Diversity of muskox Ovibos moschatus (Zimmerman, 1780) (Bovidae, Mammalia) in time and space based on cranial morphometry

Muskox Ovibos moschatus is a Pleistocene relic, which has survived only in North America and Greenland. During the Pleistocene, it was widely distributed in Eurasia and North America. To evaluate its morphological variability through time and space, we conducted an extensive morphometric study of 217 Praeovibos and Ovibos skull remains. The analyses showed that the skulls grew progressively wider from Praeovibos sp. to the Pleistocene O. moschatus, while from the Pleistocene to the recent O. moschatus, the facial regions of the skull turned narrower and shorter. We also noticed significant geographic differences between the various Pleistocene Ovibos crania. Siberian skulls were usually larger than those from Western and Central Europe. Eastern Europeanmuskoxen also exceeded in size those from the other regions of Europe. The large size of Late Pleistocene muskoxen from regions located in more continental climatic regimes was probably associated with the presence of more suitable food resources in steppe-tundra settings. Consistently, radiocarbon-dated records of this species are more numerous in colder periods, when the steppe-tundra was widely spread, and less abundant in warmer periods

Possible import routes of proteins into the cyanobacterial endosymbionts/plastids of Paulinella chromatophora

The rhizarian amoeba Paulinella chromatophora harbors two photosynthetically active and deeply integrated cyanobacterial endosymbionts acquired ~60 million years ago. Recent genomic analyses of P. chromatophora have revealed the loss of many essential genes from the endosymbiont’s genome, and have identified more than 30 genes that have been transferred to the host cell’s nucleus through endosymbiotic gene transfer (EGT). This indicates that, similar to classical primary plastids, Paulinella endosymbionts have evolved a transport system to import their nuclear-encoded proteins. To deduce how these proteins are transported, we searched for potential targeting signals in genes for 10 EGT-derived proteins. Our analyses indicate that five proteins carry potential signal peptides, implying they are targeted via the host endomembrane system. One sequence encodes a mitochondrial-like transit peptide, which suggests an import pathway involving a channel protein residing in the outer membrane of the endosymbiont. No N-terminal targeting signals were identified in the four other genes, but their encoded proteins could utilize non-classical targeting signals contained internally or in C-terminal regions. Several amino acids more often found in the Paulinella EGT-derived proteins than in their ancestral set (proteins still encoded in the endosymbiont genome) could constitute such signals. Characteristic features of the EGT-derived proteins are low molecular weight and nearly neutral charge, which both could be adaptations to enhance passage through the peptidoglycan wall present in the intermembrane space of the endosymbiont’s envelope. Our results suggest that Paulinella endosymbionts/plastids have evolved several different import routes, as has been shown in classical primary plastids

Protein translocons in photosynthetic organelles of Paulinella chromatophora

The rhizarian amoeba Paulinella chromatophora harbors two photosynthetic cyanobacterial endosymbionts (chromatophores), acquired independently of primary plastids of glaucophytes, red algae and green plants. These endosymbionts have lost many essential genes, and transferred substantial number of genes to the host nuclear genome via endosymbiotic gene transfer (EGT), including those involved in photosynthesis. This indicates that, similar to primary plastids, Paulinella endosymbionts must have evolved a transport system to import their EGT-derived proteins. This system involves vesicular trafficking to the outer chromatophore membrane and presumably a simplified Tic-like complex at the inner chromatophore membrane. Since both sequenced Paulinella strains have been shown to undergo differential plastid gene losses, they do not have to possess the same set of Toc and Tic homologs. We searched the genome of Paulinella FK01 strain for potential Toc and Tic homologs, and compared the results with the data obtained for Paulinella CCAC 0185 strain, and 72 cyanobacteria, eight Archaeplastida as well as some other bacteria. Our studies revealed that chromatophore genomes from both Paulinella strains encode the same set of translocons that could potentially create a simplified but fully-functional Tic-like complex at the inner chromatophore membranes. The common maintenance of the same set of translocon proteins in two Paulinella strains suggests a similar import mechanism and/or supports the proposed model of protein import. Moreover, we have discovered a new putative Tic component, Tic62, a redox sensor protein not identified in previous comparative studies of Paulinella translocons

Characterization of signal and transit peptides based on motif composition and taxon-specific patterns

Abstract Targeting peptides or presequences are N-terminal extensions of proteins that encode information about their cellular localization. They include signal peptides (SP), which target proteins to the endoplasmic reticulum, and transit peptides (TP) directing proteins to the organelles of endosymbiotic origin: chloroplasts and mitochondria. TPs were hypothesized to have evolved from antimicrobial peptides (AMPs), which are responsible for the host defence against microorganisms, including bacteria, fungi and viruses. In this study, we performed comprehensive bioinformatic analyses of amino acid motifs of targeting peptides and AMPs using a curated set of experimentally verified proteins. We identified motifs frequently occurring in each type of presequence showing specific patterns associated with their amino acid composition, and investigated their position within the presequence. We also compared motif patterns among different taxonomic groups and identified taxon-specific features, providing some evolutionary insights. Considering the functional relevance and many practical applications of targeting peptides and AMPs, we believe that our analyses will prove useful for their design, and better understanding of protein import mechanism and presequence evolution

Prediction of protein subplastid localization and origin with PlastoGram

Due to their complex history, plastids possess proteins encoded in the nuclear and plastid genome. Moreover, these proteins localize to various subplastid compartments. Since protein localization is associated with its function, prediction of subplastid localization is one of the most important steps in plastid protein annotation, providing insight into their potential function. Therefore, we create a novel manually curated data set of plastid proteins and build an ensemble model for prediction of protein subplastid localization. Moreover, we discuss problems associated with the task, e.g. data set sizes and homology reduction. PlastoGram classifies proteins as nuclear- or plastid-encoded and predicts their localization considering: envelope, stroma, thylakoid membrane or thylakoid lumen; for the latter, the import pathway is also predicted. We also provide an additional function to differentiate nuclear-encoded inner and outer membrane proteins. PlastoGram is available as a web server at and as an R package at . The code used for described analyses is available at

Prediction of Signal Peptides in Proteins from Malaria Parasites

Signal peptides are N-terminal presequences responsible for targeting proteins to the endomembrane system, and subsequent subcellular or extracellular compartments, and consequently condition their proper function. The significance of signal peptides stimulates development of new computational methods for their detection. These methods employ learning systems trained on datasets comprising signal peptides from different types of proteins and taxonomic groups. As a result, the accuracy of predictions are high in the case of signal peptides that are well-represented in databases, but might be low in other, atypical cases. Such atypical signal peptides are present in proteins found in apicomplexan parasites, causative agents of malaria and toxoplasmosis. Apicomplexan proteins have a unique amino acid composition due to their AT-biased genomes. Therefore, we designed a new, more flexible and universal probabilistic model for recognition of atypical eukaryotic signal peptides. Our approach called signalHsmm includes knowledge about the structure of signal peptides and physicochemical properties of amino acids. It is able to recognize signal peptides from the malaria parasites and related species more accurately than popular programs. Moreover, it is still universal enough to provide prediction of other signal peptides on par with the best preforming predictors

The Bonar Score in the Histopathological Assessment of Tendinopathy and Its Clinical Relevance - A Systematic Review

This study aimed to perform a comprehensive systematic review, which reports the role of the Bonar score in the histopathological assessment of tendinopathy and its clinical relevance. To identify all of the studies that reported relevant information on the Bonar scoring system and tendinopathy, an extensive search of the major and the most significant electronic databases (PubMed, Cochrane Central, ScienceDirect, SciELO, Web of Science) was performed. A systematic review of the literature was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The extracted data included—year of study, geographical location, type of the study, radiological modifications, gender, number of patients, region of tendinopathy, mean age, control group, characteristics of the Bonar score and alterations in the scale, mean Bonar score, number of investigators, area of tendon investigation, clinical and radiological implications. An extensive search of the databases and other sources yielded a total of 807 articles. Eighteen papers were finally included in this systematic review, and of these, 13 original papers included the clinical and radiological implications of tendinopathy. Radiological evaluation was present in eight studies (both magnetic resonance imaging (MRI) and ultrasound (US)). The clinical implications were more frequent and present in 10 studies. Using the Bonar score, it is easy to quantify the pathological changes in tendinous tissue. However, its connection with clinical and radiological evaluation is much more complicated. Based on the current state of knowledge, we concluded that the neovascularization variable in the Bonar system should be reconsidered. Ideally, the microscopic assessment score should follow the established classification scale with the radiological and clinical agreement and should have a prognostic value

Testing Antimicrobial Properties of Selected Short Amyloids

Amyloids and antimicrobial peptides (AMPs) have many similarities, e.g., both kill microorganisms by destroying their membranes, form aggregates, and modulate the innate immune system. Given these similarities and the fact that the antimicrobial properties of short amyloids have not yet been investigated, we chose a group of potentially antimicrobial short amyloids to verify their impact on bacterial and eukaryotic cells. We used AmpGram, a best-performing AMP classification model, and selected ten amyloids with the highest AMP probability for our experimental research. Our results indicate that four tested amyloids: VQIVCK, VCIVYK, KCWCFT, and GGYLLG, formed aggregates under the conditions routinely used to evaluate peptide antimicrobial properties, but none of the tested amyloids exhibited antimicrobial or cytotoxic properties. Accordingly, they should be included in the negative datasets to train the next-generation AMP prediction models, based on experimentally confirmed AMP and non-AMP sequences. In the article, we also emphasize the importance of reporting non-AMPs, given that only a handful of such sequences have been officially confirmed