Compositionally Constrained Sites Drive Long-Branch Attraction.

Accurate phylogenies are fundamental to our understanding of the pattern and process of evolution. Yet, phylogenies at deep evolutionary timescales, with correspondingly long branches, have been fraught with controversy resulting from conflicting estimates from models with varying complexity and goodness of fit. Analyses of historical as well as current empirical datasets, such as alignments including Microsporidia, Nematoda, or Platyhelminthes, have demonstrated that inadequate modeling of across-site compositional heterogeneity, which is the result of biochemical constraints that lead to varying patterns of accepted amino acids along sequences, can lead to erroneous topologies that are strongly supported. Unfortunately, models that adequately account for across-site compositional heterogeneity remain computationally challenging or intractable for an increasing fraction of contemporary datasets. Here, we introduce "compositional constraint analysis," a method to investigate the effect of site-specific constraints on amino acid composition on phylogenetic inference. We show that more constrained sites with lower diversity and less constrained sites with higher diversity exhibit ostensibly conflicting signals under models ignoring across-site compositional heterogeneity that lead to long-branch attraction artifacts and demonstrate that more complex models accounting for across-site compositional heterogeneity can ameliorate this bias. We present CAT-posterior mean site frequencies (PMSF), a pipeline for diagnosing and resolving phylogenetic bias resulting from inadequate modeling of across-site compositional heterogeneity based on the CAT model. CAT-PMSF is robust against long-branch attraction in all alignments we have examined. We suggest using CAT-PMSF when convergence of the CAT model cannot be assured. We find evidence that compositionally constrained sites are driving long-branch attraction in two metazoan datasets and recover evidence for Porifera as the sister group to all other animals. [Animal phylogeny; cross-site heterogeneity; long-branch attraction; phylogenomics.].

Carbon vacancy-assisted stabilization of individual Cu5 clusters on graphene. Insights from ab initio molecular dynamics.

Recent advances in synthesis and characterization methods have enabled the controllable fabrication of atomically precise metal clusters (AMCs) of subnanometer size that possess unique physical and chemical properties, yet to be explored. Such AMCs have potential applications in a wide range of fields, from luminescence and sensing to photocatalysis and bioimaging, making them highly desirable for further research. Therefore, there is a need to develop innovative methods to stabilize AMCs upon surface deposition, as their special properties are lost due to sintering into larger nanoparticles. To this end, dispersion-corrected density functional theory (DFT-D3) and ab initio molecular dynamics (AIMD) simulations have been employed. Benchmarking against high-level post-Hartree-Fock approaches revealed that the DFT-D3 scheme describes very well the lowest-energy states of clusters of five and ten atoms, Cu5 and Cu10. AIMD simulations performed at 400 K illustrate how intrinsic defects of graphene sheets, carbon vacancies, are capable of confining individual Cu5 clusters, thus allowing for their stabilization. Furthermore, AIMD simulations provide evidence on the dimerization of Cu5 clusters on defect-free graphene, in agreement with the ab initio predictions of (Cu5)n aggregation in the gas phase. The findings of this study demonstrate the potential of using graphene-based substrates as an effective platform for the stabilization of monodisperse atomically precise Cu5 clusters.

Catalytic activity of 1D chains of gold oxide on a stepped gold surface from density functional theory.

The rich surface chemistry of gold at the nanoscale has made it an important catalyst for low-temperature applications. Recent studies point to the possible role of self-organized structures formed by chemisorbed O atoms on the surface of gold catalysts for their catalytic activity and/or deactivation. In this study, we investigate the reactivity of a double O chain running along a step on a Au(221) surface with oxygen vacancies as a prototypical model of a 1D surface gold oxide. We compare CO and O2 adsorption on such a chain with the oxygen-free Au(221) surface model. A systematic study of the reactivity of the double chain with O vacancies was done with respect to the regular Au(221) surface using CO as a probe. The CO oxidation was investigated assuming dissociative and associative mechanisms. Remarkably, O2 adsorbs stronger on the double oxygen vacancy than on the regular Au(221) surface, and its dissociation barrier reduces significantly from 1.84 eV to 0.87 eV, whereas the CO adsorption energy is similar on these surfaces. Calculations suggest that CO oxidation should occur more efficiently on the double O vacancy than on the regular Au(221) surface due to stronger adsorption of O2 and a low activation barrier for O2 + CO surface reaction.

The role of D2 dopamine receptors in oxytocin induced place preference and anxiolytic effect.

Neuropeptide oxytocin (OT) is involved in the regulation of social and non-social behaviour. The central nucleus of amygdala (CeA), part of the limbic system, plays an important role in learning, memory, anxiety and reinforcing mechanisms. CeA has been shown to be rich in OT receptors in rodents. Our previous findings indicated that OT in the rat CeA has a dose dependent rewarding and anxiolytic effect. The aim of our present study was to examine in the CeA the possible interaction of OT and D2 dopamine (DA) receptor antagonist Sulpiride on reinforcement in place preference test and on anxiety in elevated plus maze test. Wistar rats were microinjected bilaterally with 10 ng OT. In different group of animals 4 µg D2 DA receptor antagonist was applied. Other animals received D2 DA receptor antagonist 15 min before 10 ng OT treatment or vehicle solution into the CeA. Rats receiving 10 ng OT spent significantly longer time in the treatment quadrant during the test session in conditioned place preference test. Prior treatment with D2 DA receptor antagonist blocked the rewarding effects of OT. Antagonist in itself did not influence the time rats spent in the treatment quadrant. In elevated plus maze test, rats receiving 10 ng OT spent significantly longer time on the open arms. Prior treatment with D2 DA receptor antagonist blocked the effects of OT. Our results show that DA system plays a role in positive reinforcing and anxiolytic effects of OT because D2 DA receptor antagonist can block these actions.

Correlation of natural autoantibodies and cardiovascular disease-related anti-bacterial antibodies in pericardial fluid of cardiac surgery patients.

Our previous studies showed that anti-citrate synthase (anti-CS) immunoglobulin (Ig)M natural autoantibodies are present in healthy individuals without previous antigen stimulation, but no studies have investigated their presence in the pericardial fluid (PF). Therefore, we detected the natural anti-CS IgG/M autoantibody levels in plasma and PF of cardiac surgery patients and investigated their relationship with cardiovascular disease-associated bacterial pathogens. PF and blood samples of 22 coronary artery bypass graft (CABG) and 10 aortic valve replacement (AVR) patients were tested for total Ig levels, natural autoantibodies and infection-related antibodies using enzyme-linked immunosorbent assay (ELISA) and Luminex methods. The B cell subsets were measured by flow cytometry. The total Ig subclass levels were four to eight times lower in PF than in plasma, but the natural anti-CS IgM autoantibodies showed a relative increase in PF. The frequency of CD19+ B lymphocytes was significantly lower in PF than in blood (P = 0·01), with a significant relative increase of B1 cells (P = 0·005). Mycoplasma pneumoniae antibody-positive patients had significantly higher anti-CS IgM levels. In CABG patients we found a correlation between anti-CS IgG levels and M. pneumoniae, Chlamydia pneumoniae and Borrelia burgdorferi antibody titres. Our results provide the first evidence that natural autoantibodies are present in the PF, and they show a significant correlation with certain anti-bacterial antibody titres in a disease-specific manner.

Partial Oxidation of Methanol on Gold: How Selectivity Is Steered by Low-Coordinated Sites.

Partial methanol oxidation proceeds with high selectivity to methyl formate (MeFo) on nanoporous gold (npAu) catalysts. As low-coordinated sites on npAu were suggested to affect the selectivity, we experimentally investigated their role in the isothermal selectivity for flat Au(111) and stepped Au(332) model surfaces using a molecular beam approach under well-defined conditions. Direct comparison shows that steps enhance desired MeFo formation and lower undesired overoxidation. DFT calculations reveal differences in oxygen distribution that enhance the barriers to overoxidation at steps. Thus, these results provide an atomic-level understanding of factors controlling the complex reaction network on gold catalysts, such as npAu.

Selective Oxidation of Methanol to Methyl Formate on Gold: The Role of Low-Coordinated Sites Revealed by Isothermal Pulsed Molecular Beam Experiments and AIMD Simulations.

To elucidate the role of low-coordinated sites in the partial methanol oxidation to methyl formate (MeFo), the isothermal reactivity of flat Au(111) and stepped Au(332) in pulsed molecular beam experiments was compared for a broad range of reaction conditions. Low-coordinated step sites were found to enhance MeFo selectivity, especially at low coverage conditions, as found at higher temperatures. The analysis of the transient kinetics provides evidence for the essential role of Au x O y phases for MeFo formation and the complex interplay of different oxygen species for the observed selectivity. Ab initio molecular dynamic simulations yielded microscopic insights in the formation of Au x O y phases on flat and stepped gold surfaces emphasizing the role of low-coordinated sites in their formation. Moreover, associated surface restructuring provides atomic-scale insights which align with the experimentally observed transient kinetics in MeFo formation.

Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.

In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species tree and to explain differences between them via evolutionary events including gene duplications, transfers, and losses. Here, we describe how phylogenetic reconciliation provides a natural framework for studying genome evolution and highlight recent applications including ancestral gene content inference, the rooting of species trees, and the insights into metabolic evolution and ecological transitions they yield. Reconciliation analyses have elucidated the evolution of diverse microbial lineages, from Chlamydiae to Asgard archaea, shedding light on ecological adaptation, host-microbe interactions, and symbiotic relationships. However, there are many opportunities for broader application of the approach in microbiology. Continuing improvements to make reconciliation models more realistic and scalable, and integration of ecological metadata such as habitat, pH, temperature, and oxygen use offer enormous potential for understanding the rich tapestry of microbial life.

The nature of the last universal common ancestor and its impact on the early Earth system.

The nature of the last universal common ancestor (LUCA), its age and its impact on the Earth system have been the subject of vigorous debate across diverse disciplines, often based on disparate data and methods. Age estimates for LUCA are usually based on the fossil record, varying with every reinterpretation. The nature of LUCA's metabolism has proven equally contentious, with some attributing all core metabolisms to LUCA, whereas others reconstruct a simpler life form dependent on geochemistry. Here we infer that LUCA lived ~4.2 Ga (4.09-4.33 Ga) through divergence time analysis of pre-LUCA gene duplicates, calibrated using microbial fossils and isotope records under a new cross-bracing implementation. Phylogenetic reconciliation suggests that LUCA had a genome of at least 2.5 Mb (2.49-2.99 Mb), encoding around 2,600 proteins, comparable to modern prokaryotes. Our results suggest LUCA was a prokaryote-grade anaerobic acetogen that possessed an early immune system. Although LUCA is sometimes perceived as living in isolation, we infer LUCA to have been part of an established ecological system. The metabolism of LUCA would have provided a niche for other microbial community members and hydrogen recycling by atmospheric photochemistry could have supported a modestly productive early ecosystem.

Parameter Estimation and Species Tree Rooting Using ALE and GeneRax.

ALE and GeneRax are tools for probabilistic gene tree-species tree reconciliation. Based on a common underlying statistical model of how gene trees evolve along species trees, these methods rely on gene vs. species tree discordance to infer gene duplication, transfer, and loss events, map gene family origins, and root species trees. Published analyses have used these methods to root species trees of Archaea, Bacteria, and several eukaryotic groups, as well as to infer ancestral gene repertoires. However, it was recently suggested that reconciliation-based estimates of duplication and transfer events using the ALE/GeneRax model were unreliable, with potential implications for species tree rooting. Here, we assess these criticisms and find that the methods are accurate when applied to simulated data and in generally good agreement with alternative methodological approaches on empirical data. In particular, ALE recovers variation in gene duplication and transfer frequencies across lineages that is consistent with the known biology of studied clades. In plants and opisthokonts, ALE recovers the consensus species tree root; in Bacteria-where there is less certainty about the root position-ALE agrees with alternative approaches on the most likely root region. Overall, ALE and related approaches are promising tools for studying genome evolution.

ATP synthase evolution on a cross-braced dated tree of life.

The timing of early cellular evolution, from the divergence of Archaea and Bacteria to the origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have originated prior to the Last Universal Common Ancestor (LUCA) and analyses of ATP synthase genes, together with ribosomes, have played a key role in inferring and rooting the tree of life. We reconstruct the evolutionary history of ATP synthases using an expanded taxon sampling set and develop a phylogenetic cross-bracing approach, constraining equivalent speciation nodes to be contemporaneous, based on the phylogenetic imprint of endosymbioses and ancient gene duplications. This approach results in a highly resolved, dated species tree and establishes an absolute timeline for ATP synthase evolution. Our analyses show that the divergence of ATP synthase into F- and A/V-type lineages was a very early event in cellular evolution dating back to more than 4 Ga, potentially predating the diversification of Archaea and Bacteria. Our cross-braced, dated tree of life also provides insight into more recent evolutionary transitions including eukaryogenesis, showing that the eukaryotic nuclear and mitochondrial lineages diverged from their closest archaeal (2.67-2.19 Ga) and bacterial (2.58-2.12 Ga) relatives at approximately the same time, with a slightly longer nuclear stem-lineage.

Regulatory processes of hunger motivated behavior.

While food intake and body weight are under homeostatic regulation, eating is a highly motivated and reinforced behavior that induces feelings of gratification and pleasure. The chemical senses (taste and odor) and their evaluation are essential to these functions. Brainstem and limbic glucose-monitoring (GM) neurons receiving neurochemical information from the periphery and from the local brain milieu are important controlling hunger motivation, and brain gut peptides have a modulatory role on this function. The hypothalamic and limbic forebrain areas are responsible for evaluation of reward quality and related emotions. They are innervated by the mesolimbic dopaminergic system (MLDS) and majority of GM neurons are also influenced by dopamine. Via dopamine release, the MLDS plays an essential role in rewarding-reinforcing processes of feeding and addiction. The GM network and the MLDS in the limbic system represent essential elements in the neural substrate of motivation.

A rooted phylogeny resolves early bacterial evolution.

A rooted bacterial tree is necessary to understand early evolution, but the position of the root is contested. Here, we model the evolution of 11,272 gene families to identify the root, extent of horizontal gene transfer (HGT), and the nature of the last bacterial common ancestor (LBCA). Our analyses root the tree between the major clades Terrabacteria and Gracilicutes and suggest that LBCA was a free-living flagellated, rod-shaped double-membraned organism. Contrary to recent proposals, our analyses reject a basal placement of the Candidate Phyla Radiation, which instead branches sister to Chloroflexota within Terrabacteria. While most gene families (92%) have evidence of HGT, overall, two-thirds of gene transmissions have been vertical, suggesting that a rooted tree provides a meaningful frame of reference for interpreting bacterial evolution.

[Emotional state variations in rats during recall of passive avoidance reactions after neurotensin administration into nucleus accumbens of the brain].

Behavioral effects of neurotensin administration into the nucleus accumbens were studied in rats with neurotoxic lesions of serotoninergic structures of the dorsal raphe nucleus or periaqueductal grey matter. Changes in recall of passive avoidance conditioned reactions and aftereffects of painful stimulation in the locomotor activity were studied in the "open field" and elevated plus-maze and T-maze tests. The toxin administration into the dorsal raphe nucleus did not impair the recall of the passive avoidance reactions, but enhanced the oppressive aftereffects of painful stimulation, which can specify the development of anxiety in rats. The toxin administration into the periaqueductal grey matter had an opposite effect, which can be considered as a manifestation of the panic state. Neurotensin weakened the above mentioned effects of the toxin and, depending on the evoked emotional disorders, produced the anxiolytic or antipanic effects.

Serotoninergic mechanisms of the effects of neurotensin on passive avoidance behavior in rats.

The aim of the present work was to identify the features of the actions of neurotensin on administration into the substantia nigra or dorsal cervical nucleus on the reproduction of passive avoidance reactions in rats. The results showed that the action of neurotensin administered into the substantia nigra was accompanied by sharp reductions in passive avoidance reactions, while administration into the dorsal cervical nucleus, conversely, led to increases in these reactions and slowing of their extinction. The effects of microinjections of the serotonin 5-HT(1A) receptor agonist 8-hydroxydipropylaminotetraline (8-OH-DPAT) into these brain structures were analogous to the effects of neurotensin. The different behavioral effects of administration of neurotensin corresponded to identifiable changes in the levels of serotonin and its metabolite 5-hydroxyindoleacetic acid in the caudate nuclei of the brain. These data led to the conclusion that the effects of neurotensin on passive avoidance behavior are associated with the regulation of the emotional state of the animals via actions on the functions of brain serotoninergic structures.

The role of intraamygdaloid neurotensin and dopamine interaction in conditioned place preference.

Tridecapeptide Neurotensin (NT) is widely distributed in the central nervous system where it acts as a neurotransmitter and neuromodulator. The central nucleus of amygdala (CeA), part of the limbic system, plays an important role in learning, memory, anxiety and reinforcing mechanisms. Our previous data showed that NT microinjected into the CeA has positive reinforcing properties. We supposed that these effects might be due to modulations of the mesolimbic dopamine system. The aim of our study was to examine in the CeA the possible effects of NT and dopamine interaction on reinforcement by conditioned place preference test. Male Wistar rats were microinjected bilaterally with 100 ng NT or 2 µg D1 dopamine receptor antagonist alone, or D1 dopamine antagonist 15 min before 100 ng NT treatment or vehicle solution into the CeA. Other animals received 4 µg D2 dopamine receptor antagonist Sulpiride alone, or administration of D2 dopamine receptor antagonist 15 min before 100 ng NT treatment or vehicle solution into the CeA. Rats that received 100 ng NT spent significantly more time in the treatment quadrant during the test session. Pre-treatment with the D1 dopamine antagonist, blocked the effects of NT. D2 dopamine receptor antagonist pretreatment could prevent the positive reinforcing effects of NT as well. Antagonists themselves did not influence the place preference. Our results show that the rewarding effect of NT can be due to the modulation of DA system, since its effects could be blocked by either D1 dopamine or D2 dopamine antagonist preteatment.

Substance P and neurotensin in the limbic system: Their roles in reinforcement and memory consolidation.

Substance P (SP) and neurotensin (NT) are neuropeptides isolated in the periphery and in the central nervous system. They are involved in various regulatory processes in the gastrointestinal tract, in the circulatory and respiratory systems, kidney and endocrine system. In addition to the peripheral effects, SP and NT act as neurotransmitters and neuromodulators in the central nervous system, regulating various behavioural actions, such as general and motor activity, pain, food and water intake, anxiety, reward/reinforcement and memory consolidation. In the limbic system SPergic and NTergic pathways, terminals and related receptors have been identified. According to several data of literature and to our recently published results, SP and NT have rewarding/reinforcing effects and facilitate memory consolidation in various limbic regions. In this report evidences are provided about the interaction of these neuropeptides with dopaminergic and acetylcholinergic systems. A hypothesis is presented that rewarding/reinforcing effects of SP and NT develop by modulating the mesencephalic dopaminergic system, while their mnemonic effects are mediated via the mesencephalic dopaminergic and the basal forebrain cholinergic systems.

Plasma levels of acylated ghrelin during an oral glucose tolerance test in obese children.

OBJECTIVE: Ghrelin is an acylated peptide with octanoyl modification, which is essential for its GH-releasing ability. Coexpression of GH secretagogue receptor (GHS-R) and ghrelin in the pancreas suggests that this peptide is involved in glucose metabolism. The other form of the molecule, the non-acylated ghrelin, has been reported to be devoid of any pituitaric endocrine activities. Previous reports demonstrated that plasma total ghrelin levels decrease after oral glucose administration in obese children, but no data are available about the plasma levels of acylated ghrelin. Therefore, in the present study the plasma levels of acylated ghrelin were measured in obese and control children during oral glucose tolerance test (OGTT). MATERIALS AND METHODS: Acylated ghrelin response to OGTT was evaluated in 11 obese and 9 age-matched control children. All subjects received 0.75 g/kg (maximum 75 g) glucose solution orally after an overnight fast. Acylated ghrelin, insulin, glucose, and GH were determined at 0, 30, 60 and 120 min, and leptin at 0 min of the OGTT. RESULTS: Plasma basal levels of acylated ghrelin were significantly lower in the obese children than in the controls (66.3+/-6.7 vs 97.2+/-14.4 pg/ml, p<0.05). The plasma acylated ghrelin concentration decreased significantly at 30 and 60 min in the control group (53.3+/-9.9 and 57.4+/-7.0 pg/ml, p<0.05), but not in the obese group (64.7+/-9.6 and 49.3+/-4.6 pg/ml) as compared to the basal value. In the obese group the acylated ghrelin level was significantly higher at 120 min, than at 0 min (91.6+/-9.8 vs 66.3+/-6.7 pg/ml, p<0.05). CONCLUSIONS: There was no rapid fall in plasma levels of acylated ghrelin in obese children after OGTT at 30 min, but there was an increase at 120 min, suggesting that the dynamic of the response to OGTT is slower and there is an upregulation of active ghrelin in the second half of OGTT in obese children.

[Involvement of serotoninergic brain structures in the mechanisms of neurotensin effect on passive avoidance in rats].

The purpose of the research was to reveal the features of neurotensin (administered in substantia nigra or dorsal raphe nucleus) effect on recall of passive avoidance reactions in rats. It was shown that the effect of neurotensin injected into the substantia nigra was characterized by a sharp reduction of passive avoidance reactions. On the contrary, injection of the substance in the dorsal raphe nucleus led to an intensification of these reactions and delay of their extinction. The effects of microinjections of serotonin 1A receptor agonist, 8-hydroxy-dipropylaminotetralin (8-OH-DPAT), into the mentioned brain structures was similar to that of neurotensin. Changes in the content of serotonin and its metabolite 5- hydroxyindoleacetic acid (5-HIAA) in the caudate nucleus corresponded to various behavioral effects. The conclusion was made that neurotensin effect on the passive avoidance behavior is related to regulation of emotional state of animals mediated by its action on the function of the serotoninergic brain structures.