How DNA Packaging and Processing Proteins Affect Dynamic DNA Alkylation

DNA alkylating agents are commonly considered toxic due to the irreversible nature of the lesions that they form and the failure of DNA repair enzymes to remove their lesions. However, compounds that alkylate DNA in a reversible manner may not share the same toxicity as irreversible alkylating agents. Quinone methides (QMs) are a class of transient electrophiles that reversibly alkylate DNA. A bifunctional QM conjugated to the DNA intercalator acridine (bisQMAcr) has previously been synthesized in order to examine the dynamics of reaction with DNA. BisQMAcr’s reversible chemistry facilitates its stepwise migration from one end of a duplex DNA to the other in a bipedal manner. However, bisQMAcr requires 7 days to traverse 10 base pairs, which may be too slow to be effective in vivo to evade DNA repair. Two monofunctional QMs were linked together using a flexible polyammonium alkyl chain (diQMs) to potentially facilitate faster QM migration. Additionally, BisQMs conjugated to weakly intercalative quinoxalines were synthesized to avoid the strength of acridine’s intercalation that may have suppressed QM migration. However, neither of the new QMs alkylated DNA reversibly. Thus, bisQMAcr remains the most dynamic QM synthesized to date. The environment within cells likely influences the potency of QMs’ reversible DNA alkylation, since cellular DNA is packaged around histone proteins to form nucleosomes. The assembly of DNA into nucleosomes weakens QMs’ potency as DNA alkylating agents by 90% relative to DNA free in solution. Nucleosomes possess an additional protective function against bisQMAcr’s DNA alkylation, as the histone proteins serve as terminal acceptors of bisQMAcr’s DNA adducts. BisQMAcr can release from its adducts on DNA and alkylate the histones, leaving the DNA unmodified. However, QM alkylation of the histones does not interfere with their assembly into nucleosomes, as adducts formed in the core regions of the protein that may not disrupt with the necessary DNA-protein contacts for nucleosome formation. The ability of DNA polymerases and helicases to modulate the dynamics of bisQMAcr’s DNA alkylation and of bisQMAcr’s crosslinks to inhibit replication was also investigated to determine whether biological machines may hasten QM migration. The Klenow Exo- and φ29 DNA polymerases were unable to cause bisQMAcr’s crosslinks to break apart and failed to extend DNA primers in the presence of the crosslinks. However, the T7 bacteriophage gene 4 protein (T7GP4) DNA helicase was able to unwind DNA containing reversible QM crosslinks. The helicase induced dissociation of only 40% of bisQMAcr’s crosslinks, while the remaining 60% remained intact. Irreversible DNA crosslinks formed by mechlorethamine completely resisted unwinding by the T7GP4 helicase, suggesting that only reversible crosslinks separate during DNA unwinding. Reversible QM crosslinks may not pose an absolute block to replication like many irreversible crosslinking agents do. The ability of a helicase to remove QM adducts from DNA essentially affords DNA repair without relying on specific DNA repair proteins. This work describes the potency of reversible QM alkylation in a biological setting. Transfer of reversible adducts to the histone proteins and loss of DNA adducts by helicases’ translocation may afford their repair by means of their intrinsic reversible chemistry

The Holy Grail: A road map for unlocking the climate record stored within Mars' polar layered deposits

In its polar layered deposits (PLD), Mars possesses a record of its recent climate, analogous to terrestrial ice sheets containing climate records on Earth. Each PLD is greater than 2 ​km thick and contains thousands of layers, each containing information on the climatic and atmospheric state during its deposition, creating a climate archive. With detailed measurements of layer composition, it may be possible to extract age, accumulation rates, atmospheric conditions, and surface activity at the time of deposition, among other important parameters; gaining the information would allow us to “read” the climate record. Because Mars has fewer complicating factors than Earth (e.g. oceans, biology, and human-modified climate), the planet offers a unique opportunity to study the history of a terrestrial planet’s climate, which in turn can teach us about our own planet and the thousands of terrestrial exoplanets waiting to be discovered. During a two-part workshop, the Keck Institute for Space Studies (KISS) hosted 38 Mars scientists and engineers who focused on determining the measurements needed to extract the climate record contained in the PLD. The group converged on four fundamental questions that must be answered with the goal of interpreting the climate record and finding its history based on the climate drivers. The group then proposed numerous measurements in order to answer these questions and detailed a sequence of missions and architecture to complete the measurements. In all, several missions are required, including an orbiter that can characterize the present climate and volatile reservoirs; a static reconnaissance lander capable of characterizing near surface atmospheric processes, annual accumulation, surface properties, and layer formation mechanism in the upper 50 ​cm of the PLD; a network of SmallSat landers focused on meteorology for ground truth of the low-altitude orbiter data; and finally, a second landed platform to access ~500 ​m of layers to measure layer variability through time. This mission architecture, with two landers, would meet the science goals and is designed to save costs compared to a single very capable landed mission. The rationale for this plan is presented below. In this paper we discuss numerous aspects, including our motivation, background of polar science, the climate science that drives polar layer formation, modeling of the atmosphere and climate to create hypotheses for what the layers mean, and terrestrial analogs to climatological studies. Finally, we present a list of measurements and missions required to answer the four major questions and read the climate record. 1. What are present and past fluxes of volatiles, dust, and other materials into and out of the polar regions? 2. How do orbital forcing and exchange with other reservoirs affect those fluxes? 3. What chemical and physical processes form and modify layers? 4. What is the timespan, completeness, and temporal resolution of the climate history recorded in the PLD

the geomorphology of ceres

### INTRODUCTION Observations of Ceres, the largest object in the asteroid belt, have suggested that the dwarf planet is a geologically differentiated body with a silicate core and an ice-rich mantle. Data acquired by the Dawn spacecraft were used to perform a three-dimensional characterization of the surface to determine if the geomorphology of Ceres is consistent with the models of an icy interior. ### RATIONALE Instruments on Dawn have collected data at a variety of resolutions, including both clear-filter and color images. Digital terrain models have been derived from stereo images. A preliminary 1:10 M scale geologic map of Ceres was constructed using images obtained during the Approach and Survey orbital phases of the mission. We used the map, along with higher-resolution imagery, to assess the geology of Ceres at the global scale, to identify geomorphic and structural features, and to determine the geologic processes that have affected Ceres globally. ### RESULTS Impact craters are the most prevalent geomorphic feature on Ceres, and several of the craters have fractured floors. Geomorphic analysis of the fracture patterns shows that they are similar to lunar Floor-Fractured Craters (FFCs), and an analysis of the depth-to-diameter ratios shows that they are anomalously shallow compared with average Ceres craters. Both of these factors are consistent with FFC floors being uplifted due to an intrusion of cryomagma. Kilometer-scale linear structures cross much of Ceres. Some of these structures are oriented radially to large craters and most likely formed due to impact processes. However, a set of linear structures present only on a topographically high region do not have any obvious relationship to impact craters. Geomorphic analysis suggests that they represent subsurface faults and might have formed due to crustal uplift by cryomagmatic intrusion. Domes identified across the Ceres surface present a wide range of sizes ( 100 km), basal shapes, and profiles. Whether a single formation mechanism is responsible for their formation is still an open question. Cryovolcanic extrusion is one plausible process for the larger domes, although most small mounds (<10-km diameter) are more likely to be impact debris. Differences in lobate flow morphology suggest that multiple emplacement processes have operated on Ceres, where three types of flows have been identified. Type 1 flows are morphologically similar to ice-cored flows on Earth and Mars. Type 2 flows are comparable to long-runout landslides. Type 3 flows morphologically resemble the fluidized ejecta blankets of rampart craters, which are hypothesized to form by impact into ice-rich ground. ### CONCLUSION The global trend of lobate flows suggests that differences in their geomorphology could be explained by variations in ice content and temperature at the near surface. Geomorphic and topographic analyses of the FFCs suggest that cryomagmatism is active on Ceres, whereas the large domes are possibly formed by extrusions of cryolava. Although spectroscopic analysis to date has identified water ice in only one location on Ceres, the identification of these potentially ice-related features suggests that there may be more ice within localized regions of Ceres' crust. ![Figure][1] Dawn high-altitude mapping orbit imagery (140 meters per pixel) of example morphologic features. ( A ) Occator crater; arrows point to floor fractures. ( B ) Linear structures, denoted by arrows. ( C ) A large dome at 42° N, 10° E, visible in the elevation map. ( D ) A small mound at 45.5° S, 295.7° E. ( E ) Type 1 lobate flow; arrows point to the flow front. Analysis of Dawn spacecraft Framing Camera image data allows evaluation of the topography and geomorphology of features on the surface of Ceres. The dwarf planet is dominated by numerous craters, but other features are also common. Linear structures include both those associated with impact craters and those that do not appear to have any correlation to an impact event. Abundant lobate flows are identified, and numerous domical features are found at a range of scales. Features suggestive of near-surface ice, cryomagmatism, and cryovolcanism have been identified. Although spectroscopic analysis has currently detected surface water ice at only one location on Ceres, the identification of these potentially ice-related features suggests that there may be at least some ice in localized regions in the crust. [1]: pending:ye

The Holy Grail: A road map for unlocking the climate record stored within Mars' polar layered deposits

In its polar layered deposits (PLD), Mars possesses a record of its recent climate, analogous to terrestrial ice sheets containing climate records on Earth. Each PLD is greater than 2 ​km thick and contains thousands of layers, each containing information on the climatic and atmospheric state during its deposition, creating a climate archive. With detailed measurements of layer composition, it may be possible to extract age, accumulation rates, atmospheric conditions, and surface activity at the time of deposition, among other important parameters; gaining the information would allow us to “read” the climate record. Because Mars has fewer complicating factors than Earth (e.g. oceans, biology, and human-modified climate), the planet offers a unique opportunity to study the history of a terrestrial planet’s climate, which in turn can teach us about our own planet and the thousands of terrestrial exoplanets waiting to be discovered. During a two-part workshop, the Keck Institute for Space Studies (KISS) hosted 38 Mars scientists and engineers who focused on determining the measurements needed to extract the climate record contained in the PLD. The group converged on four fundamental questions that must be answered with the goal of interpreting the climate record and finding its history based on the climate drivers. The group then proposed numerous measurements in order to answer these questions and detailed a sequence of missions and architecture to complete the measurements. In all, several missions are required, including an orbiter that can characterize the present climate and volatile reservoirs; a static reconnaissance lander capable of characterizing near surface atmospheric processes, annual accumulation, surface properties, and layer formation mechanism in the upper 50 ​cm of the PLD; a network of SmallSat landers focused on meteorology for ground truth of the low-altitude orbiter data; and finally, a second landed platform to access ~500 ​m of layers to measure layer variability through time. This mission architecture, with two landers, would meet the science goals and is designed to save costs compared to a single very capable landed mission. The rationale for this plan is presented below. In this paper we discuss numerous aspects, including our motivation, background of polar science, the climate science that drives polar layer formation, modeling of the atmosphere and climate to create hypotheses for what the layers mean, and terrestrial analogs to climatological studies. Finally, we present a list of measurements and missions required to answer the four major questions and read the climate record. 1. What are present and past fluxes of volatiles, dust, and other materials into and out of the polar regions? 2. How do orbital forcing and exchange with other reservoirs affect those fluxes? 3. What chemical and physical processes form and modify layers? 4. What is the timespan, completeness, and temporal resolution of the climate history recorded in the PLD

Mammographic density and risk of breast cancer by age and tumor characteristics

Introduction: Understanding whether mammographic density (MD) is associated with all breast tumor subtypes and whether the strength of association varies by age is important for utilizing MD in risk models. Methods: Data were pooled from six studies including 3414 women with breast cancer and 7199 without who underwent screening mammography. Percent MD was assessed from digitized film-screen mammograms using a computer-assisted threshold technique. We used polytomous logistic regression to calculate breast cancer odds according to tumor type, histopathological characteristics, and receptor (estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor (HER2)) status by age (51%) versus average density (11-25%). Women ages 2.1 cm) versus small tumors and positive versus negative lymph node status (P’s < 0.01). For women ages <55 years, there was a stronger association of MD with ER-negative breast cancer than ER-positive tumors compared to women ages 55–64 and ≥65 years (Page-interaction = 0.04). MD was positively associated with both HER2-negative and HER2-positive tumors within each age group. Conclusion: MD is strongly associated with all breast cancer subtypes, but particularly tumors of large size and positive lymph nodes across all ages, and ER-negative status among women ages <55 years, suggesting high MD may play an important role in tumor aggressiveness, especially in younger women

The absence of the queuosine tRNA modification leads to pleiotropic phenotypes revealing perturbations of metal and oxidative stress homeostasis in Escherichia coli K12

Queuosine (Q) is a conserved hypermodification of the wobble base of tRNA containing GUN anticodons but the physiological consequences of Q deficiency are poorly understood in bacteria. This work combines transcriptomic, proteomic and physiological studies to characterize a Q-deficient Escherichia coli K12 MG1655 mutant. The absence of Q led to an increased resistance to nickel and cobalt, and to an increased sensitivity to cadmium, compared to the wild-type (WT) strain. Transcriptomic analysis of the WT and Q-deficient strains, grown in the presence and absence of nickel, revealed that the nickel transporter genes (nikABCDE) are downregulated in the Q- mutant, even when nickel is not added. This mutant is therefore primed to resist to high nickel levels. Downstream analysis of the transcriptomic data suggested that the absence of Q triggers an atypical oxidative stress response, confirmed by the detection of slightly elevated reactive oxygen species (ROS) levels in the mutant, increased sensitivity to hydrogen peroxide and paraquat, and a subtle growth phenotype in a strain prone to accumulation of ROS.This work was funded by the National Institute of General Medical Sciences (NIGMS) grant GM70641, by the National Institute of Environmental Health Sciences (NIEHS) grant ES002109, by the National Science Foundation (NSF) grant CHE-2002950, by the National Research Foundation of Singapore under the Singapore-MIT Alliance for Research and Technology Antimicrobial Resistance Interdisciplinary Research Group, and by Stellate Therapeutics.Peer reviewe

Mammographic density, breast cancer risk and risk prediction

In this review, we examine the evidence for mammographic density as an independent risk factor for breast cancer, describe the risk prediction models that have incorporated density, and discuss the current and future implications of using mammographic density in clinical practice. Mammographic density is a consistent and strong risk factor for breast cancer in several populations and across age at mammogram. Recently, this risk factor has been added to existing breast cancer risk prediction models, increasing the discriminatory accuracy with its inclusion, albeit slightly. With validation, these models may replace the existing Gail model for clinical risk assessment. However, absolute risk estimates resulting from these improved models are still limited in their ability to characterize an individual's probability of developing cancer. Promising new measures of mammographic density, including volumetric density, which can be standardized using full-field digital mammography, will likely result in a stronger risk factor and improve accuracy of risk prediction models

Effect of Hydrocortisone on Mortality and Organ Support in Patients With Severe COVID-19: The REMAP-CAP COVID-19 Corticosteroid Domain Randomized Clinical Trial.

Importance: Evidence regarding corticosteroid use for severe coronavirus disease 2019 (COVID-19) is limited. Objective: To determine whether hydrocortisone improves outcome for patients with severe COVID-19. Design, Setting, and Participants: An ongoing adaptive platform trial testing multiple interventions within multiple therapeutic domains, for example, antiviral agents, corticosteroids, or immunoglobulin. Between March 9 and June 17, 2020, 614 adult patients with suspected or confirmed COVID-19 were enrolled and randomized within at least 1 domain following admission to an intensive care unit (ICU) for respiratory or cardiovascular organ support at 121 sites in 8 countries. Of these, 403 were randomized to open-label interventions within the corticosteroid domain. The domain was halted after results from another trial were released. Follow-up ended August 12, 2020. Interventions: The corticosteroid domain randomized participants to a fixed 7-day course of intravenous hydrocortisone (50 mg or 100 mg every 6 hours) (n = 143), a shock-dependent course (50 mg every 6 hours when shock was clinically evident) (n = 152), or no hydrocortisone (n = 108). Main Outcomes and Measures: The primary end point was organ support-free days (days alive and free of ICU-based respiratory or cardiovascular support) within 21 days, where patients who died were assigned -1 day. The primary analysis was a bayesian cumulative logistic model that included all patients enrolled with severe COVID-19, adjusting for age, sex, site, region, time, assignment to interventions within other domains, and domain and intervention eligibility. Superiority was defined as the posterior probability of an odds ratio greater than 1 (threshold for trial conclusion of superiority >99%). Results: After excluding 19 participants who withdrew consent, there were 384 patients (mean age, 60 years; 29% female) randomized to the fixed-dose (n = 137), shock-dependent (n = 146), and no (n = 101) hydrocortisone groups; 379 (99%) completed the study and were included in the analysis. The mean age for the 3 groups ranged between 59.5 and 60.4 years; most patients were male (range, 70.6%-71.5%); mean body mass index ranged between 29.7 and 30.9; and patients receiving mechanical ventilation ranged between 50.0% and 63.5%. For the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively, the median organ support-free days were 0 (IQR, -1 to 15), 0 (IQR, -1 to 13), and 0 (-1 to 11) days (composed of 30%, 26%, and 33% mortality rates and 11.5, 9.5, and 6 median organ support-free days among survivors). The median adjusted odds ratio and bayesian probability of superiority were 1.43 (95% credible interval, 0.91-2.27) and 93% for fixed-dose hydrocortisone, respectively, and were 1.22 (95% credible interval, 0.76-1.94) and 80% for shock-dependent hydrocortisone compared with no hydrocortisone. Serious adverse events were reported in 4 (3%), 5 (3%), and 1 (1%) patients in the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively. Conclusions and Relevance: Among patients with severe COVID-19, treatment with a 7-day fixed-dose course of hydrocortisone or shock-dependent dosing of hydrocortisone, compared with no hydrocortisone, resulted in 93% and 80% probabilities of superiority with regard to the odds of improvement in organ support-free days within 21 days. However, the trial was stopped early and no treatment strategy met prespecified criteria for statistical superiority, precluding definitive conclusions. Trial Registration: ClinicalTrials.gov Identifier: NCT02735707

Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research