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SUMMARYA unifying feature of the RAS superfamily is a functionally conserved GTPase cycle that proteins use to transition between active and inactive states. Here, we demonstrate that active site autophosphorylation of some small GTPases is an intrinsic regulatory mechanism that reduces nucleotide hydrolysis and enhances nucleotide exchange, thus altering the on/off switch that forms the basis for their signaling functions. Using x-ray crystallography, nuclear magnetic resonance spectroscopy, biolayer interferometry binding assays, and molecular dynamics on autophosphorylated mutants of H-RAS and K-RAS, we show that phosphoryl transfer from GTP requires dynamic movement of the switch II domain and that autophosphorylation promotes nucleotide exchange by opening of the active site and extraction of the stabilizing Mg. Finally, we demonstrate that autophosphorylated K-RAS exhibits altered effector interactions, including a reduced affinity for RAF proteins. Thus, autophosphorylation leads to altered active site dynamics and effector interaction properties, creating a pool of GTPases that are functionally distinct from the non-phosphorylated counterpart.

BackgroundDespite rising rates of vaccination, quarantine remains critical to control SARS-CoV-2 transmission. COVID-19 quarantine length around the world varies in part due to the limited amount of empirical data.ObjectiveTo assess post-quarantine transmission risk for various quarantine lengths.DesignCohort study.SettingFour US universities, September 2020 to February 2021.Participants3,641 students and staff were identified as close contacts to SARS-CoV-2-positive individuals. They entered strict or non-strict quarantine and were tested on average twice per week for SARS-CoV-2. Strict quarantine included designated housing with a private room, private bathroom and meal delivery. Non-strict quarantine potentially included interactions with household members.MeasurementsDates of exposure and last negative and first positive tests during quarantine.ResultsOf the 418 quarantined individuals who eventually converted to positive, 11%, 4.2%, and 1.2% were negative and asymptomatic on days 7, 10 and 14, respectively. The US CDC recently shortened its quarantine guidance from 14 to 7 days based on estimates of 2.3-8.6% post-quarantine transmission risk at day 7, significantly below the 11% risk we report here. Notably, 6% of individuals tested positive after day 7 in strict quarantine, versus 14% in non-strict quarantine. Ongoing exposure during quarantine likely explains the higher rate of COVID-19 in non-strict quarantine.LimitationsQuarantine should be longer for individuals using antigen testing, given antigen testing’s lower sensitivity than qPCR. Results apply in settings in which SAR-CoV-2 variants do not affect latent period.ConclusionsTo maintain the 5% transmission risk that the CDC used in its guidance, our data suggest that quarantine with qPCR testing 1 day before intended release should extend to 10 days for non-strict quarantine.Funding SourceNone.

The promise of biotechnology is tempered by its potential for accidental or deliberate misuse. Reliably identifying telltale signatures characteristic to different genetic designers, termed ‘genetic engineering attribution’, would deter misuse, yet is still considered unsolved. Here, we show that recurrent neural networks trained on DNA motifs and basic phenotype data can reach 70% attribution accuracy in distinguishing between over 1,300 labs. To make these models usable in practice, we introduce a framework for weighing predictions against other investigative evidence using calibration, and bring our model to within 1.6% of perfect calibration. Additionally, we demonstrate that simple models can accurately predict both the nation-state-of-origin and ancestor labs, forming the foundation of an integrated attribution toolkit which should promote responsible innovation and international security alike., The potential for accidental or deliberate misuse of biotechnology is of concern for international biosecurity. Here the authors apply machine learning to DNA sequences and associated phenotypic data to facilitate genetic engineering attribution and identify country-of-origin and ancestral lab of engineered DNA sequences.

The promise of biotechnology is tempered by its potential for accidental or deliberate misuse. Reliably identifying telltale signatures characteristic to different genetic designers, termed genetic engineering attribution, would deter misuse, yet is still considered unsolved. Here, we show that recurrent neural networks trained on DNA motifs and basic phenotype can reach 70% attribution accuracy distinguishing between over 1,300 labs. To make these models usable in practice, we introduce a framework for weighing predictions against other investigative evidence using calibration, and bring our model to within 1.6% of perfect calibration. Additionally, we demonstrate that simple models can accurately predict both the nation-state-of-origin and ancestor labs, forming the foundation of an integrated attribution toolkit which should promote responsible innovation and international security alike.

Optimal quarantine length for COVID-19 infection is unclear, in part owing to limited empirical data.To assess postquarantine transmission risk for various quarantine lengths and potential associations between quarantine strictness and transmission risk.Retrospective cohort study in 4 US universities from September 2020 to February 2021, including 3641 university students and staff who were identified as close contacts to individuals who tested positive for SARS-CoV-2 infection. Individuals were tested throughout the 10 to 14-day quarantine, and follow-up testing continued at least weekly throughout the 2020-2021 academic year.Strict quarantine, including designated housing with a private room, private bathroom, and meal delivery, vs nonstrict, which potentially included interactions with household members.Dates of last known exposure, last negative test result, and first positive test result during quarantine.This study included 301 quarantined university students and staff who tested SARS-CoV-2-positive (of 3641 quarantined total). These 301 individuals had a median (IQR) age of 22.0 (20.0-25.0) years; 131 (43.5%) identified as female; and 20 (6.6%) were staff. Of the 287 self-reporting race and ethnicity according to university-defined classifications, 21 (7.3%) were African American or Black, 60 (20.9%) Asian, 17 (5.9%) Hispanic or Latinx, 174 (60.6%) White, and 15 (5.2%) other (including multiracial and/or multiethnic). Of the 301 participants, 40 (13.3%; 95% CI, 9.9%-17.6%) had negative test results and were asymptomatic on day 7 compared with 15 (4.9%; 95% CI, 3.0%-8.1%) and 4 (1.4%; 95% CI, 0.4%-3.5%) on days 10 and 14, respectively. Individuals in strict quarantine tested positive less frequently than those in nonstrict quarantine (10% vs 12%; P = .04).To maintain the 5% transmission risk used as the basis for US Centers for Disease Control and Prevention's 7-day test-based quarantine guidance, our data suggest that quarantine with quantitative polymerase chain reaction testing 1 day before intended release should be 10 days for nonstrict quarantine and 8 days for strict quarantine, as ongoing exposure during quarantine may be associated with the higher rate of positive test results following nonstrict quarantine.

New treatments for acute ischemic stroke (AIS) have been introduced and are expected to improve patients' overall outcomes. We assessed the impact of new therapeutic strategies on outcome and cost of hospitalization among adult patients with AIS in the United States.Patients with AIS admitted in the United States in 1993-1994 and 2006-2007 were listed using the Nationwide Inpatient Survey database. We determined the rates of occurrence, hospitalization outcomes, and mean hospital charges for all patients. We further analyzed these variables in the ventilated and nonventilated patients.We identified 386,043 patients with AIS admitted in the United States in 1993-1994 and 749,766 patients in 2006-2007. The length of hospitalization was significantly higher in 1993-1994 compared with 2006-2007: 6.9 ± 4.2 days versus 4.66 ± 3 days, respectively. In-hospital mortality rate was 8.9% in 1993-1994 and 5.6% in 2006-2007 (P0.0001). There was a significant increase in mean hospital charges in 2006-2007 compared with 1993-1994 ($21,916 ± $14,117 versus $9,646 ± $5,727). The length of hospitalization was significantly shorter in 2006-2007 in nonventilated patients. There was a significant increase in mean hospital charges in 2006-2007 compared with 1993-1994 in both ventilated ($81,528 ± $64,526 versus $25,143 ± $17,172, P0.0001) and nonventilated patients ($21,085 ± $13,042 versus $10,000 ± $6,300, P0.0001). The mortality rate was significantly lower in 2006-2007 in both subgroups: 46.5% versus 59.8% in ventilated patients and 4.2% versus 8.2% in nonventilated patients (P0.0001).Our study suggests that new therapeutic strategies have improved outcomes and increased cost of hospitalization among adult patients with AIS in the United States over a period of 13 years. The hospitalization cost was significantly higher in the ventilated and nonventilated patients in 2006-2007, which may reflect the impact of new therapeutic strategies, the availability of more intensive care units and stroke centers, and the lower mortality rate in this time period.