Protein remote homology detection and structural alignment using deep learning.

Exploiting sequence-structure-function relationships in biotechnology requires improved methods for aligning proteins that have low sequence similarity to previously annotated proteins. We develop two deep learning methods to address this gap, TM-Vec and DeepBLAST. TM-Vec allows searching for structure-structure similarities in large sequence databases.

Label-free affinity screening, design and synthesis of inhibitors targeting the Mycobacterium tuberculosis L-alanine dehydrogenase.

The ability of Mycobacterium tuberculosis (Mtb) to persist in its host may enable an evolutionary advantage for drug resistant variants to emerge. A potential strategy to prevent persistence and gain drug efficacy is to directly target the activity of enzymes that are crucial for persistence. We present a method for expedited discovery and structure-based design of lead compounds by targeting the hypoxia-associated enzyme L-alanine dehydrogenase (AlaDH).

Conformational control sequence for a heteropeptoid in water: coupled NMR and Rosetta modelling.

We report a critical advance in the generation and characterization of peptoid hetero-oligomers. A library of sub-monomers with amine and carboxylate side-chains are combined in different sequences using microwave-assisted synthesis. Their sequence-structure propensity is confirmed by circular dichroism, and conformer subtypes are enumerated by NMR.

Overcoming gaps: regional collaborative to optimize capacity management and predict length of stay of patients admitted with COVID-19.

Objective: Ensuring an efficient response to COVID-19 requires a degree of inter-system coordination and capacity management coupled with an accurate assessment of hospital utilization including length of stay (LOS). We aimed to establish optimal practices in inter-system data sharing and LOS modeling to support patient care and regional hospital operations.

Materials And Methods: We completed a retrospective observational study of patients admitted with COVID-19 followed by 12-week prospective validation, involving 36 hospitals covering the upper Midwest.

Engineered pH-Sensitive Protein G/IgG Interaction.

While natural protein-protein interactions have evolved to be induced by complex stimuli, rational design of interactions that can be switched-on-demand still remain challenging in the protein design world. Here, we demonstrate that a computationally redesigned natural interface for improved binding affinity could further be mutated to adopt a pH switchable interaction. The redesigned interface of Protein G/human IgG Fc domain (referred to as PrG/hIgG), when incorporated with histidine and glutamic acid on PrG (PrG-EHHE), showed a switch in binding affinity by 50-fold when the pH was altered from mild acidic to mild basic.

The Cardiovascular Quality Improvement and Care Innovation Consortium: Inception of a Multicenter Collaborative to Improve Cardiovascular Care.

Despite decades of improvement in the quality and outcomes of cardiovascular care, significant gaps remain. Existing quality improvement strategies are often limited in scope to specific clinical conditions and episodic care. Health services and outcomes research is essential to inform gaps in care but rarely results in the development and implementation of care delivery solutions.

CD34 cell therapy significantly reduces adverse cardiac events, health care expenditures, and mortality in patients with refractory angina.

Patients with refractory angina who are suboptimal candidates for further revascularization have improved exercise time, decreased angina frequency, and reduced major adverse cardiac events with intramyocardial delivery of CD34 cells. However, the effect of CD34 cell therapy on health care expenditures before and after treatment is unknown. We determined the effect of CD34 cell therapy on cardiac-related hospital visits and costs during the 12 months following stem cell injection compared with the 12 months prior to injection.

Smart Microbial Cells Couple Catalysis and Sensing to Provide High-Throughput Selection of an Organophosphate Hydrolase.

Enzyme engineering for gain of function requires navigating a large combinatorial sequence space efficiently. Typically, many mutations are needed to get significant improvements, while a single "bad" mutation can inactivate the enzyme. To establish high-throughput screening and achieve enhanced resolution between two variants, genetic libraries of the organophosphate hydrolase enzyme paraoxonase 1 (PON1) were rapidly screened an engineered positive-feedback circuit: a -nitrophenol (PNP)-specific transcription factor (TF) regulated expression of PON1, which catalyzed paraoxon breakdown and PNP production.

Better together: Elements of successful scientific software development in a distributed collaborative community.

Many scientific disciplines rely on computational methods for data analysis, model generation, and prediction. Implementing these methods is often accomplished by researchers with domain expertise but without formal training in software engineering or computer science. This arrangement has led to underappreciation of sustainability and maintainability of scientific software tools developed in academic environments.

Unusual first presentation of a metabolic disorder.

An 8-month-old boy presented to hospital with a fever, irritability and 'back arching'. On examination, he demonstrated profound opisthotonic posturing and had tonsillitis. He had a full septic screen and was treated with broad spectrum antibiotics.

Sensor-Enabled Alleviation of Product Inhibition in Chorismate Pyruvate-Lyase.

Product inhibition is a frequent bottleneck in industrial enzymes, and testing mutations to alleviate product inhibition via traditional methods remains challenging as many variants need to be tested against multiple substrate and product concentrations. Further, traditional screening methods are conducted in vitro, and resulting enzyme variants may perform differently in vivo in the context of whole-cell metabolism and regulation. In this study, we address these two problems by establishing a high-throughput screening method to alleviate product inhibition in an industrially relevant enzyme, chorismate pyruvate-lyase (UbiC).

Use of routinely captured echocardiographic data in the diagnosis of severe aortic stenosis.

Objective: To determine the implications of applying guideline-recommended definitions of aortic stenosis to echocardiographic data captured in routine clinical care.

Methods: Retrospective observational study of 213 174 patients who underwent transthoracic echocardiographic imaging within Allina Health between January 2013 and October 2017. The sensitivity, specificity, positive predictive value, negative predictive value and accuracy of echocardiographic measures for severe aortic stenosis were determined relative to the documented interpretation of severe aortic stenosis.

A protocatechuate biosensor for KT2440 via promoter and protein evolution.

Robust fluorescence-based biosensors are emerging as critical tools for high-throughput strain improvement in synthetic biology. Many biosensors are developed in model organisms where sophisticated synthetic biology tools are also well established. However, industrial biochemical production often employs microbes with phenotypes that are advantageous for a target process, and biosensors may fail to directly transition outside the host in which they are developed.

Resource utilization and outcome among patients with selective versus nonselective troponin testing.

Objective: In patients with suspected acute coronary syndrome (ACS), troponin testing is effective for diagnosis and prognosis. Troponin testing has now expanded to include patients without suspected ACS. This nonselective troponin testing has unknown consequences for resource utilization and outcome.

Value-Based ST-Segment-Elevation Myocardial Infarction Care Using Risk-Guided Triage and Early Discharge.

Background: Prior studies suggest that low-risk ST-segment-elevation myocardial infarction (STEMI) patients undergoing primary percutaneous coronary intervention can be considered for early discharge. We describe the implementation of an STEMI risk score to decrease cost while maintaining optimal patient outcomes.

Methods And Results: We determined the impact of risk-guided STEMI care on healthcare value through the retrospective application of the Zwolle Risk Score to 967 patients receiving primary percutaneous coronary intervention between 2009 and 2011.

Value in cardiovascular care.

Healthcare value, defined as health outcomes achieved relative to the costs of care, has been proposed as a unifying approach to measure improvements in the quality and affordability of healthcare. Although value is of increasing interest to payers, many providers remain unfamiliar with how value differs from other approaches to the comparison of cost and outcomes (ie, cost-effectiveness analysis). While cost-effectiveness studies can be used by policy makers and payers to inform decisions about coverage and reimbursement for new therapies, the assessment of healthcare can guide improvements in the delivery of healthcare to achieve better outcomes at lower cost.

Design, Challenges, and Implications of Quality Improvement Projects Using the Electronic Medical Record: Case Study: A Protocol to Reduce the Burden of Postoperative Atrial Fibrillation.

Postoperative atrial fibrillation (POAF) is a frequent complication of cardiac surgery, which results in increased morbidity, mortality, length of stay, and hospital costs. We developed and followed a process map to implement a protocol to decrease POAF: (1) identify stakeholders and form a working committee, (2) formal literature and guideline review, (3) retrospective analysis of current institutional data, (4) data modeling to determine expected effects of change, (4) protocol development and implementation into the electronic medical record, and (5) ongoing review of data and protocol adjustment. Retrospective analysis demonstrated that POAF occurred in 29.

Rapid Thermostabilization of Bacillus thuringiensis Serovar Konkukian 97-27 Dehydroshikimate Dehydratase through a Structure-Based Enzyme Design and Whole Cell Activity Assay.

Thermostabilization of an enzyme with complete retention of catalytic efficiency was demonstrated on recombinant 3-dehydroshikimate dehydratase (DHSase or wtAsbF) from Bacillus thuringiensis serovar konkukian 97-27 (hereafter, B. thuringiensis 97-27). The wtAsbF is relatively unstable at 37 °C, in vitro (t = 15 min), in the absence of divalent metal.

A microbial sensor for organophosphate hydrolysis exploiting an engineered specificity switch in a transcription factor.

A whole-cell biosensor utilizing a transcription factor (TF) is an effective tool for sensitive and selective detection of specialty chemicals or anthropogenic molecules, but requires access to an expanded repertoire of TFs. Using homology modeling and ligand docking for binding pocket identification, assisted by conservative mutations in the pocket, we engineered a novel specificity in an Acinetobacter TF, PobR, to 'sense' a chemical p-nitrophenol (pNP) and measured the response via a fluorescent protein reporter expressed from a PobR promoter. Out of 10(7) variants of PobR, four were active when dosed with pNP, with two mutants showing a specificity switch from the native effector 4-hydroxybenzoate (4HB).

Rosetta comparative modeling for library design: Engineering alternative inducer specificity in a transcription factor.

Structure-based rational mutagenesis for engineering protein functionality has been limited by the scarcity and difficulty of obtaining crystal structures of desired proteins. On the other hand, when high-throughput selection is possible, directed evolution-based approaches for gaining protein functionalities have been random and fortuitous with limited rationalization. We combine comparative modeling of dimer structures, ab initio loop reconstruction, and ligand docking to select positions for mutagenesis to create a library focused on the ligand-contacting residues.