Programming Probiotics: Diet-Responsive Gene Expression and Colonization Control in Engineered S. boulardii.

Saccharomyces boulardii (Sb) is an emerging probiotic chassis for delivering biomolecules to the mammalian gut, offering unique advantages as the only eukaryotic probiotic. However, precise control over gene expression and gut residence time in Sb have remained challenging. To address this, we developed five ligand-responsive gene expression systems and repaired galactose metabolism in Sb, enabling inducible gene expression in this strain. Engineering these systems allowed us to construct AND logic gates, control the surface display of proteins, and turn on protein production in the mouse gut in response to dietary sugar. Additionally, repairing galactose metabolism expanded Sb's habitat within the intestines and resulted in galactose-responsive control over gut residence time. This work opens new avenues for precise dosing of therapeutics by Sb via control over its in vivo gene expression levels and localization within the gastrointestinal tract.

Origins and functions of eosinophils in two non-mucosal tissues.

Eosinophils are a type of granulocyte named after the presence of their eosin-stained granules. Traditionally, eosinophils have been best known to play prominent roles in anti-parasitic responses and mediating allergic reactions. Knowledge of their behaviour has expanded with time, and they are now recognized to play integral parts in the homeostasis of gastrointestinal, respiratory, skeletal muscle, adipose, and connective tissue systems. As such, they are implicated in a myriad of pathologies, and have been the target of several medical therapies. This review focuses on the lifespan of eosinophils, from their origins in the bone marrow, to their tissue-resident role. In particular, we wish to highlight the functions of eosinophils in non-mucosal tissues with skeletal muscle and the adipose tissues as examples, and to discuss the current understanding of their participation in diseased states in these tissues.

Recognition of BRAF by CDC37 and Re-Evaluation of the Activation Mechanism for the Class 2 BRAF-L597R Mutant.

The kinome specific co-chaperone, CDC37 (cell division cycle 37), is responsible for delivering BRAF (B-Rapidly Accelerated Fibrosarcoma) to the Hsp90 (heat shock protein 90) complex, where it is then translocated to the RAS (protooncogene product p21) complex at the plasma membrane for RAS mediated dimerization and subsequent activation. We identify a bipartite interaction between CDC37 and BRAF and delimitate the essential structural elements of CDC37 involved in BRAF recognition. We find an extended and conserved CDC37 motif, 20HPNID---SL--W31, responsible for recognizing the C-lobe of BRAF kinase domain, while the c-terminal domain of CDC37 is responsible for the second of the bipartite interaction with BRAF. We show that dimerization of BRAF, independent of nucleotide binding, can act as a potent signal that prevents CDC37 recognition and discuss the implications of mutations in BRAF and the consequences on signaling in a clinical setting, particularly for class 2 BRAF mutations.

Qualitative High-Throughput Analysis of Subvisible Particles in Biological Formulations Using Backgrounded Membrane Imaging.

High-throughput analysis of low-volume samples for detection of subvisible particles (SVPs) in biologic formulations remains an unmet need in the pharmaceutical industry. Some commonly used methods, such as light obscuration and microflow imaging, for SVP analysis are not high throughput and require significant amounts of sample volume, which may impede the collection of SVP data when therapeutic protein amounts are limited, typically during early stages of formulation development. We evaluated backgrounded membrane imaging (BMI) as an orthogonal method for SVP analysis and identified critical experimental parameters. Protein concentration, sample viscosity, and membrane coverage area had to be adjusted for each sample, especially those with high protein concentrations. A comparative analysis of particle counts obtained from BMI, light obscuration, and microflow imaging for five protein samples revealed that particle counts obtained with BMI were significantly higher than those acquired with the other two techniques for all particle size categories. BMI could not accurately count particles in protein-containing samples, as the image analysis software could not accurately trace the boundaries of translucent particles. Based on our results, BMI could be used as an orthogonal method for particle characterization when sample material is limited, such as during the early stages of formulation development or screening.

Natural and anthropogenic processes affecting radon releases during mining and early stage reclamation activities, Pinenut uranium mine, Arizona, USA.

Radon (Rnair) was monitored in open air in publicly accessible areas surrounding the Pinenut uranium (U) mine during mining and reclamation activities in 2015-16 to address concerns about mining related effects to areas surrounding Grand Canyon National Park (GCNP) in Arizona, USA. During July 2015, Rnair concentrations associated with the ore storage pile monitoring site were larger than those at the mine vent monitoring site and likely resulted from the relatively large amount of ore stored on site during this period. Higher wind velocities at the ore pile monitoring site generally resulted in lower Rnair concentrations; however, wind velocity did not appear to be an important factor in controlling Rnair concentrations at the mine vent monitoring site. Physical disturbances of the ore pile by heavy equipment did not coincide with elevated Rnair concentrations at the ore storage pile or mine vent monitoring sites. The relative size of the ore storage pile showed a positive trend with the daily mean Rnair concentration measured at the ore pile monitoring site. Principal component analysis (PCA) was applied to the ore pile and mine vent multivariate data sets for simultaneous comparison of all measured variables during 230 days of the study period. A significant positive coefficient for Rnair was associated with a significant negative coefficient for wind speed for principal component (PC) 2ore pile. Significant, positive PC2mine vent coefficients included Rnair, wind direction, and relative ore pile size indicating that Rnair variations at the mine vent monitoring site may be affected by Rn sourced from the ore pile. The ore pile is located about 200 m south of the mine vent Rn monitor with the prevalent wind direction coming from the south. All data generated during the field study and laboratory verification tests were published by Naftz et al. (2018) and are available online at: https://doi.org/10.5066/F79Z946T.

Correction to: Galcanezumab in episodic migraine: subgroup analyses of efficacy by high versus low frequency of migraine headaches in phase 3 studies (EVOLVE-1 & EVOLVE-2).

After publication of our article [1] we were notified that the data presented in the upper row of Fig. 7 was inadvertently the least square mean change from baseline (standard error) at Month 6 rather than the overall average of Month 3 and Month 6. The figure legend and discussion of the data in the text were and are correct. The error was only in the upper row of Fig. 7. The legend for Fig. 7 did not require revision.

Galcanezumab in episodic migraine: subgroup analyses of efficacy by high versus low frequency of migraine headaches in phase 3 studies (EVOLVE-1 & EVOLVE-2).

BACKGROUND: Patients with high-frequency episodic migraine (HFEM) have a greater disease burden than those with low-frequency episodic migraine (LFEM). Acute treatment overuse increases the risk of migraine chronification in patients with HFEM. Galcanezumab, a humanized monoclonal antibody binding calcitonin gene-related peptide (CGRP), is effective for migraine prevention with a favorable safety profile. Here, we investigate whether there are differences in galcanezumab efficacy in patients with LFEM or with HFEM. METHODS: Data were pooled from two double-blind, placebo-controlled phase 3 trials; EVOLVE-1 and EVOLVE-2. Patients were 18-65 years old, experienced 4-14 monthly migraine headache days (MHDs) for ≥1 year prior, with onset at < 50 years of age. Migraine headaches were tracked via electronic patient-reported outcome system and randomization was stratified by low (LFEM; 4-7 monthly MHDs) or high (HFEM; 8-14 monthly MHDs) frequency. Subgroup analysis compared the HFEM and LFEM subgroups with a linear or generalized linear mixed model repeated measures approach. RESULTS: The intent-to-treat patients (N = 1773) had a mean age of 41.3 years, were mostly white (75%), female (85%), and 66% of patients had HFEM. In both the LFEM and HFEM subgroups, the overall (Months 1-6) and monthly changes from baseline in monthly MHDs and monthly MHDs with acute medication use compared with placebo were statistically significantly reduced for galcanezumab 120-mg and 240-mg. Galcanezumab (120-mg and 240-mg) significantly decreased the overall and monthly MHDs with nausea and/or vomiting, and with photophobia and phonophobia versus placebo in patients with LFEM or HFEM. In both subgroups, the mean overall (Months 1-6) and monthly percentages of patients with ≥50%, ≥75%, and 100% reduction in monthly MHDs from baseline were statistically significantly greater in patients receiving either dose of galcanezumab versus placebo. Galcanezumab (120-mg and 240-mg) significantly improved the Migraine-Specific Quality of Life Questionnaire role function-restrictive domain score as well as the Migraine Disability Assessment total score versus placebo for patients with LFEM or HFEM. There were no significant subgroup-by-treatment interactions. CONCLUSIONS: Galcanezumab was as effective in patients with HFEM as in those with LFEM. Associated symptoms, quality of life, and disability were similarly improved in patients with HFEM or LFEM. TRIAL REGISTRATION: NCT02614183 , NCT02614196 .

Improved enrichment factor calculations through principal component analysis: Examples from soils near breccia pipe uranium mines, Arizona, USA.

The enrichment factor (EF) is a widely used metric for determining how much the presence of an element in a sampling media has increased relative to average natural abundance because of human activity. Calculation of an EF requires the selection of both a background composition and a reference element, choices that can strongly influence the result of the calculation. Here, it is shown how carefully applied, classical principal component analysis (PCA) examined via biplots can guide the selections of background compositions and reference elements. Elemental data were treated using the centered log ratio (CLR) transformation, and multiple subsets of major and trace elements were examined to gain different perspectives. The methodology was applied to a dataset of elemental soil concentrations from around breccia pipe uranium mines in Arizona, U.S.A., with most samples collected via incremental sampling methodology. Storage of ore at the surface creates the potential for wind dispersal of ore-derived material. Uranium was found to be the best individual tracer of dispersal of ore-derived material to nearby soils, with EF values up to 75. Sulfur, As, Mo, and Cu were also enriched but to lesser degrees. The results demonstrate several practical benefits of a PCA in these situations: (1) the ability to identify one or more elements best suited to distinguish a specific source of enrichment from background composition; (2) understanding how background compositions vary within and between sites; (3) identification of samples containing enriched or anthropogenic materials based upon their integrated, multi-element composition. Calculating the most representative EF values is useful for numerical assessment of enrichment, whether anthropogenic or natural. As shown here, however, the PCA and biplot method provide a visual approach that integrates information from all elements for a given subset of data in a manner that yields geochemical insights beyond the power of the EF.

Evaluation of aggregate and silicone-oil counts in pre-filled siliconized syringes: An orthogonal study characterising the entire subvisible size range.

Characterisation of particulates in therapeutic monoclonal antibody (mAb) formulations is routinely extended to the sub-visible size-range (0.1-10µm). Additionally, with the increased use of pre-filled syringes (PFS), particle differentiation is required between proteinaceous and non-proteinaceous particles such as silicone-oil droplets. Here, three orthogonal techniques: Raster Image Correlation Spectroscopy (RICS), Resonance Mass Measurements (RMM) and Micro-Flow Imaging (MFI), were evaluated with respect to their sub-visible particle measurement and characterisation capabilities. Particle formation in mAb PFS solutions was evaluated with increasing polysorbate-20 (PS-20) concentrations. All three techniques provided complementary but distinct information on protein aggregate and silicone-oil droplet presence. PS-20 limited the generation of mAb aggregates during agitation, while increasing the number of silicone-oil droplets (PS-20 concentration dependant). MFI and RMM revealed PS-20 lead to the formation of larger micron-sized droplets, with RICS revealing an increase in smaller sub-micron droplets. Subtle differences in data sets complicate the apparent correlation between silicone-oil sloughing and mAb aggregates' generation. RICS (though the use of a specific dye) demonstrates an improved selectivity for mAb aggregates, a broader measurement size-range and smaller sample volume requirement. Thus, RICS is proposed to add value to the currently available particle measurement techniques and enable informed decisions during mAb formulation development.

Modulation of the Hydration Water Around Monoclonal Antibodies on Addition of Excipients Detected by Terahertz Time-Domain Spectroscopy.

Terahertz time-domain spectroscopy (THz-TDS) has been shown to detect overlapping extended hydration layers around proteins. Here, we used THz-TDS to detect modulation of the extended hydration layer around monoclonal antibodies (mAbs) by the introduction of commonly used excipients. Proline and sucrose altered the hydration layer around a mAb (mAb1), which was observed as a negative shift in the plateau in absorbance above ~100 mg/mL mAb1 (~70,000 water molecules per mAb); arginine had no effect. At lower concentrations of ~10 mg/mL mAb1 (~700,000 water molecules per mAb) proline and arginine modulated the hydration layer, which was observed as a negative shift in the relative absorbance, whereas sucrose had no effect. The changes in the extended hydration layer were not translated to shifts in the thermal stability or protein:protein interaction parameter. The hydration layer of a second mAb (mAb2) was further shown to be modulated by more complex formulations composed of two or more excipients; although the differences in terahertz absorbance were not predictive of viscosity or long-term stability. THz-TDS promises to be a useful tool for understanding a protein's interaction with excipients in solution and the challenge will be to determine how to apply this knowledge to protein formulation.

Winter energetics of female Indiana bats Myotis sodalis.

Understanding physiological limits and environmental optima is critical to developing protection strategies for endangered and threatened species. One theory to explain the decline in endangered Indiana bat Myotis sodalis populations involves increasing cave temperatures in winter hibernacula. Altered cave temperatures can raise metabolism and cause more arousals in torpid bats, both of which use more fat reserves. In addition, fluctuations in cave temperatures may cause additional arousals. Our objectives were to quantify the effect of temperature and fluctuations thereof on torpid metabolism and arousal frequency in this species. Female Indiana bats (n=36) were collected from caves just before hibernation, maintained in an environmental chamber that simulated hibernacula conditions, and had skin temperature recorded every 30 min throughout the winter. One environmental chamber containing bats (n=12) was sequentially set at 8°, 6°, and 4°C over the winter. The second chamber containing bats (n=12) experienced the same mean temperatures, but temperature fluctuated ±2°C on a regular basis. Torpor bouts were longest at 4°C and were not affected by temperature fluctuations. However, the temperature fluctuations appeared to cause longer arousals. Other bats (n=12) were individually placed in metabolic chambers to calculate oxygen consumption during torpor and during arousals. Torpid metabolism was affected by temperature; at 9°C, it was higher than at 7° or 5°C. Metabolism during arousals was not different among temperature treatments, but rates were almost 200 times higher than torpid metabolic rates. We calculated a winter energy budget and, from the energetic perspective, determined an optimum hibernation temperature (3°-6°C) for female Indiana bats. These findings suggest that hibernacula that provide these conditions deserve extra protection, although other factors in addition to energetics may play a role in temperature preferences.

Causes of death and associated conditions (Codac): a utilitarian approach to the classification of perinatal deaths.

A carefully classified dataset of perinatal mortality will retain the most significant information on the causes of death. Such information is needed for health care policy development, surveillance and international comparisons, clinical services and research. For comparability purposes, we propose a classification system that could serve all these needs, and be applicable in both developing and developed countries. It is developed to adhere to basic concepts of underlying cause in the International Classification of Diseases (ICD), although gaps in ICD prevent classification of perinatal deaths solely on existing ICD codes.We tested the Causes of Death and Associated Conditions (Codac) classification for perinatal deaths in seven populations, including two developing country settings. We identified areas of potential improvements in the ability to retain existing information, ease of use and inter-rater agreement. After revisions to address these issues we propose Version II of Codac with detailed coding instructions.The ten main categories of Codac consist of three key contributors to global perinatal mortality (intrapartum events, infections and congenital anomalies), two crucial aspects of perinatal mortality (unknown causes of death and termination of pregnancy), a clear distinction of conditions relevant only to the neonatal period and the remaining conditions are arranged in the four anatomical compartments (fetal, cord, placental and maternal).For more detail there are 94 subcategories, further specified in 577 categories in the full version. Codac is designed to accommodate both the main cause of death as well as two associated conditions. We suggest reporting not only the main cause of death, but also the associated relevant conditions so that scenarios of combined conditions and events are captured.The appropriately applied Codac system promises to better manage information on causes of perinatal deaths, the conditions associated with them, and the most common clinical scenarios for future study and comparisons.

An evaluation of classification systems for stillbirth.

BACKGROUND: Audit and classification of stillbirths is an essential part of clinical practice and a crucial step towards stillbirth prevention. Due to the limitations of the ICD system and lack of an international approach to an acceptable solution, numerous disparate classification systems have emerged. We assessed the performance of six contemporary systems to inform the development of an internationally accepted approach. METHODS: We evaluated the following systems: Amended Aberdeen, Extended Wigglesworth; PSANZ-PDC, ReCoDe, Tulip and CODAC. Nine teams from 7 countries applied the classification systems to cohorts of stillbirths from their regions using 857 stillbirth cases. The main outcome measures were: the ability to retain the important information about the death using the InfoKeep rating; the ease of use according to the Ease rating (both measures used a five-point scale with a score <2 considered unsatisfactory); inter-observer agreement and the proportion of unexplained stillbirths. A randomly selected subset of 100 stillbirths was used to assess inter-observer agreement. RESULTS: InfoKeep scores were significantly different across the classifications (p < or = 0.01) due to low scores for Wigglesworth and Aberdeen. CODAC received the highest mean (SD) score of 3.40 (0.73) followed by PSANZ-PDC, ReCoDe and Tulip [2.77 (1.00), 2.36 (1.21), 1.92 (1.24) respectively]. Wigglesworth and Aberdeen resulted in a high proportion of unexplained stillbirths and CODAC and Tulip the lowest. While Ease scores were different (p < or = 0.01), all systems received satisfactory scores; CODAC received the highest score. Aberdeen and Wigglesworth showed poor agreement with kappas of 0.35 and 0.25 respectively. Tulip performed best with a kappa of 0.74. The remainder had good to fair agreement. CONCLUSION: The Extended Wigglesworth and Amended Aberdeen systems cannot be recommended for classification of stillbirths. Overall, CODAC performed best with PSANZ-PDC and ReCoDe performing well. Tulip was shown to have the best agreement and a low proportion of unexplained stillbirths. The virtues of these systems need to be considered in the development of an international solution to classification of stillbirths. Further studies are required on the performance of classification systems in the context of developing countries. Suboptimal agreement highlights the importance of instituting measures to ensure consistency for any classification system.