to his breakthrough discovery of delay-tuned neurons in the bat's auditory midbrain and cortex, Albert Feng proposed that neural computations for echo delay involve intrinsic oscillatory discharges generated in the inferior colliculus (IC). To explore further the presence of these neural oscillations, we recorded multiple unit activity with a novel annular low impedance electrode from the IC of anesthetized big brown bats and Seba's short-tailed fruit bats. In both species, responses to tones, noise bursts, and FM sweeps contain long latency components, extending up to 60 ms post-stimulus onset, organized in periodic, oscillatory-like patterns at frequencies of 360-740 Hz. Latencies of this oscillatory activity resemble the wide distributions of single neuron response latencies in the IC. In big brown bats, oscillations lasting up to 30 ms after pulse onset emerge in response to single FM pulse-echo pairs, at particular pulse-echo delays. Oscillatory responses to pulses and evoked responses to echoes overlap extensively at short echo delays (5-7 ms), creating interference-like patterns. At longer echo delays, responses are separately evident to both pulses and echoes, with less overlap. These results extend Feng's reports of IC oscillations, and point to different processing mechanisms underlying perception of short vs long echo delays.

Chromosome fusion and programmed DNA elimination shape karyotypes of parasitic nematodes.

A growing list of metazoans undergo programmed DNA elimination (PDE), where a significant amount of DNA is selectively lost from the somatic genome during development. In some nematodes, PDE leads to the removal and remodeling of the ends of all germline chromosomes. In several species, PDE also generates internal breaks that lead to sequence loss and an increased number of somatic chromosomes. The biological significance of these karyotype changes associated with PDE and the origin and evolution of nematode PDE remain largely unknown. Here, we assembled the single germline chromosome of the horse parasite Parascaris univalens and compared the karyotypes, chromosomal gene organization, and PDE features among ascarid nematodes. We show that PDE in Parascaris converts an XX/XY sex-determination system in the germline into an XX/XO system in the somatic cells. Comparisons of Ascaris, Parascaris, and Baylisascaris ascarid chromosomes suggest that PDE existed in the ancestor of these parasites, and their current distinct germline karyotypes were derived from fusion events of smaller ancestral chromosomes. The DNA breaks involved in PDE resolve these fused germline chromosomes into their pre-fusion karyotypes, leading to alterations in genome architecture and gene expression in the somatic cells. Cytological and genomic analyses further suggest that satellite DNA and the heterochromatic chromosome arms play a dynamic role in the Parascaris germline chromosome during meiosis. Overall, our results show that chromosome fusion and PDE have been harnessed in these ascarids to sculpt their karyotypes, altering the genome organization and serving specific functions in the germline and somatic cells.

The nematode Oscheius tipulae as a genetic model for programmed DNA elimination.

Programmed DNA elimination (PDE) is a notable exception to the paradigm of genome integrity. In metazoa, PDE often occurs coincident with germline to somatic cell differentiation. During PDE, portions of genomic DNA are lost, resulting in reduced somatic genomes. Prior studies have described the sequences lost, as well as chromosome behavior, during metazoan PDE. However, a system for studying the mechanisms and consequences of PDE in metazoa is lacking. Here, we present a functional and genetic model for PDE in the free-living Rhabditidae nematode Oscheius tipulae, a family that also includes Caenorhabditis elegans. O. tipulae was recently suggested to eliminate DNA. Using staged embryos and DNA FISH, we showed that O. tipulae PDE occurs during embryogenesis at the 8-16 cell stages. We identified a conserved motif, named Sequence For Elimination (SFE), for all 12 break sites on the six chromosomes at the junctions of retained and eliminated DNA. SFE mutants exhibited a "fail-to-eliminate" phenotype only at the modified sites. END-seq revealed that breaks can occur at multiple positions within the SFE, with extensive end resection followed by telomere addition to both retained and eliminated ends. We identified many functional SFEs at the chromosome ends through END-seq in the wild-type embryos, genome sequencing of SFE mutants, and comparative genomics of 23 wild isolates. We suggest that these alternative SFEs provide flexibility in the sequences eliminated and a fail-safe mechanism for PDE. These studies establish O. tipulae as a new, attractive model for studying the mechanisms and consequences of PDE in a metazoan.

Phosphorylated histone variant γH2Av is associated with chromatin insulators in Drosophila.

Chromatin insulators are responsible for orchestrating long-range interactions between enhancers and promoters throughout the genome and align with the boundaries of Topologically Associating Domains (TADs). Here, we demonstrate an association between gypsy insulator proteins and the phosphorylated histone variant H2Av (γH2Av), normally a marker of DNA double strand breaks. Gypsy insulator components colocalize with γH2Av throughout the genome, in polytene chromosomes and in diploid cells in which Chromatin IP data shows it is enriched at TAD boundaries. Mutation of insulator components su(Hw) and Cp190 results in a significant reduction in γH2Av levels in chromatin and phosphatase inhibition strengthens the association between insulator components and γH2Av and rescues γH2Av localization in insulator mutants. We also show that γH2Av, but not H2Av, is a component of insulator bodies, which are protein condensates that form during osmotic stress. Phosphatase activity is required for insulator body dissolution after stress recovery. Together, our results implicate the H2A variant with a novel mechanism of insulator function and boundary formation.

A Review of Respiratory Post-Acute Sequelae of COVID-19 (PASC) and the Potential Benefits of Pulmonary Rehabilitation.

With the SARS-CoV-2 pandemic continuing into its third year, the number of patients who survive acute COVID-19 infection but go on to develop long-term symptoms is increasing daily. Those individuals who experience one or more of a variety of persistent symptoms post-COVID-19 are now diagnosed with the syndrome called post-acute sequelae of COVID-19 (PASC), often colloquially called "Long COVID." This article discusses relevant research and current hypotheses regarding the pathophysiology and management of respiratory symptoms of PASC, in order to provide primary care physicians with context for management of this heterogeneous population. We focus on the growing body of research that supports the use of pulmonary rehabilitation for patients with PASC to improve symptoms and quality of life.

Non-invasive auditory brainstem responses to FM sweeps in awake big brown bats.

We introduce two EEG techniques, one based on conventional monopolar electrodes and one based on a novel tripolar electrode, to record for the first time auditory brainstem responses (ABRs) from the scalp of unanesthetized, unrestrained big brown bats. Stimuli were frequency-modulated (FM) sweeps varying in sweep direction, sweep duration, and harmonic structure. As expected from previous invasive ABR recordings, upward-sweeping FM signals evoked larger amplitude responses (peak-to-trough amplitude in the latency range of 3-5 ms post-stimulus onset) than downward-sweeping FM signals. Scalp-recorded responses displayed amplitude-latency trading effects as expected from invasive recordings. These two findings validate the reliability of our noninvasive recording techniques. The feasibility of recording noninvasively in unanesthetized, unrestrained bats will energize future research uncovering electrophysiological signatures of perceptual and cognitive processing of biosonar signals in these animals, and allows for better comparison with ABR data from echolocating cetaceans, where invasive experiments are heavily restricted.

Amplitude discrimination is predictably affected by echo frequency filtering in wideband echolocating bats.

Big brown bats echolocate using wideband frequency-modulated (FM) ultrasonic pulses, perceiving target range from echo delay and target size from echo amplitude. Echolocation pulses contain two prominent down-sweeping harmonics (FM1, ∼55-22 kHz; FM2, ∼100-55 kHz), which are affected differently by propagation to the target and back to the bat. Previous work demonstrates that big brown bats utilize the low frequencies in FM1 for target ranging, while FM2 only contributes if FM1 is also present. The present experiments test the hypothesis that the bat's ability to discriminate echo amplitude is also affected by selectively attenuating FM1 or FM2 in target or nontarget echoes. Bats were trained to perform an amplitude discrimination task with virtual echo targets located 83 cm away. Echo delay was fixed and echo amplitude was varied, while either FM1 or FM2 was attenuated by highpass or lowpass filtering. Bats' performance decreased when lower frequencies were attenuated in target echoes and when higher frequencies were attenuated in nontarget echoes. Performance was reversed in the opposite filtering conditions. The bat's ability to distinguish between virtual targets varying in amplitude at the same simulated range indicates a high level of focused attention for perceptual isolation of target from non-target echoes.

In-vivo functional and structural retinal imaging using multiwavelength photoacoustic remote sensing microscopy.

Many important eye diseases as well as systemic disorders manifest themselves in the retina. Retinal imaging technologies are rapidly growing and can provide ever-increasing amounts of information about the structure, function, and molecular composition of retinal tissue in-vivo. Photoacoustic remote sensing (PARS) is a novel imaging modality based on all-optical detection of photoacoustic signals, which makes it suitable for a wide range of medical applications. In this study, PARS is applied for in-vivo imaging of the retina and estimating oxygen saturation in the retinal vasculature. To our knowledge, this is the first time that a non-contact photoacoustic imaging technique is applied for in-vivo imaging of the retina. Here, optical coherence tomography is also used as a well-established retinal imaging technique to navigate the PARS imaging beams and demonstrate the capabilities of the optical imaging setup. The system is applied for in-vivo imaging of both microanatomy and the microvasculature of the retina. The developed system has the potential to advance the understanding of the ocular environment and to help in monitoring of ophthalmic diseases.

Systolic Strain by Speckle-Tracking Echocardiography Is a Feasible and Sensitive Measure of Right Ventricular Dysfunction in Acute Respiratory Failure Patients on Mechanical Ventilation.

Right ventricular (RV) dysfunction is common in acute respiratory failure and associated with worse outcomes, but it can be difficult to detect in the ICU setting. Speckle-tracking echocardiography (STE) can identify early changes in RV systolic function and be quantified as systolic strain. We measured the feasibility of RV global longitudinal systolic strain (RV GLS) in respiratory failure patients and its association with clinical outcomes. DESIGN: Retrospective cohort. SETTING: Two tertiary hospital medical ICUs in Providence, RI, from March 2015 to January 2018. PATIENTS: Two hundred twenty-three patients with acute respiratory failure requiring mechanical ventilation (MV) with available echocardiograms. MEASUREMENTS AND MAIN RESULTS: Clinical data were extracted from medical records. RV GLS was measured via STE (TOMTEC, Chicago, IL), along with standard echocardiographic measurements by two independent readers blinded to outcomes. The average age was 65 years (range, 21-90 yr), 121 (54%) were men, and the most common etiology of respiratory failure was pneumonia (n = 83, 37%). The average RV GLS was -16% (sd ± 7). The intraobserver correlation coefficients were 0.78 and 0.94, whereas the interobserver correlation coefficient was 0.61 for RV GLS. In the majority of echocardiograms (n = 178, 80%), all wall segments were tracked appropriately by operator visual inspection. Worse RV GLS was associated with greater hospital mortality (odds ratio, 1.03; 95% CI, 1.00-1.07; p = 0.03), such that every 1% decrement in RV GLS was associated with up to a 7% increase in the risk of death. RV GLS was 90% sensitive for the detection of RV dysfunction compared with tricuspid annular plane systolic excursion. CONCLUSIONS: The measurement of RV GLS by STE in subjects on MV is feasible, reproducible, and sensitive for the detection of RV dysfunction. RV GLS may predict poor outcomes in acute respiratory failure.

A Drosophila insulator interacting protein suppresses enhancer-blocking function and modulates replication timing.

Insulators play important roles in genome structure and function in eukaryotes. Interactions between a DNA binding insulator protein and its interacting partner proteins define the properties of each insulator site. The different roles of insulator protein partners in the Drosophila genome and how they confer functional specificity remain poorly understood. The Suppressor of Hairy wing [Su(Hw)] insulator is targeted to the nuclear lamina, preferentially localizes at euchromatin/heterochromatin boundaries, and is associated with the gypsy retrotransposon. Insulator activity relies on the ability of the Su(Hw) protein to bind the DNA at specific sites and interact with Mod(mdg4)67.2 and CP190 partner proteins. HP1 and insulator partner protein 1 (HIPP1) is a partner of Su(Hw), but how HIPP1 contributes to the function of Su(Hw) insulator complexes is unclear. Here, we demonstrate that HIPP1 colocalizes with the Su(Hw) insulator complex in polytene chromatin and in stress-induced insulator bodies. We find that the overexpression of either HIPP1 or Su(Hw) or mutation of the HIPP1 crotonase-like domain (CLD) causes defects in cell proliferation by limiting the progression of DNA replication. We also show that HIPP1 overexpression suppresses the Su(Hw) insulator enhancer-blocking function, while mutation of the HIPP1 CLD does not affect Su(Hw) enhancer blocking. These findings demonstrate a functional relationship between HIPP1 and the Su(Hw) insulator complex and suggest that the CLD, while not involved in enhancer blocking, influences cell cycle progression.