Optimizing Spectronaut Search Parameters to Improve Data Quality with Minimal Proteome Coverage Reductions in DIA Analyses of Heterogeneous Samples.

Data-independent acquisition has seen breakthroughs that enable comprehensive proteome profiling using short gradients. As the proteome coverage continues to increase, the quality of the data generated becomes much more relevant. Using Spectronaut, we show that the default search parameters can be easily optimized to minimize the occurrence of false positives across different samples. Using an immunological infection model system to demonstrate the impact of adjusting search settings, we analyzed Mus musculus macrophages and compared their proteome to macrophages spiked withCandida albicans. This experimental system enabled the identification of "false positives" as Candida albicans peptides and proteins should not be present in the Mus musculus-only samples. We show that adjusting the search parameters reduced "false positive" identifications by 89% at the peptide and protein level, thereby considerably increasing the quality of the data. We also show that these optimized parameters incurred a moderate cost, only reducing the overall number of "true positive" identifications across each biological replicate by <6.7% at both the peptide and protein level. We believe the value of our updated search parameters extends beyond a two-organism analysis and would be of great value to any DIA experiment analyzing heterogeneous populations of cell types or tissues.

Mitonuclear interactions impact aerobic metabolism in hybrids and may explain mitonuclear discordance in young, naturally hybridizing bird lineages.

Understanding genetic incompatibilities and genetic introgression between incipient species are major goals in evolutionary biology. Mitochondrial genes evolve rapidly and exist in dense gene networks with coevolved nuclear genes, suggesting that mitochondrial respiration may be particularly susceptible to disruption in hybrid organisms. Mitonuclear interactions have been demonstrated to contribute to hybrid dysfunction between deeply divergent taxa crossed in the laboratory, but there are few empirical examples of mitonuclear interactions between younger lineages that naturally hybridize. Here, we use controlled hybrid crosses and high-resolution respirometry to provide the first experimental evidence in a bird that inter-lineage mitonuclear interactions impact mitochondrial aerobic metabolism. Specifically, respiration capacity of the two mitodiscordant backcrosses (with mismatched mitonuclear combinations) differs from one another, although they do not differ significantly from the parental groups or mitoconcordant backcrosses as we would expect of mitonuclear disruptions. In the wild hybrid zone between these subspecies, the mitochondrial cline centre is shifted west of the nuclear cline centre, which is consistent with the direction of our experimental results. Our results therefore demonstrate asymmetric mitonuclear interactions that impact the capacity of cellular mitochondrial respiration and may help to explain the geographic discordance between mitochondrial and nuclear genomes observed in the wild.

Transcriptomic signatures of progression to TB disease among close contacts in Brazil.

BACKGROUND: Approximately 5% of people infected with Mycobacterium tuberculosis progress to tuberculosis (TB) disease without preventive therapy. There is a need for a prognostic test to identify those at highest risk of incident TB, so that therapy can be targeted. We evaluated host blood transcriptomic signatures for progression to TB disease. METHODS: Close contacts (≥4 hours exposure per week) of adult patients with culture-confirmed pulmonary TB were enrolled in Brazil. Investigation for incident, microbiologically-confirmed or clinically-diagnosed pulmonary or extra-pulmonary TB disease through 24 months of follow-up was symptom-triggered. Twenty previously validated blood TB transcriptomic signatures were measured at baseline by real-time quantitative PCR. Prognostic performance for incident TB was tested using receiver operating characteristic curve (ROC) analysis at 6, 9, 12, and 24 months of follow-up. RESULTS: Between June 2015 and June 2019, 1,854 close contacts were enrolled; Twenty-five progressed to incident TB, of whom 13 had microbiologically-confirmed disease. Baseline transcriptomic signature scores were measured in 1,789 close contacts. Prognostic performance for all signatures was best within 6 months of diagnosis. Seven signatures (Gliddon4, Suliman4, Roe3, Roe1, Penn-Nicholson6, Francisco2, and Rajan5) met the minimum World Health Organization target product profile (TPP) for a prognostic test through 6 months; three (Gliddon4, Rajan5, and Duffy9) through 9 months. None met the TPP threshold through 12 or more months of follow-up. CONCLUSIONS: Blood transcriptomic signatures may be useful for predicting TB risk within 9 months of measurement among TB-exposed contacts, to target preventive therapy administration.

Motor evoked potentials in the human upper and lower limb do not increase after single 30-minute sessions of acute intermittent hypoxia.

Acute Intermittent Hypoxia (AIH) can induce sustained facilitation of motor output in people with spinal cord injury (SCI). Most studies of corticospinal tract excitability in humans have used 9% FiO2 AIH (AIH-9%), with inconsistent outcomes. We investigated the effect of single sessions of 9% FiO2 and 12% FiO2 AIH (AIH-12%) on corticospinal excitability of a hand and leg muscle in able-bodied adults. Ten naïve participants without SCI completed three sessions comprising 15 cycles of one minute of AIH-9%, AIH-12% or sham (SHAM-21%) followed by one minute of room air (21% FiO2) in a randomised crossover design. Motor evoked potentials (MEPs, n=30, ~1mV) elicited at rest by transcranial magnetic stimulation and maximal M-waves (Mmax) evoked by peripheral nerve stimulation were measured from the first dorsal interosseous (FDI) and tibialis anterior (TA) muscles at baseline and at ~0, 20, 40, and 60 minutes post-intervention. AIH-9% induced the greatest reduction in SpO2 (to 85% vs 93% and 100% in AIH-12% and SHAM-21%, respectively; p < 0.001) and the greatest increase in ventilation (by 22% vs 12% and -3% in AIH-12% and SHAM-21%, respectively (p<0.001)). There was no difference in MEP amplitudes (%Mmax) after any of the three conditions (AIH-9%, AIH-12%, SHAM-21%) for both FDI (p=0.399) and TA (p=0.582). Despite greater cardiorespiratory changes during AIH-9%, there was no evidence of corticospinal facilitation (tested with MEPs) in this study. Further studies could explore variability in response to AIH between individuals and other methods to measure motor facilitation in people with and without spinal cord injuries.

Bicuspid Aortic Valve Disease With Early Onset Complications: Characteristics And Aortic Outcomes.

Bicuspid aortic valve (BAV) is the most common congenital heart malformation in adults but can also cause childhood-onset complications. In multicenter study, we found that adults who experience significant complications of BAV disease before age 30 are distinguished from the majority of BAV cases that manifest after age 50 by a relatively severe clinical course, with higher rates of surgical interventions, more frequent second interventions, and a greater burden of congenital heart malformations. These observations highlight the need for prompt recognition, regular lifelong surveillance, and targeted interventions to address the significant health burdens of patients with early onset BAV complications.

Embryonal sarcoma of the liver in pediatric and young adult patients: A report from Children's Oncology Group study ARST0332.

BACKGROUND: Embryonal sarcoma of the liver (ESL) is a rare mesenchymal tumor most common in childhood; the optimal treatment approach is uncertain. The clinical features and outcomes of patients with ESL enrolled in a Children's Oncology Group (COG) clinical trial that evaluated a risk-based strategy for treating soft tissue sarcomas in patients aged <30 years were evaluated. METHODS: This subset analysis included patients with ESL enrolled in COG study ARST0332. Central review of records, pathology, and imaging confirmed the diagnosis, presenting features, and surgery extent and complications. All patients received dose-intensive ifosfamide/doxorubicin chemotherapy, with cycle timing dependent on surgery and radiotherapy. Tumor resection occurred before study entry or after four cycles of chemotherapy; radiotherapy for residual tumor was optional. RESULTS: Thirty-nine eligible/evaluable patients with ESL were analyzed. All tumors were >10 cm in diameter; four were metastatic. Tumor resection was performed upfront in 23 and delayed in 16. Positive surgical margins (n = 6) and intraoperative tumor rupture (n = 6) occurred only in upfront resections. Eight patients received radiotherapy. Estimated 5-year event-free and overall survival were 79% (95% confidence interval [CI], 65%-93%) and 95% (95% CI, 87%-100%), respectively. Positive margins increased the local recurrence risk. One of 13 patients with documented hemorrhagic ascites and/or tumor rupture developed extrahepatic intra-abdominal tumor recurrence. CONCLUSIONS: The treatment strategy used in ARST0332 achieved favorable outcomes for patients with ESL despite a substantial proportion having high-risk disease features. Deferring tumor resection until after neoadjuvant chemotherapy may decrease the risk of intraoperative tumor rupture and improve the likelihood of adequate surgical margins.

Spatiotemporal binding of cyclophilin A and CPSF6 to capsid regulates HIV-1 nuclear entry and integration.

Human immunodeficiency virus type 1 (HIV-1) capsid, which is the target of the antiviral lenacapavir, protects the viral genome and binds multiple host proteins to influence intracellular trafficking, nuclear import, and integration. Previously, we showed that capsid binding to cleavage and polyadenylation specificity factor 6 (CPSF6) in the cytoplasm is competitively inhibited by cyclophilin A (CypA) binding and regulates capsid trafficking, nuclear import, and infection. Here we determined that a capsid mutant with increased CypA binding affinity had significantly reduced nuclear entry and mislocalized integration. However, disruption of CypA binding to the mutant capsid restored nuclear entry, integration, and infection in a CPSF6-dependent manner. Furthermore, relocalization of CypA expression from the cell cytoplasm to the nucleus failed to restore mutant HIV-1 infection. Our results clarify that sequential binding of CypA and CPSF6 to HIV-1 capsid is required for optimal nuclear entry and integration targeting, informing antiretroviral therapies that contain lenacapavir.

Essentiality, protein-protein interactions and evolutionary properties are key predictors for identifying cancer-associated genes using machine learning.

The distinctive nature of cancer as a disease prompts an exploration of the special characteristics the genes implicated in cancer exhibit. The identification of cancer-associated genes and their characteristics is crucial to further our understanding of this disease and enhanced likelihood of therapeutic drug targets success. However, the rate at which cancer genes are being identified experimentally is slow. Applying predictive analysis techniques, through the building of accurate machine learning models, is potentially a useful approach in enhancing the identification rate of these genes and their characteristics. Here, we investigated gene essentiality scores and found that they tend to be higher for cancer-associated genes compared to other protein-coding human genes. We built a dataset of extended gene properties linked to essentiality and used it to train a machine-learning model; this model reached 89% accuracy and > 0.85 for the Area Under Curve (AUC). The model showed that essentiality, evolutionary-related properties, and properties arising from protein-protein interaction networks are particularly effective in predicting cancer-associated genes. We were able to use the model to identify potential candidate genes that have not been previously linked to cancer. Prioritising genes that score highly by our methods could aid scientists in their cancer genes research.

Prevalence and progression of arterial calcifications on computed tomography in humans with knee osteoarthritis.

OBJECTIVES: Ectopic bone deposition plays an important role in osteoarthritis (OA) and in arterial wall disease. We aimed to investigate the prevalence and progression of arterial calcifications on whole-body computed tomography (CT) in persons with knee OA. METHODS: We included 118 (36 male) participants who satisfied the clinical American College of Rheumatology classification criteria for knee OA. Baseline investigations included Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) and Kellgren-Lawrence grading. At baseline and after two years, a whole-body CT was performed using the same scanner and protocol. Calcifications were quantified in the carotid, brachiocephalic, coronary, thoracic aortic, abdominal aortic, iliac, femoropopliteal and crural arteries. Multivariable linear and logistic regression modeling was used for analyses. RESULTS: At baseline males were 66.9 ± 7.7 and females were 68.0 ± 5.6 years old. Calcifications were common, all participants except two females had some calcification, and prevalence ranged between 41.8% and 94.4% for various arterial beds. Baseline femoropopliteal calcifications were associated with a higher Kellgren-Lawrence grade (more severe knee OA). Median annual progression rate was 13.1% in males and 15.7% in females. Structural OA severity was not associated with progression, but a five points lower (worse) WOMAC was associated with 1% faster progression of arterial calcifications (p= 0.008). CONCLUSION: Around age 70 nearly all persons with knee OA have arterial calcifications, which progress substantially. For further investigation into shared causality intervention studies are needed.

Effects of exercise interventions on brain-derived neurotrophic factor levels in overweight and obesity: A systematic review and meta-analysis.

Background: /Objective. An explosion in global obesity epidemic poses threats to the healthcare system by provoking risks of many debilitating diseases, including cognitive dysfunction. Physical activity has been shown to alleviate the deleterious effects of obesity-associated cognitive deficits across the lifespan. Given the strong neuroprotective role of brain-derived neurotrophic factor (BDNF) and exercise training as a known modulator for its elevation, this systematic review sought to examine the strength of the association between exercise and BDNF levels in healthy people with overweight and obesity. Methods: Six electronic databases (PubMed, MEDLINE, EMBASE, Web of Science, Ovid Nursing Database, and SPORTDiscus) were searched from their inceptions through December 2022. The primary outcome of interest was BDNF levels. Interventional studies (randomized and quasi-experimental) with English full text available were included. Risk of bias of the included studies was assessed using the Physiotherapy Evidence Database Scale. Data were extracted for meta-analyses by random-effects models. Results: Thirteen studies (n = 750), of which 69.2% (9/13) had low risk of bias, were included. In the meta-analysis, exercise interventions had no significant effect on resting BDNF levels (standardized mean difference: -0.30, 95% CI -0.80 to 0.21, P = 0.25). Subgroup analyses also indicated no effects of age and types of control groups being compared on moderating the association. Conclusion: To further inform the role of BDNF in obesity-related cognitive functioning, rigorous studies with larger samples of participants and raw data available were imperatively deserved.

High nest failure in a zebra finch population and persistent nest predation by a monitor lizard.

Predation is well known to have substantial effects on behaviour and fitness in many animals. In songbirds, nest predation is rarely observed directly, so that research focusses primarily on the consequences of predation and less on the behaviour of the predator. Here, we report predation data in a zebra finch (Taeniopygia catanosis) nest box population, highlighting a 22-min-long sequence, captured on video, of a sand goanna (Varanus gouldii) predating a zebra finch nest in the wild. This monitor lizard appeared to be extremely persistent with climbing and jumping up to the next box nine times, including three successive unsuccessful attempts that lead to a change in approach strategy. It removed all six nestlings from the nest box during those repeated approaches and consumed them. In combination with overall high predation rates in the study population we document here, the findings highlight the role that a single predator species can have on nest success and, thus potentially also breeding decisions and social organisation of the prey population. Specifically so in a species like the zebra finch which synchronises reproductive attempts through the use of social information acquired through nest inspections and which uses social hotspots where they could gather information on changes in local social composition due to the individualised signals they use.

The effect of potassium on aluminous phase stability in the lower mantle.

The aluminous calcium-ferrite type phase (CF) and new aluminous phase (NAL) are thought to hold the excess alumina produced by the decomposition of garnet in MORB compositions in the lower mantle. The respective stabilities of CF and NAL in the nepheline-spinel binary (NaAlSiO4-MgAl2O4) are well established. However with the addition of further components the phase relations at lower mantle conditions remain unclear. Here we investigate a range of compositions around the nepheline apex of the nepheline-kalsilite-spinel compositional join (NaAlSiO4-KAlSiO4-MgAl2O4) at 28-78 GPa and 2000 K. Our experiments indicate that even small amounts of a kalsilite (KAlSiO4) component dramatically impact phase relations. We find NAL to be stable up to at least 71 GPa in potassium-bearing compositions. This demonstrates the stabilizing effect of potassium on NAL, because NAL is not observed at pressures above 48 GPa on the nepheline-spinel binary. We also observe a broadening of the CF stability field to incorporate larger amounts of potassium with increasing pressure. For pressures below 50 GPa only minor amounts (<0.011(1)KK+Na+Mg) of potassium are soluble in CF, whereas at 68 GPa, we find a solubility in CF of at least 0.088(3)KK+Na+Mg. This indicates that CF and NAL are suitable hosts of the alkali content of MORB compositions at lower mantle conditions. For sedimentary compositions at lower mantle pressures, we expect K-Hollandite to be stable in addition to CF and NAL for pressures of 28-48 GPa, based on our simplified compositions. Supplementary Information: The online version contains supplementary material available at 10.1007/s00410-024-02129-w.

Exposure to Sublethal Concentrations of Lead (Pb) Affects Ecologically Relevant Behaviors in House Sparrows (Passer domesticus).

Global contamination of environments with lead (Pb) poses threats to many ecosystems and populations. While exposure to Pb is toxic at high concentrations, recent literature has shown that lower concentrations can also cause sublethal, deleterious effects. However, there remains relatively little causal investigation of how exposure to lower concentrations of environmental Pb affects ecologically important behaviors. Behaviors often represent first-line responses of an organism and its internal physiological, molecular, and genetic responses to a changing environment. Hence, better understanding how behaviors are influenced by pollutants such as Pb generates crucial information on how species are coping with the effects of pollution more broadly. To better understand the effects of sublethal Pb on behavior, we chronically exposed adult wild-caught, captive house sparrows (Passer domesticus) to Pb-exposed drinking water and quantified a suite of behavioral outcomes: takeoff flight performance, activity in a novel environment, and in-hand struggling and breathing rate while being handled by an experimenter. Compared to controls (un-exposed drinking water), sparrows exposed to environmentally relevant concentrations of Pb exhibited decreases in takeoff flight performance and reduced movements in a novel environment following 9-10 weeks of exposure. We interpret this suite of results to be consistent with Pb influencing fundamental neuro-muscular abilities, making it more difficult for exposed birds to mount faster movements and activities. It is likely that suppression of takeoff flight and reduced movements would increase the predation risk of similar birds in the wild; hence, we also conclude that the effects we observed could influence fitness outcomes for individuals and populations altering ecological interactions within more naturalistic settings.

A review of the effect of iron supplementation on the gut microbiota of children in developing countries and the impact of prebiotics.

Iron is essential for many physiological functions of the body, and it is required for normal growth and development. Iron deficiency (ID) is the most common form of micronutrient malnutrition and is particularly prevalent in infants and young children in developing countries. Iron supplementation is considered the most effective strategy to combat the risk of ID and ID anaemia (IDA) in infants, although iron supplements cause a range of deleterious gut-related problems in malnourished children. The purpose of this review is to assess the available evidence on the effect of iron supplementation on the gut microbiota during childhood ID and to further assess whether prebiotics offer any benefits for iron supplementation. Prebiotics are well known to improve gut-microbial health in children, and recent reports indicate that prebiotics can mitigate the adverse gut-related effects of iron supplementation in children with ID and IDA. Thus, provision of prebiotics alongside iron supplements has the potential for an enhanced strategy for combatting ID and IDA among children in the developing world. However, further understanding is required before the benefit of such combined treatments of ID in nutritionally deprived children across populations can be fully confirmed. Such enhanced understanding is of high relevance in resource-poor countries where ID, poor sanitation and hygiene, alongside inadequate access to good drinking water and poor health systems, are serious public health concerns.

Utah Latina/o/x suicide decedents less likely to die by firearm, even in rural areas: examining population-wide data from the Utah Office of the Medical Examiner.

Introduction: Suicide death remains a significantly rarer event among Latina/o/x populations compared to non-Latina/o/x populations. However, the reasons why Latina/o/x communities experience relatively lower suicide rates are not fully understood. Critical gaps exist in the examination of Latina/o/x suicide death, especially in rural settings, where suicide death by firearm is historically more common within non-Latina/o/x populations. Method: We tested whether the prevalence of Latina/o/x firearm suicide was meaningfully different in urban and rural environments and from non-Latino/a/x decedents when controlling for age, sex, and a social deprivation metric, the Area Deprivation Index. Suicide death data used in this analysis encompasses 2,989 suicide decedents ascertained in Utah from 2016 to 2019. This included death certificate data from the Utah Office of the Medical Examiner on all Utah suicide deaths linked to information by staff at the Utah Population Database. Results: Compared to non-Latina/o/x suicide decedents, Latina/o/x suicide decedents had 34.7% lower adjusted odds of dying by firearm. Additionally, among the firearm suicide decedents living only in rural counties, Latina/o/x decedents had 40.5% lower adjusted odds of dying by firearm compared to non-Latina/o/x suicide decedents. Discussion: The likelihood of firearm suicide death in Utah differed by ethnicity, even in rural populations. Our findings may suggest underlying factors contributing to lower firearm suicide rates within Latina/o/x populations, e.g., aversion to firearms or less access to firearms, especially in rural areas, though additional research on these phenomena is needed.

Toxic to the touch: The makings of lethal mantles in pitohui birds and poison dart frogs.

How do chemically defended animals resist their own toxins? This intriguing question on the concept of autotoxicity is at the heart of how species interactions evolve. In this issue of Molecular Ecology (Molecular Ecology, 2024, 33), Bodawatta and colleagues report on how Papua New Guinean birds coopted deadly neurotoxins to create lethal mantles that protect against predators and parasites. Combining chemical screening of the plumage of a diverse collection of passerine birds with genome sequencing, the researchers unlocked a deeper understanding of how some birds sequester deadly batrachotoxin (BTX) from their food without poisoning themselves. They identified that birds impervious to BTX bear amino acid substitutions in the toxin-binding site of the voltage-gated sodium channel Nav1.4, whose function is essential for proper contraction and relaxation of vertebrate muscles. Comparative genetic and molecular docking analyses show that several of the substitutions associated with insensitivity to BTX may have become prevalent among toxic birds through positive selection. Intriguingly, poison dart frogs that also co-opted BTX in their lethal mantles were found to harbour similar toxin insensitivity substitutions in their Nav1.4 channels. Taken together, this sets up a powerful model system for studying the mechanisms behind convergent molecular evolution and how it may drive biological diversity.

Interferon-gamma contributes to disease progression in the Ndufs4(-/-) model of Leigh syndrome.

AIM: Leigh syndrome (LS), the most common paediatric presentation of genetic mitochondrial dysfunction, is a multi-system disorder characterised by severe neurologic and metabolic abnormalities. Symmetric, bilateral, progressive necrotizing lesions in the brainstem are defining features of the disease. Patients are often symptom free in early life but typically develop symptoms by about 2 years of age. The mechanisms underlying disease onset and progression in LS remain obscure. Recent studies have shown that the immune system causally drives disease in the Ndufs4(-/-) mouse model of LS: treatment of Ndufs4(-/-) mice with the macrophage-depleting Csf1r inhibitor pexidartinib prevents disease. While the precise mechanisms leading to immune activation and immune factors involved in disease progression have not yet been determined, interferon-gamma (IFNγ) and interferon gamma-induced protein 10 (IP10) were found to be significantly elevated in Ndufs4(-/-) brainstem, implicating these factors in disease. Here, we aimed to explore the role of IFNγ and IP10 in LS. METHODS: To establish the role of IFNγ and IP10 in LS, we generated IFNγ and IP10 deficient Ndufs4(-/-)/Ifng(-/-) and Ndufs4(-/-)/IP10(-/-) double knockout animals, as well as IFNγ and IP10 heterozygous, Ndufs4(-/-)/Ifng(+/-) and Ndufs4(-/-)/IP10(+/-), animals. We monitored disease onset and progression to define the impact of heterozygous or homozygous loss of IFNγ and IP10 in LS. RESULTS: Loss of IP10 does not significantly impact the onset or progression of disease in the Ndufs4(-/-) model. IFNγ loss significantly extends survival and delays disease progression in a gene dosage-dependent manner, though the benefits are modest compared to Csf1r inhibition. CONCLUSIONS: IFNγ contributes to disease onset and progression in LS. Our findings suggest that IFNγ targeting therapies may provide some benefits in genetic mitochondrial disease, but targeting IFNγ alone would likely yield only modest benefits in LS.

CD39 expression by regulatory T cells participates in CD8+ T cell suppression during experimental Trypanosoma cruzi infection.

An imbalance between suppressor and effector immune responses may preclude cure in chronic parasitic diseases. In the case of Trypanosoma cruzi infection, specialized regulatory Foxp3+ T (Treg) cells suppress protective type-1 effector responses. Herein, we investigated the kinetics and underlying mechanisms behind the regulation of protective parasite-specific CD8+ T cell immunity during acute T. cruzi infection. Using the DEREG mouse model, we found that Treg cells play a role during the initial stages after T. cruzi infection, restraining the magnitude of CD8+ T cell responses and parasite control. Early Treg cell depletion increased the frequencies of polyfunctional short-lived, effector T cell subsets, without affecting memory precursor cell formation or the expression of activation, exhaustion and functional markers. In addition, Treg cell depletion during early infection minimally affected the antigen-presenting cell response but it boosted CD4+ T cell responses before the development of anti-parasite effector CD8+ T cell immunity. Crucially, the absence of CD39 expression on Treg cells significantly bolstered effector parasite-specific CD8+ T cell responses, preventing increased parasite replication in T. cruzi infected mice adoptively transferred with Treg cells. Our work underscores the crucial role of Treg cells in regulating protective anti-parasite immunity and provides evidence that CD39 expression by Treg cells represents a key immunomodulatory mechanism in this infection model.

Probabilistic Interpolation of Quantum Rotation Angles.

Quantum computing requires a universal set of gate operations; regarding gates as rotations, any rotation angle must be possible. However a real device may only be capable of B bits of resolution, i.e., it might support only 2^{B} possible variants of a given physical gate. Naive discretization of an algorithm's gates to the nearest available options causes coherent errors, while decomposing an impermissible gate into several allowed operations increases circuit depth. Conversely, demanding higher B can greatly complexify hardware. Here, we explore an alternative: probabilistic angle interpolation (PAI). This effectively implements any desired, continuously parametrized rotation by randomly choosing one of three discretized gate settings and postprocessing individual circuit outputs. The approach is particularly relevant for near-term applications where one would in any case average over many runs of circuit executions to estimate expected values. While PAI increases that sampling cost, we prove that (a) the approach is optimal in the sense that PAI achieves the least possible overhead and (b) the overhead is remarkably modest even with thousands of parametrized gates and only seven bits of resolution available. This is a profound relaxation of engineering requirements for first generation quantum computers where even 5-6 bits of resolution may suffice and, as we demonstrate, the approach is many orders of magnitude more efficient than prior techniques. Moreover we conclude that, even for more mature late noisy intermediate-scale quantum era hardware, no more than nine bits will be necessary.

Optimization of Potent Ligands for the E3 Ligase DCAF15 and Evaluation of Their Use in Heterobifunctional Degraders.

Unlocking novel E3 ligases for use in heterobifunctional PROTAC degraders is of high importance to the pharmaceutical industry. Over-reliance on the current suite of ligands used to recruit E3 ligases could limit the potential of their application. To address this, potent ligands for DCAF15 were optimized using cryo-EM supported, structure-based design to improve on micromolar starting points. A potent binder, compound 24, was identified and subsequently conjugated into PROTACs against multiple targets. Following attempts on degrading a number of proteins using DCAF15 recruiting PROTACs, only degradation of BRD4 was observed. Deconvolution of the mechanism of action showed that this degradation was not mediated by DCAF15, thereby highlighting both the challenges faced when trying to expand the toolbox of validated E3 ligase ligands for use in PROTAC degraders and the pitfalls of using BRD4 as a model substrate.