Stability of Protein Pharmaceuticals: Recent Advances.

There have been significant advances in the formulation and stabilization of proteins in the liquid state over the past years since our previous review. Our mechanistic understanding of protein-excipient interactions has increased, allowing one to develop formulations in a more rational fashion. The field has moved towards more complex and challenging formulations, such as high concentration formulations to allow for subcutaneous administration and co-formulation. While much of the published work has focused on mAbs, the principles appear to apply to any therapeutic protein, although mAbs clearly have some distinctive features. In this review, we first discuss chemical degradation reactions. This is followed by a section on physical instability issues. Then, more specific topics are addressed: instability induced by interactions with interfaces, predictive methods for physical stability and interplay between chemical and physical instability. The final parts are devoted to discussions how all the above impacts (co-)formulation strategies, in particular for high protein concentration solutions.'

Evaluating the Performance of the Astral Mass Analyzer for Quantitative Proteomics Using Data-Independent Acquisition.

We evaluate the quantitative performance of the newly released Asymmetric Track Lossless (Astral) analyzer. Using data-independent acquisition, the Thermo Scientific Orbitrap Astral mass spectrometer quantifies 5 times more peptides per unit time than state-of-the-art Thermo Scientific Orbitrap mass spectrometers, which have long been the gold standard for high-resolution quantitative proteomics. Our results demonstrate that the Orbitrap Astral mass spectrometer can produce high-quality quantitative measurements across a wide dynamic range. We also use a newly developed extracellular vesicle enrichment protocol to reach new depths of coverage in the plasma proteome, quantifying over 5000 plasma proteins in a 60 min gradient with the Orbitrap Astral mass spectrometer.

Capsaicin 8% Patch for Spinal Cord Injury Focal Neuropathic Pain, a Randomized Controlled Trial.

BACKGROUND: Neuropathic pain (NP) after spinal cord injury (SCI) exacerbates disability, decreases quality of life (QOL), and is often refractory to available therapies. Patients report willingness to trade potential recovery of strength, bowel, bladder, or sexual function for pain relief. One proposed mechanism causing NP is up-regulation of transient receptor potential vanilloid 1 (TRPV 1) proteins in uninjured C fibers and dorsal root ganglia causing neuronal excitability. Recent studies have found up-regulation of TRPV 1 proteins after SCI. OBJECTIVE: We hypothesize the application of capsaicin 8% patch (C8P), FDA approved for NP in diabetic peripheral neuropathy and post-herpetic neuralgia, will improve pain, function and QOL in persons with SCI. METHODS: Randomized single-blind crossover design in which 11 persons with SCI and NP refractory to two oral pain medications received C8P or a control low dose Capsaicin 0.025% patch (CON) over two 12-week periods. Pain (VAS, MPI-SCI), quality of life (WHO-QOL), and functional status (SCIM) were measured at 2-4-week intervals. RESULTS: There was a main treatment effect of C8P over CON on VAS and MPI-SCI outcomes with pain reduction of 35% and 29% at weeks 2 and 4, respectively. C8P also demonstrated a main treatment effect over CON on the SCIM mobility subscale. WHO-QOL scores did not improve with C8P. CONCLUSIONS: C8P improves pain and mobility for patients with SCI and refractory NP. Larger studies should be performed to evaluate impact of repeat applications and QOL outcomes.

Extreme cold consistently reduces seedling growth but has species-specific effects on browse tolerance in summer.

PREMISE OF THE STUDY: Extreme weather events can injure plants, causing decreased survival. However, we may underestimate the ecological importance of extreme events if they have strong sublethal effects that manifest after several months. We tested the hypothesis that late-winter extreme-cold events decrease the ability of woody plants to grow and tolerate stem removal in summer. METHODS: Seedlings from four temperate tree species (Abies balsamea, Pinus resinosa, P. strobus, Quercus rubra) were acclimated to winter conditions in growth chambers, and experienced 1 week of warm temperatures before being exposed to one of three 24-h extreme-cold events (minimum temperature: 8°C control, -8°C, or -16°C). Seedlings were then transferred to a greenhouse where we monitored survival and growth. Three months after the extreme-cold event, we mimicked an herbivore attack by removing either 25% or 75% of new stem growth from seedlings of two species (P. resinosa, Q. rubra). KEY RESULTS: While extreme cold had no immediate effect on seedling survival, the coldest temperature treatment reduced stem growth 51% relative to controls. Stem removal decreased P. resinosa survival in the -16°C treatment, but stem removal treatment had no effect on P. resinosa survival in the intermediate -8°C treatment or 8°C control. Stem removal did not alter Q. rubra survival. CONCLUSIONS: Ephemeral late-winter cold temperatures can have unappreciated effects on growing-season seedling dynamics, including growth and herbivory. For predicting how extreme-cold events might alter large-scale patterns of tree distribution, seedlings should be monitored throughout the growing season following extreme late-winter frosts.

Plants eavesdrop on cues produced by snails and induce costly defenses that affect insect herbivores.

Although induced defenses are widespread in plants, the degree to which plants respond to herbivore kairomones (incidental chemicals that herbivores produce independent of herbivory), the costs and benefits of responding to cues of herbivory risk, and the ecological consequences of induced defenses remain unclear. We demonstrate that undamaged tomatoes, Solanum lycopersicum, induce defenses in response to a kairomone (locomotion mucus) of snail herbivores (Helix aspersa). Induced defense had significant costs and benefits for plants: plants exposed to snail mucus or a standard defense elicitor (methyl jasmonate, MeJA) exhibited slower growth, but also experienced less herbivory by an insect herbivore (Spodoptera exigua). We also find that kairomones from molluscan herbivores lead to deleterious effects on insect herbivores mediated through changes in plant defense, i.e., mucus-induced defenses of Solanum lycopersicum-reduced growth of S. exigua. These results suggest that incidental cues of widespread generalist herbivores might be a mechanism creating variation in plant growth, plant defense, and biotic interactions.

A nonparametric Bayesian method of translating machine learning scores to probabilities in clinical decision support.

BACKGROUND: Probabilistic assessments of clinical care are essential for quality care. Yet, machine learning, which supports this care process has been limited to categorical results. To maximize its usefulness, it is important to find novel approaches that calibrate the ML output with a likelihood scale. Current state-of-the-art calibration methods are generally accurate and applicable to many ML models, but improved granularity and accuracy of such methods would increase the information available for clinical decision making. This novel non-parametric Bayesian approach is demonstrated on a variety of data sets, including simulated classifier outputs, biomedical data sets from the University of California, Irvine (UCI) Machine Learning Repository, and a clinical data set built to determine suicide risk from the language of emergency department patients. RESULTS: The method is first demonstrated on support-vector machine (SVM) models, which generally produce well-behaved, well understood scores. The method produces calibrations that are comparable to the state-of-the-art Bayesian Binning in Quantiles (BBQ) method when the SVM models are able to effectively separate cases and controls. However, as the SVM models' ability to discriminate classes decreases, our approach yields more granular and dynamic calibrated probabilities comparing to the BBQ method. Improvements in granularity and range are even more dramatic when the discrimination between the classes is artificially degraded by replacing the SVM model with an ad hoc k-means classifier. CONCLUSIONS: The method allows both clinicians and patients to have a more nuanced view of the output of an ML model, allowing better decision making. The method is demonstrated on simulated data, various biomedical data sets and a clinical data set, to which diverse ML methods are applied. Trivially extending the method to (non-ML) clinical scores is also discussed.

Climatic variation and seed persistence: freeze-thaw cycles lower survival via the joint action of abiotic stress and fungal pathogens.

Global climate change is altering thermal cycles in soils during late winter, a transition that may directly threaten seed survival via abiotic stress, facilitate infection by soil-borne pathogens, or both. Using field-collected soil and seeds of the perennial bunchgrass Elymus canadensis, we tested the hypothesis that soil freeze-thaw events limit survival within the soil through direct effects on seed persistence and amplification of soil pathogen attack using a factorial experiment that manipulated freeze-thaw cycles (constant freeze vs. freeze-thaw) and fungicide addition. Freeze-thaw treatment resulted in lower seedling emergence and delayed emergence time relative to constant-freeze controls. Fungicide-treated soils had greater emergence relative to untreated soils; the lowest seedling emergence was observed in no-fungicide, freeze-thaw-treated soils (<1 %). The strong effects of thermal variability and fungi on seeds were mitigated through interactions at the seed-soil interface, as subsequent experiments showed that fungicide and freeze-thaw treatments alone do not influence dormancy. Our work demonstrates that changes in freeze-thaw events directly limit seedling emergence, delay seedling phenology, and provide opportunities for fungal pathogens to limit seed persistence. As recruitment from seeds is a key determinant of plant population dynamics, these results suggest that climatic variation may generate unique consequences for populations under changing climate regimes.

Acute calcific longus colli tendonitis.

Acute calcific longus colli tendonitis is an inflammatory response of the neck flexor musculature. Patients present with symptoms suggestive of a retropharyngeal abscess or meningitis. Adjunctive medical imaging is required to confirm the diagnosis and dispel other, more serious and life threatening, pathologies. We present a case of acute calcific longus colli tendonitis, and provide a discussion on the topic as to avoid unnecessary medical and surgical intervention because the entity can be easily confused with more severe diseases.

Specific catalysis of asparaginyl deamidation by carboxylic acids: kinetic, thermodynamic, and quantitative structure-property relationship analyses.

Asparaginyl (Asn) deamidation could lead to altered potency, safety, and/or pharmacokinetics of therapeutic protein drugs. In this study, we investigated the effects of several different carboxylic acids on Asn deamidation rates using an IgG1 monoclonal antibody (mAb1*) and a model hexapeptide (peptide1) with the sequence YGKNGG. Thermodynamic analyses of the kinetics data revealed that higher deamidation rates are associated with predominantly more negative ΔS and, to a lesser extent, more positive ΔH. The observed differences in deamidation rates were attributed to the unique ability of each type of carboxylic acid to stabilize the energetically unfavorable transition-state conformations required for imide formation. Quantitative structure property relationship (QSPR) analysis using kinetic data demonstrated that molecular descriptors encoding for the geometric spatial distribution of atomic properties on various carboxylic acids are effective determinants for the deamidation reaction. Specifically, the number of O-O and O-H atom pairs on carboxyl and hydroxyl groups with interatomic distances of 4-5 Å on a carboxylic acid buffer appears to determine the rate of deamidation. Collectively, the results from structural and thermodynamic analyses indicate that carboxylic acids presumably form multiple hydrogen bonds and charge-charge interactions with the relevant deamidation site and provide alignment between the reactive atoms on the side chain and backbone. We propose that carboxylic acids catalyze deamidation by stabilizing a specific, energetically unfavorable transition-state conformation of l-asparaginyl intermediate II that readily facilitates bond formation between the γ-carbonyl carbon and the deprotonated backbone nitrogen for cyclic imide formation.

Invasive shrubs differentially alter autumnal activity for three common small-mammal species.

Seasonal variation in animal activity influences fitness and the intensity of ecological interactions (e.g., competition, predation), yet aspects of global change in the Anthropocene may catalyze shifts in seasonal activity. Invasive plants are components of global change and can modify animal daily activity, but their influence on animal seasonal activity is less understood. We examined how invasive woody shrubs (Autumn olive [Elaeagnus umbellata] and Amur honeysuckle [Lonicera maackii]) affect seasonal activity of three common small-mammal species by coupling experimental shrub removal with autumnal camera trapping for two consecutive years at six paired forest sites (total 12 plots). Eastern chipmunks (Tamias striatus) foraged more, and foraging was observed at least 20 days longer, in shrub-invaded forests. White-footed mice (Peromyscus leucopus) foraged more in invaded than cleared plots in one study year, but P. leucopus autumn activity timing did not differ between shrub-removal treatments. Fox squirrel (Sciurus niger) activity displayed year-specific responses to shrub removal suggesting intraannual cues (e.g., temperature) structure S. niger autumnal activity. Our work highlights how plant invasions can have species-specific effects on seasonal animal activity, may modify the timing of physiological processes (e.g., torpor), and could generate variation in animal-mediated interactions such as seed dispersal or granivory.

Complete genome sequence of Microbacterium foliorum phage Curie, a podovirus isolated from soil in Spokane, Washington.

Bacteriophage Curie is a podovirus that infects Microbacterium foliorum. The Curie genome spans 16,810 bp, has 90 bp terminal inverted repeats, and includes 23 protein-coding genes. Its genome architecture resembles phage PineapplePizza and other phi29-like phages. Together, Curie and PineapplePizza form a new actinobacteriophage Cluster GI.

Structural and metabolic transitions of C4 leaf development and differentiation defined by microscopy and quantitative proteomics in maize.

C(4) grasses, such as maize (Zea mays), have high photosynthetic efficiency through combined biochemical and structural adaptations. C(4) photosynthesis is established along the developmental axis of the leaf blade, leading from an undifferentiated leaf base just above the ligule into highly specialized mesophyll cells (MCs) and bundle sheath cells (BSCs) at the tip. To resolve the kinetics of maize leaf development and C(4) differentiation and to obtain a systems-level understanding of maize leaf formation, the accumulation profiles of proteomes of the leaf and the isolated BSCs with their vascular bundle along the developmental gradient were determined using large-scale mass spectrometry. This was complemented by extensive qualitative and quantitative microscopy analysis of structural features (e.g., Kranz anatomy, plasmodesmata, cell wall, and organelles). More than 4300 proteins were identified and functionally annotated. Developmental protein accumulation profiles and hierarchical cluster analysis then determined the kinetics of organelle biogenesis, formation of cellular structures, metabolism, and coexpression patterns. Two main expression clusters were observed, each divided in subclusters, suggesting that a limited number of developmental regulatory networks organize concerted protein accumulation along the leaf gradient. The coexpression with BSC and MC markers provided strong candidates for further analysis of C(4) specialization, in particular transporters and biogenesis factors. Based on the integrated information, we describe five developmental transitions that provide a conceptual and practical template for further analysis. An online protein expression viewer is provided through the Plant Proteome Database.

Evaluating the Performance of the Astral Mass Analyzer for Quantitative Proteomics Using Data Independent Acquisition.

We evaluate the quantitative performance of the newly released Asymmetric Track Lossless (Astral) analyzer. Using data independent acquisition, the Thermo Scientific™ Orbitrap™ Astral™ mass spectrometer quantifies 5 times more peptides per unit time than state-of-the-art Thermo Scientific™ Orbitrap™ mass spectrometers, which have long been the gold standard for high resolution quantitative proteomics. Our results demonstrate that the Orbitrap Astral mass spectrometer can produce high quality quantitative measurements across a wide dynamic range. We also use a newly developed extra-cellular vesicle enrichment protocol to reach new depths of coverage in the plasma proteome, quantifying over 5,000 plasma proteins in a 60-minute gradient with the Orbitrap Astral mass spectrometer.

Weak interactions govern the viscosity of concentrated antibody solutions: high-throughput analysis using the diffusion interaction parameter.

Weak protein-protein interactions are thought to modulate the viscoelastic properties of concentrated antibody solutions. Predicting the viscoelastic behavior of concentrated antibodies from their dilute solution behavior is of significant interest and remains a challenge. Here, we show that the diffusion interaction parameter (k(D)), a component of the osmotic second virial coefficient (B(2)) that is amenable to high-throughput measurement in dilute solutions, correlates well with the viscosity of concentrated monoclonal antibody (mAb) solutions. We measured the k(D) of 29 different mAbs (IgG(1) and IgG(4)) in four different solvent conditions (low and high ion normality) and found a linear dependence between k(D) and the exponential coefficient that describes the viscosity concentration profiles (|R| ≥ 0.9). Through experimentally measured effective charge measurements, under low ion normality where the electroviscous effect can dominate, we show that the mAb solution viscosity is poorly correlated with the mAb net charge (|R| ≤ 0.6). With this large data set, our results provide compelling evidence in support of weak intermolecular interactions, in contrast to the notion that the electroviscous effect is important in governing the viscoelastic behavior of concentrated mAb solutions. Our approach is particularly applicable as a screening tool for selecting mAbs with desirable viscosity properties early during lead candidate selection.

Selective abrogation of the uPA-uPAR interaction in vivo reveals a novel role in suppression of fibrin-associated inflammation.

The urokinase plasminogen activator receptor (uPAR) has emerged as a potential regulator of cell adhesion, cell migration, proliferation, differentiation, and cell survival in multiple physiologic and pathologic contexts. The urokinase plasminogen activator (uPA) was the first identified ligand for uPAR, but elucidation of the specific functions of the uPA-uPAR interaction in vivo has been difficult because uPA has important physiologic functions that are independent of binding to uPAR and because uPAR engages multiple ligands. Here, we developed a new mouse strain (Plau(GFDhu/GFDhu)) in which the interaction between endogenous uPA and uPAR is selectively abrogated, whereas other functions of both the protease and its receptor are retained. Specifically, we introduced 4 amino acid substitutions into the growth factor domain (GFD) of uPA that abrogate uPAR binding while preserving the overall structure of the domain. Analysis of Plau(GFDhu/GFDhu) mice revealed an unanticipated role of the uPA-uPAR interaction in suppressing inflammation secondary to fibrin deposition. In contrast, leukocyte recruitment and tissue regeneration were unaffected by the loss of uPA binding to uPAR. This study identifies a principal in vivo role of the uPA-uPAR interaction in cell-associated fibrinolysis critical for suppression of fibrin accumulation and fibrin-associated inflammation and provides a valuable model for further exploration of this multifunctional receptor.

Generalist herbivore response to volatile chemical induction varies along a gradient in soil salinization.

Elevated soil salinity directly modifies plant physiology and indirectly alters the biotic interactions that shape plant performance. However, it is unclear how soil salinization interacts with plant defenses to alter patterns of leaf consumption or herbivore survival, development, and performance. In this study, we carried out laboratory feeding trials and a common garden experiment to investigate how gradients in soil salinization interact with plant induction status (modified via exogenous application of methyl jasmonate [MeJA]) to influence feeding consumption and performance of the generalist herbivore Spodoptera exigua on tomato (Solanum lycoperscium) plants. Our results showed that S. exigua consumed less leaf tissue from tomatoes treated with ≥ 50 mM NaCl; at these higher salinity treatments, these herbivores were less likely to pupate and died more quickly. Treatment with MeJA only reduced leaf consumption in the 0 mM NaCl treatment. Our common garden study demonstrated that natural populations of leaf chewing herbivores were less likely to damage tomatoes treated with > 50 mM NaCl solutions. Treatment with MeJA in the common garden reduced damage from natural populations of herbivores, but only for salt treatments at the 50 mM NaCl concentration level and we did observe variation in herbivore damage between cohorts in common garden trials. These results suggest that both soil salinization and volatile jasmonate signals may generate complementary shifts in decreased plant quality for herbivores. Overall, our study concludes that soil salinization could be a potential driver in spatial patterns of variation in both herbivory and herbivore demography.

MnO2-Ir Nanowires: Combining Ultrasmall Nanoparticle Sizes, O-Vacancies, and Low Noble-Metal Loading with Improved Activities towards the Oxygen Reduction Reaction.

Although clean energy generation utilizing the Oxygen Reduction Reaction (ORR) can be considered a promising strategy, this approach remains challenging by the dependence on high loadings of noble metals, mainly Platinum (Pt). Therefore, efforts have been directed to develop new and efficient electrocatalysts that could decrease the Pt content (e.g., by nanotechnology tools or alloying) or replace them completely in these systems. The present investigation shows that high catalytic activity can be reached towards the ORR by employing 1.8 ± 0.7 nm Ir nanoparticles (NPs) deposited onto MnO2 nanowires surface under low Ir loadings (1.2 wt.%). Interestingly, we observed that the MnO2-Ir nanohybrid presented high catalytic activity for the ORR close to commercial Pt/C (20.0 wt.% of Pt), indicating that it could obtain efficient performance using a simple synthetic procedure. The MnO2-Ir electrocatalyst also showed improved stability relative to commercial Pt/C, in which only a slight activity loss was observed after 50 reaction cycles. Considering our findings, the superior performance delivered by the MnO2-Ir nanohybrid may be related to (i) the significant concentration of reduced Mn3+ species, leading to increased concentration of oxygen vacancies at its surface; (ii) the presence of strong metal-support interactions (SMSI), in which the electronic effect between MnOx and Ir may enhance the ORR process; and (iii) the unique structure comprised by Ir ultrasmall sizes at the nanowire surface that enable the exposure of high energy surface/facets, high surface-to-volume ratios, and their uniform dispersion.

LabKey Server: an open source platform for scientific data integration, analysis and collaboration.

BACKGROUND: Broad-based collaborations are becoming increasingly common among disease researchers. For example, the Global HIV Enterprise has united cross-disciplinary consortia to speed progress towards HIV vaccines through coordinated research across the boundaries of institutions, continents and specialties. New, end-to-end software tools for data and specimen management are necessary to achieve the ambitious goals of such alliances. These tools must enable researchers to organize and integrate heterogeneous data early in the discovery process, standardize processes, gain new insights into pooled data and collaborate securely. RESULTS: To meet these needs, we enhanced the LabKey Server platform, formerly known as CPAS. This freely available, open source software is maintained by professional engineers who use commercially proven practices for software development and maintenance. Recent enhancements support: (i) Submitting specimens requests across collaborating organizations (ii) Graphically defining new experimental data types, metadata and wizards for data collection (iii) Transitioning experimental results from a multiplicity of spreadsheets to custom tables in a shared database (iv) Securely organizing, integrating, analyzing, visualizing and sharing diverse data types, from clinical records to specimens to complex assays (v) Interacting dynamically with external data sources (vi) Tracking study participants and cohorts over time (vii) Developing custom interfaces using client libraries (viii) Authoring custom visualizations in a built-in R scripting environment. Diverse research organizations have adopted and adapted LabKey Server, including consortia within the Global HIV Enterprise. Atlas is an installation of LabKey Server that has been tailored to serve these consortia. It is in production use and demonstrates the core capabilities of LabKey Server. Atlas now has over 2,800 active user accounts originating from approximately 36 countries and 350 organizations. It tracks roughly 27,000 assay runs, 860,000 specimen vials and 1,300,000 vial transfers. CONCLUSIONS: Sharing data, analysis tools and infrastructure can speed the efforts of large research consortia by enhancing efficiency and enabling new insights. The Atlas installation of LabKey Server demonstrates the utility of the LabKey platform for collaborative research. Stable, supported builds of LabKey Server are freely available for download at http://www.labkey.org. Documentation and source code are available under the Apache License 2.0.

CYTOMEGALOVIRUS RETINITIS AFTER AN INTRAVITREAL DEXAMETHASONE IMPLANT IN AN IMMUNOCOMPETENT PATIENT.

PURPOSE: To present the case of a 71-year-old woman who developed cytomegalovirus retinitis after the administration of an intravitreal dexamethasone implant in an immunocompetent patient. METHODS: Retrospective case report. PATIENTS: Single patient with a diagnosis of cytomegalovirus retinitis associated with the intravitreal dexamethasone implant. RESULTS: The patient developed cytomegalovirus retinitis three months after an intravitreal injection of a dexamethasone implant for macular edema. The patient had no history of poor immune function and was not taking immunosuppressive medications. CONCLUSION: Cytomegalovirus retinitis has been associated with local steroid therapy. This has been described in both immunocompromised and immunocompetent patients. The intravitreal dexamethasone implant may cause local immunosuppression and result in cytomegalovirus retinitis in immunocompetent patients.