The utility of inflammation and platelet biomarkers in patients with acute coronary syndromes

Introduction

Thrombotic and inflammatory mechanisms are involved in the pathophysiology of acute coronary syndrome (ACS). The aim of the study was the evaluation of inflammation (white blood cells count/WBC, C-reactive protein/CRP, interleukin-6/IL-6) and platelet (platelet count/PLT, mean platelet volume/MPV, large platelet/LPLT, beta-thromboglobulin/β-TG) biomarkers in the groups of ACS patients depending on the severity of signs and symptoms and compared to controls without coronary artery disease.

Are rice chromosomes components of a holocentric chromosome ancestor?

Comparative genomics reveals that cereal genomes are composed of similar genomic building blocks (linkage blocks). By stacking these blocks in a unique order, it is possible to construct a single ancestral chromosome which can be cleaved to give the basic structure of the 56 different chromosomes found in wheat, rice, maize, sorghum, millet and sugarcane. The borders of linkage blocks are defined by cereal centromeric and telomeric sites. However, a number of studies have shown that telomeric heterochromatin has neocentromeric activity, implying that linkage blocks are in fact defined by centromeric-like sites with conserved sequences. The structure of the ancestral cereal genome thus resembles a holocentric chromosome, which is the chromosome structure shared by the closest relatives of the Gramineae, the Cypericeae and Juncaceae.     

Estimating abundance for a savanna elephant population using mark–resight methods: a case study for the Tembe Elephant Park, South Africa

Elephants living in dense woodlands are difficult to count. Many elephant populations in Africa occur in such conditions. Estimates of these populations based on total counts, aerial counts and dung counts often lack information on precision and accuracy. We use standard mark–recapture field methods to obtain estimates of population size with associated confidence limits. We apply this approach to a closed elephant population in the Tembe Elephant Park (300 km²), South Africa. A registration count completed in 4 months gives a known population size. We evaluate mark–recapture models against the known population size. Individual identification profiles obtained for elephants during the registration count and mark–recapture events indicate that at least 167 elephants live in the park. We consider this value as an estimate of the minimum number alive. We include 189 sightings of bulls and 37 sightings of breeding herds in the mark–recapture modelling. Of the models we test (Petersen, Schnabel, Schumacher, Jolly–Seber, Bowden's, Poisson and negative binomial), Bowden's gives an estimate closest to the registration count. Assumptions of the model are not violated. For all models except one (negative binomial), our estimates improve with increased sampling intensity. Confidence intervals do not improve with increased effort except for the Schnabel model. Mark–recapture methods should be considered as reliable estimators of population size for elephants occurring in dense woodlands and forests when other methods cannot be relied on.     

On the Trails of the Proteasome Fold: Structural and Functional Analysis of the Ancestral β-Subunit Protein Anbu

The 20S proteasome is a key player in eukaryotic and archaeal protein degradation, but its progenitor in eubacteria is unknown. Recently, the ancestral β-subunit protein (Anbu) was predicted to be the evolutionary precursor of the proteasome. We crystallized Anbu from Hyphomicrobium sp. strain MC1 in four different space groups and solved the structures by SAD-phasing and Patterson search calculation techniques. Our data reveal that Anbu adopts the classical fold of Ntn-hydrolases, but its oligomeric state differs from that of barrel-shaped proteases. In contrast to their typical architecture, the Anbu protomer is a tightly interacting dimer that can assemble into a helical superstructure. Although Anbu features a catalytic triad of Thr1O^γ, Asp17O^δ1 and Lys32N^ε, it is unable to hydrolyze standard protease substrates. The lack of activity might be caused by the incapacity of Thr1NH₂ to function as a Brønsted acid during substrate cleavage due to its missing activation via hydrogen bonding. Altogether, we demonstrate that the topology of the proteasomal fold is conserved in Anbu, but whether it acts as a protease still needs to be clarified.     

Phylogenetic distribution of regeneration and asexual reproduction in Annelida: regeneration is ancestral and fission evolves in regenerative clades

Regeneration, the ability to replace lost body structures, and agametic asexual reproduction, such as fission and budding, are post‐embryonic developmental capabilities widely distributed yet highly variable across animals. Regeneration capabilities vary dramatically both within and across phyla, but the evolution of regeneration ability has rarely been reconstructed in an explicitly phylogenetic context. Agametic reproduction appears strongly associated with high regenerative abilities, and there are also extensive developmental similarities between these two processes, suggesting that the two are evolutionarily related. However, the directionality leading to this relationship remains unclear: while it has been proposed that regeneration precedes asexual reproduction, the reverse hypothesis has also been put forward. Here, we use phylogenetically explicit methods to reconstruct broad patterns of regeneration evolution and formally test these hypotheses about the evolution of fission in the phylum Annelida (segmented worms). We compiled from the literature a large dataset of information on anterior regeneration, posterior regeneration, and fission abilities for 401 species and mapped this information onto a phylogenetic tree based on recent molecular studies. We used Markovian maximum likelihood and Bayesian MCMC methods to evaluate different models for the evolution of regeneration and fission and to estimate the likelihood of each of these traits being present at each node of the tree. Our results strongly support anterior and posterior regeneration ability being present at the basal node of the annelid tree and being lost 18 and 5 times, respectively, but never regained. By contrast, the ability to fission is reconstructed as being absent at the basal node and being gained at least 19 times, with several possible losses. Models assuming independent evolution of regeneration and fission yield significantly lower likelihoods. Our findings suggest that anterior and posterior regeneration are ancestral for Annelida and are consistent with the hypothesis that regenerative ability is required to evolve fission.     

Environmental constraints and call evolution in torrent‐dwelling frogs

Although acoustic signals are important for communication in many taxa, signal propagation is affected by environmental properties. Strong environmental constraints should drive call evolution, favoring signals with greater transmission distance and content integrity in a given calling habitat. Yet, few empirical studies have verified this prediction, possibly due to a shortcoming in habitat characterization, which is often too broad. Here we assess the potential impact of environmental constraints on the evolution of advertisement call in four groups of torrent‐dwelling frogs in the family Ranidae. We reconstruct the evolution of calling site preferences, both broadly categorized and at a finer scale, onto a phylogenetic tree for 148 species with five markers (～3600 bp). We test models of evolution for six call traits for 79 species with regard to the reconstructed history of calling site preferences and estimate their ancestral states. We find that in spite of existing morphological constraints, vocalizations of torrent‐dwelling species are most probably constrained by the acoustic specificities of torrent habitats and particularly their high level of ambient noise. We also show that a fine‐scale characterization of calling sites allows a better perception of the impact of environmental constraints on call evolution.     

Molecular systematics of New World lampropeltinine snakes (Colubridae): implications for biogeography and evolution of food habits

We used mitochondrial gene sequences to infer phylogenetic relationships among North American snakes of the colubrid tribe Lampropeltini (Arizona, Bogertophis, Cemophora , New World Elaphe, Lampropellis, Pituophis, Rhinocheilus, Senticolis, Stilosoma) , and assessed the implications of our findings for the biogeography and evolution of food habits among these serpents. The maximum likelihood phylogeny identified Rhinocheilus as the sister taxon to all other lampropeltinines, and supported the monophyly of Lampropeltis (including Stilosoma) , New World Elaphe , and Pituophis , but not that of Bogertophis. This phylogeny also suggested a sister group relationship between Cemophora and Lampropeltis , and between New World Elaphe and Pituophis , and strongly supported that Sentkolis belongs within Lampropeltini, thus contradicting previous suggestions that Senticolis is not a lampropeltinine. Using a method for approximating ancestral areas of clades, we determined that western North America was most likely the ancestral area of lampropeltinines. Our survey of published studies, combined with unpublished data, indicated that lampropeltinines as a group feed mainly on mammals, less frequently on lizards, birds, and bird eggs, and only rarely on squamate eggs, snakes, anurans, and insects. Some individual species indeed emphasize mammals in their diets, but others most frequently eat lizards, squamate eggs, bird eggs, or snakes, whereas others take two prey types with similar frequency. Our reconstruction of the evolution of food habits among lampropeltinines suggests that a diet emphasizing lizards is ancestral, and therefore diets that mosdy consist of mammals, squamate and bird eggs, and snakes are derived within the clade. In at least some species, smaller individuals prey mostly on lizards and larger ones add mammals to their diets.     

Ecological selectivity and the evolution of mammalian substrate preference across the K–Pg boundary

The Cretaceous–Paleogene (K–Pg) mass extinction 66 million years ago was characterized by a worldwide ecological catastrophe and rapid species turnover. Large‐scale devastation of forested environments resulting from the Chicxulub asteroid impact likely influenced the evolutionary trajectories of multiple clades in terrestrial environments, and it has been hypothesized to have biased survivorship in favour of nonarboreal lineages across the K–Pg boundary. Here, we evaluate patterns of substrate preferences across the K–Pg boundary among crown group mammals, a group that underwent rapid diversification following the mass extinction. Using Bayesian, likelihood, and parsimony reconstructions, we identify patterns of mammalian ecological selectivity that are broadly similar to those previously hypothesized for birds. Models based on extant taxa indicate predominant K–Pg survivorship among semi‐ or nonarboreal taxa, followed by numerous independent transitions to arboreality in the early Cenozoic. However, contrary to the predominant signal, some or all members of total‐clade Euarchonta (Primates + Dermoptera + Scandentia) appear to have maintained arboreal habits across the K–Pg boundary, suggesting ecological flexibility during an interval of global habitat instability. We further observe a pronounced shift in character state transitions away from plesiomorphic arboreality associated with the K–Pg transition. Our findings are consistent with the hypothesis that predominantly nonarboreal taxa preferentially survived the end‐Cretaceous mass extinction, and emphasize the pivotal influence of the K‐Pg transition in shaping the early evolutionary trajectories of extant terrestrial vertebrates.     

Is evolution faster at ecotones? A test using rates and tempo of diet transitions in Neotropical Sigmodontinae (Rodentia,Cricetidae)

We evaluated whether evolution is faster at ecotones as niche shifts may be needed to persist under unstable environment. We mapped diet evolution along the evolutionary history of 350 sigmodontine species. Mapping was used in three new tip‐based metrics of trait evolution – Transition Rates, Stasis Time, and Last Transition Time – which were spatialized at the assemblage level (aTR, aST, aTL). Assemblages were obtained by superimposing range maps on points located at core and ecotone of the 93 South American ecoregions. Using Linear Mixed Models, we tested whether ecotones have species with more changes from the ancestral diet (higher aTR), have maintained the current diet for a shorter time (lower aST), and have more recent transitions to the current diet (lower aLT) than cores. We found lower aTR, and higher aST and aLT at ecotones than at cores. Although ecotones are more heterogeneous, both environmentally and in relation to selection pressures they exert on organisms, ecotone species change little from the ancestral diet as generalist habits are necessary toward feeding in ephemeral environments. The need to incorporate phylogenetic uncertainty in tip‐based metrics was evident from large uncertainty detected. Our study integrates ecology and evolution by analyzing how fast trait evolution is across space.     

Alpha Satellite Insertion Close to an Ancestral Centromeric Region

Human centromeres are mainly composed of alpha satellite DNA hierarchically organized as higher-order repeats (HORs). Alpha satellite dynamics is shown by sequence homogenization in centromeric arrays and by its transfer to other centromeric locations, for example, during the maturation of new centromeres. We identified during prenatal aneuploidy diagnosis by fluorescent in situ hybridization a de novo insertion of alpha satellite DNA from the centromere of chromosome 18 (D18Z1) into cytoband 15q26. Although bound by CENP-B, this locus did not acquire centromeric functionality as demonstrated by the lack of constriction and the absence of CENP-A binding. The insertion was associated with a 2.8-kbp deletion and likely occurred in the paternal germline. The site was enriched in long terminal repeats and located ∼10 Mbp from the location where a centromere was ancestrally seeded and became inactive in the common ancestor of humans and apes 20–25 million years ago. Long-read mapping to the T2T-CHM13 human genome assembly revealed that the insertion derives from a specific region of chromosome 18 centromeric 12-mer HOR array in which the monomer size follows a regular pattern. The rearrangement did not directly disrupt any gene or predicted regulatory element and did not alter the methylation status of the surrounding region, consistent with the absence of phenotypic consequences in the carrier. This case demonstrates a likely rare but new class of structural variation that we name “alpha satellite insertion.” It also expands our knowledge on alphoid DNA dynamics and conveys the possibility that alphoid arrays can relocate near vestigial centromeric sites.