An enclosed in-gel PCR amplification cassette with multi-target, multi-sample detection for platform molecular diagnostics

This work describes a self-contained, simple, disposable, and inexpensive gel capillary cassette for DNA amplification in near point of care settings. The cassette avoids the need for pumps or valves during raw sample delivery or polymerase chain reaction (PCR) amplification steps. The cassette contains capillary reaction units that can be stored at room temperature for up to 3 months. The current cassette configuration format can simultaneously tests up to 16 patients for two or more targets, accommodates different sample types on the same cassette, has integrated positive and negative controls and allows flexibility for multiple geometries. PCR reagents in the cassette are desiccated to allow storage at room temperature with rehydration by raw sample at the time of testing. The sample is introduced to the cassette via a transfer pipette simply by capillary force. DNA amplification was carried out in a portable prototype instrument for PCR thermal cycling with fluorescence detection of amplified products by melt curve analysis. To demonstrate performance, raw genital swabs and urine were introduced to the same cassette to simultaneously detect four sexually transmitted infections. Herpes Simplex Viruses (HSV-1 and HSV-2) were detected from raw genital swabs. Ureaplasma Urealyticum (UU) and Mycoplasma Homonis (MH) were detected from raw urine. Results for multiple patients were obtained in as little as 50'. This platform allows multiparameter clinical testing with a pre-assembled cassette that requires only the introduction of raw sample. Modification of the prototype device to accommodate larger cassettes will ultimately provide high throughput simultaneous testing of even larger numbers of samples for many different targets, as is required for most clinical applications. Combinations of wax and/or polymer cassettes holding capillary reaction units are feasible. The components of the cassette are suited to mass production and robotic assembly to produce a readily manufactured disposable reaction cassette that can be configured for disease-specific testing panels. Rapid testing with a disposable reaction cassette on an inexpensive instrument will permit on the spot evaluation of patients in the clinic for faster medical decision-making and more informed therapeutic choices

Leveraging genomics to understand threats in a migratory waterbird

Understanding how risk factors affect populations across their annual cycle is a major challenge for conserving migratory birds. For example, disease outbreaks may happen on the breeding grounds, the wintering grounds, or during migration and are expected to accelerate under climate change. The ability to identify the geographic origins of impacted individuals, especially outside of breeding areas, might make it possible to predict demographic trends and inform conservation decision-making. However, such an effort is made more challenging by the degraded state of carcasses and resulting low quality of DNA available. Here, we describe a rapid and low-cost approach for identifying the origins of birds sampled across their annual cycle that is robust even when DNA quality is poor. We illustrate the approach in the common loon (Gavia immer), an iconic migratory aquatic bird that is under increasing threat on both its breeding and wintering areas. Using 300 samples collected from across the breeding range, we develop a panel of 158 single-nucleotide polymorphisms (SNP) loci with divergent allele frequencies across six genetic subpopulations. We use this SNP panel to identify the breeding grounds for 142 live nonbreeding individuals and carcasses. For example, genetic assignment of loons sampled during botulism outbreaks in parts of the Great Lakes provides evidence for the significant role the lakes play as migratory stopover areas for loons that breed across wide swaths of Canada, and highlights the vulnerability of a large segment of the breeding population to botulism outbreaks that are occurring in the Great Lakes with increasing frequency. Our results illustrate that the use of SNP panels to identify breeding origins of carcasses collected during the nonbreeding season can improve our understanding of the population-specific impacts of mortality from disease and anthropogenic stressors, ultimately allowing more effective management.Published versio

Keck Infrared Transient Survey I: Survey Description and Data Release 1

We present the Keck Infrared Transient Survey (KITS), a NASA Key Strategic Mission Support program to obtain near-infrared (NIR) spectra of astrophysical transients of all types, and its first data release, consisting of 105 NIR spectra of 50 transients. Such a data set is essential as we enter a new era of IR astronomy with the James Webb Space Telescope (JWST) and the upcoming Nancy Grace Roman Space Telescope (Roman). NIR spectral templates will be essential to search JWST images for stellar explosions of the first stars and to plan an effective Roma} SN Ia cosmology survey, both key science objectives for mission success. Between 2022 February and 2023 July, we systematically obtained 274 NIR spectra of 146 astronomical transients, representing a significant increase in the number of available NIR spectra in the literature. The first data release includes data from the 2022A semester. We systematically observed three samples: a flux-limited sample that includes all transients $<$17 mag in a red optical band (usually ZTF r or ATLAS o bands); a volume-limited sample including all transients within redshift $z < 0.01$ ($D \approx 50$ Mpc); and an SN Ia sample targeting objects at phases and light-curve parameters that had scant existing NIR data in the literature. The flux-limited sample is 39% complete (60% excluding SNe Ia), while the volume-limited sample is 54% complete and is 79% complete to $z = 0.005$. All completeness numbers will rise with the inclusion of data from other telescopes in future data releases. Transient classes observed include common Type Ia and core-collapse supernovae, tidal disruption events (TDEs), luminous red novae, and the newly categorized hydrogen-free/helium-poor interacting Type Icn supernovae. We describe our observing procedures and data reduction using Pypeit, which requires minimal human interaction to ensure reproducibility

JWST NIRSpec+MIRI Observations of the nearby Type IIP supernova 2022acko

We present JWST spectral and photometric observations of the Type IIP supernova (SN) 2022acko at ~50 days past explosion. These data are the first JWST spectral observations of a core-collapse SN. We identify ~30 different H I features, other features associated with products produced from the CNO cycle, and s-process elements such as Sc II and Ba II. By combining the JWST spectra with ground-based optical and NIR spectra, we construct a full Spectral Energy Distribution from 0.4 to 25 microns and find that the JWST spectra are fully consistent with the simultaneous JWST photometry. The data lack signatures of CO formation and we estimate a limit on the CO mass of < 10^{-8} solar mass. We demonstrate how the CO fundamental band limits can be used to probe underlying physics during stellar evolution, explosion, and the environment. The observations indicate little mixing between the H envelope and C/O core in the ejecta and show no evidence of dust. The data presented here set a critical baseline for future JWST observations, where possible molecular and dust formation may be seen

Universal DNA methylation age across mammalian tissues

Aging, often considered a result of random cellular damage, can be accurately estimated using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we demonstrate the development of universal pan-mammalian clocks, using 11,754 methylation arrays from our Mammalian Methylation Consortium, which encompass 59 tissue types across 185 mammalian species. These predictive models estimate mammalian tissue age with high accuracy (r > 0.96). Age deviations correlate with human mortality risk, mouse somatotropic axis mutations and caloric restriction. We identified specific cytosines with methylation levels that change with age across numerous species. These sites, highly enriched in polycomb repressive complex 2-binding locations, are near genes implicated in mammalian development, cancer, obesity and longevity. Our findings offer new evidence suggesting that aging is evolutionarily conserved and intertwined with developmental processes across all mammals.Publisher PDFPeer reviewe

Synaptic Transmission from Horizontal Cells to Cones Is Impaired by Loss of Connexin Hemichannels

In the vertebrate retina, horizontal cells generate the inhibitory surround of bipolar cells, an essential step in contrast enhancement. For the last decades, the mechanism involved in this inhibitory synaptic pathway has been a major controversy in retinal research. One hypothesis suggests that connexin hemichannels mediate this negative feedback signal; another suggests that feedback is mediated by protons. Mutant zebrafish were generated that lack connexin 55.5 hemichannels in horizontal cells. Whole cell voltage clamp recordings were made from isolated horizontal cells and cones in flat mount retinas. Light-induced feedback from horizontal cells to cones was reduced in mutants. A reduction of feedback was also found when horizontal cells were pharmacologically hyperpolarized but was absent when they were pharmacologically depolarized. Hemichannel currents in isolated horizontal cells showed a similar behavior. The hyperpolarization-induced hemichannel current was strongly reduced in the mutants while the depolarization-induced hemichannel current was not. Intracellular recordings were made from horizontal cells. Consistent with impaired feedback in the mutant, spectral opponent responses in horizontal cells were diminished in these animals. A behavioral assay revealed a lower contrast-sensitivity, illustrating the role of the horizontal cell to cone feedback pathway in contrast enhancement. Model simulations showed that the observed modifications of feedback can be accounted for by an ephaptic mechanism. A model for feedback, in which the number of connexin hemichannels is reduced to about 40%, fully predicts the specific asymmetric modification of feedback. To our knowledge, this is the first successful genetic interference in the feedback pathway from horizontal cells to cones. It provides direct evidence for an unconventional role of connexin hemichannels in the inhibitory synapse between horizontal cells and cones. This is an important step in resolving a long-standing debate about the unusual form of (ephaptic) synaptic transmission between horizontal cells and cones in the vertebrate retina

Universal DNA methylation age across mammalian tissues.

Aging, often considered a result of random cellular damage, can be accurately estimated using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we demonstrate the development of universal pan-mammalian clocks, using 11,754 methylation arrays from our Mammalian Methylation Consortium, which encompass 59 tissue types across 185 mammalian species. These predictive models estimate mammalian tissue age with high accuracy (r > 0.96). Age deviations correlate with human mortality risk, mouse somatotropic axis mutations and caloric restriction. We identified specific cytosines with methylation levels that change with age across numerous species. These sites, highly enriched in polycomb repressive complex 2-binding locations, are near genes implicated in mammalian development, cancer, obesity and longevity. Our findings offer new evidence suggesting that aging is evolutionarily conserved and intertwined with developmental processes across all mammals

LensWatch. I. Resolved HST Observations and Constraints on the Strongly Lensed Type Ia Supernova 2022qmx (“SN Zwicky”)

Supernovae (SNe) that have been multiply imaged by gravitational lensing are rare and powerful probes for cosmology. Each detection is an opportunity to develop the critical tools and methodologies needed as the sample of lensed SNe increases by orders of magnitude with the upcoming Vera C. Rubin Observatory and Nancy Grace Roman Space Telescope. The latest such discovery is of the quadruply imaged Type Ia SN 2022qmx (aka, “SN Zwicky”) at z = 0.3544. SN Zwicky was discovered by the Zwicky Transient Facility in spatially unresolved data. Here we present follow-up Hubble Space Telescope observations of SN Zwicky, the first from the multicycle “LensWatch (www.lenswatch.org)” program. We measure photometry for each of the four images of SN Zwicky, which are resolved in three WFC3/UVIS filters (F475W, F625W, and F814W) but unresolved with WFC3/IR F160W, and present an analysis of the lensing system using a variety of independent lens modeling methods. We find consistency between lens-model-predicted time delays (≲1 day), and delays estimated with the single epoch of Hubble Space Telescope colors (≲3.5 days), including the uncertainty from chromatic microlensing (∼1-1.5 days). Our lens models converge to an Einstein radius of θ E = ( 0.168 − 0.005 + 0.009 ) ″ , the smallest yet seen in a lensed SN system. The “standard candle” nature of SN Zwicky provides magnification estimates independent of the lens modeling that are brighter than predicted by ∼ 1.7 − 0.6 + 0.8 mag and ∼ 0.9 − 0.6 + 0.8 mag for two of the four images, suggesting significant microlensing and/or additional substructure beyond the flexibility of our image-position mass models

A JWST near- and mid-infrared nebular spectrum of the type Ia supernova 2021aefx

We present JWST near-infrared (NIR) and mid-infrared (MIR) spectroscopic observations of the nearby normal Type Ia supernova (SN) SN 2021aefx in the nebular phase at +255 days past maximum light. Our Near Infrared Spectrograph (NIRSpec) and Mid Infrared Instrument observations, combined with ground-based optical data from the South African Large Telescope, constitute the first complete optical+NIR+MIR nebular SN Ia spectrum covering 0.3–14 μm. This spectrum unveils the previously unobserved 2.5−5 μm region, revealing strong nebular iron and stable nickel emission, indicative of high-density burning that can constrain the progenitor mass. The data show a significant improvement in sensitivity and resolution compared to previous Spitzer MIR data. We identify numerous NIR and MIR nebular emission lines from iron-group elements as well as lines from the intermediate-mass element argon. The argon lines extend to higher velocities than the iron-group elements, suggesting stratified ejecta that are a hallmark of delayed-detonation or double-detonation SN Ia models. We present fits to simple geometric line profiles to features beyond 1.2 μm and find that most lines are consistent with Gaussian or spherical emission distributions, while the [Ar iii] 8.99 μm line has a distinctively flat-topped profile indicating a thick spherical shell of emission. Using our line profile fits, we investigate the emissivity structure of SN 2021aefx and measure kinematic properties. Continued observations of SN 2021aefx and other SNe Ia with JWST will be transformative to the study of SN Ia composition, ionization structure, density, and temperature, and will provide important constraints on SN Ia progenitor and explosion models

Ground-based and JWST observations of SN 2022pul. I. Unusual signatures of carbon, oxygen, and circumstellar interaction in a peculiar type Ia supernova

Nebular-phase observations of peculiar Type Ia supernovae (SNe Ia) provide important constraints on progenitor scenarios and explosion dynamics for both these rare SNe and the more common, cosmologically useful SNe Ia. We present observations from an extensive ground- and space-based follow-up campaign to characterize SN 2022pul, a super-Chandrasekhar mass SN Ia (alternatively "03fg-like" SN), from before peak brightness to well into the nebular phase across optical to mid-infrared (MIR) wavelengths. The early rise of the light curve is atypical, exhibiting two distinct components, consistent with SN Ia ejecta interacting with dense carbon–oxygen (C/O)-rich circumstellar material (CSM). In the optical, SN 2022pul is most similar to SN 2012dn, having a low estimated peak luminosity (MB = −18.9 mag) and high photospheric velocity relative to other 03fg-like SNe. In the nebular phase, SN 2022pul adds to the increasing diversity of the 03fg-like subclass. From 168 to 336 days after peak B-band brightness, SN 2022pul exhibits asymmetric and narrow emission from [O i] λλ6300, 6364 (FWHM ≈ 2000 km s−1), strong, broad emission from [Ca ii] λλ7291, 7323 (FWHM ≈ 7300 km s−1), and a rapid Fe iii to Fe ii ionization change. Finally, we present the first ever optical-to-MIR nebular spectrum of an 03fg-like SN Ia using data from JWST. In the MIR, strong lines of neon and argon, weak emission from stable nickel, and strong thermal dust emission (with T ≈ 500 K), combined with prominent [O i] in the optical, suggest that SN 2022pul was produced by a white dwarf merger within C/O-rich CSM