Expert elicitation of the timing and uncertainty to establish a geologic sequestration well for CO2 in the United States.

Many studies anticipate that carbon capture and sequestration (CCS) will be essential to decarbonizing the U.S. economy. However, prior work has not estimated the time required to develop, approve, and implement a geologic sequestration site in the United States. We generate such an estimate by identifying six clearance points that must be passed before a sequestration site can become operational. For each clearance point (CP), we elicit expert judgments of the time required in the form of probability distributions and then use stochastic simulation to combine and sum the results. We find that, on average, there is a 90% chance that the time required lies between 5.5 and 9.6 y, with an upper bound of 12 y. Even using the most optimistic expert judgements, the lower bound on time is 2.7 y, and the upper bound is 8.3 y. Using the most pessimistic judgements, the lower bound is 3.5 y and the upper bound is 19.2 y. These estimates suggest that strategies must be found to safely accelerate the process. We conclude the paper by discussing seven potential strategies.

Solar-Powered Direct Air Capture: Techno-Economic and Environmental Assessment.

Direct air capture (DAC) of CO2 has gained attention as a sustainable carbon source. One of the most promising technologies currently available is liquid solvent DAC (L-DAC), but the significant fraction of fossil CO2 in the output stream hinders its utilization in carbon-neutral fuels and chemicals. Fossil CO2 is generated and captured during the combustion of fuels to calcine carbonates, which is difficult to decarbonize due to the high temperatures required. Solar thermal energy can provide green high-temperature heat, but it flourishes in arid regions where environmental conditions are typically unfavorable for L-DAC. This study proposes a solar-powered L-DAC approach and develops a model to assess the influence of the location and plant capacity on capture costs. The performed life cycle assessment enables the comparison of technologies based on net CO2 removal, demonstrating that solar-powered L-DAC is not only more environmentally friendly but also more cost-effective than conventional L-DAC.

CRISPR/Cas9 screens unravel miR-3689a-3p regulating sorafenib resistance in hepatocellular carcinoma via suppressing CCS/SOD1-dependent mitochondrial oxidative stress.

AIMS: Therapeutic outcome of sorafenib in hepatocellular carcinoma (HCC) is undermined by the development of drug resistance. This study aimed to identify the critical microRNA (miRNA) which is responsible for sorafenib resistance at the genomic level. METHODS: CRISPR/Cas9 screen followed by gain- and loss-of-function assays both in vitro and in vivo were applied to identify the role of miR-3689a-3p in mediating sorafenib response in HCC. The upstream and downstream molecules of miR-3689a-3p and their mechanism of action were investigated. RESULTS: CRISPR/Cas9 screening identified miR-3689a-3p was the most up-regulated miRNA in sorafenib sensitive HCC. Knockdown of miR-3689a-3p significantly increased sorafenib resistance, while its overexpression sensitized HCC response to sorafenib treatment. Proteomic analysis revealed that the effect of miR-3689a-3p was related to the copper-dependent mitochondrial superoxide dismutase type 1 (SOD1) activity. Mechanistically, miR-3689a-3p targeted the 3'UTR of the intracellular copper chaperone for superoxide dismutase (CCS) and suppressed its expression. As a result, miR-3689a-3p disrupted the intracellular copper trafficking and reduced SOD1-mediated scavenge of mitochondrial oxidative stress that eventually caused HCC cell death in response to sorafenib treatment. CCS overexpression blunted sorafenib response in HCC. Clinically, miR-3689a-3p was down-regulated in HCC and predicted favorable prognosis for HCC patients. CONCLUSION: Our findings provide comprehensive evidence for miR-3689a-3p as a positive regulator and potential druggable target for improving sorafenib treatment in HCC.

RBS and ABS Coordinated Control Strategy Based on Explicit Model Predictive Control.

During the braking process of electric vehicles, both the regenerative braking system (RBS) and anti-lock braking system (ABS) modulate the hydraulic braking force, leading to control conflict that impacts the effectiveness and real-time capability of coordinated control. Aiming to enhance the coordinated control effectiveness of RBS and ABS within the electro-hydraulic composite braking system, this paper proposes a coordinated control strategy based on explicit model predictive control (eMPC-CCS). Initially, a comprehensive braking control framework is established, combining offline adaptive control law generation, online optimized control law application, and state compensation to effectively coordinate braking force through the electro-hydraulic system. During offline processing, eMPC generates a real-time-oriented state feedback control law based on real-world micro trip segments, improving the adaptiveness of the braking strategy across different driving conditions. In the online implementation, the developed three-dimensional eMPC control laws, corresponding to current driving conditions, are invoked, thereby enhancing the potential for real-time braking strategy implementation. Moreover, the state error compensator is integrated into eMPC-CCS, yielding a state gain matrix that optimizes the vehicle braking status and ensures robustness across diverse braking conditions. Lastly, simulation evaluation and hardware-in-the-loop (HIL) testing manifest that the proposed eMPC-CCS effectively coordinates the regenerative and hydraulic braking systems, outperforming other CCSs in terms of braking energy recovery and real-time capability.

Ion mobility mass spectrometry in the omics era: Challenges and opportunities for metabolomics and lipidomics.

Researchers worldwide are taking advantage of novel, commercially available, technologies, such as ion mobility mass spectrometry (IM-MS), for metabolomics and lipidomics applications in a variety of fields including life, biomedical, and food sciences. IM-MS provides three main technical advantages over traditional LC-MS workflows. Firstly, in addition to mass, IM-MS allows collision cross-section values to be measured for metabolites and lipids, a physicochemical identifier related to the chemical shape of an analyte that increases the confidence of identification. Second, IM-MS increases peak capacity and the signal-to-noise, improving fingerprinting as well as quantification, and better defining the spatial localization of metabolites and lipids in biological and food samples. Third, IM-MS can be coupled with various fragmentation modes, adding new tools to improve structural characterization and molecular annotation. Here, we review the state-of-the-art in IM-MS technologies and approaches utilized to support metabolomics and lipidomics applications and we assess the challenges and opportunities in this growing field.

Trends in Off-Label Indications of Non-Vitamin K Antagonist Oral Anticoagulants in Acute Coronary Syndrome.

Acute coronary syndrome (ACS) is a leading cause of mortality worldwide. Despite optimal antiplatelet therapy recommendation after ischemic events, recurrent thrombotic complications rate remains high. The recurrent events maybe in part due to increased thrombin levels during ACS which may underscore the need for an additional anticoagulation therapy. Given the advantages of non-vitamin K antagonist oral anticoagulants (NOACs) over warfarin, they have the potential to prevent thrombus formation, in the presence or absence of atrial fibrillation, but at the cost of increased risk of bleeding. NOACs have also shown a promising efficacy in managing left ventricular thrombus and a potential benefit in avoiding stent thrombosis after percutaneous coronary revascularization. Taken as a whole, NOACs are increasingly used for off-licence indications, and continue to evolve as essential therapy in preventing and treating thrombotic events. Herein, this review discusses NOACs off-label indications in the setting of ischemic coronary disease.

Cost and Life Cycle Emissions of Ethanol Produced with an Oxyfuel Boiler and Carbon Capture and Storage.

Decarbonization of transportation fuels represents one of the most vexing challenges for climate change mitigation. Biofuels derived from corn starch have offered modest life cycle greenhouse gas (GHG) emissions reductions over fossil fuels. Here we show that capture and storage of CO2 emissions from corn ethanol fermentation achieves ∼58% reduction in the GHG intensity (CI) of ethanol at a levelized cost of 52 $/tCO2e abated. The integration of an oxyfuel boiler enables further CO2 capture at modest cost. This system yields a 75% reduction in CI to 15 gCO2e/MJ at a minimum ethanol selling price (MESP) of $2.24/gallon ($0.59/L), a $0.31/gallon ($0.08/L) increase relative to the baseline no intervention case. The levelized cost of carbon abatement is 84 $/tCO2e. Sensitivity analysis reveals that carbon-neutral or even carbon-negative ethanol can be achieved when oxyfuel carbon capture is stacked with low-CI alternatives to grid power and fossil natural gas. Conservatively, fermentation and oxyfuel CCS can reduce the CI of conventional ethanol by a net 44-50 gCO2/MJ. Full implementation of interventions explored in the sensitivity analysis would reduce CI by net 79-85 gCO2/MJ. Integrated oxyfuel and fermentation CCS is shown to be cost-effective under existing U.S. policy, offering near-term abatement opportunities.

Peptide collision cross sections of 22 post-translational modifications.

Recent advances have rekindled the interest in ion mobility as an additional dimension of separation in mass spectrometry (MS)-based proteomics. Ion mobility separates ions according to their size and shape in the gas phase. Here, we set out to investigate the effect of 22 different post-translational modifications (PTMs) on the collision cross section (CCS) of peptides. In total, we analyzed ~4300 pairs of matching modified and unmodified peptide ion species by trapped ion mobility spectrometry (TIMS). Linear alignment based on spike-in reference peptides resulted in highly reproducible CCS values with a median coefficient of variation of 0.26%. On a global level, we observed a redistribution in the m/z vs. ion mobility space for modified peptides upon changes in their charge state. Pairwise comparison between modified and unmodified peptides of the same charge state revealed median shifts in CCS between -1.4% (arginine citrullination) and +4.5% (O-GlcNAcylation). In general, increasing modified peptide masses were correlated with higher CCS values, in particular within homologous PTM series. However, investigating the ion populations in more detail, we found that the change in CCS can vary substantially for a given PTM and is partially correlated with the gas phase structure of its unmodified counterpart. In conclusion, our study shows PTM- and sequence-specific effects on the cross section of peptides, which could be further leveraged for proteome-wide PTM analysis.

Short-term outcomes after heart transplantation using donor hearts preserved with ex vivo perfusion.

The standard Conventional Cold Storage (CCS) during heart transplantation procurement is associated with time-dependent ischemic injury to the graft, which is a significant independent risk factor for post-transplant early morbidity and mortality - especially when cold ischemic time exceeds four hours. Since 2018, Rigshospitalet (Copenhagen, Denmark) has been utilising ex vivo perfusion (Organ Care System, OCS) in selected cases. The objective of this study was to compare the short-term clinical outcomes of patients transplanted with OCS compared to CCS. Methods: This retrospective single-centre study was based on consecutive patients undergoing a heart transplant between January 2018 and April 2021. Patients were selected for the OCS group when the cold ischemic time was expected to exceed four hours. The primary outcome measure was six-month event-free survival. Results: In total, 48 patients were included in the study; nine were transplanted with an OCS heart. The two groups had no significant differences in baseline characteristics. Six-month event-free survival was 77.8% [95% CI: 54.9-100%] in the OCS group and 79.5% [95% CI: 67.8-93.2%] in the CCS group (p = 0.91). While the OCS group had a median out-of-body time that was 183 min longer (p < 0.0001), the cold ischemic time was reduced by 51 min (p = 0.007). Conclusion: In a Scandinavian setting, our data confirms that utilising OCS in heart procurement allows for a longer out-of-body time and a reduced cold ischemic time without negatively affecting safety or early post-transplant outcomes.

Comparison of the efficacy of costoclavicular space brachial plexus blockade with 0.5% versus 0.375% ropivacaine: a randomized, double-blind, single-centre, noninferiority clinical trial.

PURPOSE: Recently, more attention has been given to the costoclavicular space (CCS) as an alternative pathway for ultrasound-guided brachial plexus block (BPB). While 0.5% ropivacaine was used in most related studies, research has shown effective ultrasound-guided supraclavicular BPB using lower local anesthetic concentrations, and our preliminary data have indicated that 0.375% ropivacaine may be effective when given in the CCS. Hence, we hypothesized that the efficacy of 0.375% ropivacaine would be noninferior compared with 0.5% in ultrasound-guided BPB via the CCS. METHODS: We conducted a randomized, double-blind, single-centre, noninferiority clinical trial. Seventy patients undergoing elective forearm or hand surgery were randomly assigned to receive either 20 mL of 0.375% ropivacaine (experimental group) or 0.5% ropivacaine (control group) in the CCS for BPB. We assessed sensory and motor blockade at five, ten, 15, 20, 25, and 30 min after the injection. The primary outcome was the rate of successful BPB. Secondary outcomes included onset time, duration of sensory and motor blockade, and adverse reactions. The depth from the skin to the CCS was also recorded during the procedure. RESULTS: A total of 69 patients were evaluable for block success. There was one failed block in both groups, yielding a BPB block success rate of 97% in both groups. 0.375% Ropivacaine was noninferior to 0.5% ropivacaine (P = 0.98). There was no significant difference in the median [interquartile range (IQR)] onset time of sensory-motor blockade in the experimental group (15 [15-20] min; N = 34) compared with the control group (15 [13-20] min; N = 33; Mann-Whitney test, P = 0.48). The median [IQR] duration of sensory blockade was significantly shorter in the experimental group (455 [398-490] min vs 610 [570-655] min in the control group; Hodges-Lehmann estimator of the difference, 165 min; 95.08% confidence interval (CI), 130 to 195; P < 0.001). Likewise, the median [IQR] duration of motor blockade was significantly shorter in the experimental group (470 [409-500] min vs 625 [578-665] min in the control group; Hodges-Lehmann estimator of the difference, 165 min; 95.08% CI, 130 to 195; P < 0.001). There were no adverse reactions directly related to the technique or the ropivacaine injection in either group. CONCLUSIONS: 0.375% Ropivacainewas noninferior to 0.5% ropivacaine with regard to rate of successful ultrasound-guided costoclavicular BPB. STUDY REGISTRATION: chictr.org.cn (ChiCTR20000306570); registered 8 March 2020.

RéSUMé: OBJECTIF: L'espace costo-claviculaire (ECC) a récemment bénéficié d'un regain d'intérêt comme voie de substitution pour le bloc du plexus brachial (BPB) échoguidé. La ropivacaïne 0,5 % a été utilisée dans la majorité des études sur ce sujet, mais la recherche a montré un BPB supra-claviculaire échoguidé efficace en utilisant de plus faibles concentrations d'anesthésique local et nos données préliminaires ont indiqué que la ropivacaïne à 0,375 % pouvait être efficace en administration dans l'ECC. En conséquence, nous avons émis l'hypothèse selon laquelle l'efficacité de la ropivacaïne 0,375 % serait non inférieure à la ropivacaïne 0,5 % dans le BPB échoguidé via l'ECC. MéTHODES: Nous avons mené un essai clinique monocentrique de non-infériorité, randomisée en double insu. Soixante-dix patients subissant une chirurgie élective de l'avant-bras ou de la main ont été randomisés dans un groupe recevant 20 mL de ropivacaïne 0,375 % (groupe expérimental) ou de ropivacaïne 0,5 % (groupe contrôle) dans l'ECC pour un BPB. Nous avons évalué les blocs sensoriel et moteur à 5, 10, 15, 20, 25 et 30 minutes après l'injection. Le critère d'évaluation principal était le taux de succès du BPB. Les critères d'évaluation secondaires étaient, notamment, le délai d'action, la durée des blocs sensoriel et moteur, et les événements indésirables. La profondeur de la peau à l'ECC a aussi été consignée pendant la procédure. RéSULTATS: Un total de 69 patients était évaluable pour le succès du bloc. Il y a eu un échec du bloc dans chacun des deux groupes, ramenant le taux de succès du BPB à 97 % dans les deux groupes. La ropivacaïne 0,375 % a été non inférieure à la ropivacaïne 0,5 % (P = 0,98). Il n'y a pas eu de différence significative concernant le délai d'action médian (plage interquartile [PIQ]) du bloc sensori-moteur dans le groupe expérimental (15 [15 à 20] minutes; n = 34) comparativement au groupe contrôle (15 [13 à 20] minutes; n = 33; test de Mann­Whitney, P = 0,48). La durée médiane [PIQ] du bloc sensitif a été significativement plus courte dans le groupe expérimental (455 [398 à 490] minutes contre 610 [570 à 655] minutes dans le groupe contrôle; estimateur de la différence de Hodges­Lehmann, 165 minutes; intervalle de confiance [IC] à 95,08 % : 130 à 195; P < 0,001). De même, la durée médiane [PIQ] du bloc moteur a été significativement plus courte dans le groupe expérimental (470 [409 à 500] minutes contre 625 [578 à 665] minutes dans le groupe contrôle; estimateur de la différence de Hodges­Lehmann, 165 minutes; IC à 95,08 %, 130 à 195; P < 0,001). Il n'y a pas eu d'événement indésirable directement lié à la technique ou à l'injection de ropivacaïne dans l'un ou l'autre groupe. CONCLUSIONS: La ropivacaïne 0,375 % a été non inférieure à la ropivacaïne 0,5 % en ce qui concerne le taux de succès du BPB costo-claviculaire échoguidé. ENREGISTREMENT DE L'éTUDE: chictr.org.cn (ChiCTR20000306570); Enregistrée le 8 mars 2020.

Student-led clinic cervical cancer screening-medical students' views on progression of learning, quality of Pap smears and women´s experiences of the visit - a mixed methods study.

BACKGROUND: Student-led clinics (SLC) have been described, but not in gynecology. Gynecology is a subject typically covered in the last terms of medical training, however it includes few opportunities for students to tackle all phases of a consultation and a shortage of opportunities to perform gynecological examinations. Therefore, we started a student-led clinic for cervical cancer screening (SLC-CCS) in Linköping, Sweden and aimed to evaluate students' views on the progression of learning, the quality of the Papanicolaou (Pap) smear, and women´s experiences of the visit, using mixed methodology. METHODS: The implementation of the SLC-CCS is described in detail. Students (n = 61) taking part in the SLC-CCS between January and May 2021 were invited to participate in a follow-up discussion (n = 24) focused around four themes: attitudes and expectations prior to participation, experiences of the patient encounter, organization of the placement, and reflections on and suggestions for further development of the placements. The group meetings were conducted in Swedish, recorded, transcribed verbatim and subjected to a qualitative, descriptive thematic analysis. Thematic analysis is considered an appropriate method of analysis for seeking to understand experiences, thoughts, or behaviors across a data set. The proportion of Pap smears lacking cells from the squamous epithelium during the study period was compared with data from the same clinic before the SLC-CCS started. A validated questionnaire on women's experience of the Pap smear visit was provided. Answers were compared between women who had the Pap smear taken by a student or a healthcare provider. RESULTS: Three different themes were generated: growing confidence in the clinical situation, embodied awareness of variation in anatomy, doubting accuracy of one's own performance. The percentage of Pap smears lacking cells from the squamous epithelium were equal (2%) during the study period compared to the period before the SLC-CCS started (p = 0.28). No difference was found in the satisfaction index between the women examined by a student, those examined by a healthcare provider, or women who did not know who the examiner was (p = 0.112). CONCLUSIONS: The students expressed a growing confidence in the clinical situation and there was high satisfaction from the women. The quality of the Pap smears taken by the students was equal to the quality of those taken by the health care staff. All these findings indicate that high patient safety was maintained during this activity support the recommendation to include SLC-CCS as part of the medical training.

CCS-GAN: COVID-19 CT Scan Generation and Classification with Very Few Positive Training Images.

We present a novel algorithm that is able to generate deep synthetic COVID-19 pneumonia CT scan slices using a very small sample of positive training images in tandem with a larger number of normal images. This generative algorithm produces images of sufficient accuracy to enable a DNN classifier to achieve high classification accuracy using as few as 10 positive training slices (from 10 positive cases), which to the best of our knowledge is one order of magnitude fewer than the next closest published work at the time of writing. Deep learning with extremely small positive training volumes is a very difficult problem and has been an important topic during the COVID-19 pandemic, because for quite some time it was difficult to obtain large volumes of COVID-19-positive images for training. Algorithms that can learn to screen for diseases using few examples are an important area of research. Furthermore, algorithms to produce deep synthetic images with smaller data volumes have the added benefit of reducing the barriers of data sharing between healthcare institutions. We present the cycle-consistent segmentation-generative adversarial network (CCS-GAN). CCS-GAN combines style transfer with pulmonary segmentation and relevant transfer learning from negative images in order to create a larger volume of synthetic positive images for the purposes of improving diagnostic classification performance. The performance of a VGG-19 classifier plus CCS-GAN was trained using a small sample of positive image slices ranging from at most 50 down to as few as 10 COVID-19-positive CT scan images. CCS-GAN achieves high accuracy with few positive images and thereby greatly reduces the barrier of acquiring large training volumes in order to train a diagnostic classifier for COVID-19.

Identification of the GDP-L-Galactose Phosphorylase Gene as a Candidate for the Regulation of Ascorbic Acid Content in Fruits of Capsicum annuum L.

Ascorbic acid (AsA) is an antioxidant with significant functions in both plants and animals. Despite its importance, there has been limited research on the molecular basis of AsA production in the fruits of Capsicum annuum L. In this study, we used Illumina transcriptome sequencing (RNA-seq) technology to explore the candidate genes involved in AsA biosynthesis in Capsicum annuum L. A total of 8272 differentially expressed genes (DEGs) were identified by the comparative transcriptome analysis. Weighted gene co-expression network analysis identified two co-expressed modules related to the AsA content (purple and light-cyan modules), and eight interested DEGs related to AsA biosynthesis were selected according to gene annotations in the purple and light-cyan modules. Moreover, we found that the gene GDP-L-galactose phosphorylase (GGP) was related to AsA content, and silencing GGP led to a reduction in the AsA content in fruit. These results demonstrated that GGP is an important gene controlling AsA biosynthesis in the fruit of Capsicum annuum L. In addition, we developed capsanthin/capsorubin synthase as the reporter gene for visual analysis of gene function in mature fruit, enabling us to accurately select silenced tissues and analyze the results of silencing. The findings of this study provide the theoretical basis for future research to elucidate AsA biosynthesis in Capsicum annuum L.

Cronkhite-Canada Syndrome- The first case from Pakistan: a case report.

Chronkhite-Canada Syndrome is characterised by diffuse gastrointestinal polyposis, dystrophic changes of the fingernails, cutaneous hyperpigmentation, alopecia, diarrhoea, weight loss, and abdominal pain. This disease is also associated with peripheral neuropathies and autoimmune disorders. Its association with other diseases may cause the polyps to turn into malignant tumours and worsen the condition. The first-line treatment is a combination of prednisone and mesalamine. NSAIDs and antibiotic administration is based on the symptoms and needs of patients. Here, we describe a 51-year-old male who presented to us with abdominal pain and significant weight loss. His physical examination showed dystrophic nails, alopecia and hyperpigmentation. Endoscopy and colonoscopy showed multiple polyps. His manifestations were consistent with Cronkhite-Canada syndrome. We prescribed oral corticosteroids, which improved his condition.

The use of the femoral neck system (FNS) leads to better outcomes in the surgical management of femoral neck fractures in adults compared to fixation with cannulated screws: A systematic review and meta-analysis.

BACKGROUND: Intracapsular femoral neck fractures are challenging to treat, with outcomes depending on the quality of reduction, and the stability of fixation. Cannulated cancellous screws (CCS) are the most commonly used implants to fix these fractures, but failure rates are significant. The recently introduced femoral neck system (FNS) may be a better option than CCS fixation and this review attempts to compare the results. METHODS: Four electronic databases were searched for eligible articles that had comparative data on the outcomes of fixation of adult femoral neck fractures with FNS and CCS. Data on various outcome parameters were collected. Meta-analysis was conducted using a random-effects model with 95% confidence intervals. RESULTS: Eight studies with 509 cases having a mean age of 50.8 years were included for final analysis. FNS was found to be associated with significantly reduced complication rates (p < 0.001), decreased incidence of postoperative femoral neck shortening (p < 0.001), quicker time to fracture union (p = 0.002), and better functional outcome scores (p < 0.001) compared to cannulated screws. FNS was also associated with a shorter operating time (mean difference 6.65 min) although not statistically significant (p = 0.24). CCS group had significantly reduced mean blood loss (p < 0.001). CONCLUSION: The available literature supports FNS as a better option for adult femoral neck fractures, with a lower complication rate, quicker union, and better clinical outcomes. LEVEL OF EVIDENCE: Level 3.

Nanohydrophobic Interaction Chromatography Coupled to Ultraviolet Photodissociation Mass Spectrometry for the Analysis of Intact Proteins in Low Charge States.

The direct correlation between proteoforms and biological phenotype necessitates the exploration of mass spectrometry (MS)-based methods more suitable for proteoform detection and characterization. Here, we couple nano-hydrophobic interaction chromatography (nano-HIC) to ultraviolet photodissociation MS (UVPD-MS) for separation and characterization of intact proteins and proteoforms. High linearity, sensitivity, and sequence coverage are obtained with this method for a variety of proteins. Investigation of collisional cross sections of intact proteins during nano-HIC indicates semifolded conformations in low charge states, enabling a different dimension of separation in comparison to traditional, fully denaturing reversed-phase separations. This method is demonstrated for a mixture of intact proteins from Escherichia coli ribosomes; high sequence coverage is obtained for a variety of modified and unmodified proteoforms.

USP11 mediates repair of DNA-protein cross-links by deubiquitinating SPRTN metalloprotease.

DNA-protein cross-links (DPCs) are toxic DNA lesions that interfere with DNA metabolic processes such as replication, transcription, and recombination. USP11 deubiquitinase participates in DNA repair, but the role of USP11 in DPC repair is not known. SPRTN is a replication-coupled DNA-dependent metalloprotease that cleaves proteins cross-linked to DNA to promote DPC repair. SPRTN function is tightly regulated by a monoubiquitin switch that controls SPRTN auto-proteolysis and chromatin accessibility during DPC repair. Previously, VCPIP1 and USP7 deubiquitinases have been shown to regulate SPRTN. Here, we identify USP11 as an SPRTN deubiquitinase. USP11 interacts with SPRTN and cleaves monoubiquitinated SPRTN in cells and in vitro. USP11 depletion impairs SPRTN deubiquitination and promotes SPRTN auto-proteolysis in response to formaldehyde-induced DPCs. Loss of USP11 causes an accumulation of unrepaired DPCs and cellular hypersensitivity to treatment with DPC-inducing agents. Our findings show that USP11 regulates SPRTN auto-proteolysis and SPRTN-mediated DPC repair to maintain genome stability.

Structural insights revealed by the cocrystal structure of CCS1477 in complex with CBP bromodomain.

Inhibition of the bromodomain of the CREB (cyclic-AMP response element-binding protein) binding protein (CBP) is a particularly promising new therapeutic approach for cancer. Benzimidazole derivatives CCS1477 and its analogues (8 and 9) are highly potent and selective CBP bromodomain inhibitors, with Kd values of 26.4, 37.0, and 34.3 nM in ITC assay, respectively. Among these compounds, CCS1477 is undergoing phase Ib/IIa clinical trials for the treatment of various cancers. Thus, we determined the co-crystal structures of CCS1477 and its analogues in complex with CBP bromodomain and revealed the detailed binding modes. Furthermore, overlapping with other reported co-crystal structures allowed us to identify that interaction with Arg1173, LPF shelf, and ZA channel was critical for keeping strong biological activity and selectivity. Collectively, this study provided a structural basis for CBP bromodomain inhibitors design.

THE IMS PARADOX: A PERSPECTIVE ON STRUCTURAL ION MOBILITY-MASS SPECTROMETRY.

Studies of large proteins, protein complexes, and membrane protein complexes pose new challenges, most notably the need for increased ion mobility (IM) and mass spectrometry (MS) resolution. This review covers evolutionary developments in IM-MS in the authors' and key collaborators' laboratories with specific focus on developments that enhance the utility of IM-MS for structural analysis. IM-MS measurements are performed on gas phase ions, thus "structural IM-MS" appears paradoxical-do gas phase ions retain their solution phase structure? There is growing evidence to support the notion that solution phase structure(s) can be retained by the gas phase ions. It should not go unnoticed that we use "structures" in this statement because an important feature of IM-MS is the ability to deal with conformationally heterogeneous systems, thus providing a direct measure of conformational entropy. The extension of this work to large proteins and protein complexes has motivated our development of Fourier-transform IM-MS instruments, a strategy first described by Hill and coworkers in 1985 (Anal Chem, 1985, 57, pp. 402-406) that has proved to be a game-changer in our quest to merge drift tube (DT) and ion mobility and the high mass resolution orbitrap MS instruments. DT-IMS is the only method that allows first-principles determinations of rotationally averaged collision cross sections (CSS), which is essential for studies of biomolecules where the conformational diversities of the molecule precludes the use of CCS calibration approaches. The Fourier transform-IM-orbitrap instrument described here also incorporates the full suite of native MS/IM-MS capabilities that are currently employed in the most advanced native MS/IM-MS instruments. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.

Integrating ion mobility into comprehensive multidimensional metabolomics workflows: critical considerations.

BACKGROUND: Ion mobility (IM) separation capabilities are now widely available to researchers through several commercial vendors and are now being adopted into many metabolomics workflows. The added peak capacity that ion mobility offers with minimal compromise to other analytical figures-of-merit has provided real benefits to sensitivity and structural selectivity and have allowed more specific metabolite annotations to be assigned in untargeted workflows. One of the greatest promises of contemporary IM-enabled instrumentation is the capability of operating multiple analytical dimensions inline with minimal sample volumes, which has the potential to address many grand challenges currently faced in the omics fields. However, comprehensive operation of multidimensional mass spectrometry comes with its own inherent challenges that, beyond operational complexity, may not be immediately obvious to practitioners of these techniques. AIM OF REVIEW: In this review, we outline the strengths and considerations for incorporating IM analysis in metabolomics workflows and provide a critical but forward-looking perspective on the contemporary challenges and prospects associated with interpreting IM data into chemical knowledge. KEY SCIENTIFIC CONCEPTS OF REVIEW: We outline a strategy for unifying IM-derived collision cross section (CCS) measurements obtained from different IM techniques and discuss the emerging field of high resolution ion mobility (HRIM) that is poised to address many of the contemporary challenges associated with ion mobility metabolomics. Whereas the LC step limits the throughput of comprehensive LC-IM-MS, the higher peak capacity of HRIM can allow fast LC gradients or rapid sample cleanup via solid-phase extraction (SPE) to be utilized, significantly improving the sample throughput.