Engineered domain-based assays to identify individual antibodies in oligoclonal combinations targeting the same protein

Quantitation of individual monoclonal antibodies (mAbs) within a combined antibody drug product is required for preclinical and clinical drug development. We have developed two antitoxins, XOMA 3B and XOMA 3E, each consisting of three mAbs that neutralize type B and type E botulinum neurotoxin (BoNT/B and BoNT/E) to treat serotype B and E botulism. To develop mAb-specific binding assays for each antitoxin, we mapped the epitopes of the six mAbs. Each mAb bound an epitope on either the BoNT light chain (LC) or translocation domain (H_N). Epitope mapping data were used to design LC-H_N domains with orthogonal mutations to make them specific for only one mAb in either XOMA 3B or XOMA 3E. Mutant LC-H_N domains were cloned, expressed, and purified from Escherichia coli. Each mAb bound only to its specific domain with affinity comparable to the binding to holotoxin. Further engineering of domains allowed construction of enzyme-linked immunosorbent assays (ELISAs) that could characterize the integrity, binding affinity, and identity of each of the six mAbs in XOMA 3B and 3E without interference from the three BoNT/A mAbs in XOMA 3AB. Such antigen engineering is a general method allowing quantitation and characterization of individual mAbs in a mAb cocktail that bind the same protein.     

An increased requirement for methionine by transformed rat liver epithelial cells in vitro

The growth of two normal and four transformed rat liver epithelial cell lines in a methionine-containing medium and a methionine-deficient medium supplemented with homocysteine was examined. The growth rates of the normal cells on the homocysteine-supplemented medium were approximately one-half the growth rates shown by the same cells in the methionine-containing medium. In contrast, three of the four transformed cell lines studied showed virtually no growth on the homocysteine-supplemented medium, although they grew quite rapidly on the methionine-containing medium. The fourth, transformed by N-methyl-N-nitrosourea, was able to grow on the homocysteine-supplemented medium at about one-third the rate as on the methionine-containing medium. Thus, transformed rat liver epithelial cells resemble other malignant cells in their reduced capacity to grow on homocysteine in the absence of methionine.     

Nitrite effect on nitrous oxide emission from denitrifying activated sludge

Laboratory-scale experiments were conducted to examine the N₂O emission during the denitrification process. For each of the 6 runs carried out, synthetic effluent was fed in a 10 l batch mixed liquor to investigate the effect of nitrite on N₂O emission and Helium was continuously bubbled through the reactor at constant rate (0.12 l/min) to favour N₂O transfer and detection. An increasing COD/NO₃⁻-N influent ratio from 3 to 7 was firstly applied (runs 1–3). Secondly, NO₂⁻ pulse additions were performed during run 4 and 5 (10 and 20 mg N/l, respectively). Finally, the reactor was fed with influent containing both NO₂⁻ and NO₃⁻. We showed that N₂O emission was detected shortly after NO₂⁻ accumulation, few minutes after the substrate feeding. The highest emission occurred at the lower COD/NO₃⁻-N ratio (=3) and at the higher NO₂⁻ addition (20 mg N/l). In addition, the higher nitrogen conversion to N₂O gas (14.4%) was obtained with an influent containing initially both NO₂⁻ and NO₃⁻. Our results suggest a direct effect of the NO₂⁻ concentration on the N₂O emission. We have also confirmed the inhibitory effect of NO₂⁻ concentration on N₂O reduction.     

Accuracy of diagnostic registers and management of chronic obstructive pulmonary disease: the Devon primary care audit

Background

Guidelines on COPD diagnosis and management encourage primary care physicians to detect the disease at an early stage and to treat patients according to their condition and needs. Problems in guideline implementation include difficulties in diagnosis, using spirometry and the disputed role of reversibility testing. These lead to inaccurate diagnostic registers and inadequacy of administered treatments. This study represents an audit of COPD diagnosis and management in primary care practices in Devon.

Methods

Six hundred and thirty two patients on COPD registers in primary care practices were seen by a visiting Respiratory Specialist Nurse. Diagnoses were made according to the NICE guidelines. Reversibility testing was carried out either routinely or based on clinical indication in two sub-samples. Dyspnoea was assessed. Data were entered into a novel IT-based software which computed guideline-based treatment recommendations. Current and recommended treatments were compared.

Results

Five hundred and eighty patients had spirometry. Diagnoses of COPD were confirmed in 422 patients (73%). Thirty nine patients were identified as asthma only, 94 had normal spirometry, 23 were restrictive and 2 had a cardiac disorder. Reversibility testing changed diagnosis of 11% of patients with airflow obstruction, and severity grading in 18%. Three quarters of patients with COPD had been offered practical help with smoking cessation. Short and long-acting anticholinergics and long acting beta-2 agonists had been under-prescribed; in 15–18% of patients they were indicated but not received. Inhaled steroids had been over-prescribed (recommended in 17%; taken by 60%), whereas only 4% of patients with a chronic productive cough were receiving mucolytics. Pulmonary rehabilitation was not available in some areas and was under-used in other areas.

Conclusion

Diagnostic registers of COPD in primary care contain mistakes leading to inaccurate prevalence estimates and inappropriate treatment decisions. Use of pre-bronchodilator readings for diagnosis overestimates the prevalence and severity in a significant minority, thus post bronchodilator readings should be used. Management of stable COPD does often not correspond to guidelines. The IT system used in this study has the potential to improve diagnosis and management of COPD in primary care.     

Protein kinase A and two phosphatases are components of the inositol 1,4,5-trisphosphate receptor macromolecular signaling complex

The inositol 1,4,5-trisphosphate receptor (IP3R) is a ubiquitously expressed intracellular calcium (Ca(2+)) release channel on the endoplasmic reticulum. IP3Rs play key roles in controlling Ca(2+) signals that activate numerous cellular functions including T cell activation, neurotransmitter release, oocyte fertilization and apoptosis. There are three forms of IP3R, all of which are ligand-gated channels activated by the second messenger inositol 1,4,5-trisphosphate. Channel function is modulated via cross-talk with other signaling pathways including those mediated by kinases and phosphatases. In particular IP3Rs are known to be regulated by cAMP-dependent protein kinase (PKA) phosphorylation. In the present study we show that PKA and the protein phosphatases PP1 and PP2A are components of the IP3R1 macromolecular signaling complex. PKA phosphorylation of IP3R1 increases channel activity in planar lipid bilayers. These studies indicate that regulation of IP3R1 function via PKA phosphorylation involves components of a macromolecular signaling complex.     

Tree diversity,tree height and environmental harshness in eastern and western North America

Does variation in environmental harshness explain local and regional species diversity gradients? We hypothesise that for a given life form like trees, greater harshness leads to a smaller range of traits that are viable and thereby also to lower species diversity. On the basis of a strong dependence of maximum tree height on site productivity and other measures of site quality, we propose maximum tree height as an inverse measure of environmental harshness for trees. Our results show that tree species richness is strongly positively correlated with maximum tree height across multiple spatial scales in forests of both eastern and western North America. Maximum tree height co‐varied with species richness along gradients from benign to harsh environmental conditions, which supports the hypothesis that harshness may be a general mechanism limiting local diversity and explaining diversity gradients within a biogeographic region.     

Translational control of coronaviruses

Coronaviruses represent a large family of enveloped RNA viruses that infect a large spectrum of animals. In humans, the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic and is genetically related to SARS-CoV and Middle East respiratory syndrome-related coronavirus (MERS-CoV), which caused outbreaks in 2002 and 2012, respectively. All viruses described to date entirely rely on the protein synthesis machinery of the host cells to produce proteins required for their replication and spread. As such, virus often need to control the cellular translational apparatus to avoid the first line of the cellular defense intended to limit the viral propagation. Thus, coronaviruses have developed remarkable strategies to hijack the host translational machinery in order to favor viral protein production. In this review, we will describe some of these strategies and will highlight the role of viral proteins and RNAs in this process.     

Stream carbon and nitrogen supplements during leaf litter decomposition: contrasting patterns for two foundation species

Leaf litter decomposition plays a major role in nutrient dynamics in forested streams. The chemical composition of litter affects its processing by microorganisms, which obtain nutrients from litter and from the water column. The balance of these fluxes is not well known, because they occur simultaneously and thus are difficult to quantify separately. Here, we examined C and N flow from streamwater and leaf litter to microbial biofilms during decomposition. We used isotopically enriched leaves (¹³C and ¹⁵N) from two riparian foundation tree species: fast-decomposing Populus fremontii and slow-decomposing Populus angustifolia, which differed in their concentration of recalcitrant compounds. We adapted the isotope pool dilution method to estimate gross elemental fluxes into litter microbes. Three key findings emerged: litter type strongly affected biomass and stoichiometry of microbial assemblages growing on litter; the proportion of C and N in microorganisms derived from the streamwater, as opposed to the litter, did not differ between litter types, but increased throughout decomposition; gross immobilization of N from the streamwater was higher for P. fremontii compared to P. angustifolia, probably as a consequence of the higher microbial biomass on P. fremontii. In contrast, gross immobilization of C from the streamwater was higher for P. angustifolia, suggesting that dissolved organic C in streamwater was used as an additional energy source by microbial assemblages growing on slow-decomposing litter. These results indicate that biofilms on decomposing litter have specific element requirements driven by litter characteristics, which might have implications for whole-stream nutrient retention.