Probing binding mechanism of interleukin-6 and olokizumab: in silico design of potential lead antibodies for autoimmune and inflammatory diseases

Computer-aided antibody engineering has been successful in the design of new biologics for disease diagnosis and therapeutic interventions. Interleukin-6 (IL-6), a well-recognized drug target for various autoimmune and inflammatory diseases such as rheumatoid arthritis, multiple sclerosis, and psoriasis, was investigated in silico to design potential lead antibodies. Here, crystal structure of IL-6 along with monoclonal antibody olokizumab was explored to predict antigen–antibody (Ag???Ab)-interacting residues using DiscoTope, Paratome, and PyMOL. Tyr56, Tyr103 in heavy chain and Gly30, Ile31 in light chain of olokizumab were mutated with residues Ser, Thr, Tyr, Trp, and Phe. A set of 899 mutant macromolecules were designed, and binding affinity of these macromolecules to IL-6 was evaluated through Ag???Ab docking (ZDOCK, ClusPro, and Rosetta server), binding free-energy calculations using Molecular Mechanics/Poisson Boltzman Surface Area (MM/PBSA) method, and interaction energy estimation. In comparison to olokizumab, eight newly designed theoretical antibodies demonstrated better result in all assessments. Therefore, these newly designed macromolecules were proposed as potential lead antibodies to serve as a therapeutics option for IL-6-mediated diseases.     

Asymptotic distributions of kappa statistics and their differences with many raters,many rating categories and two conditions

In clinical research and in more general classification problems, a frequent concern is the reliability of a rating system. In the absence of a gold standard, agreement may be considered as an indication of reliability. When dealing with categorical data, the well‐known kappa statistic is often used to measure agreement. The aim of this paper is to obtain a theoretical result about the asymptotic distribution of the kappa statistic with multiple items, multiple raters, multiple conditions, and multiple rating categories (more than two), based on recent work. The result settles a long lasting quest for the asymptotic variance of the kappa statistic in this situation and allows for the construction of asymptotic confidence intervals. A recent application to clinical endoscopy and to the diagnosis of inflammatory bowel diseases (IBDs) is shortly presented to complement the theoretical perspective.     

Endoparasites observed within invertebrates used as live food items for captive wild birds: Overview and potential risks

To monitor and evaluate potential risks to birds’ health, invertebrate species that have been used as live food items had their body contents searched for endoparasites. The contents of approximately 10,000 invertebrates were analyzed. A principal component analysis was performed to study the relationship between the presence/absence of endoparasites and the characteristics of the invertebrates. In most of them, including the species preferred by birds such as caterpillars, waxworms, mealworms, most grasshoppers, and spiders, no organism was identified. Such findings suggest a low potential for parasite transmission associated with its consumption by birds. Although they had unknown or even unlikely implications for the birds’ health, gregarines, oxyurides Leidynema sp., and digenetic trematodes Monolecithotrema sp. were found in samples from woodlice, cockroaches, and centipedes, respectively. The only avian parasites observed in this study were Heterakis gallinarum in samples from earthworms and Acuaria spiralis from woodlice. Suggestively, soil invertebrates showed a higher prevalence of endoparasites and may represent a higher potential risk in comparison to the other categories of invertebrates sampled herein. Detritivory and collected origin were also explanatory variables related to the presence of endoparasites in the current study.     

Automated identification of diseases related to lymph system from lymphography data using artificial immune recognition system with fuzzy resource allocation mechanism (fuzzy-AIRS)

Artificial immune recognition system (AIRS) classification algorithm, which has an important place among classification algorithms in the field of artificial immune systems, has showed an effective and intriguing performance on the problems it was applied. AIRS was previously applied to some medical classification problems including breast cancer, Cleveland heart disease, diabetes and it obtained very satisfactory results. So, AIRS proved to be an efficient artificial intelligence technique in medical field. In this study, the resource allocation mechanism of AIRS was changed with a new one determined by fuzzy-logic. This system, named as fuzzy-AIRS was used as a classifier in the diagnosis of lymph diseases, which is of great importance in medicine. The classifications of lymph diseases dataset taken from University of California at Irvine (UCI) Machine Learning Repository were done using 10-fold cross-validation method. Reached classification accuracies were evaluated by comparing them with reported classifiers in UCI web site in addition to other systems that are applied to the related problems. Also, the obtained classification performances were compared with AIRS with regard to the classification accuracy, number of resources and classification time. While only AIRS algorithm obtained 83.138% classification accuracy, fuzzy-AIRS classified the lymph diseases dataset with 90.00% accuracy. For lymph diseases dataset, fuzzy-AIRS obtained the highest classification accuracy according to the UCI web site. Beside of this success, fuzzy-AIRS gained an important advantage over the AIRS by means of classification time. By reducing classification time as well as obtaining high classification accuracies in the applied datasets, fuzzy-AIRS classifier proved that it could be used as an effective classifier for medical problems.     

Female choice linked to male dorsal fin height in a shortfin molly

Sexual selection is a possible mechanism of speciation. This could be true even in systems where female mate choice has not been clearly observed, because pre-existing biases may be expressed if female decision-making results in male trait evolution. In some mollies, males have enlarged dorsal fins and courtship display is the prevailing mating process. In others, male dominance is thought to play a greater role. We tested females of a species in the latter group, Poecilia mexicana, for consistent preference related to dorsal fin morphology. We found that females were biased toward larger dorsal fins. This latent preference could be an important driver in trait evolution.     

A positive association between oviposition and fruit set: female choice or manipulation?

The relationship between where a female chooses to oviposit and her larvae’s performance at those sites is critical to both the ecology and evolution of plant-insect interactions. For predispersal seed predators that do not themselves pollinate their host and whose larvae are sessile, females must be able to predict which flowers will ultimately be pollinated and set fruit, or be able to manipulate flowers in some way to ensure they set fruit. Otherwise, their offspring will perish. Here we describe the results of an experiment in which we tested if female Hylemya (Diptera: Anthomyiidae) are choosing oviposition sites wisely, or if they are manipulating flowers of their host, Ipomopsis aggregata (Polemoniaceae), in some way to ensure fruit set. Previous work in this system established a positive correlation between oviposition and fruit set. By bagging females on flowers, we removed their ability to choose flowers on which to oviposit. We found that flowers females oviposited on, whether bagged (”no choice”) or unbagged (”female choice”), had a significantly higher probability of setting fruit than ”control” flowers that we bagged but did not cage females on. In addition, we tested if Hylemya prefer particular architectural locations of flowers and if those locations correspond with higher than average fruit set. Although flowers at the distal end of the plant, and those most proximal to the main stem, were more likely to set fruit overall, Hylemya was no more likely to oviposit on those flowers than others on the plant. Taken together, our results suggest that Hylemya is somehow able to manipulate its host to ensure fruit set and thus the provisioning of their larvae. Received: 3 December 1999 / Accepted: 23 March 2000     

NMR Structural and Biophysical Analysis of the Disease-Linked Inner Mitochondrial Membrane Protein MPV17

MPV17 is an integral inner mitochondrial membrane protein, whose loss-of-function is linked to the hepatocerebral form of the mitochondrial-DNA-depletion syndrome, leading to a tissue-specific reduction of mitochondrial DNA and organ failure in infants. Several disease-causing mutations in MPV17 have been identified and earlier studies with reconstituted protein suggest that MPV17 forms a high conductivity channel in the membrane. However, the molecular and structural basis of the MPV17 functionality remain only poorly understood. In order to make MPV17 accessible to high-resolution structural studies, we here present an efficient protocol for its high-level production in E. coli and refolding into detergent micelles. Using biophysical and NMR methods, we show that refolded MPV17 in detergent micelles adopts a compact structure consisting of six membrane-embedded α-helices. Furthermore, we demonstrate that MPV17 forms oligomers in a lipid bilayer that are further stabilized by disulfide-bridges. In line with these findings, MPV17 could only be inserted into lipid nanodiscs of 8–12 nm in diameter if intrinsic cysteines were either removed by mutagenesis or blocked by chemical modification. Using this nanodisc reconstitution approach, we could show that disease-linked mutations in MPV17 abolish its oligomerization properties in the membrane. These data suggest that, induced by oxidative stress, MPV17 can alter its oligomeric state from a properly folded monomer to a disulfide-stabilized oligomeric pore which might be required for the transport of metabolic DNA precursors into the mitochondrial matrix to compensate for the damage caused by reactive oxygen species.     

Host identification in unfed ticks from stable isotope compositions (δ13C and δ15N)

Determination of the ratios of natural stable isotopes (¹³C/¹²C and ¹⁵N/¹⁴N) in unfed Ixodes ricinus nymphs and adults, which, in their previous stage, fed on captive wild rodents (Apodemus sylvaticus and Myodes glareolus), wild birds (Parus major and Cyanistes caeruleus) or domestic ruminants (Ovis aries and Bos taurus), demonstrated that it is possible to identify each host category with confidence. First, the tick–blood spacing, which is the difference between values obtained from ticks and the blood of hosts that they had fed on in the previous stage, was consistent (152 spacings investigated from 15 host individuals in total). Second, potential confounding factors (tick age and sex) did not affect the discriminatory power of the isotope patterns, nor did different rearing conditions (room temperature vs. 4 °C) or the duration of development (maximum of 430 days). The findings that the tick–blood isotope spacings, across a diverse range of hosts, were similar and predictable, and that confounders had little or no effect on this, strongly support the usage of the isotope approach. Because each of the host categories has a different role in the population dynamics of I. ricinus and in tick‐borne pathogen ecology, the method described here has great potential for the clarification of tick and tick‐borne pathogen ecology in the field.