Adeno-associated virus (AAV) capsids can deliver transformative gene therapies, but our understanding of AAV biology remains incomplete. We generated the complete first-order AAV2 capsid fitness ...landscape, characterizing all single-codon substitutions, insertions, and deletions across multiple functions relevant for in vivo delivery. We discovered a frameshifted gene in the VP1 region that expresses a membrane-associated accessory protein that limits AAV production through competitive exclusion. Mutant biodistribution revealed the importance of both surface-exposed and buried residues, with a few phenotypic profiles characterizing most variants. Finally, we algorithmically designed and experimentally verified a diverse in vivo targeted capsid library with viability far exceeding random mutagenesis approaches. These results demonstrate the power of systematic mutagenesis for deciphering complex genomes and the potential of empirical machine-guided protein engineering.
The effect of anthropogenic aerosols on cloud droplet concentrations and radiative properties is the source of one of the largest uncertainties in the radiative forcing of climate over the industrial ...period. This uncertainty affects our ability to estimate how sensitive the climate is to greenhouse gas emissions. Here we perform a sensitivity analysis on a global model to quantify the uncertainty in cloud radiative forcing over the industrial period caused by uncertainties in aerosol emissions and processes. Our results show that 45 per cent of the variance of aerosol forcing since about 1750 arises from uncertainties in natural emissions of volcanic sulphur dioxide, marine dimethylsulphide, biogenic volatile organic carbon, biomass burning and sea spray. Only 34 per cent of the variance is associated with anthropogenic emissions. The results point to the importance of understanding pristine pre-industrial-like environments, with natural aerosols only, and suggest that improved measurements and evaluation of simulated aerosols in polluted present-day conditions will not necessarily result in commensurate reductions in the uncertainty of forcing estimates.
We present CO(2−1) and adjacent continuum observations of seven nearby radio-quiet type-2 quasars (QSO2s) obtained with ALMA at ∼0.2″ resolution (370 pc at
z
∼ 0.1). These QSO2s are luminous (
L
...OIII
> 10
8.5
L
⊙
∼
M
B
< −23), and their host galaxies massive (
M
*
∼ 10
11
M
⊙
). The CO morphologies are diverse, including disks and interacting systems. Two of the QSO2s are red early-type galaxies with no CO(2–1) detected. In the interacting galaxies, the central kiloparsec contains 18–25% of the total cold molecular gas, whereas in the spirals it is only ∼5–12%. J1010+0612 and J1430+1339 show double-peaked CO flux maps along the major axis of the CO disks that do not have an optical counterpart at the same angular resolution. Based on our analysis of the ionized and molecular gas kinematics and millimeter continuum emission, these CO morphologies are most likely produced by active galactic nucleus (AGN) feedback in the form of outflows, jets, and/or shocks. The CO kinematics of the QSO2s with CO(2−1) detections are dominated by rotation but also reveal noncircular motions. According to our analysis, these noncircular motions correspond to molecular outflows that are mostly coplanar with the CO disks in four of the QSO2s, and either to a coplanar inflow or vertical outflow in the case of J1010+0612. These outflows represent 0.2–0.7% of the QSO2s’ total molecular gas mass and have maximum velocities of 200–350 km s
−1
, radii from 0.4 to 1.3 kpc, and outflow mass rates of 8–16
M
⊙
yr
−1
. These outflow properties are intermediate between those of the mild molecular outflows measured for Seyfert galaxies and the fast and energetic outflows shown by ultra-luminous infrared galaxies. This suggests that it is not only AGN luminosity that drives massive molecular outflows. Other factors such as jet power, coupling between winds, jets, and/or ionized outflows and the CO disks, and amount or geometry of dense gas in the nuclear regions might also be relevant. Thus, although we do not find evidence for a significant impact of quasar feedback on the total molecular gas reservoirs and star formation rates, it appears to be modifying the distribution of cold molecular gas in the central kiloparsec of the galaxies.
Modern experimental technologies can assay large numbers of biological sequences, but engineered protein libraries rarely exceed the sequence diversity of natural protein families. Machine learning ...(ML) models trained directly on experimental data without biophysical modeling provide one route to accessing the full potential diversity of engineered proteins. Here we apply deep learning to design highly diverse adeno-associated virus 2 (AAV2) capsid protein variants that remain viable for packaging of a DNA payload. Focusing on a 28-amino acid segment, we generated 201,426 variants of the AAV2 wild-type (WT) sequence yielding 110,689 viable engineered capsids, 57,348 of which surpass the average diversity of natural AAV serotype sequences, with 12-29 mutations across this region. Even when trained on limited data, deep neural network models accurately predict capsid viability across diverse variants. This approach unlocks vast areas of functional but previously unreachable sequence space, with many potential applications for the generation of improved viral vectors and protein therapeutics.
We explored whether breast cancer outcomes are associated with endoxifen and other metabolites of tamoxifen and examined potential correlates of endoxifen concentration levels in serum including ...cytochrome P450 2D6 (CYP2D6) metabolizer phenotype and body mass index (BMI). Concentration levels of tamoxifen, endoxifen, 4‐hydroxytamoxifen (4OH‐tamoxifen), and N‐desmethyltamoxifen (ND‐tamoxifen) were measured from samples taken from 1,370 patients with estrogen receptor (ER)‐positive breast cancer who were participating in the Women's Healthy Eating and Living (WHEL) Study. We tested these concentration levels for possible associations with breast cancer outcomes and found that breast cancer outcomes were not associated with the concentration levels of tamoxifen, 4‐hydroxytamoxifen, and ND‐tamoxifen. For endoxifen, a threshold was identified, with women in the upper four quintiles of endoxifen concentration appearing to have a 26% lower recurrence rate than women in the bottom quintile (hazard ratio (HR) = 0.74; 95% confidence interval (CI), (0.55–1.00)). The predictors of this higher‐risk bottom quintile were poor/intermediate metabolizer genotype, higher BMI, and lower tamoxifen concentrations as compared with the mean for the cohort as a whole. This study suggests that there is a minimal concentration threshold above which endoxifen is effective against the recurrence of breast cancer and that ~80% of tamoxifen takers attain this threshold.
Clinical Pharmacology & Therapeutics (2011) 89 5, 718–725. doi:10.1038/clpt.2011.32
Tackling the climate emergency is now a key target for the healthcare sector. Avoiding inhalational anaesthesia is often cited as an important element of reducing anaesthesia-related emissions. ...However, evidence supporting this is based on adult practice. The aim of this study was to identify the difference in carbon footprint of inhalational and i.v. anaesthesia when used in children.
We used mathematical simulation models to compare general anaesthetic techniques in children weighing 5-50 kg for TIVA, i.v. induction then inhalational maintenance, inhalational induction then i.v. maintenance, and inhalational induction and maintenance. We simulated inhalational induction with sevoflurane alone, and co-induction with sevoflurane and nitrous oxide, and both remifentanil-propofol and propofol-only i.v. anaesthesia. For each technique, we drew on previously published life-cycle data to calculate carbon dioxide equivalents for anaesthetic durations up to 480 min.
TIVA with propofol and remifentanil had a smaller carbon footprint over a typical anaesthetic duration of 60 min (1.26 kg carbon dioxide equivalents CO
e for a 20 kg child) than i.v. induction followed by inhalational maintenance (2.58 kg CO
e) or inhalational induction and maintenance (2.98 kg CO
e). Inhalational induction followed by i.v. maintenance only had a lower carbon footprint than inhalational induction and maintenance when used in longer procedures (>77 min for children 5-20 kg; >105 min for children 30-50 kg).
In a simulation study, i.v. anaesthesia had climate benefits in paediatric anaesthesia. However, when used after inhalational induction, benefits were only achieved in longer procedures. These findings provide evidence-based guidance for reducing the environmental impact of paediatric anaesthesia, but these will require confirmation using real-world data.
The Cosmics Leaving OUtdoor Droplets (CLOUD) experiment was created to systematically test the link between galactic cosmic rays (GCR) and climate, specifically, the connection of ions from GCR to ...aerosol nucleation and cloud condensation nuclei (CCN), the particles on which cloud droplets form. The CLOUD experiment subsequently unlocked many of the mysteries of nucleation and growth in our atmosphere, and it has improved our understanding of human influences on climate. Their most recent publication (Gordon et al. 2017, https://doi.org/10.1002/2017JD026844) provides their first estimate of the GCR‐CCN connection, and they show that CCN respond too weakly to changes in GCR to yield a significant influence on clouds and climate.
Key Points
The CLOUD experiment was designed to probe connections between galactic cosmic rays, aerosols, and clouds
The experiment has led to significant advances in our understanding of aerosol nucleation and growth, and aerosol effects on climate
CLOUD recently found that the impact of decadal fluctuations of galactic cosmic rays on aerosols would have a limited impact on clouds
ABSTRACT
Radio-loud active galaxies have two accretion modes radiatively inefficient (RI) and radiatively efficient (RE), with distinct optical and infrared signatures, and two jet dynamical ...behaviours, which in arcsec- to arcmin-resolution radio surveys manifest primarily as centre- or edge-brightened structures Fanaroff–Riley (FR) class I and II. The nature of the relationship between accretion mode and radio morphology (FR class) has been the subject of long debate. We present a comprehensive investigation of this relationship for a sample of 286 well-resolved radio galaxies in the LOFAR Two-metre Sky Survey Deep Fields (LoTSS-Deep) first data release, for which robust morphological and accretion mode classifications have been made. We find that two-thirds of luminous FRII radio galaxies are RI, and identify no significant differences in the visual appearance or source dynamic range (peak/mean surface brightness) of the RI and RE FRIIs, demonstrating that both RI and RE systems can produce FRII structures. We also find a significant population of low-luminosity FRIIs (predominantly RI), supporting our earlier conclusion that FRII radio structures can be produced at all radio luminosities. We demonstrate that in the luminosity range where both morphologies are present, the probability of producing FRI or FRII radio morphology is directly linked to stellar mass, while across all morphologies and luminosities, RE accretion occurs in systems with high specific star formation rate, presumably because this traces fuel availability. In summary, the relationship between accretion mode and radio morphology is very indirect, with host-galaxy environment controlling these two key parameters in different ways.
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