A Combined Experimental and Computational Exploration of Heteroleptic cis-PdLL' Coordination Cages through Geometric Complementarity.

Heteroleptic (mixed-ligand) coordination cages are of interest as host systems with more structurally and functionally complex cavities than homoleptic architectures. The design of heteroleptic cages, however, is far from trivial. In this work, we experimentally probed the self-assembly of Pd(II) ions with binary ligand combinations in a combinatorial fashion to search for new cis-PdLL' heteroleptic cages.

Supramolecular and molecular capsules, cages and containers.

Stemming from early seminal notions of molecular recognition and encapsulation, three-dimensional, cavity-containing capsular compounds and assemblies have attracted intense interest due to the ability to modulate chemical and physical properties of species encapsulated within these confined spaces compared to bulk environments. With such a diverse range of covalent motifs and non-covalent (supramolecular) interactions available to assemble building blocks, an incredibly wide-range of capsular-type architectures have been developed. Furthermore, synthetic tunability of the internal environments gives chemists the opportunity to engineer systems for uses in sensing, sequestration, catalysis and transport of molecules, just to name a few.

Expedient Decagram-Scale Synthesis of Robust Organic Cages That Bind Sulfate Strongly and Selectively in Water.

Selective anion recognition remains a key challenge in supramolecular chemistry: only a very small number of systems that can function in water are known, and these nearly always preferentially bind hydrophobic anions. In this work, we report three robust hexa-cationic cages that can be prepared on scales up to 14 g in two simple and high-yielding steps from commercially available materials. One of these cages displays unusually strong sulfate binding in water ( = 12,000 M), and demonstrates high selectivity for this anion over HPO/HPO in DMSO/buffer mixtures.

metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data.

Background: Genomic Observatories (GOs) are sites of long-term scientific study that undertake regular assessments of the genomic biodiversity. The European Marine Omics Biodiversity Observation Network (EMO BON) is a network of GOs that conduct regular biological community samplings to generate environmental and metagenomic data of microbial communities from designated marine stations around Europe. The development of an effective workflow is essential for the analysis of the EMO BON metagenomic data in a timely and reproducible manner.

Data-specific substitution models improve protein-based phylogenetics.

Calculating amino-acid substitution models that are specific for individual protein data sets is often difficult due to the computational burden of estimating large numbers of rate parameters. In this study, we tested the computational efficiency and accuracy of five methods used to estimate substitution models, namely Codeml, FastMG, IQ-TREE, P4 (maximum likelihood), and P4 (Bayesian inference). Data-specific substitution models were estimated from simulated alignments (with different lengths) that were generated from a known simulation model and simulation tree.

Continuous observations of the surface energy budget and meteorology over the Arctic sea ice during MOSAiC.

The Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) was a yearlong expedition supported by the icebreaker R/V Polarstern, following the Transpolar Drift from October 2019 to October 2020. The campaign documented an annual cycle of physical, biological, and chemical processes impacting the atmosphere-ice-ocean system. Of central importance were measurements of the thermodynamic and dynamic evolution of the sea ice.

Right Internal Mammary Artery Occlusion in a Patient With Failed Left Internal Mammary Artery Coronary Artery Bypass Graft Surgery Post a Laparoscopic Appendectomy for Acute Appendicitis.

Patients who present with acute myocardial infarction are often urgently evaluated for possible revascularization via coronary artery bypass graft surgery (CABG), percutaneous coronary intervention (PCI), or medical therapy alone. CABG has been shown to provide symptomatic relief as well as increased long-term survival for patients with multivessel coronary artery disease (CAD). Though venous grafts can be used to revascularize the ischemic territory, long-term patency is most successful when using pedicled coronary grafts such as the left internal mammary artery (LIMA) or right internal mammary artery (RIMA) graft.

Integrated phylogenomic analyses unveil reticulate evolution in Parthenocissus (Vitaceae), highlighting speciation dynamics in the Himalayan-Hengduan Mountains.

Hybridization caused by frequent environmental changes can lead both to species diversification (speciation) and to speciation reversal (despeciation), but the latter has rarely been demonstrated. Parthenocissus, a genus with its trifoliolate lineage in the Himalayan-Hengduan Mountains (HHM) region showing perplexing phylogenetic relationships, provides an opportunity for investigating speciation dynamics based on integrated evidence. We investigated phylogenetic discordance and reticulate evolution in Parthenocissus based on rigorous analyses of plastome and transcriptome data.

Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus.

Background: The order and orientation of genes encoded by animal mitogenomes are typically conserved, although there is increasing evidence of multiple rearrangements among mollusks. The mitogenome from a Brazilian brown mussel (hereafter named B1) classified as Linnaeus, 1758 and assembled from Illumina short-length reads revealed an unusual gene order very different from other congeneric species. Previous mitogenomic analyses based on the Brazilian specimen and other Mytilidae suggested the polyphyly of the genus .

Recoding Amino Acids to a Reduced Alphabet may Increase or Decrease Phylogenetic Accuracy.

Common molecular phylogenetic characteristics such as long branches and compositional heterogeneity can be problematic for phylogenetic reconstruction when using amino acid data. Recoding alignments to reduced alphabets before phylogenetic analysis has often been used both to explore and potentially decrease the effect of such problems. We tested the effectiveness of this strategy on topological accuracy using simulated data on four-taxon trees.

Odontogenic Infection Complicated by Cervicofacial Necrotizing Fasciitis in a Healthy Young Female.

Necrotizing fasciitis (NF) is a critical and rapidly progressive infection of the skin and soft tissue, and it is associated with a high mortality rate. NF of the cervicofacial region is uncommon due to the rich vascular supply of the head and neck, which promotes an efficient immune response to infection. Patients who are immunocompromised or have comorbidities affecting the vasculature, such as diabetes mellitus or peripheral vascular disease, are at an increased risk of more severe disease and outcome.

Successful spinal cord stimulation for chronic pancreatitis and post-laminectomy pain.

Approximately one in five adults in the United States experiences chronic pain. Over the last 50 years, spinal cord stimulation has become increasingly recognized as a minimally invasive, efficacious treatment modality for the management of chronic pain. The authors report a case study of a 46-year-old female in the first documented spinal cord stimulation simultaneously targeting intractable neuropathic and visceral pain caused by post-laminectomy syndrome and chronic pancreatitis, respectively.

Biochemical and molecular responses of the Mediterranean mussel (Mytilus galloprovincialis) to short-term exposure to three commonly prescribed drugs.

Pharmaceuticals represent a group of emerging contaminants. The short-term effect (3 and 7 days) of warfarin (1 and 10 mg L), dexamethasone (0.392 and 3.

Inferring the Deep Past from Molecular Data.

There is an expectation that analyses of molecular sequences might be able to distinguish between alternative hypotheses for ancient relationships, but the phylogenetic methods used and types of data analyzed are of critical importance in any attempt to recover historical signal. Here, we discuss some common issues that can influence the topology of trees obtained when using overly simple models to analyze molecular data that often display complicated patterns of sequence heterogeneity. To illustrate our discussion, we have used three examples of inferred relationships which have changed radically as models and methods of analysis have improved.

Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals.

Background: In octocorals (Cnidaria Octocorallia), the functional relationship between host health and its symbiotic consortium has yet to be determined. Here, we employed comparative metagenomics to uncover the distinct functional and phylogenetic features of the microbiomes of healthy Eunicella gazella, Eunicella verrucosa, and Leptogorgia sarmentosa tissues, in contrast with the microbiomes found in seawater and sediments. We further explored how the octocoral microbiome shifts to a pathobiome state in E.

Author Correction: Phylogenomics provides robust support for a two-domains tree of life.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Uncovering the shell game with barcodes: diversity of meiofaunal Caecidae snails (Truncatelloidea, Caenogastropoda) from Central America.

Caecidae is a species-rich family of microsnails with a worldwide distribution. Typical for many groups of gastropods, caecid taxonomy is largely based on overt shell characters. However, identification of species using shell characteristics is problematic due to their rather uniform, tubular shells, the presence of different growth stages, and a high degree of intraspecific variability.

Prokaryotic diversity in stream sediments affected by acid mine drainage.

The microbial communities in mining impacted areas rely on a variety of mechanisms to survive in such extreme environments. In this work, a meta-taxonomic approach using 16S rRNA gene sequences was used to investigate the prokaryotic diversity of sediment samples from water bodies affected by acid mine drainage at the São Domingos mining area in the south of Portugal. Samples were collected in summer and winter from the most contaminated sites from where the water flows downstream to the freshwater of Chança's river reservoir.

The Chloroplast Land Plant Phylogeny: Analyses Employing Better-Fitting Tree- and Site-Heterogeneous Composition Models.

The colonization of land by descendants of charophyte green algae marked a turning point in Earth history that enabled the development of the diverse terrestrial ecosystems we see today. Early land plants diversified into three gametophyte-dominant lineages, namely the hornworts, liverworts, and mosses, collectively known as bryophytes, and a sporophyte-dominant lineage, the vascular plants, or tracheophytes. In recent decades, the prevailing view of evolutionary relationships among these four lineages has been that the tracheophytes were derived from a bryophyte ancestor.

The mitochondrial phylogeny of land plants shows support for Setaphyta under composition-heterogeneous substitution models.

Congruence among analyses of plant genomic data partitions (nuclear, chloroplast and mitochondrial) is a strong indicator of accuracy in plant molecular phylogenetics. Recent analyses of both nuclear and chloroplast genome data of land plants (embryophytes) have, controversially, been shown to support monophyly of both bryophytes (mosses, liverworts, and hornworts) and tracheophytes (lycopods, ferns, and seed plants), with mosses and liverworts forming the clade Setaphyta. However, relationships inferred from mitochondria are incongruent with these results, and typically indicate paraphyly of bryophytes with liverworts alone resolved as the earliest-branching land plant group.

Phylogenomics provides robust support for a two-domains tree of life.

Hypotheses about the origin of eukaryotic cells are classically framed within the context of a universal 'tree of life' based on conserved core genes. Vigorous ongoing debate about eukaryote origins is based on assertions that the topology of the tree of life depends on the taxa included and the choice and quality of genomic data analysed. Here we have reanalysed the evidence underpinning those claims and apply more data to the question by using supertree and coalescent methods to interrogate >3,000 gene families in archaea and eukaryotes.